[R] Conjoint Analysis in R??
Pls advise how I can use R in conjoint analysis?? regds Faisal Afzal Siddiqui Karachi, Pakistan Looking for last minute shopping deals? __ 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 interpolate a plot with a logistic curve
Dear Simone, you can use the package 'drc' to fit a logistic model, that is a non-linear regression model based on the equation c+(d-c)/(1+exp(b(x-e))), to your data (below named 'simone'): ## Fitting a 4-parameter logistic model (also called Boltzmann model) simone.m1 - drm(size~x, data=simone, fct=B.4()) ## Plotting the data together with the fitted curve plot(simone.m1, log=) The fit is not great due to the bend. Christian __ 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] correlation coefficient from qq plot
You could use the qqnorm function to obtain the correlation, as: qqp=qqnorm(rstudent(regrname)) cor(qqp$x,qqp$y) If you do not want see the plot (as the qq.plot is richer): qqp=qqnorm(rstudent(regrname), plot.it=F) domenico vistocco Tom Fitzhugh wrote: Hi, I am trying to figure out how to get the correlation coefficient for a QQ plot (residual plot). So to be more precise, I am creating the plot like this: qq.plot(rstudent(regrname), main = rformula, col=1) But want to also access (or compute) the correlation coefficient for that plot. Thanks, Tom [[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-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 CMD Build feature searches or requests
Hello, I'm missing two features in R CMD build: 1) Easy building of Windows/zip packaged package version alongside the *nix-style *.tar.gz. Right now I'm doing a scripted version of R CMD build PACKAGE R CMD INSTALL PACKAGE mkdir tmp cp -r /usr/local/lib/R/site-library/PACKAGE tmp/PACKAGE cd tmp zip -r PACKAGE_EXTRACTEDVERSION.zip PACKAGE mv *.zip .. cd .. rm -rf tmp I was wondering whether it wouldn't be helpfull to others maintaining packages not requiring genuine cross-compilation (only containing R code) to deal with this via an option to R CMD build. Something like '-zip-package' might do it ... 2) My scripted solution right now also automatically increments version numbers and adjusts dates in PACKAGE/man/PACKAGE-package.Rd and PACKAGE/DESCRIPTION, ensuring progressing and continuous package naming. Would be nice to have an R CMD build-option to take care of that too ... Please let me know what you think or where to find the functionality in case I overlooked it. Thanks, Joh __ 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] Using panel.densityplot with stripplot
Hi Deepayan! thank you! panel.violin with the following modification works as I want: grid.polyline(x = dx.list[[i]], y = dy.list[[i]], ... instead of grid.polygon(x = c(dx.list[[i]], rev(dx.list[[i]])), y = c(dy.list[[i]], -rev(dy.list[[i]])), ... From examples I would have thought I would need to do... What examples? The examples for writing your own panel functions. I was not aware that there were different expectations regarding arguments. panel.stripplot and panel.densityplot have entirely different expectations about what the y-range of the panel is going to be, and they cannot be mixed. But is there a technical reason for making this distinction? It seemed to me that most panel functions can deal with x and y parameters and that panel.densityplot could make use of the same mechanisms as panel.violin to subdivide based on factor y. Again many thanks for the fast response, Christopher -- Christopher Oezbek Arbeitsgruppe Software Engineering Institut für Informatik Freie Universität Berlin Takustr. 9, 14195 Berlin, Germany +49 30 838 75242, Raum 008 http://www.inf.fu-berlin.de/~oezbek/ __ 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] Using expression in Hmisc Key()
Hi Dieter,
I actually solved *my* problem:
Key(x = 0.667, y = 0.833, lev = c(expression(italic(b)),
expression(italic(c)), expression(italic(d))),
other = list(title = expression(italic(v)), cex.title = 1))
I was able to figure this out only by looking at the code for Key(),
because I hadn't come across the 'lev' argument in the documentation
(in fact Key does not appear in the list of functions of Hmisc; I
discovered its usefulness by consulting the examples for xYplot()). I
would have expected this argument to be called 'labels' (see
help(labels)), (or at least 'levels'):
function (x = NULL, y = NULL, lev = c(b, c, d), cex = c(0.7,
0.7, 0.7), col = c(2, 4, 9), font = c(1, 1, 1), pch = c(1, 2, 16),
other = NULL)
{
…
}
…
Note that the NULL setting of the parameter may be useful for
programming, but it is not useful to anyone reading the code. How is
one to proceed after having read help(NULL)?
At the same time, I have no grounds for complaining about the
documentation for Key(): Frank Harrell is giving away his work. His
examples are extensive, and his functions always work as advertised.
Sometimes they also work as not advertised.
This is one of the cases where I wish there were a function that
exercised all the arguments of a graphics function by visualizing
the effect of changing two or three levels of each argument (one by
one, of course). This might have the side effect of allowing authors
to shorten documentation. I have in mind adding a method to each
graphics function, and having the author specify the two or three
instructive levels of each argument. See the exhaustive exploration by
J.R. Lobry, A.B. Dufour D. Chessel of the graphical parameters
accessible by par(), at
http://pbil.univ-lyon1.fr/R/fichestd/tdr75.pdf
On Dec 6, 2007, at 2:17 AM, Dieter Menne wrote:
Michael Kubovy kubovy at virginia.edu writes:
Dear r-helpers,
How do I tell xYplot() and Key() that I want the labels in italic?
Key(x = 0.667, y = 0.833, other = list(title = expression(italic(v)),
cex.title = 1,
labels = c(expression(italic(b)), expression(italic(c)),
expression(italic(d)
dev.off()
Michael,
I have submit a similar case last week to the Bug tracker. Maybe you
can raise
that enhancement request to defect
http://biostat.mc.vanderbilt.edu/trac/Hmisc/ticket/21
Dieter
---
The Key function generated by some plot commands should have a ...
parameter.
Otherwise, the ... in rlegend is useless, and it would be nice to be
able to
suppress the box, for example.
Key = function (x = NULL, y = NULL, lev = c(No Fail, Fail), pch
= c(16, 1))
{ .. part omitted
rlegend(x, y, legend = lev, pch = pch, ...) invisible()
}
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
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[R] colour coded points in biplot
Dear all I tried to make a biplot with color coded labels but I was not successful. Searching archives I found that it is probably not so simple. I found http://tolstoy.newcastle.edu.au/R/help/05/01/10661.html which recommends eqscplot eqscplot(fit$score[,1], fit$score[,2], pch = 20, col=c(rep(2,10), rep(3,40)), cex=2) http://tolstoy.newcastle.edu.au/R/help/05/01/10661.html or I can use plot itself, but then I was not able to find how to add arrows. The closest I get is fit-(princomp(USArrests, cor = TRUE)) biplot(fit , xlabs=rep(, 50)) points(fit$score[,1], fit$score[,2], pch = 20, col=c(rep(2,10), rep(3,40)), cex=2) and use some suitable scaling before calling points. My question is if there is some other easier approach to get color coded points in biplot? Petr Pikal [EMAIL PROTECTED] __ 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] Segmented regression
Dear Brendan,
I am not sure to understand your code..
