Re: [R] ANCOVA for linear regressions without intercept
Thanks Bert. I have read ?formula again and again, and I'm still struggling; lm(body_length ~ head_length-1) This removes intercept from each individual regression (for male, female, unknown). When they are taken together, lm(body_length ~ sex*head_length) This shows differences in slopes and intercepts between the regressions (but I want to compare the slopes of the regressions WITHOUT intercepts). If I put lm(body_length ~ sex:head_length-1) This shows slopes for each sex without intercepts, but NOT differences in the slope between the regressions. I also tried lm(body_length ~ sex*head_length-1) lm(body_length ~ sex*head_length-sex-1) But none of them worked. Would anyone be able to help me? All I want to do is to compare the slopes of three linear regressions that go through the origin (0,0) so that I can say if their difference is significant or not. Thanks for your help. From: Bert Gunter [mailto:gunter.ber...@gene.com] Sent: Friday, 1 April 2011 12:56 AM To: Yusuke Fukuda Cc: r-help@r-project.org Subject: Re: [R] ANCOVA for linear regressions without intercept If you haven't already received an answer, a careful reading of ?formula will provide it. -- Bert On Wed, Mar 30, 2011 at 11:42 PM, Yusuke Fukuda yusuke.fuk...@nt.gov.au wrote: Hello R experts I have two linear regressions for sexes (Male, Female, Unknown). All have a good correlation between body length (response variable) and head length (explanatory variable). I know it is not recommended, but for a good practical reason (the purpose of study is to find a single conversion factor from head length to body length), the regressions need to go through the origin (0 intercept). Is it possible to do ANCOVA for these regressions without intercepts? When I do summary(lm(body length ~ sex*head length)) this will include the intercepts as below Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -6.49697 1.68497 -3.856 0.000118 *** sexMale -9.39340 1.97760 -4.750 2.14e-06 *** sexUnknown -1.33791 2.35453 -0.568 0.569927 head_length 7.12307 0.05503 129.443 2e-16 *** sexMale:head_length 0.31631 0.06246 5.064 4.37e-07 *** sexUnknown:head_length 0.19937 0.07022 2.839 0.004556 ** --- Is there any way I can remove the intercepts so that I can simply compare the slopes with no intercept taken into account? Thanks for help in advance. Yusuke Fukuda __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Men by nature long to get on to the ultimate truths, and will often be impatient with elementary studies or fight shy of them. If it were possible to reach the ultimate truths without the elementary studies usually prefixed to them, these would not be preparatory studies but superfluous diversions. -- Maimonides (1135-1204) Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] principal components
HI all, I am trying to compute the EOF of a matrix using prcomp but unable to get the expansion co-efficients. is it possible using prcomp or are there any other methods thanks nuncio -- Nuncio.M Research Scientist National Center for Antarctic and Ocean research Head land Sada Vasco da Gamma Goa-403804 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple lattice question
-Mensaje original-
De: Peter Ehlers [mailto:ehl...@ucalgary.ca]
Enviado el: jueves, 31 de marzo de 2011 18:09
Para: Rubén Roa
CC: r-help@r-project.org
Asunto: Re: [R] Simple lattice question
On 2011-03-31 06:58, Rubén Roa wrote:
Thanks Peters!
Just a few minor glitches now:
require(lattice)
data-
data.frame(SP=sort(rep(as.factor(c('A','B','C','D','E')),12)),
x=rpois(60,10),
y=rep(c(rep(0,4),rep(10,4),rep(20,4)),5),
z=rep(1:4,15))
xyplot(x~y|SP,data=data,groups=z,layout=c(2,3),pch=1:4,lty=1:4
,col='black',type='b',
key=list(x = .65, y = .75, corner = c(0, 0), points=TRUE,
lines=TRUE, pch=1:4, lty=1:4, type='b',
text=list(lab = as.character(unique(data$z)
I have an extra column of symbols on the legend,
and,
would like to add a title to the legend. Such as 'main' for plots.
Any suggestions?
for key(), make 'lines' into a list:
xyplot(x~y|SP,data=data,groups=z,layout=c(2,3),
pch=1:4,lty=1:4,col='black',type='b',
key=list(x = .65, y = .75, corner = c(0, 0),
title=title here, cex.title=.9, lines.title=3,
lines=list(pch=1:4, lty=1:4, type='b'),
text=list(lab = as.character(unique(data$z)
Peter Ehlers
... that works. Thanks Peter (sorry I misspelled your name b4). The clean code
is now:
require(lattice)
data - data.frame(SP=sort(rep(as.factor(c('A','B','C','D','E')),12)),
x=rpois(60,10),
y=rep(c(rep(0,4),rep(10,4),rep(20,4)),5),
z=rep(1:4,15))
xyplot(x~y|SP,data=data,groups=z,layout=c(2,3),pch=1:4,lty=1:4,col='black',type='b',
key=list(x = .65, y = .75, corner = c(0, 0),
lines=list(pch=1:4, lty=1:4, type='b'),
title=expression(CO^2),
text=list(lab = as.character(unique(data$z)
David's code works too (thanks to you too!) and is somewhat shorter
xyplot(x~y|SP, data=data,groups=z, layout=c(2,3),
par.settings=simpleTheme(pch=1:4,lty=1:4,col='black'), type=b,
auto.key = list(x = .6, y = .7, lines=TRUE, corner = c(0, 0)))
but the lines and symbols are on different columns, and the line types look as
if they were in bold.
Rubén
Dr. Rubén Roa-Ureta
AZTI - Tecnalia / Marine Research Unit
Txatxarramendi Ugartea z/g
48395 Sukarrieta (Bizkaia)
SPAIN
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Re: [R] Assign Names of columns in data.frame dinamically
Hi Marcos,
I'd be glad to help, but your example is not usable for anyone but
yourself - I don't have the files that your code reads and I don't have
any idea what the resulting data frames look like. Please provide
examples of the data and the result.
Andreas
Marcos Amaris Gonzalez schrieb:
Hello List.
I have many files of ECG, each one with 7 column and I need only the
second column and the name of each ECG. I am doing this but althought
I have various days trying this i haven't gotten, so I ask help with
this, if somebody cans help me I'll be so thankfully.
rm(list=ls())
# loadEcgFiles - function(Dir=.) {
Dir - .;
txtfiles - list.files(paste(Dir),'.txt$');
ecg = data.frame(ncol=1);
len = length(txtfiles);
for (i in 1:5 ) {
# i - 1;
filename = paste(projectDir, / ,
txtfiles[i],sep='');
sample = read.table(filename, nrow=75000);
sampleName = filename; sampleName=gsub(./,
,sampleName); sampleName=gsub(.txt, , sampleName);
temp - sample$V2;
names(temp) - sampleName;
ecg = cbind(ecg, temp);
#}
Thanks and sorry for my english.
---
Marcos Amaris González - Linux Counter #462840
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[R] TV VECM (formerly: VECM with UNRESTRICTED TREND)
Dear Renoir,
are you referring to:
http://econ.la.psu.edu/~hbierens/TVCOINT.PDF
?
If so, no, but you could up this framework fairly easily and hereby employ the
functions of urca. But this should already be evident from the package's
manual.
Best,
Bernhard
-Ursprüngliche Nachricht-
Von: renoir vieira [mailto:renoirvie...@gmail.com]
Gesendet: Donnerstag, 31. März 2011 22:27
An: Grzegorz Konat
Cc: Pfaff, Bernhard Dr.; r-help@r-project.org
Betreff: Re: [R] VECM with UNRESTRICTED TREND
Dear Pfaff,
Would that be possible to fit a Time varying VECM using urca?
Yours,
Renoir
On Thursday, March 31, 2011, Grzegorz Konat
grzegorz.ko...@ibrkk.pl wrote:
The code you gave me works fine with Finland, but the same
for my data
- does not!
I do:
library(urca)
data(my.data)
dat1 - my.data[, c(dY, X, dM)]
trend - matrix(1:nrow(dat1), ncol = 1)
colnames(trend) - trd
yxm.vecm - ca.jo(dat1, type = trace, ecdet = const, K
= 2, spec =
longrun, dumvar = trend)
and the result is again:
Error in r[i1, , drop = FALSE] - r[-nrow(r):-(nrow(r) - lag
+ 1L), ,
drop = FALSE] :
non-numeric argument to binary operator
I attach my dataset in xls format. If you have 5 minutes
and wish to
check it out, I'd be extremely grateful!
Best,
Greg
2011/3/31 Pfaff, Bernhard Dr. bernhard_pf...@fra.invesco.com
Well, without further information, I do not know, but try the
following
library(urca)
example(ca.jo)
trend - matrix(1:nrow(sjf), ncol = 1)
colnames(trend) - trd
ca.jo(sjf, type = trace, ecdet = const, K = 2, spec =
longrun,
dumvar = trend)
Best,
Bernhard
--
*Von:* Grzegorz Konat [mailto:grzegorz.ko...@ibrkk.pl]
*Gesendet:* Donnerstag, 31. März 2011 14:40
*An:* Pfaff, Bernhard Dr.; r-help@r-project.org
*Betreff:* Re: [R] VECM with UNRESTRICTED TREND
'time' was a trend variable from my.data set. Equivalent to the
output of the command 'matrix' you just gave me.
So now I did:
library(urca)
data(my.data)
names(my.data)
attach(my.data)
dat1 - my.data[, c(dY, X, dM)]
mat1 - matrix(seq(1:nrow(dat1)), ncol = 1)
args('ca.jo')
yxm.vecm - ca.jo(dat1, type = trace, ecdet = const, K
= 2, spec
= longrun, dumvar=mat1)
and the output is:
Error in r[i1, , drop = FALSE] - r[-nrow(r):-(nrow(r) -
lag + 1L), ,
drop = FALSE] :
non-numeric argument to binary operator In addition: Warning
message:
In ca.jo(dat1, type = trace, ecdet = const, K = 2, spec =
longrun,
:
No column names in 'dumvar', using prefix 'exo' instead.
What do I do wrong?
Best,
Greg
2011/3/31 Pfaff, Bernhard Dr. bernhard_pf...@fra.invesco.com
Hello Bernhard,
thank You so much one again! Now I (more or less) understand the
idea, but still have problem with its practical application.
I do (somewhat following example 8.1 in your textbook):
library(urca)
data(my.data)
names(my.data)
attach(my.data)
dat1 - my.data[, c(dY, X, dM)]
dat2 - cbind(time)
What is 'time'? Just employ matrix(seq(1:nrow(dat1)),
ncol = 1) for
creating the trend variable.
Best,
Bernhard
args('ca.jo')
yxm.vecm - ca.jo(dat1, type = trace, ecdet = trend,
K = 2, spec
= longrun, dumvar=dat2)
The above code produces following output:
Error in r[i1, , drop = FALSE] - r[-nrow(r):-(nrow(r) -
lag + 1L),
, drop = FALSE] :
non-numeric argument to binary operator
What does that mean? Should I use cbind command to dat1
as well? And
doesn't it transform the series into series of integer numbers?
Thank you once again (especially for your patience).
Best,
Greg
2011/3/31 Pfaff, Bernhard Dr. bernhard_pf...@fra.invesco.com
Hello Greg,
you include your trend as a (Nx1) matrix and use this
for 'dumvar'.
The matrix 'dumvar' is just added to the VECM as deterministic
regressors and while you are referring to case 5, this
is basically
what you are after, if I am not mistaken. But we aware that this
implies a quadratic trend for the levels
*
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[R] Using a variable in a covariance structure and as a predictor - is this OK?
Dear list, I have the model below which i am using to account for spatial autocorrelation: exponential -corExp(form = ~ Longitude + Latitude) explanation_mod_all - gls(Lower_PD~Area+Elevation+Temperature+Preceipitation+Agriculture+Urban+Human.footprint+Population, correlation = exponential) I want to see if Latitude and Longitude are significant, is it statistically and methodologically correct to add them to the model i.e explanation_mod_all - gls(Lower_PD~Area+Elevation+Temperature+Preceipitation+Agriculture+Urban+Human.footprint+Population+Longitude+Latitude, correlation = exponential) ? Thanks Chris __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] pROC 1.4.3: compare two ROC curves in R
Dear R users,
pROC is a package to compare, visualize, and smooth receiver operating
characteristic (ROC) curves.
The package provides the following features:
* Partial or full area under the curve (AUC) computation
* Comparison of two ROC curves (curves and AUC)
* Calculating and plotting confidence intervals
* Smoothing of the ROC curve
* Coordinates extraction ('coords' function).
The main feature of pROC is the comparison between two ROC curves. Three
methods are currently implemented for both paired and unpaired ROC curves:
* Bootstrap for full and partial AUC and smoothed ROC curves
* DeLong [1] method for full AUC
* Venkatraman [2, 3].
Confidence intervals can be computed with bootstrap for both empirical
or smoothed ROC curves:
* partial or full AUC (also with DeLong [1] method for full AUC)
* ROC coordinates (thresholds, sensitivity or specificity).
You can find more information in our paper [4] and on pROC website:
http://www.expasy.org/tools/pROC/
Hope you'll find it useful!
Xavier Robin
--
References:
[1] DeLong ER, DeLong DM, Clarke-Pearson DL (1988) Comparing the areas
under two or more correlated receiver operating characteristic curves: a
nonparametric approach. Biometrics 44, 837–845.
[2] Venkatraman ES,Begg CB (1996) A distribution-free procedure for
comparing receiver operating characteristic curves from a paired
experiment. Biometrika 83, 835–848.
[3] Venkatraman ES (2000) A Permutation Test to Compare Receiver
Operating Characteristic Curves. Biometrics 56, 1134–1138.
[4] Robin X, Turck N, Hainard A, et al. (2011). pROC: an open-source
package for R and S+ to analyze and compare ROC curves. BMC
Bioinformatics, 12, 77. http://dx.doi.org/10.1186/1471-2105-12-77
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Re: [R] How to update R?
On Thu, Mar 31, 2011 at 9:04 PM, Shi, Tao shida...@yahoo.com wrote: This question has been asked by many people already. The easiest way is: 1) install the new version 2) copy all or the libraries that you installed later from the library folder of older version to the new version 3) uninstall the old version 4) do a library update in the new version On Windows, I've found that it is actually better to uninstall the old version first. Uninstalling removes file associations for .Rdata and other files even if a more recent version of R is present (although perhaps there is a way to tell it not to) but this won't be a problem if you do it in the following order: 3) uninstall the old version 1) install the new version 2) copy all or the libraries that you installed later from the library folder of older version to the new version 4) do a library update in the new version Kenn __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] MySql Versus R
Dear R Users, I use for my data crunching a combination of MySQL and GNU R. I have to handle huge/ middle seized data which is stored in a MySql database, R executes a SQL command to fetch the data and does the plotting with the build in R plotting functions. The (low level) calculations like summing, dividing, grouping, sorting etc. can be done either with the sql command on the MySQL side or on the R side. My question is what is faster for this low level calculations / data rearrangement MySQL or R? Is there a general rule of thumb what to shift to the MySql side and what to the R side? Thanks Henri __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MySql Versus R
On Fri, Apr 1, 2011 at 1:46 PM, Henri Mone henrim...@gmail.com wrote: Dear R Users, I use for my data crunching a combination of MySQL and GNU R. I have to handle huge/ middle seized data which is stored in a MySql database, R executes a SQL command to fetch the data and does the plotting with the build in R plotting functions. The (low level) calculations like summing, dividing, grouping, sorting etc. can be done either with the sql command on the MySQL side or on the R side. My question is what is faster for this low level calculations / data rearrangement MySQL or R? Is there a general rule of thumb what to shift to the MySql side and what to the R side? Thanks Henri __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. I would assume RDBMS have advanced memory management capabilities and are designed for the manipulation and handling of large amounts of data. These are primary features for most database management server software. This way the database management server software should (in most cases) be used to store, manipulate then return only the processed and qualifying records to the client or other application for further specialized processing and/or data visualization. Allan. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] programming: telling a function where to look for the entered variables
Hi there,
Could someone help me with the following programming problem..?
I have written a function that works for my intended purpose, but it
is quite closely tied to a particular dataframe and the names of the
variables in this dataframe. However, I'd like to use the same
function for different dataframes and variables. My problem is that
I'm not quite sure how to tell my function in which dataframe the
entered variables are located.
Here's some reproducible data and the function:
# create reproducible data
set.seed(124)
xvar - sample(0:3, 1000, replace = T)
yvar - sample(0:1, 1000, replace=T)
zvar - rnorm(100)
lvar - sample(0:1, 1000, replace=T)
Fulldf - as.data.frame(cbind(xvar,yvar,zvar,lvar))
Fulldf$xvar - factor(xvar, labels=c(blue,green,red,yellow))
Fulldf$yvar - factor(yvar, labels=c(area1,area2))
Fulldf$lvar - factor(lvar, labels=c(yes,no))
and here's the function in the form that it currently works: from a
subset of the dataframe Fulldf, a contingency table is created (in my
actual data, several other operations are then performed on that
contingency table, but these are not relevant for the problem in
question, therefore I've deleted it) .
# function as it currently works: tailored to a particular dataframe (Fulldf)
myfunct - function(subgroup){ # enter a particular subgroup for which
the contingency table should be calculated (i.e. a particular value of
the factor lvar)
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
#restrict dataframe to given subgroup and two columns of the original
dataframe
Data.tmp - na.omit(Data.tmp) # exclude missing values
indextable - table(Data.tmp$xvar, Data.tmp$yvar) # make contingency table
return(indextable)
}
#Since I need to use the function with different dataframes and
variable names, I'd like to be able to tell my function the name of
the dataframe and variables it should use for calculating the index.
This is how I tried to modify the first part of the #function, but it
didn't work:
# function as I would like it to work: independent of any particular
dataframe or variable names (doesn't work)
myfunct.better - function(subgroup, lvarname, yvarname, dataframe){
#enter the subgroup, the variable names to be used and the dataframe
in which they are found
Data.tmp - subset(dataframe, lvarname==subgroup, select=c(xvar,
deparse(substitute(yvarname # trying to subset the given dataframe
for the given subgroup of the given variable. The variable xvar
happens to have the same name in all dataframes) but the variable
yvarname has different names in the different dataframes
Data.tmp - na.omit(Data.tmp)
indextable - table(Data.tmp$xvar, Data.tmp$yvarname) # create the
contingency table on the basis of the entered variables
return(indextable)
}
calling
myfunct.better(yes, lvarname=lvar, yvarname=yvar, dataframe=Fulldf)
results in the following error:
Error in `[.data.frame`(x, r, vars, drop = drop) :
undefined columns selected
My feeling is that R doesn't know where to look for the entered
variables (lvar, yvar), but I'm not sure how to solve this problem. I
tried using with() and even attach() within the function, but that
didn't work.
Any help is greatly appreciated.
Best,
Esther
P.S.:
Are there books that elaborate programming in R for beginners -- and I
mean things like how to best use vectorization instead of loops and
general best practice tips for programming. Most of the books I've
been looking at focus on applying R for particular statistical
analyses, and only comparably briefly deal with more general
programming aspects. I was wondering if there's any books or tutorials
out there that cover the latter aspects in a more elaborate and
systematic way...?