It seems to me that your are interested in fitting a one-breakpoint
segmented relationship in each level of your grouping variable
If this is the case, the correct code is below.
In order to fit a segmented relationship in each group you have to
define the relevant variable before fitting, and to constrain the last
slope to be zero you have to consider the `minus' variable..(I discuss
these points in the submitted Rnews article..If you are interested, let
me know off list).
If my code does not fix your problem, please let me know,
Best,
vito
##--define the group-specific segmented variable:
X-model.matrix(~0+factor(group),data=df)*df$tt
df$tt.KV-X[,1] #KV
df$tt.KW-X[,2] #KW
df$tt.WC-X[,3] #WC
##-fit the unconstrained model
olm-lm(y~group+tt.KV+tt.KW+tt.WC,data=df)
os-segmented(olm,seg.Z=~tt.KV+tt.KW+tt.WC,psi=list(tt.KV=350,
tt.KW=500, tt.WC=350))
#have a look to results:
with(df,plot(tt,y))
with(subset(df,group==RKW),points(tt,y,col=2))
with(subset(df,group==RKV),points(tt,y,col=3))
points(df$tt[df$group==RWC],fitted(os)[df$group==RWC],pch=20)
points(df$tt[df$group==RKW],fitted(os)[df$group==RKW],pch=20,col=2)
points(df$tt[df$group==RKV],fitted(os)[df$group==RKV],pch=20,col=3)
#constrain the last slope in group KW
tt.KW.minus- -df$tt.KW
olm1-lm(y~group+tt.KV+tt.WC,data=df)
os1-segmented(olm1,seg.Z=~tt.KV+tt.KW.minus+tt.WC,psi=list(tt.KV=350,
tt.KW.minus=-500, tt.WC=350))
#check..:-)
slope(os1)
with(df,plot(tt,y))
with(subset(df,group==RKW),points(tt,y,col=2))
with(subset(df,group==RKV),points(tt,y,col=3))
points(df$tt[df$group==RWC],fitted(os1)[df$group==RWC],pch=20)
points(df$tt[df$group==RKW],fitted(os1)[df$group==RKW],pch=20,col=2)
points(df$tt[df$group==RKV],fitted(os1)[df$group==RKV],pch=20,col=3)
Power, Brendan D (Toowoomba) ha scritto:
Hello all,
I have 3 time series (tt) that I've fitted segmented regression models
to, with 3 breakpoints that are common to all, using code below
(requires segmented package). However I wish to specifiy a zero
coefficient, a priori, for the last segment of the KW series (green)
only. Is this possible to do with segmented? If not, could someone point
in a direction?
The final goal is to compare breakpoint sets for differences from those
derived from other data.
Thanks in advance,
Brendan.
library(segmented)
df-data.frame(y=c(0.12,0.12,0.11,0.19,0.27,0.28,0.35,0.38,0.46,0.51,0.5
8,0.59,0.60,0.57,0.64,0.68,0.72,0.73,0.78,0.84,0.85,0.83,0.86,0.88,0.88,
0.95,0.95,0.93,0.92,0.97,0.86,1.00,0.85,0.97,0.90,1.02,0.95,0.54,0.53,0.
50,0.60,0.70,0.74,0.78,0.82,0.88,0.83,1.00,0.85,0.96,0.84,0.86,0.82,0.86
,0.84,0.84,0.84,0.77,0.69,0.61,0.67,0.73,0.65,0.55,0.58,0.56,0.60,0.50,0
.50,0.42,0.43,0.44,0.42,0.40,0.51,0.60,0.63,0.71,0.74,0.82,0.82,0.85,0.8
9,0.91,0.87,0.91,0.93,0.95,0.95,0.97,1.00,0.96,0.90,0.86,0.91,0.94,0.96,
0.88,0.88,0.88,0.92,0.82,0.85),
tt=c(141.6,141.6,141.6,183.2,212.8,227.0,242.4,271.5,297.4,312.3,331.4,3
42.4,346.3,356.6,371.6,408.8,408.8,419.5,434.4,464.5,492.6,521.7,550.5,5
50.3,565.4,588.0,602.9,623.7,639.6,647.9,672.6,680.6,709.7,709.7,750.2,7
50.2,750.2,141.6,141.6,141.6,183.2,212.8,227.0,242.4,271.5,297.4,312.3,3
31.4,342.4,346.3,356.6,371.6,408.8,408.8,419.5,434.4,464.5,492.6,521.7,5
50.5,550.3,565.4,588.0,602.9,623.7,639.6,647.9,672.6,680.6,709.7,709.7,1
41.6,141.6,141.6,183.2,212.8,227.0,242.4,271.5,297.4,312.3,331.4,342.4,3
46.3,356.6,371.6,408.8,408.8,419.5,434.4,464.5,492.6,521.7,550.5,550.3,5
65.4,588.0,602.9,623.7,639.6,647.9,672.6,709.7),
group=c(rep(RKW,37),rep(RWC,34),rep(RKV,32)))
init.bp - c(297.4,639.6,680.6)
lm.1 - lm(y~tt+group,data=df)
seg.1 - segmented(lm.1, seg.Z=~tt, psi=list(tt=init.bp))
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 6.0
year 2007
month 10
day03
svn rev43063
language R
version.string R version 2.6.0 (2007-10-03)
DISCLAIMER**...{{dropped:15}}
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--
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Dip.to Sc Statist e Matem `Vianelli'
Università di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 6626240
fax: 091 485726/485612
[R] Building package - tab delimited example data issue
Hello, I'm trying to integrate example data in the shape of a tab delimited ASCII file into my package and therefore dropped it into the data subdirectory. The build works out just fine, but when I attempt to install I get: ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 500 elements Calls: Anonymous ... Anonymous - switch - assign - read.table - scan Execution halted ERROR: installing package indices failed ** Removing '/usr/local/lib/R/site-library/MaxQuantUtils' ** Restoring previous '/usr/local/lib/R/site-library/MaxQuantUtils' Accordingly the check delivers: ... * checking whether package 'MaxQuantUtils' can be installed ... ERROR Can anyone tell me what I'm doing wrong? build/install witout the ASCII file works just fine. Joh __ 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] Conjoint Analysis in R??
http://tolstoy.newcastle.edu.au/R/help/05/06/6104.html http://tolstoy.newcastle.edu.au/R/help/05/06/6103.html domenico faisal afzal siddiqui wrote: Pls advise how I can use R in conjoint analysis?? regds Faisal Afzal Siddiqui Karachi, Pakistan Looking for last minute shopping deals? __ 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] Conjoint Analysis in R??
Faisal, can you elaborate further on your conjoint design there is bayesm which offers a hierarchical bayes approach to analysing choice data MLogit available through zelig (see below) http://gking.harvard.edu/zelig/docs/index.html MNP as a standalone package for the probit model thanks Paul - Original Message - From: faisal afzal siddiqui [EMAIL PROTECTED] To: R Help [EMAIL PROTECTED] Sent: Thursday, December 06, 2007 6:00 PM Subject: [R] Conjoint Analysis in R?? Pls advise how I can use R in conjoint analysis?? regds Faisal Afzal Siddiqui Karachi, Pakistan Looking for last minute shopping deals? __ 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] Building package - tab delimited example data issue
Johannes Graumann wrote:
Hello,
I'm trying to integrate example data in the shape of a tab delimited ASCII
file into my package and therefore dropped it into the data subdirectory.
The build works out just fine, but when I attempt to install I get:
** building package indices ...
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
line 1 did not have 500 elements
Calls: Anonymous ... Anonymous - switch - assign - read.table - scan
Execution halted
ERROR: installing package indices failed
** Removing '/usr/local/lib/R/site-library/MaxQuantUtils'
** Restoring previous '/usr/local/lib/R/site-library/MaxQuantUtils'
Accordingly the check delivers:
...
* checking whether package 'MaxQuantUtils' can be installed ... ERROR
Can anyone tell me what I'm doing wrong? build/install witout the ASCII file
works just fine.
Joh
If you had looked at help(data), you would have found a list of which
file formats it supports and how they are read. Hint: TAB-delimited
files are not among them. *Whitespace* separated files work, using
read.table(filename, header=TRUE), but that is not a superset of
TAB-delimited data if there are empty fields.
A nice trick is to figure out how to read the data from the command line
and drop the relevant code into a mydata.R file (assuming that the
actual data file is mydata.txt). This gets executed when the data is
loaded (by data(mydata) or when building the lazyload database) because
.R files have priority over .txt.
This is quite general and allows a nice way of incorporating data
management while retaining the original data source:
more ISwR/data/stroke.R
stroke - read.csv2(stroke.csv, na.strings=.)
names(stroke) - tolower(names(stroke))
stroke - within(stroke,{
sex - factor(sex,levels=0:1,labels=c(Female,Male))
dgn - factor(dgn)
coma - factor(coma, levels=0:1, labels=c(No,Yes))
minf - factor(minf, levels=0:1, labels=c(No,Yes))
diab - factor(diab, levels=0:1, labels=c(No,Yes))
han - factor(han, levels=0:1, labels=c(No,Yes))
died - as.Date(died, format=%d.%m.%Y)
dstr - as.Date(dstr,format=%d.%m.%Y)
dead - !is.na(died) died as.Date(1996-01-01)
died[!dead] - NA
})
head ISwR/data/stroke.csv
SEX;DIED;DSTR;AGE;DGN;COMA;DIAB;MINF;HAN
1;7.01.1991;2.01.1991;76;INF;0;0;1;0
1;.;3.01.1991;58;INF;0;0;0;0
1;2.06.1991;8.01.1991;74;INF;0;0;1;1
0;13.01.1991;11.01.1991;77;ICH;0;1;0;1
0;23.01.1996;13.01.1991;76;INF;0;1;0;1
1;13.01.1991;13.01.1991;48;ICH;1;0;0;1
0;1.12.1993;14.01.1991;81;INF;0;0;0;1
1;12.12.1991;14.01.1991;53;INF;0;0;1;1
0;.;15.01.1991;73;ID;0;0;0;1
--
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c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] R function for percentrank
MS == Marc Schwartz [EMAIL PROTECTED] on Wed, 05 Dec 2007 12:43:50 -0600 writes: [] MS Martin, MS Thanks for the corrections. In hindsight, now seeing the intended use of MS ecdf() in the fashion you describe above, it is now clear that my MS approach in response to David's query was un-needed and over the top. MS Yuck is quite appropriate... :-) MS As I was going through this exercise, it did seem overly complicated, MS given R's usual elegant philosophy about such things. I suppose if I had MS looked at the source for plot.stepfun(), it would have been more evident MS as to how the y values are acquired. MS In reviewing the examples in ?ecdf, I think that an example using MS something along the lines of the discussion here more explicitly, would MS be helpful. It is not crystal clear from the examples, that one can use MS ecdf() in this fashion, though the use of 12 * Fn(tt) hints at it. MS Perhaps: MS ##-- Simple didactical ecdf example: MS x - rnorm(12) MS Fn - ecdf(x) MS Fn MS Fn(x) # returns the percentiles for x MS ... Thank you, Marc for the above proposal, to make the examples more crystal clear :-) I've now amended the R-devel version of help(ecdf) accordingly. MS Thanks again Martin and no offense taken... :-) I'm glad. You're welcome! Martin __ 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] Building package - tab delimited example data issue
G'day Peter,
On Thu, 06 Dec 2007 11:52:46 +0100
Peter Dalgaard [EMAIL PROTECTED] wrote:
If you had looked at help(data), you would have found a list of which
file formats it supports and how they are read. Hint: TAB-delimited
files are not among them. [...]
On the other hand, Writing R Extensions has stated since a long time
(and still does):
The @file{data} subdirectory is for additional data files the package
makes available for loading using @code{data()}. Currently, data files
can have one of three types as indicated by their extension: plain R
code (@file{.R} or @file{.r}), tables (@file{.tab}, @file{.txt}, or
@file{.csv}), or @code{save()} images (@file{.RData} or @file{.rda}).
Now in my book, .csv files contain comma separated values, .tab files
contain values separated by TABs and .txt files are pure text files,
presumably values separated by any kind of white space.