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Re: [R] MySql Versus R
On Fri, 1 Apr 2011, Henri Mone wrote: Dear R Users, I use for my data crunching a combination of MySQL and GNU R. I have to handle huge/ middle seized data which is stored in a MySql database, R executes a SQL command to fetch the data and does the plotting with the build in R plotting functions. The (low level) calculations like summing, dividing, grouping, sorting etc. can be done either with the sql command on the MySQL side or on the R side. My question is what is faster for this low level calculations / data rearrangement MySQL or R? Is there a general rule of thumb what to shift to the MySql side and what to the R side? The data transfer costs almost always dominate here: since such low-level computations would almost always be a trivial part of the total costs, you should do things which can reduce the size (e.g. summarizations) in the DBMS. I do wonder what you think the R-sig-db list is for if not questions such as this one. Please subscribe and use it next time. Thanks Henri -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MySql Versus R
On Fri, Apr 1, 2011 at 6:46 AM, Henri Mone henrim...@gmail.com wrote: Dear R Users, I use for my data crunching a combination of MySQL and GNU R. I have to handle huge/ middle seized data which is stored in a MySql database, R executes a SQL command to fetch the data and does the plotting with the build in R plotting functions. The (low level) calculations like summing, dividing, grouping, sorting etc. can be done either with the sql command on the MySQL side or on the R side. My question is what is faster for this low level calculations / data rearrangement MySQL or R? Is there a general rule of thumb what to shift to the MySql side and what to the R side? The sqldf package makes it easy to use sqlite, h2 or postgresql from R to carry out data manipulation tasks and this has facilitated some benchmarks by users using sqlite's capability of using an in memory database. In the cases cited on the sqldf home page sqlite was faster than R despite the overhead of moving the data into the database and out again. See http://sqldf.googlecode.com In general the answer would depend on the database, what has been cached, the particular query, size of data and how well you had optimized your sql and R queries. There are entire books on optimizing MySQL so this is an extensive subject. Various comparisons of different approaches can easily result in different ordering from fastest to slowest based on what would appear to be relatively minor aspects of the problem so you would have to benchmark the important queries to really get an answer that pertains to your situation. Check out the rbenchmark package for this which makes it relatively simple to do. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MySql Versus R
On Fri, Apr 1, 2011 at 11:46 AM, Henri Mone henrim...@gmail.com wrote: Dear R Users, I use for my data crunching a combination of MySQL and GNU R. I have to handle huge/ middle seized data which is stored in a MySql database, R executes a SQL command to fetch the data and does the plotting with the build in R plotting functions. The (low level) calculations like summing, dividing, grouping, sorting etc. can be done either with the sql command on the MySQL side or on the R side. My question is what is faster for this low level calculations / data rearrangement MySQL or R? Is there a general rule of thumb what to shift to the MySql side and what to the R side? Given that you are already set up to test this yourself, why don't you? SELECT everything from a table and add it in R, and then SELECT sum(everything) from a table and compare the time (obviously your example might be more complex). Post some benchmark test results together with your hardware spec. Probably best to the db-flavour R mailing list. Is the MySQl server running locally, ie on the same machine? Maybe PostgreSQL will be even faster? So many of these questions are problem-specific and hardware-setup related. You can get massive speedups by having more RAM, or more disk, or spreading your giant database onto multiple servers. Rules of thumb are rare in this world, since everyone's thumbs are different sizes and are being stuck into different sized problems. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] programming: telling a function where to look for the entered variables
See the warning in ?subset.
Passing the column name of lvar is not the same as passing the 'contextual
column' (as I coin it in these circumstances).
You can solve it by indeed using [] instead.
For my own comfort, here is the relevant line from your original function:
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
Which should become something like (untested but should be close):
Data.tmp - Fulldf[Fulldf[,lvar]==subgroup, c(xvar,yvar)]
This should be a lot easier to translate based on column names, as the
column names are now used as such.
HTH,
Nick Sabbe
--
ping: nick.sa...@ugent.be
link: http://biomath.ugent.be
wink: A1.056, Coupure Links 653, 9000 Gent
ring: 09/264.59.36
-- Do Not Disapprove
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of E Hofstadler
Sent: vrijdag 1 april 2011 13:09
To: r-help@r-project.org
Subject: [R] programming: telling a function where to look for the entered
variables
Hi there,
Could someone help me with the following programming problem..?
I have written a function that works for my intended purpose, but it
is quite closely tied to a particular dataframe and the names of the
variables in this dataframe. However, I'd like to use the same
function for different dataframes and variables. My problem is that
I'm not quite sure how to tell my function in which dataframe the
entered variables are located.
Here's some reproducible data and the function:
# create reproducible data
set.seed(124)
xvar - sample(0:3, 1000, replace = T)
yvar - sample(0:1, 1000, replace=T)
zvar - rnorm(100)
lvar - sample(0:1, 1000, replace=T)
Fulldf - as.data.frame(cbind(xvar,yvar,zvar,lvar))
Fulldf$xvar - factor(xvar, labels=c(blue,green,red,yellow))
Fulldf$yvar - factor(yvar, labels=c(area1,area2))
Fulldf$lvar - factor(lvar, labels=c(yes,no))
and here's the function in the form that it currently works: from a
subset of the dataframe Fulldf, a contingency table is created (in my
actual data, several other operations are then performed on that
contingency table, but these are not relevant for the problem in
question, therefore I've deleted it) .
# function as it currently works: tailored to a particular dataframe
(Fulldf)
myfunct - function(subgroup){ # enter a particular subgroup for which
the contingency table should be calculated (i.e. a particular value of
the factor lvar)
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
#restrict dataframe to given subgroup and two columns of the original
dataframe
Data.tmp - na.omit(Data.tmp) # exclude missing values
indextable - table(Data.tmp$xvar, Data.tmp$yvar) # make contingency table
return(indextable)
}
#Since I need to use the function with different dataframes and
variable names, I'd like to be able to tell my function the name of
the dataframe and variables it should use for calculating the index.
This is how I tried to modify the first part of the #function, but it
didn't work:
# function as I would like it to work: independent of any particular
dataframe or variable names (doesn't work)
myfunct.better - function(subgroup, lvarname, yvarname, dataframe){
#enter the subgroup, the variable names to be used and the dataframe
in which they are found
Data.tmp - subset(dataframe, lvarname==subgroup, select=c(xvar,
deparse(substitute(yvarname # trying to subset the given dataframe
for the given subgroup of the given variable. The variable xvar
happens to have the same name in all dataframes) but the variable
yvarname has different names in the different dataframes
Data.tmp - na.omit(Data.tmp)
indextable - table(Data.tmp$xvar, Data.tmp$yvarname) # create the
contingency table on the basis of the entered variables
return(indextable)
}
calling
myfunct.better(yes, lvarname=lvar, yvarname=yvar, dataframe=Fulldf)
results in the following error:
Error in `[.data.frame`(x, r, vars, drop = drop) :
undefined columns selected
My feeling is that R doesn't know where to look for the entered
variables (lvar, yvar), but I'm not sure how to solve this problem. I
tried using with() and even attach() within the function, but that
didn't work.
Any help is greatly appreciated.
Best,
Esther
P.S.:
Are there books that elaborate programming in R for beginners -- and I
mean things like how to best use vectorization instead of loops and
general best practice tips for programming. Most of the books I've
been looking at focus on applying R for particular statistical
analyses, and only comparably briefly deal with more general
programming aspects. I was wondering if there's any books or tutorials
out there that cover the latter aspects in a more elaborate and
systematic way...?
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cox Proportional Hazards model with a time-varying covariate
The R results I'm getting are similar to the SAS results but not very close. For example, my coefficient for TRT is .2913 in R but SAS gives .3450. I'd like to be able to run the R Code with method = exact to make it as same as the AS example but I can't seem to get it to work You need to read the documentation more carefully. The exact partial likelihood (Cox's label, not mine), which is appropriate for data on a discreete time scale, is invoked by the exact option for ties in R and by using the discrete option in SAS. (In hindsight I actually like their choice of a label somewhat better, since users more often make the correct association of method to data.) This method can take nearly forever to compute, however, when there are a lot of subjects tied at a given time. For instance at time 20 your data set has 10 events out of 77 subjects; the term in the exact partial likelihood requires a sum over all the possible subsets of 10 chosen from 77, approximately 10^12 terms: you might retire before it finishes. The exact marginal likelihood proposed by Prentice is invoked in SAS using ties=exact, it is not implimented in R. I have never found any compelling reason to program it. Statistical comment: in statistics an exact method means that the solution can be computed exactly, the label has absolutely no connection with the question of whether the method is a sensible thing to do. In the case of a Cox model, I prefer and strongly recommend using the Efron approximation for ties, this is the default in R. The Breslow approximation is usually quite good enough, this is the default in SAS. Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: wireframe eats up points; how to make points on wireframe visible?
On Thu, Mar 31, 2011 at 3:26 AM, Marius Hofert m_hof...@web.de wrote:
Dear Deepayan,
thanks for answering. It's never too late to be useful.
I see your point in the minimal example. I checked the z-axis limits in my
original problem for the point to be inside and it wasn't there. I can't
easily
reproduce it from the minimal example though. I'll get back to you if I run
into
this problem again.
In the example below, both points are shown. Although one lies clearly
below/under
the surface, it looks as if it lies above. One would probably have to plot
this
point first so that the wire frame is above the point. But still, this is
misleading since the eye believes that the wireframe is *not* transparent.
This
happens because the lines connecting (0,1,0)--(1,1,0)--(1,0,0) [dashed ones]
are
not completely visible [also not the one from (1,1,0) to (1,1,1)]. How can I
make
them visible even if they lie behind/under the wireframe? I tried to work with
col=transparent and with alpha=... but neither did work as I expected.
My goal is to make the small rectangles between the wire transparent.
I also use these plots in posters with a certain gradient-like background
color
and so it's a bit annoying that the rectangles are filled with white color.
Yes, that probably needs a new argument; the default computation is a
bit of a hack. You can try the following workaround for now:
wireframe(z~x*y, pts=pts, aspect=1, scales=list(col=1, arrows=FALSE),
zlim=c(0,1),
par.settings = list(background = list(col = #ff11)), ## - NEW
panel.3d.wireframe = function(x,y,z,xlim,ylim,zlim,xlim.scaled,
ylim.scaled,zlim.scaled,pts,...){
panel.3dwire(x=x, y=y, z=z, xlim=xlim, ylim=ylim, zlim=zlim,
xlim.scaled=xlim.scaled, ylim.scaled=ylim.scaled,
zlim.scaled=zlim.scaled, ...)
panel.3dscatter(x=pts[,1], y=pts[,2], z=pts[,3],
xlim=xlim, ylim=ylim, zlim=zlim,
xlim.scaled=xlim.scaled, ylim.scaled=ylim.scaled,
zlim.scaled=zlim.scaled, type=p, col=c(2,3),
cex=1.8, pch=c(3,4), .scale=TRUE, ...)
})
col = #ff00 instead will give you full transparency (but
transparent will not work), and col = #ff77 will be less
transparent and so on.
-Deepayan
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] programming: telling a function where to look for the entered variables
Thanks Nick and Juan for your replies.
Nick, thanks for pointing out the warning in subset(). I'm not sure
though I understand the example you provided -- because despite using
subset() rather than bracket notation, the original function (myfunct)
does what is expected of it. The problem I have is with the second
function (myfunct.better), where variable names + dataframe are not
fixed within the function but passed to the function when calling it
-- and even with bracket notation I don't quite manage to tell R where
to look for the columns that related to the entered column names.
(but then perhaps I misunderstood you)
This is what I tried (using bracket notation):
myfunct.better(dataframe, subgroup, lvarname,yvarname){
Data.tmp - dataframe[dataframe[,deparse(substitute(lvarname))]==subgroup,
c(xvar,deparse(substitute(yvarname)))]
}
but this creates an empty contingency table only -- perhaps because my
use of deparse() is flawed (I think what is converted into a string is
lvarname and yvarname, rather than the column names that these two
function-variables represent in the dataframe)?
2011/4/1 Nick Sabbe nick.sa...@ugent.be:
See the warning in ?subset.
Passing the column name of lvar is not the same as passing the 'contextual
column' (as I coin it in these circumstances).
You can solve it by indeed using [] instead.
For my own comfort, here is the relevant line from your original function:
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
Which should become something like (untested but should be close):
Data.tmp - Fulldf[Fulldf[,lvar]==subgroup, c(xvar,yvar)]
This should be a lot easier to translate based on column names, as the
column names are now used as such.
HTH,
Nick Sabbe
--
ping: nick.sa...@ugent.be
link: http://biomath.ugent.be
wink: A1.056, Coupure Links 653, 9000 Gent
ring: 09/264.59.36
-- Do Not Disapprove
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of E Hofstadler
Sent: vrijdag 1 april 2011 13:09
To: r-help@r-project.org
Subject: [R] programming: telling a function where to look for the entered
variables
Hi there,
Could someone help me with the following programming problem..?
I have written a function that works for my intended purpose, but it
is quite closely tied to a particular dataframe and the names of the
variables in this dataframe. However, I'd like to use the same
function for different dataframes and variables. My problem is that
I'm not quite sure how to tell my function in which dataframe the
entered variables are located.
Here's some reproducible data and the function:
# create reproducible data
set.seed(124)
xvar - sample(0:3, 1000, replace = T)
yvar - sample(0:1, 1000, replace=T)
zvar - rnorm(100)
lvar - sample(0:1, 1000, replace=T)
Fulldf - as.data.frame(cbind(xvar,yvar,zvar,lvar))
Fulldf$xvar - factor(xvar, labels=c(blue,green,red,yellow))
Fulldf$yvar - factor(yvar, labels=c(area1,area2))
Fulldf$lvar - factor(lvar, labels=c(yes,no))
and here's the function in the form that it currently works: from a
subset of the dataframe Fulldf, a contingency table is created (in my
actual data, several other operations are then performed on that
contingency table, but these are not relevant for the problem in
question, therefore I've deleted it) .
# function as it currently works: tailored to a particular dataframe
(Fulldf)
myfunct - function(subgroup){ # enter a particular subgroup for which
the contingency table should be calculated (i.e. a particular value of
the factor lvar)
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
#restrict dataframe to given subgroup and two columns of the original
dataframe
Data.tmp - na.omit(Data.tmp) # exclude missing values
indextable - table(Data.tmp$xvar, Data.tmp$yvar) # make contingency table
return(indextable)
}
#Since I need to use the function with different dataframes and
variable names, I'd like to be able to tell my function the name of
the dataframe and variables it should use for calculating the index.
This is how I tried to modify the first part of the #function, but it
didn't work:
# function as I would like it to work: independent of any particular
dataframe or variable names (doesn't work)
myfunct.better - function(subgroup, lvarname, yvarname, dataframe){
#enter the subgroup, the variable names to be used and the dataframe
in which they are found
Data.tmp - subset(dataframe, lvarname==subgroup, select=c(xvar,
deparse(substitute(yvarname # trying to subset the given dataframe
for the given subgroup of the given variable. The variable xvar
happens to have the same name in all dataframes) but the variable
yvarname has different names in the different dataframes
Data.tmp - na.omit(Data.tmp)
indextable - table(Data.tmp$xvar, Data.tmp$yvarname) # create the
contingency table on the basis of the entered variables
return(indextable)
}
Re: [R] programming: telling a function where to look for the entered variables
This should be a version that does what you want.
Because you named the variable lvarname, I assumed you were already passing
lvar instead of trying to pass lvar (without the quotes), which is in no
way a 'name'.
myfunct.better - function(subgroup, lvarname, xvarname, yvarname,
dataframe)
{
#enter the subgroup, the variable names to be used and the dataframe
#in which they are found
Data.tmp - Fulldf[Fulldf[,lvarname]==subgroup,
c(xvarname,yvarname)]
Data.tmp -na.omit(Data.tmp)
indextable - table(Data.tmp[,xvarname], Data.tmp[,yvarname]) #
create the contingency
#table on the basis of the entered variables
#actually, if I remember well, you could simply use
indextable-table(Data.tmp) here
#that would allow for some more simplifications (replace xvarname
and yvarname by
#columnsOfInterest or similar, and pass that instead of c(xvarname,
yvarname) )
return(indextable)
}
myfunct.better(yes, lvarname=lvar, xvarname=xvar, yvarname=yvar,
dataframe=Fulldf)
HTH,
Nick Sabbe
--
ping: nick.sa...@ugent.be
link: http://biomath.ugent.be
wink: A1.056, Coupure Links 653, 9000 Gent
ring: 09/264.59.36
-- Do Not Disapprove
-Original Message-
From: irene.p...@googlemail.com [mailto:irene.p...@googlemail.com] On Behalf
Of E Hofstadler
Sent: vrijdag 1 april 2011 14:28
To: Nick Sabbe
Cc: r-help@r-project.org
Subject: Re: [R] programming: telling a function where to look for the
entered variables
Thanks Nick and Juan for your replies.
Nick, thanks for pointing out the warning in subset(). I'm not sure
though I understand the example you provided -- because despite using
subset() rather than bracket notation, the original function (myfunct)
does what is expected of it. The problem I have is with the second
function (myfunct.better), where variable names + dataframe are not
fixed within the function but passed to the function when calling it
-- and even with bracket notation I don't quite manage to tell R where
to look for the columns that related to the entered column names.
(but then perhaps I misunderstood you)
This is what I tried (using bracket notation):
myfunct.better(dataframe, subgroup, lvarname,yvarname){
Data.tmp - dataframe[dataframe[,deparse(substitute(lvarname))]==subgroup,
c(xvar,deparse(substitute(yvarname)))]
}
but this creates an empty contingency table only -- perhaps because my
use of deparse() is flawed (I think what is converted into a string is
lvarname and yvarname, rather than the column names that these two
function-variables represent in the dataframe)?
2011/4/1 Nick Sabbe nick.sa...@ugent.be:
See the warning in ?subset.
Passing the column name of lvar is not the same as passing the 'contextual
column' (as I coin it in these circumstances).
You can solve it by indeed using [] instead.
For my own comfort, here is the relevant line from your original function:
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
Which should become something like (untested but should be close):
Data.tmp - Fulldf[Fulldf[,lvar]==subgroup, c(xvar,yvar)]
This should be a lot easier to translate based on column names, as the
column names are now used as such.
HTH,
Nick Sabbe
--
ping: nick.sa...@ugent.be
link: http://biomath.ugent.be
wink: A1.056, Coupure Links 653, 9000 Gent
ring: 09/264.59.36
-- Do Not Disapprove
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf Of E Hofstadler
Sent: vrijdag 1 april 2011 13:09
To: r-help@r-project.org
Subject: [R] programming: telling a function where to look for the entered
variables
Hi there,
Could someone help me with the following programming problem..?
I have written a function that works for my intended purpose, but it
is quite closely tied to a particular dataframe and the names of the
variables in this dataframe. However, I'd like to use the same
function for different dataframes and variables. My problem is that
I'm not quite sure how to tell my function in which dataframe the
entered variables are located.
Here's some reproducible data and the function:
# create reproducible data
set.seed(124)
xvar - sample(0:3, 1000, replace = T)
yvar - sample(0:1, 1000, replace=T)
zvar - rnorm(100)
lvar - sample(0:1, 1000, replace=T)
Fulldf - as.data.frame(cbind(xvar,yvar,zvar,lvar))
Fulldf$xvar - factor(xvar, labels=c(blue,green,red,yellow))
Fulldf$yvar - factor(yvar, labels=c(area1,area2))
Fulldf$lvar - factor(lvar, labels=c(yes,no))
and here's the function in the form that it currently works: from a
subset of the dataframe Fulldf, a contingency table is created (in my
actual data, several other operations are then performed on that
contingency table, but these are not relevant for the problem in
question, therefore I've deleted it) .
# function as it currently works: tailored to a particular dataframe
(Fulldf)
myfunct - function(subgroup){ #
Re: [R] Linear Model with curve fitting parameter?