Thus, I think that the expectation that TAB-delimited file formats
should work is not unreasonable; I was long time ago bitten by this
too. Then I realised that the phrase one of the three types should
probably be interpreted as implying that .tab, .txt and .csv files are
all of the same type and, apparently, should contain values separated
by whitespace. I admit that I never tested whether .csv files would
lead to the same problems as TAB delimited .tab files. Rather, I decided
in the end that the safest option, i.e. to avoid misleading file
extensions, would be to use .rda files in the future.
Cheers,
Berwin
=== Full address =
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Dept of Statistics and Applied Probability+65 6515 6650 (self)
Faculty of Science FAX : +65 6872 3919
National University of Singapore
6 Science Drive 2, Blk S16, Level 7 e-mail: [EMAIL PROTECTED]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] colour coded points in biplot
If you are using correspondence analysis you could see the plot.ca function in the ca library. Petr PIKAL wrote: Dear all I tried to make a biplot with color coded labels but I was not successful. Searching archives I found that it is probably not so simple. I found http://tolstoy.newcastle.edu.au/R/help/05/01/10661.html which recommends eqscplot eqscplot(fit$score[,1], fit$score[,2], pch = 20, col=c(rep(2,10), rep(3,40)), cex=2) http://tolstoy.newcastle.edu.au/R/help/05/01/10661.html or I can use plot itself, but then I was not able to find how to add arrows. The closest I get is fit-(princomp(USArrests, cor = TRUE)) biplot(fit , xlabs=rep(, 50)) points(fit$score[,1], fit$score[,2], pch = 20, col=c(rep(2,10), rep(3,40)), cex=2) and use some suitable scaling before calling points. My question is if there is some other easier approach to get color coded points in biplot? Petr Pikal [EMAIL PROTECTED] __ 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] how to interpolate a plot with a logistic curve
Dear Christian, it works great, and it is simple to understand, thank you very much. just a detail, is it possible to plot just the fitted curve and not the data? it's because I would like to have data in black and the fitted curve in red.. I don't know how to pick up the single parts, if I simply wrote plot(simone.m1, log=, col=red) everything became red.. thank in advance, Simone Il giorno 06/dic/07, alle ore 09:00, Christian Ritz ha scritto: Dear Simone, you can use the package 'drc' to fit a logistic model, that is a non- linear regression model based on the equation c+(d-c)/(1+exp(b(x- e))), to your data (below named 'simone'): ## Fitting a 4-parameter logistic model (also called Boltzmann model) simone.m1 - drm(size~x, data=simone, fct=B.4()) ## Plotting the data together with the fitted curve plot(simone.m1, log=) The fit is not great due to the bend. Christian __ 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 interpolate a plot with a logistic curve
Dear Christian, it works great, and it is simple to understand, thank you very much. just a detail, is it possible to plot just the fitted curve and not the data? it's because I would like to have data in black and the fitted curve in red.. I don't know how to pick up the single parts, if I simply wrote plot(simone.m1, log=, col=red) everything became red.. thank in advance, Simone Il giorno 06/dic/07, alle ore 09:00, Christian Ritz ha scritto: Dear Simone, you can use the package 'drc' to fit a logistic model, that is a non- linear regression model based on the equation c+(d-c)/(1+exp(b(x- e))), to your data (below named 'simone'): ## Fitting a 4-parameter logistic model (also called Boltzmann model) simone.m1 - drm(size~x, data=simone, fct=B.4()) ## Plotting the data together with the fitted curve plot(simone.m1, log=) The fit is not great due to the bend. Christian __ 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] $ operator is invalid for atomic vectors, returning NULL - what is the right thing to do then?
Dear all, Starting from a recent version of R, the $ became unusable on atomic vectors, e.g. x - c(a=1,b=2) x$a NULL Warning message: In x$a : $ operator is invalid for atomic vectors, returning NULL I can of course do x['a'] - but that requires more typing (5 characters rather than 2). Apologies if I've missed a an announcement regarding this, but 1) Is there an alternative to the ['a'] and 2) Why was this change made? Regards Søren __ 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] Nine questions about methods and generics
I have a series of question about methods and generics.
The questions are interspersed in some text which explains
what I want to do, how it works now and why I do not
understand well why it works. Questions are written
Q1 and so on up to Q9 and always start a new line.
The concrete problem is this: it has become customary
after a meta-analysis to quote various statistics
to give a picture of the degree of heterogeneity.
Initially I wrote a function which calculated these given
the heterogeneity chi-squared Q and the number of studies k.
It then occurred to me that it would be convenient to
have functions which take the objects returned by
the various functions in the package rmeta (available
from CRAN) and perform the calculation on them.
So after plagiarising some ideas from rmeta
I wrote
hetero - function(x, ...) {
UseMethod(hetero)
}
Q1 - have I created a generic called hetero? If so
what is the correct idiom: created, declared, ...?
Q2 - if I go class(hetero) it returns function rather
than generic. Is that what I should expect?
I then called my original function hetero.default
hetero.default - function(Q = NULL, k = NULL, conflevel = 0.95) {
# some code left out here which computes values in the list res
class(res) - meta.hetero
res
}
Q3 was it a good idea to have it return an object of class
meta.hetero or would it have been better to call it hetero
now if I go
hetero(14.4, 24)
I get what I expected
I then provide a new function
hetero.meta.summaries - function(obj, ...) {
# some code to calculate Q and k
res - hetero.default(Q, k, ...)
res
}
which also seems to do what I wanted. There are also
similar functions hetero.meta.MH and hetero.meta.DSL
to operate on the other classes of object returned in rmeta.
The problem is that I do not really understand why it all works
and suspect it could easily stop working.
At this point I decided that if all else fails I should read the
documentation. The manual pages (the things you get
with ?UseMethod) describe what the functions do but
do not give me a series of steps to salvation.
I found S Programming (VR) much clearer now I knew where to
look but I think VR underestimate the depths of my
ignorance.
Q4 VR seems to suggest that I should have called the first
argument to hetero, hetero.default and hetero.meta.summaries
the same (possibly x or object) yet it seems to work.
Q5 Does it matter?
If it does matter which should I choose?
I also decide to look at R-extensions which seems
to suggest that I should be using NextMethod and
also has dire warnings about having different argument
lists to the various methods.
I found R-extensions much the least helpful
of the three sources I tried.
Q6 should I be using NextMethod?
Q7 if what I have created are methods which are
displayed by methods(hetero) why is it UseMethod not
usemethod? (I note that ?Methods tells me about something
different from ?methods.)
Q8 I have used a ... argument for hetero.meta.summaries
but not for hetero.default. Was that wise? R-extensions
has some stern things to say here which I do not really
understand.
Q9 is there somewhere else I could have looked
bearing in mind my comments above about the
manual pages, VR and R-extensions? Or shall
I just keep reading VR until the penny drops?
For the record:
S Programming (VR) means
@BOOK{venables00,
author = {Venables, W N and Ripley, B D},
year = 2000,
title = {S programming},
publisher = {Springer-Verlag},
address = {New York},
keywords = {statistics general; software}
}
The heterogeneity statistics are explained in
@ARTICLE{higgins02,
author = {Higgins, J P T and Thompson, S G},
year = 2002,
title = {Quantifying heterogeneity in a meta--analysis},
journal = {Statistics in Medicine},
volume = 21,
pages = {1539--1558},
keywords = {meta-analysis, heterogeneity}
}
I am using 2.6.1 under XP Professional.
My knowledge of computer science is frozen at about 1975.
Michael Dewey
http://www.aghmed.fsnet.co.uk
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Re: [R] $ operator is invalid for atomic vectors, returning NULL - what is the right thing to do then?
On Thu, 6 Dec 2007, Søren Højsgaard wrote: Dear all, Starting from a recent version of R, From R 2.5.0, not so recent. the $ became unusable on atomic vectors, e.g. x - c(a=1,b=2) x$a NULL Warning message: In x$a : $ operator is invalid for atomic vectors, returning NULL I can of course do x['a'] - but that requires more typing (5 characters rather than 2). Apologies if I've missed a an announcement regarding this, but 1) Is there an alternative to the ['a'] and 2) Why was this change made? It has always returned NULL on atomic vectors: see the help page. E.g. in R 2.0.0 from 2004: x - c(a=1,b=2) x$a NULL x['a'] a 1 The warning was added three versions of R ago: the announcement is in the NEWS file for 2.5.0. USER-VISIBLE CHANGES o Using $ on an atomic vector now raises a warning, as does use on an S4 class for which a method has not been defined. I think you have exemplified the answer to your question '2)': because users misunderstood what it did. In R 2.7.0 this will be an error, since package programmers did not seem to be heeding the warnings. -- Brian D. Ripley, [EMAIL PROTECTED] 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] R function for percentrank
On Dec 6, 2007 6:11 AM, Martin Maechler [EMAIL PROTECTED] wrote: MS == Marc Schwartz [EMAIL PROTECTED] on Wed, 05 Dec 2007 12:43:50 -0600 writes: [] MS Martin, MS Thanks for the corrections. In hindsight, now seeing the intended use of MS ecdf() in the fashion you describe above, it is now clear that my MS approach in response to David's query was un-needed and over the top. MS Yuck is quite appropriate... :-) MS As I was going through this exercise, it did seem overly complicated, MS given R's usual elegant philosophy about such things. I suppose if I had MS looked at the source for plot.stepfun(), it would have been more evident MS as to how the y values are acquired. MS In reviewing the examples in ?ecdf, I think that an example using MS something along the lines of the discussion here more explicitly, would MS be helpful. It is not crystal clear from the examples, that one can use MS ecdf() in this fashion, though the use of 12 * Fn(tt) hints at it. MS Perhaps: MS ##-- Simple didactical ecdf example: MS x - rnorm(12) MS Fn - ecdf(x) MS Fn MS Fn(x) # returns the percentiles for x MS ... Thank you, Marc for the above proposal, to make the examples more crystal clear :-) I've now amended the R-devel version of help(ecdf) accordingly. Since the above does not actually reproduce percentrank in the case of ties, the change that would facilitate this particularly would be to add a ties = excelpercentrank to approx. See my solution earlier in this thread. __ 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] $ operator is invalid for atomic vectors, returning NULL
On 06-Dec-07 12:04:56, Søren Højsgaard wrote: Dear all, Starting from a recent version of R, the $ became unusable on atomic vectors, e.g. x - c(a=1,b=2) x$a NULL Warning message: In x$a : $ operator is invalid for atomic vectors, returning NULL I can of course do x['a'] - but that requires more typing (5 characters rather than 2). Apologies if I've missed a an announcement regarding this, but 1) Is there an alternative to the ['a'] and 2) Why was this change made? While Brian has answered your query from a more technical point of view, there's an implication you should consider. x$a always (as far as I know)[*] has been unusable, in that it returns NULL, and not what you expected to get. The only thing that's (relatively) new is that you now get a warning. [*] Certainly as early as R-1.6.2 (Jan 2003), as I've just checked. Previously, you were not getting a warning. So, if you were using the likes of x$a in code, and getting no warnings, possibly your code was generating results derived from NULL values rather than from the values you expected it to be using. Perhaps you should check back! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 06-Dec-07 Time: 12:39:49 -- XFMail -- __ 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] Building package - tab delimited example data issue
Berwin A Turlach wrote:
G'day Peter,
On Thu, 06 Dec 2007 11:52:46 +0100
Peter Dalgaard [EMAIL PROTECTED] wrote:
If you had looked at help(data), you would have found a list of which
file formats it supports and how they are read. Hint: TAB-delimited
files are not among them. [...]
On the other hand, Writing R Extensions has stated since a long time
(and still does):
The @file{data} subdirectory is for additional data files the package
makes available for loading using @code{data()}. Currently, data files
can have one of three types as indicated by their extension: plain R
code (@file{.R} or @file{.r}), tables (@file{.tab}, @file{.txt}, or
@file{.csv}), or @code{save()} images (@file{.RData} or @file{.rda}).
Now in my book, .csv files contain comma separated values, .tab files
contain values separated by TABs and .txt files are pure text files,
presumably values separated by any kind of white space.
Thus, I think that the expectation that TAB-delimited file formats
should work is not unreasonable; I was long time ago bitten by this
too. Then I realised that the phrase one of the three types should
probably be interpreted as implying that .tab, .txt and .csv files are
all of the same type and, apparently, should contain values separated
by whitespace. I admit that I never tested whether .csv files would
lead to the same problems as TAB delimited .tab files. Rather, I decided
in the end that the safest option, i.e. to avoid misleading file
extensions, would be to use .rda files in the future.
Now had you lived in the Western world ... (Hey, what's that? New
address!) ... then you would have known better than to have any trust in
file extensions. At the time they apparently figured that the .CSV
standard was so good that it was even better to have two of them (double
standards are twice as good, right?), depending on whether you were in
England or in Denmark, I lost faith completely. (In this country you can
export to a text file with SAS and then NOT read it with SPSS and vice
versa on the same Windows machine).
Actually, R is a bit perverse about .csv too since it expects
_semicolon_ field separator, but not the comma decimal separator which
usually accompanies it. The reason for this is lost in the mists of time
-- the datasets in current versions of R do not include any .csv files.