Setting Z=Q-A would be the incorrect dimensions. I could Z=Q/A. Is fitting a nls model the same as fitting an ols? These data are hydraulic data from ~47 sites. To access predictive ability I am removing one site fitting a new model and then accessing the fit with a myriad of model assessment criteria. I should get the same answer with ols vs nls? Thank you for all of your help. Stephen On Thu, Mar 31, 2011 at 8:34 PM, Steven McKinney smckin...@bccrc.ca wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of stephen sefick Sent: March-31-11 3:38 PM To: R help Subject: [R] Linear Model with curve fitting parameter? I have a model Q=K*A*(R^r)*(S^s) A, R, and S are data I have and K is a curve fitting parameter. I have linearized as log(Q)=log(K)+log(A)+r*log(R)+s*log(S) I have taken the log of the data that I have and this is the model formula without the K part lm(Q~offset(A)+R+S, data=x) What is the formula that I should use? Let Z = Q - A for your logged data. Fitting lm(Z ~ R + S, data = x) should yield intercept parameter estimate = estimate for log(K) R coefficient parameter estimate = estimate for r S coefficient parameter estimate = estimate for s Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre Thanks for all of your help. I can provide a subset of data if necessary. -- Stephen Sefick | Auburn University | | Biological Sciences | | 331 Funchess Hall | | Auburn, Alabama | | 36849 | |___| | sas0...@auburn.edu | | http://www.auburn.edu/~sas0025 | |___| Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick | Auburn University | | Biological Sciences | | 331 Funchess Hall | | Auburn, Alabama | | 36849 | |___| | sas0...@auburn.edu | | http://www.auburn.edu/~sas0025 | |___| Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple lattice question
Ruben,
One more thing you might try is to add a 'size' component to
the lines list. The default is size=5, but since you have
enought space in the plot, try size=8 or 9; the line types
will show up more clearly:
lines=list(pch=1:4, lty=1:4, type='b', size=8),
Peter Ehlers
On 2011-03-31 23:28, Rubén Roa wrote:
-Mensaje original-
De: Peter Ehlers [mailto:ehl...@ucalgary.ca]
Enviado el: jueves, 31 de marzo de 2011 18:09
Para: Rubén Roa
CC: r-help@r-project.org
Asunto: Re: [R] Simple lattice question
On 2011-03-31 06:58, Rubén Roa wrote:
Thanks Peters!
Just a few minor glitches now:
require(lattice)
data-
data.frame(SP=sort(rep(as.factor(c('A','B','C','D','E')),12)),
x=rpois(60,10),
y=rep(c(rep(0,4),rep(10,4),rep(20,4)),5),
z=rep(1:4,15))
xyplot(x~y|SP,data=data,groups=z,layout=c(2,3),pch=1:4,lty=1:4
,col='black',type='b',
key=list(x = .65, y = .75, corner = c(0, 0), points=TRUE,
lines=TRUE, pch=1:4, lty=1:4, type='b',
text=list(lab = as.character(unique(data$z)
I have an extra column of symbols on the legend,
and,
would like to add a title to the legend. Such as 'main' for plots.
Any suggestions?
for key(), make 'lines' into a list:
xyplot(x~y|SP,data=data,groups=z,layout=c(2,3),
pch=1:4,lty=1:4,col='black',type='b',
key=list(x = .65, y = .75, corner = c(0, 0),
title=title here, cex.title=.9, lines.title=3,
lines=list(pch=1:4, lty=1:4, type='b'),
text=list(lab = as.character(unique(data$z)
Peter Ehlers
... that works. Thanks Peter (sorry I misspelled your name b4). The clean code
is now:
require(lattice)
data- data.frame(SP=sort(rep(as.factor(c('A','B','C','D','E')),12)),
x=rpois(60,10),
y=rep(c(rep(0,4),rep(10,4),rep(20,4)),5),
z=rep(1:4,15))
xyplot(x~y|SP,data=data,groups=z,layout=c(2,3),pch=1:4,lty=1:4,col='black',type='b',
key=list(x = .65, y = .75, corner = c(0, 0),
lines=list(pch=1:4, lty=1:4, type='b'),
title=expression(CO^2),
text=list(lab = as.character(unique(data$z)
David's code works too (thanks to you too!) and is somewhat shorter
xyplot(x~y|SP, data=data,groups=z, layout=c(2,3),
par.settings=simpleTheme(pch=1:4,lty=1:4,col='black'), type=b,
auto.key = list(x = .6, y = .7, lines=TRUE, corner = c(0, 0)))
but the lines and symbols are on different columns, and the line types look as
if they were in bold.
Rubén
Dr. Rubén Roa-Ureta
AZTI - Tecnalia / Marine Research Unit
Txatxarramendi Ugartea z/g
48395 Sukarrieta (Bizkaia)
SPAIN
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[R] useR! 2011 abstract deadline extended by 2 days
useR! 2011 Conference, University of Warwick, Coventry, UK 16-18 August, 2011 (International R user conference; see http://www.r-project.org/conferences.html for the history.) The abstract submission period for this year's useR! conference, which was due to end today, is *extended* by 2 days. The FINAL DEADLINE is: Monday 4 April at 0900 GMT. For all conference information, including the abstract submission details, please see http://www.warwick.ac.uk/statsdept/useR-2011/ David Firth (for the useR! 2011 organisers) -- Professor David Firth http://go.warwick.ac.uk/dfirth __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Syntax coloring in R console
Dear all, I am a happy user of R console, but I would like to see syntax coloring. I use R 2.12 in Ubuntu Linux. I have found the packages xterm256 and highlight, but I was not able to figure out how to use it to highlight the syntax in console output. Also, I tried several GUI interfaces, but I was not able to find something that suits me better than the default R console. R cmdr is definitely not for me, as I don't want to fundamentally change the way I am managing my data in R. Rkwrd seems to be nice (from screenshots), but its installation requires all the base KDE libraries, which I don't want to install. I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice xscale.components: different ticks on top/bottom axis
On Fri, Mar 11, 2011 at 12:28 AM, boris.vasil...@forces.gc.ca wrote:
Good afternoon,
I am trying to create a plot where the bottom and top axes have the same
scale but different tick marks. I tried user-defined xscale.component
function but it does not produce desired results. Can anybody suggest
where my use of xscale.component function is incorrect?
For example, the code below tries to create a plot where horizontal axes
limits are c(0,10), top axis has ticks at odd integers, and bottom axis
has ticks at even integers.
library(lattice)
df - data.frame(x=1:10,y=1:10)
xscale.components.A - function(...,user.value=NULL) {
# get default axes definition list; print user.value
ans - xscale.components.default(...)
print(user.value)
# start with the same definition of bottom and top axes
ans$top - ans$bottom
# - bottom labels
ans$bottom$labels$at - seq(0,10,by=2)
ans$bottom$labels$labels - paste(B,seq(0,10,by=2),sep=-)
# - top labels
ans$top$labels$at - seq(1,9,by=2)
ans$top$labels$labels - paste(T,seq(1,9,by=2),sep=-)
# return axes definition list
return(ans)
}
oltc - xyplot(y~x,data=df,
scales=list(x=list(limits=c(0,10),at=0:10,alternating=3)),
xscale.components=xscale.components.A,
user.value=1)
print(oltc)
The code generates a figure with incorrectly placed bottom and top
labels. Bottom labels B-0, B-2, ... are at 0, 1, ... and top labels
T-1, T-3, ... are at 0, 1, ... When axis-function runs out of
labels, it replaces labels with NA.
It appears that lattice uses top$ticks$at to place labels and
top$labels$labels for labels. Is there a way to override this behaviour
(other than to expand the labels$labels vector to be as long as
ticks$at vector and set necessary elements to )?
Well, top|bottom$ticks$at is used to place the ticks, and $labels$at
is used to place the labels. They should typically be the same, but
you have changed one and not the other. Everything seems to work if
you set $ticks$at to the same values as $labels$at:
## - bottom labels
+ ans$bottom$ticks$at - seq(0,10,by=2)
ans$bottom$labels$at - seq(0,10,by=2)
ans$bottom$labels$labels - paste(B,seq(0,10,by=2),sep=-)
## - top labels
+ ans$top$ticks$at - seq(1,9,by=2)
ans$top$labels$at - seq(1,9,by=2)
ans$top$labels$labels - paste(T,seq(1,9,by=2),sep=-)
Also, can user-parameter be passed into xscale.components() function?
(For example, locations and labels of ticks on the top axis). In the
code above, print(user.value) returns NULL even though in the xyplot()
call user.value is 1.
No. Unrecognized arguments are passed to the panel function only, not
to any other function. However, you can always define an inline
function:
oltc - xyplot(y~x,data=df,
scales=list(x=list(limits=c(0,10), at = 0:10, alternating=3)),
xscale.components = function(...)
xscale.components.A(..., user.value=1))
Hope that helps (and sorry for the late reply).
-Deepayan
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Re: [R] programming: telling a function where to look for the entered variables
2011/4/1 Nick Sabbe nick.sa...@ugent.be:
This should be a version that does what you want.
Indeed it does, thank you very much!
Because you named the variable lvarname, I assumed you were already passing
lvar instead of trying to pass lvar (without the quotes), which is in no
way a 'name'.
Sorry about that, I can see how my variable names were somewhat confusing.
Many thanks once again!
-Original Message-
From: irene.p...@googlemail.com [mailto:irene.p...@googlemail.com] On Behalf
Of E Hofstadler
Sent: vrijdag 1 april 2011 14:28
To: Nick Sabbe
Cc: r-help@r-project.org
Subject: Re: [R] programming: telling a function where to look for the
entered variables
Thanks Nick and Juan for your replies.
Nick, thanks for pointing out the warning in subset(). I'm not sure
though I understand the example you provided -- because despite using
subset() rather than bracket notation, the original function (myfunct)
does what is expected of it. The problem I have is with the second
function (myfunct.better), where variable names + dataframe are not
fixed within the function but passed to the function when calling it
-- and even with bracket notation I don't quite manage to tell R where
to look for the columns that related to the entered column names.
(but then perhaps I misunderstood you)
This is what I tried (using bracket notation):
myfunct.better(dataframe, subgroup, lvarname,yvarname){
Data.tmp - dataframe[dataframe[,deparse(substitute(lvarname))]==subgroup,
c(xvar,deparse(substitute(yvarname)))]
}
but this creates an empty contingency table only -- perhaps because my
use of deparse() is flawed (I think what is converted into a string is
lvarname and yvarname, rather than the column names that these two
function-variables represent in the dataframe)?
2011/4/1 Nick Sabbe nick.sa...@ugent.be:
See the warning in ?subset.
Passing the column name of lvar is not the same as passing the 'contextual
column' (as I coin it in these circumstances).
You can solve it by indeed using [] instead.
For my own comfort, here is the relevant line from your original function:
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
Which should become something like (untested but should be close):
Data.tmp - Fulldf[Fulldf[,lvar]==subgroup, c(xvar,yvar)]
This should be a lot easier to translate based on column names, as the
column names are now used as such.
HTH,
Nick Sabbe
--
ping: nick.sa...@ugent.be
link: http://biomath.ugent.be
wink: A1.056, Coupure Links 653, 9000 Gent
ring: 09/264.59.36
-- Do Not Disapprove
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf Of E Hofstadler
Sent: vrijdag 1 april 2011 13:09
To: r-help@r-project.org
Subject: [R] programming: telling a function where to look for the entered
variables
Hi there,
Could someone help me with the following programming problem..?
I have written a function that works for my intended purpose, but it
is quite closely tied to a particular dataframe and the names of the
variables in this dataframe. However, I'd like to use the same
function for different dataframes and variables. My problem is that
I'm not quite sure how to tell my function in which dataframe the
entered variables are located.
Here's some reproducible data and the function:
# create reproducible data
set.seed(124)
xvar - sample(0:3, 1000, replace = T)
yvar - sample(0:1, 1000, replace=T)
zvar - rnorm(100)
lvar - sample(0:1, 1000, replace=T)
Fulldf - as.data.frame(cbind(xvar,yvar,zvar,lvar))
Fulldf$xvar - factor(xvar, labels=c(blue,green,red,yellow))
Fulldf$yvar - factor(yvar, labels=c(area1,area2))
Fulldf$lvar - factor(lvar, labels=c(yes,no))
and here's the function in the form that it currently works: from a
subset of the dataframe Fulldf, a contingency table is created (in my
actual data, several other operations are then performed on that
contingency table, but these are not relevant for the problem in
question, therefore I've deleted it) .
# function as it currently works: tailored to a particular dataframe
(Fulldf)
myfunct - function(subgroup){ # enter a particular subgroup for which
the contingency table should be calculated (i.e. a particular value of
the factor lvar)
Data.tmp - subset(Fulldf, lvar==subgroup, select=c(xvar,yvar))
#restrict dataframe to given subgroup and two columns of the original
dataframe
Data.tmp - na.omit(Data.tmp) # exclude missing values
indextable - table(Data.tmp$xvar, Data.tmp$yvar) # make contingency table
return(indextable)
}
#Since I need to use the function with different dataframes and
variable names, I'd like to be able to tell my function the name of
the dataframe and variables it should use for calculating the index.
This is how I tried to modify the first part of the #function, but it
didn't work:
# function as I would like it to work: independent of any particular
[R] Information theoretic approach in GLS
Dear R-Users, Am I right if I say that comparisons among gls models with differing fixed effects, but same correlation stuctures, fitted by REML is not meaningful? I need to use ML fit to get comparable AIC, BIC values? And the same is applied to likelihood ratio statistics? I don't really know what's the differece between the two fitting methods. Does anybody have a good documentation for understanding them? Would much esaier to understand restrictions of REMLfit if I see the mathematical background of it. Cheers, Balazs [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] guidelines for using the R logo
Hello, I am writing an R-guide which is addressed especially for students of German Universities (http://www.rrzn.uni-hannover.de/buch.html?no_cache=1titel=statistik_r). For the title page, I want to use the R logo. I found a similar question in the R mailing list about the same topic. The answer was that the usage of the logo is OK. However, this already a few years ago and I was wondering wether this is still up-to-date or wether there are any guidelines I would violate when using the logo. Thanks -- Johannes Hain University of Wuerzburg Chair of Mathematics VIII (Statistics) +49 931 31-84969 Empfehlen Sie WEB.DE DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! [1]https://freundschaftswerbung.web.de References 1. https://freundschaftswerbung.web.de/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
RStudio is a new interface. I just started using it and find it very good. You might want to check it out. It does have Ubuntu capabilities, but you have be sure that your graphic drivers are the same as is specified in the RStudio system. Hope this helps Steve Friedman Ph. D. Ecologist / Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 January Weiner january.weiner@m piib-berlin.mpg.d To er-h...@stat.math.ethz.ch Sent by: cc r-help-bounces@r- project.org Subject [R] Syntax coloring in R console 04/01/2011 06:32 AM Dear all, I am a happy user of R console, but I would like to see syntax coloring. I use R 2.12 in Ubuntu Linux. I have found the packages xterm256 and highlight, but I was not able to figure out how to use it to highlight the syntax in console output. Also, I tried several GUI interfaces, but I was not able to find something that suits me better than the default R console. R cmdr is definitely not for me, as I don't want to fundamentally change the way I am managing my data in R. Rkwrd seems to be nice (from screenshots), but its installation requires all the base KDE libraries, which I don't want to install. I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Hello On Fri, Apr 1, 2011 at 12:32 PM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: I have found the packages xterm256 and highlight, but I was not able to figure out how to use it to highlight the syntax in console output. I've been in this position before, without finding a solution for syntax highlighting in the default R console. Also, I tried several GUI interfaces, but I was not able to find something that suits me better than the default R console. R cmdr is definitely not for me, as I don't want to fundamentally change the way I am managing my data in R. Rkwrd seems to be nice (from screenshots), but its installation requires all the base KDE libraries, which I don't want to install. Recently RStudio was introduced [1] and, although beta, it received quasi-unanimous acclaim from the community, so you risk finding it useful too. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice (panel.3dscatter): how to make plot symbol thicker?