There are, however, six .tab files, three of which are not
tab-separated, but I don't actually think there was ever a standard to
the effect that they should be (.tab just means that it is a _table_).
So, you really need to read the help page for data, which does have the
exact info. The passage you cite from the manual could do with a
rephrasing, although it probably isn't technically incorrect. As it
stands, it reminds me a bit of the old Monty Python sketch:
Our *three* weapons are fear, surprise, and ruthless efficiency...and
an almost fanatical devotion to the Pope Our *four*...no...
*Amongst* our weapons Amongst our weaponry...are such elements as
fear, surprise I'll come in again
(There really are 3 data TYPES, but 4 FORMATS and, er, diverse EXTENSIONS)
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] differences in using source() or console
Dear all, Is there *any* reason explaining what I describe below? I have the following line myfun(x) If I type them directly in R (or copy/past), it works.. However if I type in R 2.6.1 source(code.R) ##code.R includes the above line Error in inherits(x, data.frame) : object d not found namely myfun() does not work correctly. In particular the non-working line inside myfun() is update(eval(x$call$obj), data=d) #d is created in myfun() My question is: why the problem occurs just via source()ing??? many thanks, vito Vito M.R. Muggeo Dip.to Sc Statist e Matem `Vianelli' Università di Palermo viale delle Scienze, edificio 13 90128 Palermo - ITALY tel: 091 6626240 fax: 091 485726/485612 __ 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] R2HTML how to pair graphic.png and table
Dear list, i have this problem: how to pair a graphic.png and a table in R2HTML ? The better showing of a mutiple analysis is sometimes to mate graphic and table Can anyone help me in this task ?? In the example below graphisc and table are subsequent and not pair.. directory=getwd() myfile-file.path(directory,testHTML.html) HTMLoutput=file.path(directory,testHTML.html) graf=graf.png png(file.path(directory,graf)) plot(c(1:12)) dev.off() tab-as.matrix(c(1:12)) HTMLInsertGraph(graf,tab,file=HTMLoutput,caption=Esempio di grafico) browseURL(myfile) Thanks in advance Roberto Iacopetti -- View this message in context: http://www.nabble.com/R2HTML--how-to-pair-graphic.png-and-table-tf4956321.html#a14193218 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.
[R] 64-bit R question in Leopard
Hi, All; I've compiled and installed successfully presumably 64-bit R on Leopard. But when I tried to run R, I got the following error: /usr/bin/R: line 179: /Library/Frameworks/R.framework/Resources/etc/ i386/ldpaths: No such file or directory Here is the configuration I used: CONFIG_SHELL=/bin/bash ../R-devel/configure r_arch=x86_64 LDFLAGS=-L/ usr/local/lib64 -L/usr/X11R6/lib CC='gcc-4.2 -g -O3' CXX='g++-4.2 -g - O3' F77='gfortran -g -O3' FC='gfortran -g -O3' --with-blas='-framework vecLib' --with-lapack Thanks in advance Tae-Hoon Chung __ 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] Building package - tab delimited example data issue
Johannes Graumann wrote:
On Thursday 06 December 2007 11:52:46 Peter Dalgaard wrote:
Johannes Graumann wrote:
Hello,
I'm trying to integrate example data in the shape of a tab delimited
ASCII file into my package and therefore dropped it into the data
subdirectory. The build works out just fine, but when I attempt to
install I get:
** building package indices ...
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
line 1 did not have 500 elements
Calls: Anonymous ... Anonymous - switch - assign - read.table -
scan Execution halted
ERROR: installing package indices failed
** Removing '/usr/local/lib/R/site-library/MaxQuantUtils'
** Restoring previous '/usr/local/lib/R/site-library/MaxQuantUtils'
Accordingly the check delivers:
...
* checking whether package 'MaxQuantUtils' can be installed ... ERROR
Can anyone tell me what I'm doing wrong? build/install witout the ASCII
file works just fine.
Joh
If you had looked at help(data), you would have found a list of which
file formats it supports and how they are read. Hint: TAB-delimited
files are not among them. *Whitespace* separated files work, using
read.table(filename, header=TRUE), but that is not a superset of
TAB-delimited data if there are empty fields.
A nice trick is to figure out how to read the data from the command line
and drop the relevant code into a mydata.R file (assuming that the
actual data file is mydata.txt). This gets executed when the data is
loaded (by data(mydata) or when building the lazyload database) because
.R files have priority over .txt.
This is quite general and allows a nice way of incorporating data
management while retaining the original data source:
more ISwR/data/stroke.R
stroke - read.csv2(stroke.csv, na.strings=.)
names(stroke) - tolower(names(stroke))
stroke - within(stroke,{
sex - factor(sex,levels=0:1,labels=c(Female,Male))
dgn - factor(dgn)
coma - factor(coma, levels=0:1, labels=c(No,Yes))
minf - factor(minf, levels=0:1, labels=c(No,Yes))
diab - factor(diab, levels=0:1, labels=c(No,Yes))
han - factor(han, levels=0:1, labels=c(No,Yes))
died - as.Date(died, format=%d.%m.%Y)
dstr - as.Date(dstr,format=%d.%m.%Y)
dead - !is.na(died) died as.Date(1996-01-01)
died[!dead] - NA
})
head ISwR/data/stroke.csv
SEX;DIED;DSTR;AGE;DGN;COMA;DIAB;MINF;HAN
1;7.01.1991;2.01.1991;76;INF;0;0;1;0
1;.;3.01.1991;58;INF;0;0;0;0
1;2.06.1991;8.01.1991;74;INF;0;0;1;1
0;13.01.1991;11.01.1991;77;ICH;0;1;0;1
0;23.01.1996;13.01.1991;76;INF;0;1;0;1
1;13.01.1991;13.01.1991;48;ICH;1;0;0;1
0;1.12.1993;14.01.1991;81;INF;0;0;0;1
1;12.12.1991;14.01.1991;53;INF;0;0;1;1
0;.;15.01.1991;73;ID;0;0;0;1
Thanks for your help. Very insightfull and your version of RTFM was not
to harsh either ;0)
Part of what I want to achieve with the inclusion of the file is to be
able to showcase a read-in function for the particular data type. Is there
a slick way - sticking to your example - to reference the 'stroke.csv'
directly? I'd like to put in the example of some function.Rd something
analogous to # Use function to read in file:
result - function(link to 'stroke.csv' in installed ISwR package)
Without having to resort to accepting the example as No Run.