On Fri, Mar 11, 2011 at 12:29 PM, Marius Hofert m_hof...@web.de wrote: Dear Deepayan, many thanks for answering. Another thing I am wondering is the following: I know you can have (3d-like) crosses in the wireframe plot. But are there any other 3d-like plot symbols? Of course one can use different colors to distinguish between several points. The problem is that most of the scientific journals do not allow colors [or it's expensive]. I am thus wondering if the plot symbols have equivalent 3d-versions. It looks a bit odd to draw a 2d cross in a 3d wireframe. Or a circle. Concerning the circle, it could be a small ball in 3d for example. Is there anything like this? No, at least not easily. The 3D crosses are done by mapping each point into 3 perpendicular line segments, then projecting the endpoints into the 2D space, and then joining them. This is hardcoded in panel.3dscatter() -- search for the section inside 'if (cross)'. For other 3D plotting characters, you need to replicate this process (which is not really that difficult, but a bit tedious). If you are going to be doing a lot of fancy 3D graphics, I would strongly suggest considering rgl, which is a real 3D graphics system. Proper 3D graphics are difficult in systems based on vector graphics (like R graphics). -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] controlling the labels width of a barplot
Dear all, I am trying the barplot command but some of the labels are disappearing as there is not enough place on the graph to put them all. Here is an example of code that doesn't show all the labels: barplot(sort(runif(9,0,0.2),decreasing=TRUE),xlim=c(0,20),width=2,names.arg=c(first name,second name,third name,fourth name,fifth name,sixth name,seventh name,eigth name,nineth name)) Does someone know a way to control the size of the font in the barplot function, or to give them an inclination angle? Many thanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] controlling the labels width of a barplot
Try the cex.names argument in barplot function. On Fri, Apr 1, 2011 at 10:34 AM, Samuel Le samuel...@srlglobal.com wrote: Dear all, I am trying the barplot command but some of the labels are disappearing as there is not enough place on the graph to put them all. Here is an example of code that doesn't show all the labels: barplot(sort(runif(9,0,0.2),decreasing=TRUE),xlim=c(0,20),width=2,names.arg=c(first name,second name,third name,fourth name,fifth name,sixth name,seventh name,eigth name,nineth name)) Does someone know a way to control the size of the font in the barplot function, or to give them an inclination angle? Many thanks, Samuel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] XYPlot Conditioning Variable in Specific, Non-Alphanumeric Order. -- Resending with corrected .txt file
On Sat, Mar 19, 2011 at 2:53 AM, Guy Jett gj...@itsi.com wrote: Due to an error on my part, I have renamed the previously attached file from T_5-04b_LTC-SE-SO-Compared.csv to T_5-04b_LTC-SE-SO-Compared.txt. It remains a comma-delimited file so the extension can be changed and used per the script, or loaded separately. My sincere apologies, Guy -Original Message- From: Guy Jett Sent: Friday, March 18, 2011 1:13 PM To: 'r-help@R-project.org' Subject: XYPlot Conditioning Variable in Specific, Non-Alphanumeric Order. # I need to create an xyplot() where I control the specific order of # both my conditioning variables. The default code below plots the # data correctly (dispersed across all 14 columns), but fails in two # ways. Both the primary conditioning variable (Transect), and the # secondary conditioning variable (Offset) are in alphanumeric order, # rather than the specific order I need. # Here is a call to the input datafile, which should be attached. You may rename that .txt file to .csv for processing in the following line. df - read.csv(file = T_5-04b_LTC-SE-SO-Compared.csv) # Basic default plot (correct data, incorrect layout): xyplot((sbd+sed)/2 ~ Result | Offset+Transect, groups = PARLABEL, as.table = TRUE, data = df, layout = c(14,4), type = b) # I attempted to control the order following the method described in # the thread [R] xyplot() - can you control how the plots are # ordered?, but I appear to be missing, or misunderstanding # something. The modeled code is here. It does put all the # individual 'lattices'(?) in the needed order, BUT the graphics # for the individual sets dump all the measurements into a single # cell, on the diagonal, as if it's treating the conditioning # variables as an [i,j] index. Again not what I want. # Draft code (incorrect data, correct layout): Transects - c(LNF02, LSF02, LUR01, LURT1, LUR03, LUR05, LUR09, LUR11, LUR12, LUR15, LUR16, LUR21, LURT3, LUR25, LURT4, LUR28, LUR36, LUR38, LUR46, LURT5, LUR48, LLR04, LLR10, LLR11, LLRT1, LLR17, LLRT2, LLR18, LLRT3, LLR19) Transects - factor(Transects, levels = Transects) Offsets - c(T, U, V, Y, Z, A, B, C, D, E, F, G, H) Offsets - factor(Offsets, levels = Offsets) xyplot((sbd+sed)/2 ~ Result | Offsets+Transects, groups = PARLABEL, as.table = TRUE, data = df, layout = c(13,5), type = b) # What I am looking for is a combination of the default plot, but ordered in # the layout of the second code fragment. You need to specify the order of the levels explicitly (to override the default). Here is how to do it for one, you can similarly do the other: levels(df$Offset) [1] T U V Y Z A B C D E F G H df$Offset - factor(df$Offset, + levels = c(T, U, V, Y, Z, A, +B, C, D, E, F, G, H)) levels(df$Offset) [1] T U V Y Z A B C D E F G H Once you make these changes, your original call should work as desired. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice histogram function and groups
On Sat, Mar 19, 2011 at 6:11 AM, Evans, David G (DFG) david.ev...@alaska.gov wrote: Hi, From the following code (tweaked from another user): variable-sample(rep(1:2,100)) individual-rep(1:3, length(variable)) group-rep(LETTERS[1:2],length(variable)/2) mydata-data.frame(variable,individual,group) individual-as.factor(individual) group-as.factor(group) histogram(~variable|individual+group) I get six panels, one for each of individuals 1-3 in group A and one for each of individuals 1-3 in group B . What I want is three panels , one for each individual, but with A and B paired in the same panel. I think the groups=argument does this sort of superposition for other lattice functions. But not for histogram (intentionally). See http://tolstoy.newcastle.edu.au/R/e2/help/07/04/14490.html -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Large number of Y and X variables
Hello I have two issues 1. I have a linear model with several thousands of Y and X variables, so if I do not want to write them down one by one in the lm(Y ~ X) model how should I go about it. 2. Also, if I suspect that some of the Y variables could not be independent, what function should I apply? Regards Rosario __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Recently RStudio was introduced [1] and, although beta, it received quasi-unanimous acclaim from the community, so you risk finding it useful too. Dear Liviu, RStudio might be a fine program, but it does not feature syntax highlighting, which is the only thing I am missing from R Console (it only colors the commands typed). Moreover, the very idea of squeezing all R windows into one window-desktop would be counterproductive in my particular case. Thank you anyways! j. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] converting affybatch object to matrix
I have an Affybatch object called batch : batch AffyBatch object size of arrays=1050x1050 features (196 kb) cdf=HuGene-1_0-st-v1 (32321 affyids) number of samples=384 number of genes=32321 annotation=hugene10stv1 notes= Is there a way of converting a portion of this data into a matrix? More specifically, a matrix where the 384 samples are columns and the 32321 genes are rows? The exprs function returns a matrix that has 384 columns but for some reason there are 1050^2 rows. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] read.table question #only need to change column names
Hi all, I have a huge data set. All I want to do is to change the column names of the it. So if I use read.table, I can read the data in and change colnames and then write back, such as, t - read.table(a.txt, header = T, sep = \t) colnames(t) colnames(t) - c() # new column names write.table(t, a.txt, quote = F, sep = \t, row.names = F, col.names = T) My question is that is there a better to do this without reading in and write out data entirely? Thanks. Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Dear January, Have a look at Eclipse with the STAT-ET plugin http://www.walware.de/goto/statet Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens January Weiner Verzonden: vrijdag 1 april 2011 15:48 Aan: r-h...@stat.math.ethz.ch Onderwerp: Re: [R] Syntax coloring in R console Recently RStudio was introduced [1] and, although beta, it received quasi-unanimous acclaim from the community, so you risk finding it useful too. Dear Liviu, RStudio might be a fine program, but it does not feature syntax highlighting, which is the only thing I am missing from R Console (it only colors the commands typed). Moreover, the very idea of squeezing all R windows into one window-desktop would be counterproductive in my particular case. Thank you anyways! j. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rexcel path problem
Hi,
I am running a test to call an R script with in excel using VBA. My VBA
code is shown bellow. The middle section of this mail also includes the
content of my Rscript. The bottom part shows the error message form the
R console.
It seems that Excel is opening the R console without any problems.
The problem I am seeing is that Rinterface.RRun instruction is
interpreting the \T part of the path as an R command. It does not
recognize the X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\ as a one single string, or path.
Any ideas how can I fix the problem?
Thanks ,'
Jorge
VB code
Sub tester()
Rinterface.StartRServer
Rinterface.RRun
(source('X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\toto.R'))
Rinterface.StopRServer
End Sub
R cript code toto.R
path = getwd()
setwd(path)
a = 5
b=5
x = matrix(rnorm(a*b),a,b)
a = 5
b=5
y = matrix(rnorm(a*b),a,b)
z = x %*% y
savefile = paste(path,/,testresults.csv,sep=)
write.csv(z, file = savefile)
Rconsole message
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Loading required package: rcom
Loading required package: rscproxy
Error: '\T' is an unrecognized escape in character string starting
source('X:\T
Jorge Nieves
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rexcel path problem
Jorge,
This looks like an R on Windows problem, it is unrelated to VBA.
You have the statement
(source('X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\toto.R'))
which is invalid R. You need to use either forward slashes or
double-back-slashes in R commands.
See the R for Windows FAQ 2.16.
Further RCOM questions should be addressed to the rcom list. You can sign
up at
rcom.univie.ac.at
Rich
On Fri, Apr 1, 2011 at 10:12 AM, Jorge Nieves jorge.nie...@moorecap.comwrote:
Hi,
I am running a test to call an R script with in excel using VBA. My VBA
code is shown bellow. The middle section of this mail also includes the
content of my Rscript. The bottom part shows the error message form the
R console.
It seems that Excel is opening the R console without any problems.
The problem I am seeing is that Rinterface.RRun instruction is
interpreting the \T part of the path as an R command. It does not
recognize the X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\ as a one single string, or path.
Any ideas how can I fix the problem?
Thanks ,'
Jorge
VB code
Sub tester()
Rinterface.StartRServer
Rinterface.RRun
(source('X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\toto.R'))
Rinterface.StopRServer
End Sub
R cript code toto.R
path = getwd()
setwd(path)
a = 5
b=5
x = matrix(rnorm(a*b),a,b)
a = 5
b=5
y = matrix(rnorm(a*b),a,b)
z = x %*% y
savefile = paste(path,/,testresults.csv,sep=)
write.csv(z, file = savefile)
Rconsole message
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Loading required package: rcom
Loading required package: rscproxy
Error: '\T' is an unrecognized escape in character string starting
source('X:\T
Jorge Nieves
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
On Fri, Apr 1, 2011 at 3:48 PM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: RStudio might be a fine program, but it does not feature syntax highlighting, which is the only thing I am missing from R Console (it only colors the commands typed). The idea is that you shouldn't use the R console for you main programming needs, but only for quick and dirty checks. For the bulk of programming tasks you are invited to use the integrated editor (File New Script). The editor window does feature syntax highlighting, and a very helpful completion mechanism (via tab). Sending lines for execution to the terminal is as easy as clicking 'run lines' or ctrl+enter. If you're not a fan of keeping scripts for your projects you can easily use temporary files that you don't save. Moreover, the very idea of squeezing all R windows into one window-desktop would be counterproductive in my particular case. Notice that all panes are freely resizable and can be resized to the point of becoming hidden. Future releases will give more control over the panes layout (I think). Regards Liviu Thank you anyways! j. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rexcel path problem
On 01-04-2011, at 16:12, Jorge Nieves wrote:
Hi,
I am running a test to call an R script with in excel using VBA. My VBA
code is shown bellow. The middle section of this mail also includes the
content of my Rscript. The bottom part shows the error message form the
R console.
It seems that Excel is opening the R console without any problems.
The problem I am seeing is that Rinterface.RRun instruction is
interpreting the \T part of the path as an R command. It does not
recognize the X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\ as a one single string, or path.
Any ideas how can I fix the problem?
Thanks ,'
Jorge
VB code
Sub tester()
Rinterface.StartRServer
Rinterface.RRun
(source('X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\toto.R'))
Rinterface.StopRServer
End Sub
R cript code toto.R
path = getwd()
setwd(path)
a = 5
b=5
x = matrix(rnorm(a*b),a,b)
a = 5
b=5
y = matrix(rnorm(a*b),a,b)
z = x %*% y
savefile = paste(path,/,testresults.csv,sep=)
write.csv(z, file = savefile)
Rconsole message
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Loading required package: rcom
Loading required package: rscproxy
Error: '\T' is an unrecognized escape in character string starting
source('X:\T
R is just telling you that it doesn't recognize \T as a valid escape sequence
in a character string.
See R for Windows FAQ 2.16 and 5.1.
Use \\ instead of a single \ as path separator or use the forward slash /.
Berend
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Colour makes my life; but not my bwplot (panel.violin)
On Fri, Mar 25, 2011 at 3:59 PM, JP jeanpaul.ebe...@inhibox.com wrote:
Hi there David,
Many thanks for your time and reply
I created a small test set, and ran your proposed solution... and this is
what I get http://i.imgur.com/vlsSQ.png
This is not what I want - I want separate grp_1 and grp_2 panels and in each
panel a red violin plot and a blue one. So like this --
http://i.imgur.com/NnsE0.png but with red for condition_a and blue for
condition_b. You would think that something like this is trivial to
achieve... I just spent a whole day on this :(( Maybe I am just thick
I included the test data I am using:
# some dummy data
p - rep(c(rep(condition_a, 4), rep(condition_b, 4)), 2)
q - c(rep(grp_1, 8), rep(grp_2, 8))
r - rnorm(16)
test_data - data.frame(p, q, r)
# your solution
bwplot(r ~ p,
groups = q,
data=test_data,
col = c(red, blue),
panel=panel.superpose,
panel.groups = function(..., box.ratio){
panel.violin(..., cut = 1, varwidth = FALSE, box.ratio = box.ratio)
panel.bwplot(..., box.ratio = .1)
},
par.settings = list(plot.symbol = list(pch = 21, col = gray),
box.rectangle = list(col = black), # not sure these are working
properly
box.umbrella = list(col = black))
)
Umm, isn't this slight modification of the above what you want (only
first two lines changed -- your formula with the right 'groups'
variable)?
bwplot(r ~ p | q,
groups = p,
data=test_data,
col = c(red, blue),
panel=panel.superpose,
panel.groups = function(..., box.ratio){
panel.violin(..., cut = 1, varwidth = FALSE, box.ratio = box.ratio)
panel.bwplot(..., box.ratio = .1)
},
par.settings = list(plot.symbol = list(pch = 21, col = gray),
box.rectangle = list(col = black),
box.umbrella = list(col = black))
)
Some further modifications will get you closer to David's solution:
bwplot(r ~ p | q,
groups = p,
data=test_data,
col = c(red, blue),
fill = c(red, blue),
panel=panel.superpose,
panel.groups = function(..., box.ratio, col, pch){
panel.violin(..., cut = 1, varwidth = FALSE, box.ratio =
box.ratio, col = col)
panel.bwplot(..., box.ratio = .1, col = black, pch = 16)
},
par.settings = list(plot.symbol = list(pch = 21, col = gray),
box.rectangle = list(col = black),
box.umbrella = list(col = black))
)
-Deepayan
# my non working one for completeness
bwplot(r ~ p | q,
data=test_data,
col = c(red, blue),
panel = function(..., box.ratio){
panel.violin(..., cut = 1, varwidth = FALSE, box.ratio = box.ratio)
panel.bwplot(..., box.ratio = .1)
},
par.settings = list(plot.symbol = list(pch = 21, col = gray),
box.rectangle = list(col = black), # not sure these are working properly
box.umbrella = list(col = black))
)
On 24 March 2011 21:59, David Winsemius dwinsem...@comcast.net wrote:
On Mar 24, 2011, at 1:37 PM, JP wrote:
Using Trellis, am successfully setting up a number of panels (25) in which
I
have two box and violin plots.
I would like to colour - one plot as RED and the other as BLUE (in each
panel). I can do that with the box plots, but the violin density areas
just
take on one colour.
My basic call is as follows:
I took the suggestion of Sarkar's:
http://finzi.psych.upenn.edu/Rhelp10/2010-April/234191.html
Identified with a search on: panel.violin color
a bit of trial and error with a re-worked copy of the `singer`
data.frame meant I encountered errors and needed to throw out some of your
pch arguments, and suggest this reworking of your code:
bwplot(rmsd ~ file , groups= code,
data=spread_data.filtered, col = c(red, blue),
panel=panel.superpose,
panel.groups = function(..., box.ratio){
panel.violin(..., cut = 1, varwidth = FALSE,
box.ratio = box.ratio)
panel.bwplot(..., box.ratio = .1)
},
par.settings = list(plot.symbol = list(pch = 21, col = gray),
box.rectangle = list(col = black), # not sure these are working
properly
box.umbrella = list(col = black))
)
Obviously it cannot be tested without some data, but I did get alternating
colors to the violin plots. There is an modifyList functionthat you might
want to look up in the archives for changing par.settings:
http://search.r-project.org/cgi-bin/namazu.cgi?query=par.settings+modifyListmax=100result=normalsort=scoreidxname=functionsidxname=Rhelp08idxname=Rhelp10idxname=Rhelp02
--
David Winsemius, MD
West Hartford, CT
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
(+44 / 0) 1865 262 034
This email and any files transmitted with it are confide...{{dropped:22}}
__
R-help@r-project.org mailing list
Re: [R] Rexcel path problem
Use / instead of \ in the path.
---
Jeff Newmiller The . . Go Live...
DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
Jorge Nieves jorge.nie...@moorecap.com wrote:
Hi, I am running a test to call an R script with in excel using VBA. My VBA
code is shown bellow. The middle section of this mail also includes the content
of my Rscript. The bottom part shows the error message form the R console. It
seems that Excel is opening the R console without any problems. The problem I
am seeing is that Rinterface.RRun instruction is interpreting the \T part of
the path as an R command. It does not recognize the
X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home models\ as a one single
string, or path. Any ideas how can I fix the problem? Thanks ,' Jorge VB code
Sub tester() Rinterface.StartRServer Rinterface.RRun
(source('X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home models\toto.R'))
Rinterface.StopRServer End Sub R cript code toto.R path = getwd() setwd(path)
a = 5 b=5 x = matrix(rnorm(a*b),a,b) a = 5 b=5 y = matrix(rnorm(a*b),a,b) z = x
%*% y savefile = paste(path,/,testresults.csv,sep=) write.csv(z, file =
savefile) Rconsole messa
ge Type
'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an
HTML browser interface to help. Type 'q()' to quit R. Loading required package:
rcom Loading required package: rscproxy Error: '\T' is an unrecognized escape
in character string starting source('X:\T Jorge Nieves
[[alternative HTML version
deleted]]_
R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rexcel path problem
Jorge:
You can run save your scripts in the same folder where your wokbook is and run
it like this:
Sub Scatter()
Call rinterface.StartRServer
'Put the dataframe into R
Call rinterface.PutDataframe(scatter, DownRightFrom(Range(RData!A1)),
WithRowNames:=False)
Call rinterface.RRun(attach(scatter))
'Run the RScatter script
rinterface.RunRFile ThisWorkbook.Path \RScatter.r
Call rinterface.StopRServer
End Sub
I
Felipe D. Carrillo
Supervisory Fishery Biologist
Department of the Interior
US Fish Wildlife Service
California, USA
http://www.fws.gov/redbluff/rbdd_jsmp.aspx
- Original Message
From: Jorge Nieves jorge.nie...@moorecap.com
To: r-h...@stat.math.ethz.ch
Sent: Fri, April 1, 2011 7:12:39 AM
Subject: [R] Rexcel path problem
Hi,
I am running a test to call an R script with in excel using VBA. My VBA
code is shown bellow. The middle section of this mail also includes the
content of my Rscript. The bottom part shows the error message form the
R console.
It seems that Excel is opening the R console without any problems.
The problem I am seeing is that Rinterface.RRun instruction is
interpreting the \T part of the path as an R command. It does not
recognize the X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\ as a one single string, or path.
Any ideas how can I fix the problem?
Thanks ,'
Jorge
VB code
Sub tester()
Rinterface.StartRServer
Rinterface.RRun
(source('X:\Trading\Energy\JorgeSpace\TMPholder\cpixe\home
models\toto.R'))
Rinterface.StopRServer
End Sub
R cript code toto.R
path = getwd()
setwd(path)
a = 5
b=5
x = matrix(rnorm(a*b),a,b)
a = 5
b=5
y = matrix(rnorm(a*b),a,b)
z = x %*% y
savefile = paste(path,/,testresults.csv,sep=)
write.csv(z, file = savefile)
Rconsole message
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Loading required package: rcom
Loading required package: rscproxy
Error: '\T' is an unrecognized escape in character string starting
source('X:\T
Jorge Nieves
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] choosing best 'match' for given factor
Interesting variety of solutions! Thanks very much.
Murali
-Original Message-
From: Henrique Dallazuanna [mailto:www...@gmail.com]
Sent: 31 March 2011 18:26
To: Menon Murali
Cc: r-help@r-project.org
Subject: Re: [R] choosing best 'match' for given factor
Try this:
bestMatch - function(search, match) {
colnames(match)[pmax(apply(match[,search], 2, which.max) - 1, 1)]
}
On Thu, Mar 31, 2011 at 11:46 AM, murali.me...@avivainvestors.com wrote:
Folks,
I have a 'matching' matrix between variables A, X, L, O:
a - structure(c(1, 0.41, 0.58, 0.75, 0.41, 1, 0.6, 0.86, 0.58,
0.6, 1, 0.83, 0.75, 0.86, 0.83, 1), .Dim = c(4L, 4L), .Dimnames = list(
c(A, X, L, O), c(A, X, L, O)))
a
A X L O
A 1.00 0.41 0.58 0.75
X 0.41 1.00 0.60 0.86
L 0.58 0.75 1.00 0.83
O 0.60 0.86 0.83 1.00
And I have a search vector of variables
v - c(X, O)
I want to write a function bestMatch(searchvector, matchMat) such that for
each variable in searchvector, I get the variable that it has the highest
match to - but searching only among variables to the left of it in the
'matching' matrix, and not matching with any variable in searchvector itself.
So in the above example, although X has the highest match (0.86) with O,
I can't choose O as it's to the right of X (and also because O is in the
searchvector v already); I'll have to choose A.
For O, I will choose L, the variable it's best matched with - as it can't
match X already in the search vector.
My function bestMatch(v, a) will then return c(A, L)
My matrix a is quite large, and I have a long list of search vectors v, so I
need an efficient method.
I wrote this:
bestMatch - function(searchvector, matchMat) {
sapply(searchvector, function(cc) {
y - matchMat[!(rownames(matchMat) %in%
searchvector) (index(rownames(matchMat)) match(cc, rownames(matchMat))),
cc, drop = FALSE];
rownames(y)[which.max(y)]
})
}
Any advice?
Thanks,
Murali
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] bwplot [lattice]: how to get different y-axis scales for each row?