Answering to myself and staying with the same example:
system.file(data/stroke.csv,package=ISwR)
allows direct access to the example file (name).
Joh
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Re: [R] R2HTML how to pair graphic.png and table
Hi Roberto, here is a way that presumes you know some (basic) HTML tags: library(R2HTML) directory=getwd() myfile-file.path(directory,testHTML.html) HTMLoutput=file.path(directory,testHTML.html) graf=graf.png png(file.path(directory,graf)) plot(c(1:12)) dev.off() tab-as.matrix(c(1:12)) cat(table border=0td width=50%,file=HTMLoutput, append=TRUE) HTMLInsertGraph(graf,file=HTMLoutput,caption=Esempio di grafico) cat(/tdtd width=50%,file=HTMLoutput, append=TRUE) HTML(tab,file=HTMLoutput) cat(/td/table,file=HTMLoutput, append=TRUE) browseURL(myfile) I had already though I should include a function like layout for plots, i will have a look at that when some time is available. Best, Eric 2007/12/6, Roberto Iacopetti [EMAIL PROTECTED]: Dear list, i have this problem: how to pair a graphic.png and a table in R2HTML ? The better showing of a mutiple analysis is sometimes to mate graphic and table Can anyone help me in this task ?? In the example below graphisc and table are subsequent and not pair.. directory=getwd() myfile-file.path(directory,testHTML.html) HTMLoutput=file.path(directory,testHTML.html) graf=graf.png png(file.path(directory,graf)) plot(c(1:12)) dev.off() tab-as.matrix(c(1:12)) HTMLInsertGraph(graf,tab,file=HTMLoutput,caption=Esempio di grafico) browseURL(myfile) Thanks in advance Roberto Iacopetti -- View this message in context: http://www.nabble.com/R2HTML--how-to-pair-graphic.png-and-table-tf4956321.html#a14193218 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. -- Eric Lecoutre Consultant - Business Decision Business Intelligence Customer Intelligence [[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] $ operator is invalid for atomic vectors, returning NULL - what is the right thing to do then?
On 12/6/2007 7:04 AM, Søren Højsgaard wrote: Dear all, Starting from a recent version of R, the $ became unusable on atomic vectors, e.g. x - c(a=1,b=2) x$a NULL Warning message: In x$a : $ operator is invalid for atomic vectors, returning NULL I can of course do x['a'] - but that requires more typing (5 characters rather than 2). Apologies if I've missed a an announcement regarding this, but 1) Is there an alternative to the ['a'] and 2) Why was this change made? There's an announcement in the NEWS file for 2.6.0 DEPRECATED DEFUNCT o $ on an atomic vector now gives a warning that it is 'invalid'. It remains deprecated, but may be removed in R = 2.7.0. and an update in R-devel saying that in fact it has been made defunct there. In answer to your questions: 1) I don't think so, other than x[1]. 2) I don't remember the details, other than it was to avoid confusion. Maybe someone else can summarize the discussion? Duncan Murdoch __ 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] hclust in heatmap.2
affy snp wrote: Dear list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! From the help page: Arguments: x: numeric matrix of the values to be plotted. Rowv: determines if and how the _row_ dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and reordering is done. If a 'dendrogram', then it is used as-is, ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector. Best, Allen [[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. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 __ 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] R2HTML how to pair graphic.png and table
You could use a table with one row and two columns:
HTML(TABLETD,file=HTMLoutput)
HTML(tab,file=HTMLoutput)
HTML(/TDTD,file=HTMLoutput)
HTMLInsertGraph(graf,file=HTMLoutput,caption=Esempio di grafico)
HTML(/TD/TABLE,file=HTMLoutput)
domenico
PS:
You could create a function if this is a common operation:
tableGraph=function(tab2Html,graph2Html,fileHtml){
HTML(TABLETD,file=fileHtml)
HTML(tab2Html,file=HTMLoutput)
HTML(/TDTD,file=HTMLoutput)
HTMLInsertGraph(graph2Html,file=fileHtml,caption=Esempio di grafico)
HTML(/TD/TABLE,file=fileHtml)
}
and then:
tableGraph(tab,graf,HTMLoutput)
Roberto Iacopetti wrote:
Dear list,
i have this problem:
how to pair a graphic.png and a table in R2HTML ?
The better showing of a mutiple analysis is sometimes to mate graphic and
table
Can anyone help me in this task ??
In the example below graphisc and table are subsequent and not pair..
directory=getwd()
myfile-file.path(directory,testHTML.html)
HTMLoutput=file.path(directory,testHTML.html)
graf=graf.png
png(file.path(directory,graf))
plot(c(1:12))
dev.off()
tab-as.matrix(c(1:12))
HTMLInsertGraph(graf,tab,file=HTMLoutput,caption=Esempio di grafico)
browseURL(myfile)
Thanks in advance
Roberto Iacopetti
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Re: [R] Building package - tab delimited example data issue
Johannes Graumann wrote:
Johannes Graumann wrote:
On Thursday 06 December 2007 11:52:46 Peter Dalgaard wrote:
Johannes Graumann wrote:
Hello,
I'm trying to integrate example data in the shape of a tab delimited
ASCII file into my package and therefore dropped it into the data
subdirectory. The build works out just fine, but when I attempt to
install I get:
** building package indices ...
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
line 1 did not have 500 elements
Calls: Anonymous ... Anonymous - switch - assign - read.table -
scan Execution halted
ERROR: installing package indices failed
** Removing '/usr/local/lib/R/site-library/MaxQuantUtils'
** Restoring previous '/usr/local/lib/R/site-library/MaxQuantUtils'
Accordingly the check delivers:
...
* checking whether package 'MaxQuantUtils' can be installed ... ERROR
Can anyone tell me what I'm doing wrong? build/install witout the ASCII
file works just fine.
Joh
If you had looked at help(data), you would have found a list of which
file formats it supports and how they are read. Hint: TAB-delimited
files are not among them. *Whitespace* separated files work, using
read.table(filename, header=TRUE), but that is not a superset of
TAB-delimited data if there are empty fields.
A nice trick is to figure out how to read the data from the command line
and drop the relevant code into a mydata.R file (assuming that the
actual data file is mydata.txt). This gets executed when the data is
loaded (by data(mydata) or when building the lazyload database) because
.R files have priority over .txt.