On Sun, Mar 27, 2011 at 8:50 PM, Marius Hofert m_hof...@web.de wrote: Dear expeRts, I partially managed to obtain what I wanted by using latticeExtra. However, the following questions remain: 1) why do not all x-axis labels appear? [compare bw and bw2] You have unnecessarily asked for relation=free for the x-axis (even though they don't change across panels), and then tried to combine them using combineLimits(), which doesn't know how to handle categorical axes. Change to using relation=free for the y-axis only, and you should be fine. bw - bwplot(error ~ methods | attr * groups, data=df, as.table=TRUE, notch=TRUE, scales = list(y = list(alternating = c(1,1), tck=c(1,0), relation = free))) 2) Can I have the y-axis labels on the right margin/side of the plot? Changing the alternating argument does not do the job since relation=free No. (Well, you can provide your own axis() function to do it, in which case you will need to allocate space too.) -Deepayan Cheers, Marius library(lattice) library(latticeExtra) ## build example data set dim - c(100, 6, 4, 3) # n, groups, methods, attributes dimnames - list(n=paste(n=, seq_len(100), sep=), groups=paste(group=, seq_len(6), sep=), methods=paste(method=, seq_len(4), sep=), attr=paste(attribute=, seq_len(3), sep=)) set.seed(1) data - rexp(prod(dim)) arr - array(data=data, dim=dim, dimnames=dimnames) arr[,2,,] - arr[,2,,]*10 arr[,4,2,2] - arr[,4,2,2]*10 z - abs(sweep(arr, 3, 1)) df - as.data.frame.table(z, responseName=error) ## box plot bw - bwplot(error ~ methods | attr * groups, data=df, as.table=TRUE, notch=TRUE, scales=list(y=list(alternating=c(1,1), tck=c(1,0)), relation=free)) (bw2 - useOuterStrips(combineLimits(bw, extend=FALSE On 2011-03-26, at 09:34 , Marius Hofert wrote: Dear expeRts, How can I get ... (1) different y-axis scales for each row (2) while having the same y-axis scales for different columns? I coulnd't manage to do this with relation=free [which gives (1) but not (2)]. I also tried relation=sliced, but it did not give the same y-axis scales within each row (see the fourth row). Further, it separates the panels. Cheers, Marius ## minimal example: library(lattice) ## build example data set dim - c(100, 6, 2, 3) # n, groups, methods, attributes dimnames - list(n=paste(n=, seq_len(100), sep=), groups=paste(group=, seq_len(6), sep=), methods=paste(method=, seq_len(2), sep=), attr=paste(attribute=, seq_len(3), sep=)) set.seed(1) data - rexp(prod(dim)) arr - array(data=data, dim=dim, dimnames=dimnames) arr[,2,,] - arr[,2,,]*10 arr[,4,2,2] - arr[,4,2,2]*10 z - abs(sweep(arr, 3, 1)) df - as.data.frame.table(z, responseName=error) ## box plot bwplot(error ~ methods | attr * groups, data=df, as.table=TRUE, notch=TRUE, scales=list(alternating=c(1,1), tck=c(1,0))) ## with relation=sliced bwplot(error ~ methods | attr * groups, data=df, as.table=TRUE, notch=TRUE, scales=list(alternating=c(1,1), tck=c(1,0), relation=sliced)) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting symbols and colors based upon data values
Thanks to Deepayan for sending me the code for the correct approach
using subscripts.
On Mar 13, 2011, at 9:46 PM, David Winsemius wrote:
On Mar 13, 2011, at 8:51 PM, Mark Linderman wrote:
David, thank you for your quick reply. I spent a few minutes
getting your
command to work with some sparse synthetic data, and then spent
several
hours trying to figure out why my data didn't work (at least for
symbols,
colors look okay). I have massaged my data to where it is
practically
indistinguishable from the synthetic data - yet it still doesn't
work.
Attached are the two data files that can be plotted as follows:
broken = read.table(broken.table,header=TRUE)
works = read.table(works.table,header=TRUE)
xyplot(Y ~ X | A, data=works, pch=works$C , col=works$B)
xyplot(Y ~ X | A, data=broken, pch=broken$C , col=broken$B)
xyplot(Y ~ X | A, data=works, pch=works$C , col=as.character(works$B),
panel = function(..., pch, col, subscripts) {
panel.xyplot(..., pch = pch[subscripts], col =
col[subscripts])
})
--
David (for Deepayan Sarkar)
I get the same problem and after experimenting for a while I think I
can solve it by randomizing the order of the entries:
broken - broken[sample(417), ]
xyplot(Y ~ X | A, data=broken, pch=broken$C, col=broken$B)
Why xyplot should fail to properly assign pch values just because
all 1's are at the beginning seems to me to be a bug.
--
David.
After confirming the the problem recurs when re-order()-ed by broken
$C, I am appending dput( ordered-broken) for others to experiment
dput(broken[order(broken$C), ])
structure(list(rown = c(91L, 193L, 128L, 8L, 143L, 46L, 60L,
99L, 112L, 67L, 25L, 15L, 188L, 93L, 115L, 4L, 190L, 64L, 147L,
119L, 82L, 120L, 23L, 139L, 28L, 42L, 180L, 24L, 145L, 71L, 13L,
95L, 94L, 104L, 149L, 74L, 32L, 184L, 11L, 114L, 90L, 70L, 63L,
141L, 192L, 126L, 153L, 172L, 26L, 151L, 109L, 133L, 79L, 35L,
61L, 43L, 52L, 29L, 30L, 80L, 154L, 7L, 121L, 122L, 106L, 182L,
16L, 2L, 175L, 34L, 102L, 174L, 117L, 178L, 100L, 68L, 48L, 31L,
53L, 168L, 59L, 165L, 123L, 69L, 55L, 62L, 163L, 39L, 108L, 96L,
97L, 113L, 87L, 164L, 169L, 33L, 118L, 45L, 148L, 129L, 22L,
116L, 101L, 157L, 191L, 89L, 75L, 156L, 137L, 183L, 98L, 150L,
124L, 144L, 127L, 155L, 57L, 36L, 14L, 161L, 187L, 138L, 111L,
146L, 20L, 107L, 140L, 110L, 125L, 41L, 105L, 159L, 103L, 132L,
44L, 166L, 56L, 171L, 195L, 40L, 135L, 5L, 58L, 37L, 54L, 83L,
17L, 142L, 77L, 162L, 170L, 160L, 78L, 38L, 194L, 21L, 167L,
27L, 81L, 185L, 47L, 66L, 73L, 3L, 134L, 158L, 51L, 173L, 50L,
18L, 12L, 6L, 189L, 72L, 85L, 65L, 92L, 179L, 86L, 49L, 130L,
177L, 152L, 176L, 9L, 10L, 76L, 88L, 131L, 181L, 19L, 186L, 136L,
1L, 84L, 366L, 235L, 196L, 224L, 206L, 288L, 204L, 274L, 199L,
239L, 271L, 295L, 266L, 305L, 284L, 340L, 268L, 296L, 293L, 262L,
300L, 212L, 336L, 208L, 358L, 242L, 221L, 237L, 369L, 292L, 201L,
338L, 233L, 217L, 227L, 225L, 270L, 267L, 345L, 205L, 219L, 278L,
337L, 230L, 380L, 291L, 229L, 367L, 339L, 241L, 228L, 263L, 349L,
348L, 371L, 202L, 207L, 351L, 282L, 222L, 200L, 213L, 285L, 375L,
302L, 231L, 223L, 386L, 352L, 363L, 353L, 357L, 359L, 350L, 283L,
362L, 218L, 198L, 374L, 301L, 286L, 364L, 368L, 220L, 298L, 280L,
214L, 273L, 303L, 382L, 354L, 238L, 373L, 234L, 356L, 216L, 289L,
370L, 381L, 343L, 361L, 306L, 281L, 203L, 341L, 355L, 346L, 272L,
264L, 360L, 334L, 210L, 197L, 342L, 299L, 378L, 236L, 333L, 294L,
347L, 275L, 385L, 365L, 209L, 297L, 240L, 265L, 379L, 304L, 269L,
372L, 384L, 344L, 287L, 332L, 376L, 261L, 377L, 383L, 215L, 232L,
277L, 276L, 211L, 290L, 335L, 226L, 279L, 399L, 307L, 395L, 400L,
411L, 388L, 319L, 403L, 320L, 309L, 318L, 407L, 402L, 308L, 326L,
251L, 260L, 246L, 408L, 331L, 312L, 387L, 414L, 253L, 315L, 413L,
416L, 327L, 393L, 322L, 390L, 317L, 389L, 249L, 325L, 329L, 398L,
397L, 323L, 396L, 255L, 415L, 245L, 391L, 412L, 259L, 417L, 311L,
392L, 409L, 328L, 254L, 248L, 310L, 258L, 405L, 324L, 250L, 406L,
316L, 394L, 257L, 404L, 243L, 252L, 410L, 313L, 256L, 330L, 321L,
244L, 401L, 247L, 314L), X = c(0.701250601327047, 0.164821685524657,
0.606994603062049, 0.863256110809743, 0.956295087235048,
0.94587846682407,
0.838799783028662, 0.523805776145309, 0.562612239504233,
0.0359199855010957,
0.142975208582357, 0.459868715610355, 0.579013091977686,
0.384347806917503,
0.161508617224172, 0.96426909067668, 0.504280025139451,
0.438289026031271,
0.373645842541009, 0.439572562696412, 0.25889431219548,
0.0467256724368781,
0.365111395483837, 0.40517632686533, 0.847934616263956,
0.0139284294564277,
0.228810637025163, 0.976755930809304, 0.537870434345677,
0.831849699141458,
0.735547028947622, 0.107985522132367, 0.200033176457509,
0.250281900400296,
0.578671747585759, 0.289995870785788, 0.440369168063626,
0.364585015457124,
0.905479809269309, 0.446940524037927, 0.658691298449412,
0.0173427225090563,
0.24269335786812, 0.430798843270168, 0.164247164269909,
0.357896727975458,
0.381168011575937, 0.466935358708724, 0.598047381266952,
Re: [R] read.table question #only need to change column names
On Apr 1, 2011, at 10:00 AM, hongsheng wu wrote: Hi all, I have a huge data set. All I want to do is to change the column names of the it. So if I use read.table, I can read the data in and change colnames and then write back, such as, t - read.table(a.txt, header = T, sep = \t) colnames(t) colnames(t) - c() # new column names write.table(t, a.txt, quote = F, sep = \t, row.names = F, col.names = T) My question is that is there a better to do this without reading in and write out data entirely? With an editor. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Dear January, Have you looked at Emacs + ESS? http://ess.r-project.org/ It highlights in the text editor and the actual R process besides coming with a rich set of features and a mailing list filled with helpful Emacs R users. I've tried several different interfaces and ended up being happiest by far with Emacs + ESS. I also seem to recall Kate or Kedit at least highlighted .R files, but I am not in a position to check right now. Happy hunting, Josh On Fri, Apr 1, 2011 at 3:32 AM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: Dear all, I am a happy user of R console, but I would like to see syntax coloring. I use R 2.12 in Ubuntu Linux. I have found the packages xterm256 and highlight, but I was not able to figure out how to use it to highlight the syntax in console output. Also, I tried several GUI interfaces, but I was not able to find something that suits me better than the default R console. R cmdr is definitely not for me, as I don't want to fundamentally change the way I am managing my data in R. Rkwrd seems to be nice (from screenshots), but its installation requires all the base KDE libraries, which I don't want to install. I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a statistical problem - more statistical strategy for making quality control
Dear R-listers, I would like to have your helps on make a good strategy of quality control by several quality control variables. This means I need a good strategy to choose cutoff for each quality control variables, or make cutoff for all such quality control variables in one time. For quality control, we employed several values. Each production has each value of such variables: (1) concordance, (float, from 0 to 1, but 0.5 is the expected best one). (2) coverage, (integer, =1, more large more better) (3) base quality, (integer, 1 to 40, more large more better) Here, concordance may be the most important variable for quality control. The best product determined by concordance are those have values of 0.5. Obviously, smaller ones (0.1) and bigger ones (0.9) are not good. Coverage may also play an important role, like the products which have 0.5 vale for concordance and 0.1 coverage may not be the good calls. While, base quality is the same with converage. The bigger base quality should be the products which are better. Here, I want to find a good strategy to set a cutoff to our products based on these three or just concordance and coverage variables. I prefer a more statistical way. Would you please give me any ideas/directions on my problems? Thanks in advance. ### # as an example, I create a dummy data for my question. product-1:100 concordance-rnorm(100, mean=0.2) coverage-sample(1:50, 100, replace = T) base.quality-sample(1:40, 100, replace = T) dummy - cbind(product, concordance, coverage, base.quality) Best, Jian-Feng, Mao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Am 01.04.2011 17:02, schrieb Joshua Wiley: Dear January, Have you looked at Emacs + ESS? http://ess.r-project.org/ It highlights in the text editor and the actual R process besides coming with a rich set of features and a mailing list filled with helpful Emacs R users. I've tried several different interfaces and ended up being happiest by far with Emacs + ESS. I also seem to recall Kate or Kedit at least highlighted .R files, but I am not in a position to check right now. Another vote for Emacs + ESS here. I think sooner or later you'll need some kind of editor (with built-in syntax highlighing) to save your code. The naked R console won't do it forever :) Although I didn't like Emacs at first because of its steep learning curve, after a while you'll love the keyboard shortcuts for everything. Also, this add-on is very useful. It makes Shift-Enter send your lines to R (and a bit more): http://www.kieranhealy.org/blog/archives/2009/10/12/make-shift-enter-do-a-lot-in-ess/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Connect observed values by a smooth curve, is there any method to get coordinate value of arbitrary point on the curve?
Dear Prof. Murdoch and Dr. Winsemius, Thank you very much for your suggestion. They were big help. One of my friends told me another approach by using smooth.spline. Here is the code: x - c(1,2,3,4,5,6) y - c(1,4,9,16,25,36) sp - smooth.spline(x,y) x - seq(1, 6, length=100) pred - predict(sp, x) real - x^2 err - real - pred$y cbind(pred$x, pred$y, real, err) plot(pred) Thank a lot. Have a nice weekend :) Wang Zhipeng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] regression line on boxplots
Dear R users, I'm trying to add a regression line on my boxplots (something like:boxplot(c(1:3),c(4:6),c(5:8))) But I can't see it. Please help !!! It's not a April fool's joke!!! Yan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Simple AR(2)
Hello list, we are beginners in R and we are trying to fit the following time series: * x - c(1.89, 2.46, 3.23, 3.95, 4.56, 5.07, 5.62, 6.16, 6.26, 6.56, 6.98, 7.36, 7.53, 7.84, 8.09)* The reason for choosing the present time series is that the we have previously calculated analytically the autoregressive coefficients using the direct inversion method as *1.1, 0.765, 0.1173*. Since those coefficients fits well our time series, we wanted to learn how to do it in R and check that it would give us the same autoregressive coefficients as the direct inversion method. So as first step in R we have initially applied the OLS method and obtained the following autoregression coefficients: * ar(x, method=ols, order.max=2, demean=FALSE, intercept=TRUE)* *Call:**ar(x = x, order.max = 2, method = ols, demean = FALSE, intercept = TRUE)* *Coefficients:* *1 2 **0.8049 0.0834 * *Intercept: 1.103 (0.2321) * *Order selected 2 sigma^2 estimated as 0.009756* Those are very close to the ones obtained with the direct inversion method so the fitting is good. Then we tried to apply the other techniques available in R, namely Yule/Walker, Burg, MLE, obtaining different coefficients, which do not give a good fit of the series at all. * ar(x, method=yw, order.max=2, demean=FALSE, intercept=TRUE)* *Call:**ar(x = x, order.max = 2, method = yw, demean = FALSE, intercept = TRUE)* *Coefficients:* *1 **0.9305 * *Order selected 1 sigma^2 estimated as 5.368* Please can anybody help us telling how to get a reasonable good fit with YW, Burg and MLE, reporting also the code that needs to be used and commenting the coefficients obtained by comparing those with the ones obtained with OLS. Thanks in advance. Fabio [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cox Proportional Hazards model with a time-varying covariate
Hi Terry and Kevin,  Thanks for your replies to my post. And thanks particularly to Terry for pointing out my confusion about the exact partial likelihood vs. the exact marginal likelihood. I'm learning and so am likely to be confused about such things from time to time.  I had thought that a good way to see if I was replicating the results would be to use the Efron approximation in both R and SAS. I tried this just now and obtained a similar pattern of differences in the results. Please bear with me. I hope I'm not doing something silly.  Below are my results in each program. I got the results for R simply by running the code I sent earlier. I got the results in SAS by changing TIES = EXACT to TIES = EFRON.  Should I be getting results as different as these? Or does this suggest that there is some problem in how I've set up my data in R? I've looked over my data In R and everything looks fine, but maybe I've missed something.  Thanks,  Paul  summary(model) Call: coxph(formula = Surv(START, STOP, STATUS) ~ TRT + DENS + INFCTN,    data = vitclear)  n= 167          coef exp(coef) se(coef)     z Pr(|z|) TRT    0.2913   1.3382  0.1782 1.635   0.102 DENS  -0.1762   0.8384  0.1739 -1.013   0.311 INFCTN 0.1192   1.1266  0.1912 0.624   0.533       exp(coef) exp(-coef) lower .95 upper .95 TRT      1.3382    0.7473   0.9436    1.898 DENS     0.8384    1.1927   0.5963    1.179 INFCTN   1.1266    0.8876   0.7746    1.639 Rsquare= 0.024  (max possible= 0.999 ) Likelihood ratio test= 4.12 on 3 df,  p=0.2486 Wald test           = 4.12 on 3 df,  p=0.2485 Score (logrank) test = 4.15 on 3 df,  p=0.2460   Cox Proportional Hazards Model 09:01 Friday, April 1, 2011 1 Example 22.2: Hyalurise in Vitreous Hemorrhage The PHREG Procedure Model Information Data Set WORK.VITCLEAR Dependent Variable RSPTIM Censoring Variable CENS Censoring Value(s) 0 Ties Handling EFRON ã Number of Observations Read 143 Number of Observations Used 143 ã Summary of the Number of Event and Censored Values Percent Stratum CENTER Total Event Censored Censored 1 A 60 45 15 25.00 2 B 37 30 7 18.92 3 C 46 39 7 15.22 --- Total 143 114 29 20.28 ã Convergence Status Convergence criterion (GCONV=1E-8) satisfied. ã ã ã Cox Proportional Hazards Model 09:01 Friday, April 1, 2011 2 Example 22.2: Hyalurise in Vitreous Hemorrhage The PHREG Procedure Model Fit Statistics Without With Criterion Covariates Covariates -2 LOG L 711.142 706.171 AIC 711.142 712.171 SBC 711.142 720.379 ã Testing Global Null Hypothesis: BETA=0 Test Chi-Square DF Pr ChiSq Likelihood Ratio 4.9712 3 0.1739 Score 4.9604 3 0.1747 Wald 4.9151 3 0.1781 ã Analysis of Maximum Likelihood Estimates Parameter Standard Hazard Parameter DF Estimate Error Chi-Square Pr ChiSq Ratio TRT 1 0.34437 0.19562 3.0988 0.0783 1.411 DENS 1 -0.23832 0.19585 1.4807 0.2237 0.788 INFCTN 1 0.12819 0.27780 0.2129 0.6445 1.137 ã  [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Dear Liviu, thanks for the programming tip! However, I do all my editing in vim, which has had syntax highlighting for quite a while, as well as auto-completion and a number of other goodies. But while I do most of my programing in vim, I do most of my scientific studies simply using the R interface and keeping a manually edited lab book apart from the scripts. Clearly, one can do as much with Rstudio -- I just don't see any advantages, but I do see a disadvantage in my specific case: all sub-windows are confined to the desktop. In other words, having multiple plots on one monitor and a terminal with R command line is not possible. A question, though. Given that I have projects assorted in various directories, how can I start RStudio opening a project stored in .RData and .Rhistory of a given directory? I.e., how can I make RStudio open the current directory (like R does), and not $HOME? Thanks nonetheless, j. On Fri, Apr 1, 2011 at 4:20 PM, Liviu Andronic landronim...@gmail.com wrote: On Fri, Apr 1, 2011 at 3:48 PM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: RStudio might be a fine program, but it does not feature syntax highlighting, which is the only thing I am missing from R Console (it only colors the commands typed). The idea is that you shouldn't use the R console for you main programming needs, but only for quick and dirty checks. For the bulk of programming tasks you are invited to use the integrated editor (File New Script). The editor window does feature syntax highlighting, and a very helpful completion mechanism (via tab). Sending lines for execution to the terminal is as easy as clicking 'run lines' or ctrl+enter. If you're not a fan of keeping scripts for your projects you can easily use temporary files that you don't save. Moreover, the very idea of squeezing all R windows into one window-desktop would be counterproductive in my particular case. Notice that all panes are freely resizable and can be resized to the point of becoming hidden. Future releases will give more control over the panes layout (I think). Regards Liviu Thank you anyways! j. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
Re: [R] regression line on boxplots
On Apr 1, 2011, at 11:24 AM, Yan Jiao wrote: boxplot(c(1:3),c(4:6),c(5:8)) df - structure(list(grp = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3), val = c(1L, 2L, 3L, 4L, 5L, 6L, 5L, 6L, 7L, 8L)), .Names = c(grp, val), row.names = c(NA, -10L), class = data.frame) boxplot(val~grp,data=df) lm(val~grp, data=df) #Call: #lm(formula = val ~ grp, data = df) #Coefficients: #(Intercept) grp #0.04348 2.21739 ?abline abline(reg=lm(val~grp, data=df) ) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] regression line on boxplots
Am 01.04.2011 11:24, schrieb Yan Jiao: Dear R users, I'm trying to add a regression line on my boxplots (something like:boxplot(c(1:3),c(4:6),c(5:8))) But I can't see it. Please help !!! It's not a April fool's joke!!! Your sample data does not make any sense (at least to me). I would do it as follows: set.seed(8) df - data.frame(y = rnorm(100), x = factor(rep(1:4))) boxplot(y ~ x, data = df) regline - lm(y ~ as.numeric(x), data = df) abline(regline) HTH, Bernd __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Syntax coloring in R console
Please move this thread off r-help. It's about Rstudio, not R. -- Bert On Fri, Apr 1, 2011 at 8:05 AM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: Dear Liviu, thanks for the programming tip! However, I do all my editing in vim, which has had syntax highlighting for quite a while, as well as auto-completion and a number of other goodies. But while I do most of my programing in vim, I do most of my scientific studies simply using the R interface and keeping a manually edited lab book apart from the scripts. Clearly, one can do as much with Rstudio -- I just don't see any advantages, but I do see a disadvantage in my specific case: all sub-windows are confined to the desktop. In other words, having multiple plots on one monitor and a terminal with R command line is not possible. A question, though. Given that I have projects assorted in various directories, how can I start RStudio opening a project stored in .RData and .Rhistory of a given directory? I.e., how can I make RStudio open the current directory (like R does), and not $HOME? Thanks nonetheless, j. On Fri, Apr 1, 2011 at 4:20 PM, Liviu Andronic landronim...@gmail.com wrote: On Fri, Apr 1, 2011 at 3:48 PM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: RStudio might be a fine program, but it does not feature syntax highlighting, which is the only thing I am missing from R Console (it only colors the commands typed). The idea is that you shouldn't use the R console for you main programming needs, but only for quick and dirty checks. For the bulk of programming tasks you are invited to use the integrated editor (File New Script). The editor window does feature syntax highlighting, and a very helpful completion mechanism (via tab). Sending lines for execution to the terminal is as easy as clicking 'run lines' or ctrl+enter. If you're not a fan of keeping scripts for your projects you can easily use temporary files that you don't save. Moreover, the very idea of squeezing all R windows into one window-desktop would be counterproductive in my particular case. Notice that all panes are freely resizable and can be resized to the point of becoming hidden. Future releases will give more control over the panes layout (I think). Regards Liviu Thank you anyways! j. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web :
Re: [R] Syntax coloring in R console
On Fri, Apr 1, 2011 at 5:05 PM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: Dear Liviu, thanks for the programming tip! However, I do all my editing in vim, which has had syntax highlighting for quite a while, as well as auto-completion and a number of other goodies. But while I do most of my programing in vim, For info, vim has plug-in for R. I do most of my scientific studies simply using the R interface and keeping a manually edited lab book apart from the scripts. Clearly, one can do as much with Rstudio -- I just don't see any advantages, but I do see a disadvantage in my specific case: all sub-windows are confined to the desktop. In other words, having multiple plots on one monitor and a terminal with R command line is not possible. I see. This would be more of a hack, but you could use playwith as an external graphics device. Otherwise, there seems to be an easy hack: x11() plot(1:10) A question, though. Given that I have projects assorted in various directories, how can I start RStudio opening a project stored in .RData and .Rhistory of a given directory? I.e., how can I make RStudio open the current directory (like R does), and not $HOME? This is a known issue and the RStudio devels plan to address this. Currently I simply open RStudio in $HOME (and make sure that there is no existent .RData there), then open the .RData from my project's directory (by clicking on it in the right-hand Files pane) and then in the same pane I hit More Set as working dir. A bit cumbersome, but seems to work, and a small price to pay for all the available functionality. Regards Liviu Thanks nonetheless, j. On Fri, Apr 1, 2011 at 4:20 PM, Liviu Andronic landronim...@gmail.com wrote: On Fri, Apr 1, 2011 at 3:48 PM, January Weiner january.wei...@mpiib-berlin.mpg.de wrote: RStudio might be a fine program, but it does not feature syntax highlighting, which is the only thing I am missing from R Console (it only colors the commands typed). The idea is that you shouldn't use the R console for you main programming needs, but only for quick and dirty checks. For the bulk of programming tasks you are invited to use the integrated editor (File New Script). The editor window does feature syntax highlighting, and a very helpful completion mechanism (via tab). Sending lines for execution to the terminal is as easy as clicking 'run lines' or ctrl+enter. If you're not a fan of keeping scripts for your projects you can easily use temporary files that you don't save. Moreover, the very idea of squeezing all R windows into one window-desktop would be counterproductive in my particular case. Notice that all panes are freely resizable and can be resized to the point of becoming hidden. Future releases will give more control over the panes layout (I think). Regards Liviu Thank you anyways! j. [1] http://alternativeto.net/software/rstudio/about Regards Liviu I tried JGR, the GUI for R, but I have found the following problems with this package: - I was not able to change the background color from a repulsive grey, - apparently, GNU readline is not implemented in that package, that is, there is no functionality similar to ctrl-r (which searches through the history for matching commands), something I use frequently, and - tab expansion is of limited use (e.g. doesn't browse files in the current directory when expanding quoted arguments e.g. in read.table). All in all, I'd be happy to continue using the plain R console, but syntax highlighting would be nice. Any advice would be extremely welcome. Kind regards, January sessionInfo() R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 LC_MONETARY=C [6] LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail -- Dr. January Weiner 3 -- Max Planck Institute for Infection Biology Charitéplatz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 __ R-help@r-project.org mailing list
Re: [R] ANCOVA for linear regressions without intercept
See inline. On 2011-03-31 22:22, Yusuke Fukuda wrote: Thanks Bert. I have read ?formula again and again, and I'm still struggling; lm(body_length ~ head_length-1) This removes intercept from each individual regression (for male, female, unknown). When they are taken together, lm(body_length ~ sex*head_length) This shows differences in slopes and intercepts between the regressions (but I want to compare the slopes of the regressions WITHOUT intercepts). If I put lm(body_length ~ sex:head_length-1) This shows slopes for each sex without intercepts, but NOT differences in the slope between the regressions. You probably want: lm(body_length ~ head_length + sex:head_length-1) or, in short form: lm(body_length ~ head_length/sex-1) You might then compare the model 'without intercepts' (i.e. with intercepts forced to zero) with a model that includes intercepts. If the intercepts turn out to be significantly nonzero, what will you do? Peter Ehlers I also tried lm(body_length ~ sex*head_length-1) lm(body_length ~ sex*head_length-sex-1) But none of them worked. Would anyone be able to help me? All I want to do is to compare the slopes of three linear regressions that go through the origin (0,0) so that I can say if their difference is significant or not. Thanks for your help. From: Bert Gunter [mailto:gunter.ber...@gene.com] Sent: Friday, 1 April 2011 12:56 AM To: Yusuke Fukuda Cc: r-help@r-project.org Subject: Re: [R] ANCOVA for linear regressions without intercept If you haven't already received an answer, a careful reading of ?formula will provide it. -- Bert On Wed, Mar 30, 2011 at 11:42 PM, Yusuke Fukudayusuke.fuk...@nt.gov.au wrote: Hello R experts I have two linear regressions for sexes (Male, Female, Unknown). All have a good correlation between body length (response variable) and head length (explanatory variable). I know it is not recommended, but for a good practical reason (the purpose of study is to find a single conversion factor from head length to body length), the regressions need to go through the origin (0 intercept). Is it possible to do ANCOVA for these regressions without intercepts? When I do summary(lm(body length ~ sex*head length)) this will include the intercepts as below Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept)-6.496971.68497 -3.856 0.000118 *** sexMale-9.393401.97760 -4.750 2.14e-06 *** sexUnknown -1.337912.35453 -0.568 0.569927 head_length 7.123070.05503 129.443 2e-16 *** sexMale:head_length 0.316310.06246 5.064 4.37e-07 *** sexUnknown:head_length 0.199370.07022 2.839 0.004556 ** --- Is there any way I can remove the intercepts so that I can simply compare the slopes with no intercept taken into account? Thanks for help in advance. Yusuke Fukuda __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear Model with curve fitting parameter?
On 2011-04-01 05:44, stephen sefick wrote: Setting Z=Q-A would be the incorrect dimensions. I could Z=Q/A. Is fitting a nls model the same as fitting an ols? These data are hydraulic data from ~47 sites. To access predictive ability I am removing one site fitting a new model and then accessing the fit with a myriad of model assessment criteria. I should get the same answer with ols vs nls? Thank you for all of your help. No, ols and nls won't give the same result. If you use ols on the logged data, you're assuming additive errors on the log scale. With nls, you assume additive errors on the original scale. But your model looks simple enough - why not run it through both functions and see what the difference is. Ultimately, everything depends on what assumptions you're comfortable with. Peter Ehlers Stephen On Thu, Mar 31, 2011 at 8:34 PM, Steven McKinneysmckin...@bccrc.ca wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of stephen sefick Sent: March-31-11 3:38 PM To: R help Subject: [R] Linear Model with curve fitting parameter? I have a model Q=K*A*(R^r)*(S^s) A, R, and S are data I have and K is a curve fitting parameter. I have linearized as log(Q)=log(K)+log(A)+r*log(R)+s*log(S) I have taken the log of the data that I have and this is the model formula without the K part lm(Q~offset(A)+R+S, data=x) What is the formula that I should use? Let Z = Q - A for your logged data. Fitting lm(Z ~ R + S, data = x) should yield intercept parameter estimate = estimate for log(K) R coefficient parameter estimate = estimate for r S coefficient parameter estimate = estimate for s Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre Thanks for all of your help. I can provide a subset of data if necessary. -- Stephen Sefick | Auburn University | | Biological Sciences | | 331 Funchess Hall | | Auburn, Alabama | | 36849 | |___| | sas0...@auburn.edu | | http://www.auburn.edu/~sas0025 | |___| Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R/Finance 2011 Conference Agenda
R community: We're excited to post a preliminary agenda for the upcoming 3rd conference on R and Applied Finance, to be held in Chicago on April 29th and 30th. In addition to keynotes from John Bollinger, Mebane Faber, Stefano Iacus and Louis Kates, we are excited to have 31 additional talks covering the state of R and applied finance. This represents a phenomenal opportunity to meet and interact with some of the leading contributors in the field of finance, all with relevant contributions using R. We expect more than 200 participants from industry, government, and academia for the 2 day event. In addition, a conference dinner Friday evening in the heart of the financial district along Chicago's picturesque river will offer an unprecedented opportunity to enjoy amazing food, drink and conversation. http://www.rinfinance.com/agenda/index.html Registration is open, though pre-conference workshops are rapidly filling up. Register now and join your fellow colleagues at R/Finance 2011! http://www.rinfinance.com/register/ Thanks to our 2011 Co-Sponsors and Sponsors: International Center for Futures and Derivatives at UIC REvolution Analytics OneMarketData RStudio lemnica __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to paste a vector of expressions and a character vector?
Dear expeRts, I know I can't paste expressions in the normal way, but I just couldn't figure out how to get the following (I want to paste a character vector to an expression vector) right with bquote() or substitute. vec1 - c(a, expression(tilde(b)), c) vec2 - c(1, 2, 3) main - as.expression(paste(vec1, vec2)) plot(0,0, main=main[2]) Cheers, Marius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] regular expression
Great. thank you Bernd! Learned a new thing here.
John
From: Bernd Weiss bernd.we...@uni-koeln.de
Cc: r-help@r-project.org
Sent: Thu, March 31, 2011 6:19:25 PM
Subject: Re: [R] regular expression
Am 31.03.2011 21:06, schrieb array chip:
Ok then this code didn't do what I wanted. I want not including
'arg' before '.symptom', not individual letters of arg, but rather
as a word.
Bill Dunlap suggested using invert=T, it works for single 1
condition, but not for 2 conditions here: not including arg before
., but at the same time, does include .symptom.
Any other suggestions would be appreciated
This does work (but I am by no means an expert in regex...). I am using
'negative lookbehind'[1] to define an expression like 'arg'.
grep('(?!(arg))\\.symptom',arg.symptom,value=T, perl = T)
character(0)
grep('(?!(arg))\\.symptom',liver.symptom,value=T, perl = T)
[1] liver.symptom
Bernd
[1] http://www.regular-expressions.info/lookaround.html
[[alternative HTML version deleted]]
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Re: [R] regular expression
Try this also:
grep(arg, arg.symptom, value = TRUE, invert = TRUE)
character(0)
grep(arg, liver.symptom, value = TRUE, invert = TRUE)
[1] liver.symptom
On Fri, Apr 1, 2011 at 1:33 PM, array chip arrayprof...@yahoo.com wrote:
Great. thank you Bernd! Learned a new thing here.
John
From: Bernd Weiss bernd.we...@uni-koeln.de
Cc: r-help@r-project.org
Sent: Thu, March 31, 2011 6:19:25 PM
Subject: Re: [R] regular expression
Am 31.03.2011 21:06, schrieb array chip:
Ok then this code didn't do what I wanted. I want not including
'arg' before '.symptom', not individual letters of arg, but rather
as a word.
Bill Dunlap suggested using invert=T, it works for single 1
condition, but not for 2 conditions here: not including arg before
., but at the same time, does include .symptom.
Any other suggestions would be appreciated
This does work (but I am by no means an expert in regex...). I am using
'negative lookbehind'[1] to define an expression like 'arg'.
grep('(?!(arg))\\.symptom',arg.symptom,value=T, perl = T)
character(0)
grep('(?!(arg))\\.symptom',liver.symptom,value=T, perl = T)
[1] liver.symptom
Bernd
[1] http://www.regular-expressions.info/lookaround.html
[[alternative HTML version deleted]]
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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[R] Fisher's test
I have a matrix with 2 columns and I want to do fishers exact test for these with the totals for each row being 100 say. The data has the form: 23 12 32 21 12 2 and these represents the tables: 23 12 77 88 32 21 78 79 12 2 88 98 How do I use apply to speed up aclculation of the fisher.exact test? -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] mean in the boxplot
Dear R users, How to show mean in the boxplot instead of median ? Many thanks Yan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to paste a vector of expressions and a character vector?
On Apr 1, 2011, at 12:32 PM, Marius Hofert wrote: Dear expeRts, I know I can't paste expressions in the normal way, but I just couldn't figure out how to get the following (I want to paste a character vector to an expression vector) right with bquote() or substitute. vec1 - c(a, expression(tilde(b)), c) vec2 - c(1, 2, 3) main - as.expression(paste(vec1, vec2)) plot(0,0, main=main[2]) Do not use `paste` ... it coerces your expression to a character value ... use `c` instead: main - as.expression(c(vec1, vec2)) plot(1,1, main=main[2]) And then, even the as.expression is superfluous: main - c(vec1, vec2) plot(1,1, main=main[2]) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mean in the boxplot
On Apr 1, 2011, at 1:20 PM, Yan Jiao wrote: Dear R users, How to show mean in the boxplot instead of median ? Read ... help(boxplot) Use boxplot to create a set of values, substitute th emean for the groups then pass the mangled set of values to bxp(). -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to paste a vector of expressions and a character vector?
Dear David, thanks for your reply. The paste() meant to paste the vectors vec1 and vec2 together, so main should be a vector of length 3 of the form a 1, b 2, c 3 # with b being tilde(b) However, with c() it is a vector of length 6: expression(a, tilde(b), c, 1, 2, 3) Do you know a solution for that? Cheers, Marius On 2011-04-01, at 19:22 , David Winsemius wrote: On Apr 1, 2011, at 12:32 PM, Marius Hofert wrote: Dear expeRts, I know I can't paste expressions in the normal way, but I just couldn't figure out how to get the following (I want to paste a character vector to an expression vector) right with bquote() or substitute. vec1 - c(a, expression(tilde(b)), c) vec2 - c(1, 2, 3) main - as.expression(paste(vec1, vec2)) plot(0,0, main=main[2]) Do not use `paste` ... it coerces your expression to a character value ... use `c` instead: main - as.expression(c(vec1, vec2)) plot(1,1, main=main[2]) And then, even the as.expression is superfluous: main - c(vec1, vec2) plot(1,1, main=main[2]) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to paste a vector of expressions and a character vector?
On Apr 1, 2011, at 1:56 PM, Marius Hofert wrote: Dear David, thanks for your reply. The paste() meant to paste the vectors vec1 and vec2 together, so main should be a vector of length 3 of the form a 1, b 2, c 3 # with b being tilde(b) However, with c() it is a vector of length 6: expression(a, tilde(b), c, 1, 2, 3) lls -c(a, tilde(b),c) mains - bquote(.(parse(text=paste(lls,~,nns,sep=))) ) mains #expression(a~1, tilde(b)~2, c~3) #attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 #- mains[2] #expression(tilde(b)~2) plot(0,0, main=mains[2]) This would also work: mains2 - as.expression(parse(text=paste(lls,~,nns,sep=))) mains2 expression(a~1, tilde(b)~2, c~3) attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 I try to avoid using spaces in expressions and instead use ~'s because I don't really understand how spaces get parsed in expression operations, and I do know how plotmath operations work with ~. Do you know a solution for that? Cheers, Marius On 2011-04-01, at 19:22 , David Winsemius wrote: On Apr 1, 2011, at 12:32 PM, Marius Hofert wrote: Dear expeRts, I know I can't paste expressions in the normal way, but I just couldn't figure out how to get the following (I want to paste a character vector to an expression vector) right with bquote() or substitute. vec1 - c(a, expression(tilde(b)), c) vec2 - c(1, 2, 3) main - as.expression(paste(vec1, vec2)) plot(0,0, main=main[2]) Do not use `paste` ... it coerces your expression to a character value ... use `c` instead: main - as.expression(c(vec1, vec2)) plot(1,1, main=main[2]) And then, even the as.expression is superfluous: main - c(vec1, vec2) plot(1,1, main=main[2]) -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to paste a vector of expressions and a character vector?
On Apr 1, 2011, at 2:34 PM, David Winsemius wrote: On Apr 1, 2011, at 1:56 PM, Marius Hofert wrote: Dear David, thanks for your reply. The paste() meant to paste the vectors vec1 and vec2 together, so main should be a vector of length 3 of the form a 1, b 2, c 3 # with b being tilde(b) However, with c() it is a vector of length 6: expression(a, tilde(b), c, 1, 2, 3) Forgot one variable, nns: lls -c(a, tilde(b),c) nns -1:3 mains - bquote(.(parse(text=paste(lls,~,nns,sep=))) ) mains #expression(a~1, tilde(b)~2, c~3) #attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 #- mains[2] #expression(tilde(b)~2) plot(0,0, main=mains[2]) This would also work: mains2 - as.expression(parse(text=paste(lls,~,nns,sep=))) mains2 expression(a~1, tilde(b)~2, c~3) attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 I try to avoid using spaces in expressions and instead use ~'s because I don't really understand how spaces get parsed in expression operations, and I do know how plotmath operations work with ~. Do you know a solution for that? Cheers, Marius On 2011-04-01, at 19:22 , David Winsemius wrote: On Apr 1, 2011, at 12:32 PM, Marius Hofert wrote: Dear expeRts, I know I can't paste expressions in the normal way, but I just couldn't figure out how to get the following (I want to paste a character vector to an expression vector) right with bquote() or substitute. vec1 - c(a, expression(tilde(b)), c) vec2 - c(1, 2, 3) main - as.expression(paste(vec1, vec2)) plot(0,0, main=main[2]) Do not use `paste` ... it coerces your expression to a character value ... use `c` instead: main - as.expression(c(vec1, vec2)) plot(1,1, main=main[2]) And then, even the as.expression is superfluous: main - c(vec1, vec2) plot(1,1, main=main[2]) -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to paste a vector of expressions and a character vector?
On Apr 1, 2011, at 2:34 PM, David Winsemius wrote: On Apr 1, 2011, at 1:56 PM, Marius Hofert wrote: Dear David, thanks for your reply. The paste() meant to paste the vectors vec1 and vec2 together, so main should be a vector of length 3 of the form a 1, b 2, c 3 # with b being tilde(b) However, with c() it is a vector of length 6: expression(a, tilde(b), c, 1, 2, 3) lls -c(a, tilde(b),c) nns - 1:3 #Even easier would be: mains3 - parse(text=paste(lls,~,nns,sep=)) mains3 expression(a~1, tilde(b)~2, c~3) attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 mains - bquote(.(parse(text=paste(lls,~,nns,sep=))) ) mains #expression(a~1, tilde(b)~2, c~3) #attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 #- mains[2] #expression(tilde(b)~2) plot(0,0, main=mains[2]) This would also work: mains2 - as.expression(parse(text=paste(lls,~,nns,sep=))) mains2 expression(a~1, tilde(b)~2, c~3) attr(,srcfile) text attr(,wholeSrcref) a~1 tilde(b)~2 c~3 I try to avoid using spaces in expressions and instead use ~'s because I don't really understand how spaces get parsed in expression operations, and I do know how plotmath operations work with ~. Do you know a solution for that? Cheers, Marius On 2011-04-01, at 19:22 , David Winsemius wrote: On Apr 1, 2011, at 12:32 PM, Marius Hofert wrote: Dear expeRts, I know I can't paste expressions in the normal way, but I just couldn't figure out how to get the following (I want to paste a character vector to an expression vector) right with bquote() or substitute. vec1 - c(a, expression(tilde(b)), c) vec2 - c(1, 2, 3) main - as.expression(paste(vec1, vec2)) plot(0,0, main=main[2]) Do not use `paste` ... it coerces your expression to a character value ... use `c` instead: main - as.expression(c(vec1, vec2)) plot(1,1, main=main[2]) And then, even the as.expression is superfluous: main - c(vec1, vec2) plot(1,1, main=main[2]) -- David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] filled contour plot with contour lines
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp - get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
The routine will work in a modified form without adding the coordinates
(the axis lines) but when I include these the routine produces various
errors, such as dimension mismatch, or unexpected end encountered.
I tried to follow the example on filled.contour help page.
Thanks in advance
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear Model with curve fitting parameter?
-Original Message- From: stephen sefick [mailto:ssef...@gmail.com] Sent: April-01-11 5:44 AM To: Steven McKinney Cc: R help Subject: Re: [R] Linear Model with curve fitting parameter? Setting Z=Q-A would be the incorrect dimensions. I could Z=Q/A. I suspect this is confusion about what Q is. I was presuming that the Q in this following formula was log(Q) with Q from the original data. I have taken the log of the data that I have and this is the model formula without the K part lm(Q~offset(A)+R+S, data=x) If the model is Q=K*A*(R^r)*(S^s) then log(Q) = log(K) + log(A) + r*log(R) + s*log(S) Rearranging yields log(Q) - log(A) = log(K) + r*log(R) + s*log(S) so what I labeled 'Z' below is Z = log(Q) - log(A) = log(Q/A) so Z = log(K) + r*log(R) + s*log(S) and a linear model fit of Z ~ log(R) + log(S) will yield parameter estimates for the linear equation E(Z) = B0 + B1*log(R) + B2*log(S) (E(Z) = expected value of Z) so B0 estimate is an estimate of log(K) B1 estimate is an estimate of r B2 estimate is an estimate of s More details and careful notation will eventually lead to a reasonable description and analysis strategy. Best Steve McKinney Is fitting a nls model the same as fitting an ols? These data are hydraulic data from ~47 sites. To access predictive ability I am removing one site fitting a new model and then accessing the fit with a myriad of model assessment criteria. I should get the same answer with ols vs nls? Thank you for all of your help. Stephen On Thu, Mar 31, 2011 at 8:34 PM, Steven McKinney smckin...@bccrc.ca wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of stephen sefick Sent: March-31-11 3:38 PM To: R help Subject: [R] Linear Model with curve fitting parameter? I have a model Q=K*A*(R^r)*(S^s) A, R, and S are data I have and K is a curve fitting parameter. I have linearized as log(Q)=log(K)+log(A)+r*log(R)+s*log(S) I have taken the log of the data that I have and this is the model formula without the K part lm(Q~offset(A)+R+S, data=x) What is the formula that I should use? Let Z = Q - A for your logged data. Fitting lm(Z ~ R + S, data = x) should yield intercept parameter estimate = estimate for log(K) R coefficient parameter estimate = estimate for r S coefficient parameter estimate = estimate for s Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre Thanks for all of your help. I can provide a subset of data if necessary. -- Stephen Sefick | Auburn University | | Biological Sciences | | 331 Funchess Hall | | Auburn, Alabama | | 36849 | |___| | sas0...@auburn.edu | | http://www.auburn.edu/~sas0025 | |___| Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick | Auburn University | | Biological Sciences | | 331 Funchess Hall | | Auburn, Alabama | | 36849 | |___| | sas0...@auburn.edu | | http://www.auburn.edu/~sas0025 | |___| Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science.
Re: [R] Fisher's test
On 2011-04-01 10:19, Jim Silverton wrote: I have a matrix with 2 columns and I want to do fishers exact test for these with the totals for each row being 100 say. The data has the form: 23 12 32 21 12 2 and these represents the tables: 23 12 77 88 32 21 78 79 12 2 88 98 How do I use apply to speed up aclculation of the fisher.exact test? apply(yourMatrix, 1, function(x) fisher.test(cbind(x, 100 - x))) or, if you only want the P-value: apply(yourMatrix, 1, function(x) fisher.test(cbind(x, 100 - x))$p.value) Peter Ehlers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice xscale.components: different ticks on top/bottom axis
On Fri, Mar 11, 2011 at 12:28 AM,
boris.vasil...@forces.gc.ca wrote:
Good afternoon,
I am trying to create a plot where the bottom and top axes have the
same scale but different tick marks. I tried user-defined
xscale.component function but it does not produce desired results.
Can anybody suggest where my use of xscale.component
function is incorrect?
For example, the code below tries to create a plot where horizontal
axes limits are c(0,10), top axis has ticks at odd integers, and
bottom axis has ticks at even integers.
library(lattice)
df - data.frame(x=1:10,y=1:10)
xscale.components.A - function(...,user.value=NULL) {
# get default axes definition list; print user.value
ans - xscale.components.default(...)
print(user.value)
# start with the same definition of bottom and top axes
ans$top - ans$bottom
# - bottom labels
ans$bottom$labels$at - seq(0,10,by=2)
ans$bottom$labels$labels - paste(B,seq(0,10,by=2),sep=-)
# - top labels
ans$top$labels$at - seq(1,9,by=2)
ans$top$labels$labels - paste(T,seq(1,9,by=2),sep=-)
# return axes definition list
return(ans)
}
oltc - xyplot(y~x,data=df,
scales=list(x=list(limits=c(0,10),at=0:10,alternating=3)),
xscale.components=xscale.components.A,
user.value=1)
print(oltc)
The code generates a figure with incorrectly placed bottom and top
labels. Bottom labels B-0, B-2, ... are at 0, 1, ... and top
labels T-1, T-3, ... are at 0, 1, ... When axis-function runs out
of labels, it replaces labels with NA.
It appears that lattice uses top$ticks$at to place labels and
top$labels$labels for labels. Is there a way to override this
behaviour (other than to expand the labels$labels vector to be as
long as ticks$at vector and set necessary elements to )?
Well, top|bottom$ticks$at is used to place the ticks, and
$labels$at is used to place the labels. They should typically
be the same, but you have changed one and not the other.
Everything seems to work if you set $ticks$at to the same
values as $labels$at:
## - bottom labels
+ ans$bottom$ticks$at - seq(0,10,by=2)
ans$bottom$labels$at - seq(0,10,by=2)
ans$bottom$labels$labels - paste(B,seq(0,10,by=2),sep=-)
## - top labels
+ ans$top$ticks$at - seq(1,9,by=2)
ans$top$labels$at - seq(1,9,by=2)
ans$top$labels$labels - paste(T,seq(1,9,by=2),sep=-)
Also, can user-parameter be passed into xscale.components()
function? (For example, locations and labels of ticks on the top
axis). In the code above, print(user.value) returns NULL even
though in the xyplot() call user.value is 1.
No. Unrecognized arguments are passed to the panel function
only, not to any other function. However, you can always
define an inline
function:
oltc - xyplot(y~x,data=df,
scales=list(x=list(limits=c(0,10), at = 0:10,
alternating=3)),
xscale.components = function(...)
xscale.components.A(..., user.value=1))
Hope that helps (and sorry for the late reply).
-Deepayan
Deepyan,
Thank you very much for your reply. It makes things a bit clearer.
It other words in the list prepared by xscale.components(), vectors
top|bottom$ticks$at and top|bottom$labels$at must be the same. If only
every second tick is to be labelled then every second label should be set
explicitly to empty strings:
ans$bottom$ticks$at - seq(0,10,by=1)
ans$bottom$labels$at - seq(0,10,by=1)
ans$bottom$labels$labels - paste(B,seq(0,10,by=1),sep=-)
# replace B-1, B-3, ... with
ans$bottom$labels$labels[seq(2,11,by=2)] -
Sincerely,
Boris.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] mean in the boxplot
On 2011-04-01 10:28, David Winsemius wrote: On Apr 1, 2011, at 1:20 PM, Yan Jiao wrote: Dear R users, How to show mean in the boxplot instead of median ? Read ... help(boxplot) Use boxplot to create a set of values, substitute th emean for the groups then pass the mangled set of values to bxp(). Another option is to add the means as points after plotting the boxplot with: boxplot() points(1:n, Means) This is particularly useful if you want both the medians and the means on the plot. If you don't want the median line, you can get rid of it by setting medcol=transparent in the boxplot() call. But then again, the whole point of a boxplot is to represent general distributional shape for which the median is surely more effective. Peter Ehlers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] XYPlot Conditioning Variable in Specific, Non-Alphanumeric Order. -- Resending with corrected .txt file
Thank you very much Deepayan. This does exactly what I needed! Cheers, Guy Jett gj...@itsi.com -Original Message- From: Deepayan Sarkar [mailto:deepayan.sar...@gmail.com] Sent: Friday, April 01, 2011 6:51 AM To: Guy Jett Cc: r-help@R-project.org Subject: Re: [R] XYPlot Conditioning Variable in Specific, Non-Alphanumeric Order. -- Resending with corrected .txt file snip You need to specify the order of the levels explicitly (to override the default). Here is how to do it for one, you can similarly do the other: levels(df$Offset) [1] T U V Y Z A B C D E F G H df$Offset - factor(df$Offset, + levels = c(T, U, V, Y, Z, A, +B, C, D, E, F, G, H)) levels(df$Offset) [1] T U V Y Z A B C D E F G H Once you make these changes, your original call should work as desired. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] filled contour plot with contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) { loop stuff }
Peter Ehlers
On 2011-04-01 11:48, steve_fried...@nps.gov wrote:
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp- get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
The routine will work in a modified form without adding the coordinates
(the axis lines) but when I include these the routine produces various
errors, such as dimension mismatch, or unexpected end encountered.
I tried to follow the example on filled.contour help page.
Thanks in advance
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] filled contour plot with contour lines
Hi Peter,
Thanks for taking the time to consider the problem. I realize the procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in size to
pull data into this process. Nobody in their right mind should work with
such things. It's a spatial temporal database with 10 years of daily data
in a irregular area spanning 405 x 287 cells.
Anyway, I tried your suggestion adding a { in front of the for loop and a
closing } following the last line.
It did not work.
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Peter Ehlers
ehlers@ucalgary.
caTo
steve_fried...@nps.gov
04/01/2011 05:08 steve_fried...@nps.gov
PM cc
r-help@r-project.org
r-help@r-project.org
Subject
Re: [R] filled contour plot with
contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) { loop stuff }
Peter Ehlers
On 2011-04-01 11:48, steve_fried...@nps.gov wrote:
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp- get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
The routine will work in a modified form without adding the coordinates
(the axis lines) but when I include these the routine produces various
errors, such as dimension mismatch, or unexpected end encountered.
I tried to follow the example on filled.contour help page.
Thanks in advance
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] function in argument
Hi, I tried to pass the function dist() as an argument, but got an error
message. However, almost the same code with mean() as the function to be
passed,
it works ok.
foo-function (x,
xfun = dist)
{
xfun(x)
}
foo(matrix(1:100,nrow=5))
Error in foo(matrix(1:100, nrow = 5)) : could not find function xfun
foo-function (x,
xfun = mean)
{
xfun(x)
}
foo(1:10)
[1] 5.5
what am I missing here?
Thanks
John
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] hc2Newick is different than th hclust dendrogram
Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: hc - hclust(dist(C)) plot(hc) with the: write(hc2Newick(hc),file='test.newick') both things draw completely different trees... I have also tried with the raw distance matrix D and also the agnes function, but the same happens. The hclus and agnes dendrogram is logical, whereas the newick tree is not. Thanks for any help! -- Jose Sergio Hleap Lozano, M. Sc. Ph. D. Student, Dalhousie University Researcher, SQUALUS Foundation __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] filled contour plot with contour lines
Hi Peter,
Thanks for taking the time to consider the problem. I realize the procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in size to
pull data into this process. Nobody in their right mind should work with
such things. It's a spatial temporal database with 10 years of daily data
in a irregular area spanning 405 x 287 cells.
Anyway, I tried your suggestion adding a { in front of the for loop and a
closing } following the last line.
It did not work.
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Peter Ehlers
ehlers@ucalgary.
caTo
steve_fried...@nps.gov
04/01/2011 05:08 steve_fried...@nps.gov
PM cc
r-help@r-project.org
r-help@r-project.org
Subject
Re: [R] filled contour plot with
contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) { loop stuff }
Peter Ehlers
On 2011-04-01 11:48, steve_fried...@nps.gov wrote:
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp- get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
The routine will work in a modified form without adding the coordinates
(the axis lines) but when I include these the routine produces various
errors, such as dimension mismatch, or unexpected end encountered.
I tried to follow the example on filled.contour help page.
Thanks in advance
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] qcc.overdispersion-test
Hi all, I have made an overdispersion test for a data set and get the following result Overdispersion test Obs.Var/Theor.Var Statistic p-value poisson data 16.24267 47444.85 0 after deleting the outliers from the data set I get the following result Overdispersion test Obs.Var/Theor.Var Statistic p-value poisson data 16.27106 0 1 The problem is that the overdispersion parameter does not really change, but how could the p-value and the statistic change so that the null hypothesis is accepted?? I would be very grateful if someone could help me? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] filled contour plot with contour lines
On Apr 1, 2011, at 5:38 PM, steve_fried...@nps.gov wrote:
Hi Peter,
Thanks for taking the time to consider the problem. I realize the
procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in
size to
pull data into this process. Nobody in their right mind should work
with
such things. It's a spatial temporal database with 10 years of daily
data
in a irregular area spanning 405 x 287 cells.
Anyway, I tried your suggestion adding a { in front of the for loop
and a
closing } following the last line.
That suggestion was probably intended to get you a more informative
error message:
for(j in 1:(varsize[4]-1) )
temp - get.var.ncdf(
nc=input,
varid=p_foraging,
c(1,1,j),
c(varsize[1], varsize[2], 1)
)
# I think Peter is correct. That loop will complete before the call to
filled.contour,
# so you will only have the last version of temp plot.
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title( main =
paste(Everglades Wood Stork Foraging Potential \nYear,
(2000+j)),
#that double call to title looks incomplete as well. The comma looks
premature.
# Shouldn't it be something like:
plot.title = bquote(Everglades Wood Stork Foraging Potential
\nYear, .(2000+j) )
#(And since the for loop is already complete `j` will not exist.
# Which is probably the source of the error you are getting.)
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
It did not work.
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Peter Ehlers
ehlers@ucalgary.
caTo
steve_fried...@nps.gov
04/01/2011 05:08 steve_fried...@nps.gov
PM cc
r-help@r-project.org
r-help@r-project.org
Subject
Re: [R] filled contour plot with
contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) { loop stuff }
Peter Ehlers
On 2011-04-01 11:48, steve_fried...@nps.gov wrote:
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp- get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
The routine will work in a modified form without adding the
coordinates
(the axis lines) but when I include these the routine produces
various
errors, such as dimension mismatch, or unexpected end
encountered.
I tried to follow the example on filled.contour help page.
Thanks in advance
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
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PLEASE do read the posting guide
Re: [R] filled contour plot with contour lines
Steve,
I use filled.contour but have a semicolon, ;, between the two
axis calls. Do you need one after
axis(1, seq(45 , 58, by = 1))
?
Clint
--
Clint BowmanINTERNET: cl...@ecy.wa.gov
Air Quality Modeler INTERNET: cl...@math.utah.edu
Department of Ecology VOICE: (360) 407-6815
PO Box 47600FAX:(360) 407-7534
Olympia, WA 98504-7600
USPS: PO Box 47600, Olympia, WA 98504-7600
Parcels:300 Desmond Drive, Lacey, WA 98503-1274
On Fri, 1 Apr 2011, steve_fried...@nps.gov wrote:
Hi Peter,
Thanks for taking the time to consider the problem. I realize the procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in size to
pull data into this process. Nobody in their right mind should work with
such things. It's a spatial temporal database with 10 years of daily data
in a irregular area spanning 405 x 287 cells.
Anyway, I tried your suggestion adding a { in front of the for loop and a
closing } following the last line.
It did not work.
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Peter Ehlers
ehlers@ucalgary.
caTo
steve_fried...@nps.gov
04/01/2011 05:08 steve_fried...@nps.gov
PM cc
r-help@r-project.org
r-help@r-project.org
Subject
Re: [R] filled contour plot with
contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) { loop stuff }
Peter Ehlers
On 2011-04-01 11:48, steve_fried...@nps.gov wrote:
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp- get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
The routine will work in a modified form without adding the coordinates
(the axis lines) but when I include these the routine produces various
errors, such as dimension mismatch, or unexpected end encountered.
I tried to follow the example on filled.contour help page.
Thanks in advance
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] function in argument
On Apr 1, 2011, at 5:56 PM, array chip wrote:
Hi, I tried to pass the function dist() as an argument, but got an
error
message. However, almost the same code with mean() as the function
to be passed,
it works ok.
foo-function (x,
xfun = dist)
{
xfun(x)
}
foo(matrix(1:100,nrow=5))
Error in foo(matrix(1:100, nrow = 5)) : could not find function xfun
Works on my machine.
foo(matrix(1:100,nrow=5))
1 2 3 4
2 4.472136
3 8.944272 4.472136
4 13.416408 8.944272 4.472136
5 17.888544 13.416408 8.944272 4.472136
You have probably overwritten `dist` with a non-functional object.
Try rm(dist) and re-run:
foo-function (x,
xfun = mean)
{
xfun(x)
}
foo(1:10)
[1] 5.5
what am I missing here?
Thinking about your full workspace, I would guess.
--
David Winsemius, MD
West Hartford, CT
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] function in argument
OK, I figured it out, need to add stats::: before dist
foo-function (x,
xfun = stats:::dist)
{
xfun(x)
}
John
To: r-help@r-project.org
Sent: Fri, April 1, 2011 2:56:06 PM
Subject: [R] function in argument
Hi, I tried to pass the function dist() as an argument, but got an error
message. However, almost the same code with mean() as the function to be
passed,
it works ok.
foo-function (x,
xfun = dist)
{
xfun(x)
}
foo(matrix(1:100,nrow=5))
Error in foo(matrix(1:100, nrow = 5)) : could not find function xfun
foo-function (x,
xfun = mean)
{
xfun(x)
}
foo(1:10)
[1] 5.5
what am I missing here?
Thanks
John
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] function in argument
Or:
foo-function (x, xfun = dist) {
match.fun(xfun)(x)
}
On Fri, Apr 1, 2011 at 7:06 PM, array chip arrayprof...@yahoo.com wrote:
OK, I figured it out, need to add stats::: before dist
foo-function (x,
xfun = stats:::dist)
{
xfun(x)
}
John
To: r-help@r-project.org
Sent: Fri, April 1, 2011 2:56:06 PM
Subject: [R] function in argument
Hi, I tried to pass the function dist() as an argument, but got an error
message. However, almost the same code with mean() as the function to be
passed,
it works ok.
foo-function (x,
xfun = dist)
{
xfun(x)
}
foo(matrix(1:100,nrow=5))
Error in foo(matrix(1:100, nrow = 5)) : could not find function xfun
foo-function (x,
xfun = mean)
{
xfun(x)
}
foo(1:10)
[1] 5.5
what am I missing here?
Thanks
John
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Lattice wireframe or cloud plot with different colours by a group
I have a question about wireframe 3-D plots and how to apply colors. I have a large dataset of river flow (m^3/s) over time, and I have coded these flows based on their height. I would like to produce a wireframe plot that colors the graph based on the flow code, i.e. I would like high flows to be red, medium to be green and low flows to be blue. Here is some sample data with the basic wireframe plot: flow.dat=cbind.data.frame(flow=sin(2*pi/53*c(1:3000))+1,day=as.numeric(format(as.Date(c(1:3000)), format=%j)), year=as.numeric(format(as.Date(c(1:3000)), format=%Y)),grp=c(rep(c(1.high,2.med,3.low),1000))) wireframe(flow~day*year, data=flow.dat, shade=T) Is there any way to specify what colours are passed to the plot? I.e. wireframe(flow~day*year, data=flow.dat, shade=T, groups=grp, col.group=c(#FF3030,#551A8B,#43CD80)) I would also be happy if I could do this with a cloud plot, but I can't get the colors to plot correctly. cloud(flow~day*year, data=flow.dat, shade=T, groups=grp, col.group=c(#FF3030,#43CD80,#1E90FF), pch=20) Any help is much appreciated! Thank you. -Pam Allen allen_...@hotmail.com -- View this message in context: http://r.789695.n4.nabble.com/Lattice-wireframe-or-cloud-plot-with-different-colours-by-a-group-tp3421296p3421296.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] filled contour plot with contour lines
Steve,
I was just about to send off another suggestion which
began with ...
Try the following or wait for David W. to chime in.
But I see that he's already done that. Anyway, in case
it's still of some use:
First I would check that you don't have a variable 'T' in
your workspace. (Never use T in place of TRUE.)
Then I would check that x and y are as they should be.
Then I would make sure that temp is of the correct type
(a matrix) by letting j take a few values (1,2,varsize[4]-1),
generating temp, and running str(temp). I assume that
varsize[4] is = 2.
Then I would run the following stripped-down version of
your loop (note that I modified your contour() call):
for(j in 1:2) {
temp - get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1)
)
filled.contour(x,
y,
temp,
plot.axes = { contour(x, y, temp, add = TRUE)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1))
}
}
If that gives reasonable results, you can add the prettyfying
statements back in. If you still get errors, then either I'm
out-to-lunch (quite possible!) or you need to use debug() to
figure out what's going on.
Peter Ehlers
On 2011-04-01 14:59, David Winsemius wrote:
On Apr 1, 2011, at 5:38 PM, steve_fried...@nps.gov wrote:
Hi Peter,
Thanks for taking the time to consider the problem. I realize the
procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in
size to
pull data into this process. Nobody in their right mind should work
with
such things. It's a spatial temporal database with 10 years of daily
data
in a irregular area spanning 405 x 287 cells.
Anyway, I tried your suggestion adding a { in front of the for loop
and a
closing } following the last line.
That suggestion was probably intended to get you a more informative
error message:
for(j in 1:(varsize[4]-1) )
temp- get.var.ncdf(
nc=input,
varid=p_foraging,
c(1,1,j),
c(varsize[1], varsize[2], 1)
)
# I think Peter is correct. That loop will complete before the call to
filled.contour,
# so you will only have the last version of temp plot.
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title( main =
paste(Everglades Wood Stork Foraging Potential \nYear,
(2000+j)),
#that double call to title looks incomplete as well. The comma looks
premature.
# Shouldn't it be something like:
plot.title = bquote(Everglades Wood Stork Foraging Potential
\nYear, .(2000+j) )
#(And since the for loop is already complete `j` will not exist.
# Which is probably the source of the error you are getting.)
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
It did not work.
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Peter Ehlers
ehlers@ucalgary.
ca To
steve_fried...@nps.gov
04/01/2011 05:08steve_fried...@nps.gov
PM cc
r-help@r-project.org
r-help@r-project.org
Subject
Re: [R] filled contour plot with
contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) { loop stuff }
Peter Ehlers
On 2011-04-01 11:48, steve_fried...@nps.gov wrote:
I'm stumped, can anyone find my error in this sequence.
for(j in 1:(varsize[4]-1))
temp- get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1))
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title(main = paste(Everglades Wood Stork
Foraging Potential \nYear, (2000+j)),
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
[R] package MICE, squeeze function, calling several variables at once
Hello everyone!I have a data set with missing observations that I am trying to impute. I am using MICE and I would like the imputed values to all be positive. I have two types of variables: prices (P1 to P136) and quantities (Q1 to Q136) and I also want the range of these two types to be different. Besides these variables. I am using the squeeze function but I am unable to set it such that I don't have to write the names of all the variables. Also note that I do not have all the 136 Ps and Qs because since some were completely missing, I had to drop those variables. But my first Q is called Q1 and the last one Q136 and similarly for P. I apologize if I am making a silly little error since I am still learning R. This is the code that I have and the error that I am getting: #Program starts here#Read data into Rdf - read.table(F:\\testC2S4\\new_C2-S4_head_data.txt, header = TRUE); #, stringsAsFactors = TRUEdfPZ - df[ ,1:3]dfDV - df[ ,277:311]dfPtemp - df[ ,seq(4, 275, by = 2)]dfP - dfPtemp[, sapply(dfPtemp, function(x) !all(is.na(x)))]dfQtemp - df[ ,seq(5, 275, by = 2)]dfQ - dfQtemp[, sapply(dfQtemp, function(x) !all(is.na(x)))]remove(dfPtemp, dfQtemp) NewPrimal - data.frame(c(dfPZ, dfQ, dfP, dfDV), row.names = NULL, check.rows = F, check.names = F) remove(dfPZ, dfQ, dfP, dfDV) library(mice)# setting up the default settings for the imputationini - mice(NewPrimal, seed = 52275,imputationMethod = norm, maxit=0,pred = quickpred(NewPrimal, mincor = 0.25, minpuc = 0.95,include = c(blnNewYearsDay, blnValentinesDay, blnStPatricksDay, blnEaster, blnMothersDay, blnMemorialDay, blnFathersDay, blnIndependenceDay, blnLaborDay, blnThanksgiving, blnChristmas, Qtr1, Qtr2, Qtr3, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec), exclude = c(ActualWeekEndingDate, CompanyID, PriceZoneID, Date, Year)), print=FALSE) meth - ini$meth # naming the default method in inipred - ini$pred # naming the matrix of default predictors in inipost - ini$post# naming the default post processing method in inipost[Q1:Q136] - imp[[j]][,i] - squeeze(imp[[j]][,i],c(0,351000)) #setting the range for quantitypost[P1:P136] - imp[[j]][,i] - squeeze(imp[[j]][,i],c(0,50)) #setting the range for price # calling mice to impute given default settings:impNP - mice(NewPrimal, meth = meth, maxit=5, pred = pred, post = post) ##My error warningError in Q1:Q136 : NA/NaN argument In addition: Warning messages: 1: In post[Q1:Q136] - imp[[j]][,i] - squeeze(imp[[j]][,i],c(0,351000)) : NAs introduced by coercion 2: In post[Q1:Q136] - imp[[j]][,i] - squeeze(imp[[j]][,i],c(0,351000)) : NAs introduced by coercion Any ideas? Thank you and have a great weekend! Rita If you think education is expensive, try ignorance--Derek Bok [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] filled contour plot with contour lines
Hi Peter and everyone else who has offered suggestions. I am now at home
and will try your suggestions this evening.
The initial effort with the stripped down verion I have used earlier did
access the file correctly so I have no reason to think it is not formatted
correctly. That however is always a worthy check in all applications. I
appreciate the reminder.
Steve
friedman.st...@gmail.com
517-648-6290
-Original message-
From: Peter Ehlers ehl...@ucalgary.ca
To: David Winsemius dwinsem...@comcast.net
Cc: r-help@r-project.org r-help@r-project.org
Sent: Fri, Apr 1, 2011 22:49:38 GMT+00:00
Subject: Re: [R] filled contour plot with contour lines
Steve,
I was just about to send off another suggestion which
began with ...
Try the following or wait for David W. to chime in.
But I see that he's already done that. Anyway, in case
it's still of some use:
First I would check that you don't have a variable 'T' in
your workspace. (Never use T in place of TRUE.)
Then I would check that x and y are as they should be.
Then I would make sure that temp is of the correct type
(a matrix) by letting j take a few values (1,2,varsize[4]-1),
generating temp, and running str(temp). I assume that
varsize[4] is = 2.
Then I would run the following stripped-down version of
your loop (note that I modified your contour() call):
for(j in 1:2) {
temp - get.var.ncdf(nc=input,
varid=p_foraging,c(1,1,j),c(varsize[1],varsize[2],1)
)
filled.contour(x,
y,
temp,
plot.axes = { contour(x, y, temp, add = TRUE)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1))
}
}
If that gives reasonable results, you can add the prettyfying
statements back in. If you still get errors, then either I'm
out-to-lunch (quite possible!) or you need to use debug() to
figure out what's going on.
Peter Ehlers
On 2011-04-01 14:59, David Winsemius wrote:
On Apr 1, 2011, at 5:38 PM, steve_fried...@nps.gov wrote:
Hi Peter,
Thanks for taking the time to consider the problem. I realize the
procedure
is not reproducible. I use a 4 dimensional netCDF file (4.2 GB) in
size to
pull data into this process. Nobody in their right mind should work
with
such things. It's a spatial temporal database with 10 years of daily
data
in a irregular area spanning 405 x 287 cells.
Anyway, I tried your suggestion adding a { in front of the for loop
and a
closing } following the last line.
That suggestion was probably intended to get you a more informative
error message:
for(j in 1:(varsize[4]-1) )
temp- get.var.ncdf(
nc=input,
varid=p_foraging,
c(1,1,j),
c(varsize[1], varsize[2], 1)
)
# I think Peter is correct. That loop will complete before the call to
filled.contour,
# so you will only have the last version of temp plot.
filled.contour(x, y, temp, color = terrain.colors,
plot.title = title( main =
paste(Everglades Wood Stork Foraging Potential \nYear,
(2000+j)),
#that double call to title looks incomplete as well. The comma looks
premature.
# Shouldn't it be something like:
plot.title = bquote(Everglades Wood Stork Foraging Potential
\nYear, .(2000+j) )
#(And since the for loop is already complete `j` will not exist.
# Which is probably the source of the error you are getting.)
xlab = UTM East, ylab = UTM North) ,
plot.axes = { contour(temp, add=T)
axis(1, seq(45 , 58, by = 1))
axis(2, seq(280,400, by = 1)) },
key.title = title(main=Probability) ,
key.axes = axis(4, seq(0 , 1 , by = 0.1))
It did not work.
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Peter Ehlers
ehlers@ucalgary.
ca To
steve_fried...@nps.gov
04/01/2011 05:08steve_fried...@nps.gov
PM cc
r-help@r-project.org
r-help@r-project.org
Subject
Re: [R] filled contour plot with
contour lines
Aren't you missing a set of parentheses?
I can't run your code since it's not reproducible, but to
my aging eyes it seems that you need a set of '{}' around
the contents of your loop:
for(j in 1:(varsize[4]-1)) {
Re: [R] Lattice wireframe or cloud plot with different colours by a group
On Apr 1, 2011, at 6:21 PM, Pam Allen wrote: I have a question about wireframe 3-D plots and how to apply colors. I have a large dataset of river flow (m^3/s) over time, and I have coded these flows based on their height. I would like to produce a wireframe plot that colors the graph based on the flow code, i.e. I would like high flows to be red, medium to be green and low flows to be blue. Here is some sample data with the basic wireframe plot: flow.dat=cbind.data.frame(flow=sin(2*pi/53*c(1:3000)) +1,day=as.numeric(format(as.Date(c(1:3000)), format=%j)), year=as.numeric(format(as.Date(c(1:3000)), format=%Y)),grp=c(rep(c(1.high,2.med,3.low),1000))) It does not look to me that high flows are properly grouped with `grp`. wireframe(flow~day*year, data=flow.dat, shade=T) wireframe(flow~day*year, data=flow.dat, drape=TRUE, col.regions=c(#FF3030,#551A8B,#43CD80), at=c(0,.6,1.3,1.8)) Because of the coding at the corner and the long thin polygons you have specified with your day*year splits you get slanting colors. Is there any way to specify what colours are passed to the plot? I.e. wireframe(flow~day*year, data=flow.dat, shade=T, groups=grp, col.group=c(#FF3030,#551A8B,#43CD80)) I would also be happy if I could do this with a cloud plot, but I can't get the colors to plot correctly. cloud(flow~day*year, data=flow.dat, shade=T, groups=grp, col.group=c(#FF3030,#43CD80,#1E90FF), pch=20) Any help is much appreciated! Thank you. -Pam Allen allen_...@hotmail.com -- View this message in context: http://r.789695.n4.nabble.com/Lattice-wireframe-or-cloud-plot-with-different-colours-by-a-group-tp3421296p3421296.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Putting a loop in a function
I'm stuck here. The following code works great if I just use it on the
command line in a 'for' loop. Once I try to define it as a function as seen
below, I get bad results. I'm trying to return a vector of column indices
based on a short string that is contained in a selection (length of about
70) of long column names that changes from time to time. Is there an
existing function that will do this for me? The more I think about this
problem, the more I feel there has to be a function out there. I've not
found it.
ind - function(col, string, vector){ # this is really the problem. I don't
feel like I'm declaring these arguments properly.
indices - vector(mode = 'numeric') # I am not entirely confident that
this use is necessary. Is indices - c() okay?
for (i in 1:length(col)){
num - regexpr(str, col[i])
if (num != -1){
indices - c(vector, i) # I've also had success with indices -
append(indices, i)
}
}
indices
}
ind(d[,'Column.I.want'], 'string', 'output.vector')
Am I wrong here? I've read that the last statement in the function is what
it will return, and what I want is a vector of integers.
Thanks,
-Ben
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Putting a loop in a function
Hi Ben,
I am having some trouble figuring out what it is exactly you want. A
workable example would be nice and then (even if just manually) typed
out what you would like it to return based on a given input. I almost
think you just want grep().
grep(test, c(test, not, test2, not), value = TRUE)
[1] test test2
using your example:
grep(string, d[,Column.You.Want], value = TRUE)
On Fri, Apr 1, 2011 at 5:39 PM, Ben Hunter bjameshun...@gmail.com wrote:
I'm stuck here. The following code works great if I just use it on the
command line in a 'for' loop. Once I try to define it as a function as seen
below, I get bad results. I'm trying to return a vector of column indices
based on a short string that is contained in a selection (length of about
70) of long column names that changes from time to time. Is there an
existing function that will do this for me? The more I think about this
problem, the more I feel there has to be a function out there. I've not
found it.
ind - function(col, string, vector){ # this is really the problem. I don't
feel like I'm declaring these arguments properly.
indices - vector(mode = 'numeric') # I am not entirely confident that
this use is necessary. Is indices - c() okay?
indices - c() would sort of work, but vector() is better. Also, if
you actually want your function to be returning integers, you should
instatiate indices as an integer class vector, not numeric.
for (i in 1:length(col)){
num - regexpr(str, col[i])
str() is a function, and as far as I can tell, a variable str is not
defined anywhere in your function or your functions argument. Did you
mean string?
if (num != -1){
indices - c(vector, i) # I've also had success with indices -
append(indices, i)
why are you combining vector with i over and over? This will give
you something like:
c(vector, i1, vector, i2, vector, i3, etc.) except obviously
replace i1, i3 with their values and vector with its value. Is that
what you want?
}
}
indices
}
ind(d[,'Column.I.want'], 'string', 'output.vector')
Am I wrong here? I've read that the last statement in the function is what
it will return, and what I want is a vector of integers.
yes, if return() is not explicitly specified inside the function, then
it will return the output of the last statement.
Thanks,
Thank you for providing code of what you tried. For future reference,
it is good to at least provide useable input data and then show us
what the output you would like is. For example: Blah blah blah, I
have a vector d - c(1, 2, 3), how can I find the average of this
(i.e., 2)? To which you would get the answer: mean(d) or some such.
If grep() is not actually what you are after, can you let us know a
little bit more about what you want?
Hope this helps,
Josh
-Ben
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--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
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