This is quite general and allows a nice way of incorporating data
management while retaining the original data source:
more ISwR/data/stroke.R
stroke - read.csv2(stroke.csv, na.strings=.)
names(stroke) - tolower(names(stroke))
stroke - within(stroke,{
sex - factor(sex,levels=0:1,labels=c(Female,Male))
dgn - factor(dgn)
coma - factor(coma, levels=0:1, labels=c(No,Yes))
minf - factor(minf, levels=0:1, labels=c(No,Yes))
diab - factor(diab, levels=0:1, labels=c(No,Yes))
han - factor(han, levels=0:1, labels=c(No,Yes))
died - as.Date(died, format=%d.%m.%Y)
dstr - as.Date(dstr,format=%d.%m.%Y)
dead - !is.na(died) died as.Date(1996-01-01)
died[!dead] - NA
})
head ISwR/data/stroke.csv
SEX;DIED;DSTR;AGE;DGN;COMA;DIAB;MINF;HAN
1;7.01.1991;2.01.1991;76;INF;0;0;1;0
1;.;3.01.1991;58;INF;0;0;0;0
1;2.06.1991;8.01.1991;74;INF;0;0;1;1
0;13.01.1991;11.01.1991;77;ICH;0;1;0;1
0;23.01.1996;13.01.1991;76;INF;0;1;0;1
1;13.01.1991;13.01.1991;48;ICH;1;0;0;1
0;1.12.1993;14.01.1991;81;INF;0;0;0;1
1;12.12.1991;14.01.1991;53;INF;0;0;1;1
0;.;15.01.1991;73;ID;0;0;0;1
Thanks for your help. Very insightfull and your version of RTFM was not
to harsh either ;0)
Part of what I want to achieve with the inclusion of the file is to be
able to showcase a read-in function for the particular data type. Is there
a slick way - sticking to your example - to reference the 'stroke.csv'
directly? I'd like to put in the example of some function.Rd something
analogous to # Use function to read in file:
result - function(link to 'stroke.csv' in installed ISwR package)
Without having to resort to accepting the example as No Run.
Answering to myself and staying with the same example:
system.file(data/stroke.csv,package=ISwR)
allows direct access to the example file (name).
Yes, but...
This works right until you turn on LazyData for your package, then you
end up with only
00Index Rdata.rdb Rdata.rds Rdata.rdx
in the data directory. Use the inst source subdir for files you want
to have installed explicitly.
Also, in principle, it is
system.file(data, stroke.csv, package=ISwR)
although platforms that do not understand / as the path separator are
rare nowadays.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] Junk or not Junk ???
Loren Engrav wrote: Thank you As per advice from several R users I have set r-project.org, stat.math.ethz.ch,fhcrc.org, stat.ethz.ch, math.ethz.ch, hypatia.math.ethz.ch all to be safe domains But still some R emails go to Junk and require to be found manually I have explored the issue with Univ Wash computing to no avail Is this just how it is or have I still missed the fix to keep R emails out of junk? __ 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 suspect most people that stay on this list read most posts through a news reader... you might consider doing the same. I can't even imagine keeping up with the daily deluge of individual emails. http://www.nabble.com/R-help-f13820.html http://news.gmane.org/gmane.comp.lang.r.general - David Hewitt Virginia Institute of Marine Science http://www.vims.edu/fish/students/dhewitt/ -- View this message in context: http://www.nabble.com/Junk-or-not-Junk-tf4940701.html#a14193897 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.
[R] Vertical text in a plot
Hi, Consider this simple plot: plot(1:25,runif(25,0,1),ylab=First Y-axis label,xaxt=n) I want to add an additional axis as axis(4,at=seq(0.2,1,.2), labels=1:5) I have no idea how to add now the title of the new axis as Second Y-axis label. I want this text to be vertically directed from bottom to top. I can't find the function in text() to write vertically. Any ideas? Thanks, Marcin __ 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] 64-bit R compiling problem on Leopard
Hi, All; I've compiled and installed successfully presumably 64-bit R on Leopard. But when I tried to run R, I got the following error: /usr/bin/R: line 179: /Library/Frameworks/R.framework/Resources/etc/ i386/ldpaths: No such file or directory Here is the configuration I used: CONFIG_SHELL=/bin/bash ../R-devel/configure r_arch=x86_64 LDFLAGS=-L/ usr/local/lib64 -L/usr/X11R6/lib CC='gcc-4.2 -g -O3' CXX='g++-4.2 -g - O3' F77='gfortran -g -O3' FC='gfortran -g -O3' --with-blas='-framework vecLib' --with-lapack Thanks in advance Tae-Hoon Chung Korea Centers for Disease Control Prevention (KCDC) Korea National Institute of Health (KNIH) Center for Genome Sciences, Biobank for Health Sciences 194 Tongil-ro, Eunpyoung-gu, Seoul, 122-701, Korea Tel 82-2-380-2252 Fax 82-2-354-1078 Mobile 82-10-8011-1036 __ 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] Building package - tab delimited example data issue
Peter Dalgaard wrote: Answering to myself and staying with the same example: system.file(data/stroke.csv,package=ISwR) allows direct access to the example file (name). Yes, but... This works right until you turn on LazyData for your package, then you end up with only 00Index Rdata.rdb Rdata.rds Rdata.rdx in the data directory. How would you do it in that case? Use the inst source subdir for files you want to have installed explicitly. Well: you provided the example ;0) - sort of ... Also, in principle, it is system.file(data, stroke.csv, package=ISwR) although platforms that do not understand / as the path separator are rare nowadays. Thanks for that hint! Joh __ 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] R2HTML how to pair graphic.png and table
Eric, your code work well for my need, i'm not skillful in html environment, but your functions in R2HTML give simple many output requirements thanks Roberto Eric Lecoutre wrote: Hi Roberto, here is a way that presumes you know some (basic) HTML tags: library(R2HTML) directory=getwd() myfile-file.path(directory,testHTML.html) HTMLoutput=file.path(directory,testHTML.html) graf=graf.png png(file.path(directory,graf)) plot(c(1:12)) dev.off() tab-as.matrix(c(1:12)) cat(table border=0td width=50%,file=HTMLoutput, append=TRUE) HTMLInsertGraph(graf,file=HTMLoutput,caption=Esempio di grafico) cat(/tdtd width=50%,file=HTMLoutput, append=TRUE) HTML(tab,file=HTMLoutput) cat(/td/table,file=HTMLoutput, append=TRUE) browseURL(myfile) I had already though I should include a function like layout for plots, i will have a look at that when some time is available. Best, Eric 2007/12/6, Roberto Iacopetti [EMAIL PROTECTED]: Dear list, i have this problem: how to pair a graphic.png and a table in R2HTML ? The better showing of a mutiple analysis is sometimes to mate graphic and table Can anyone help me in this task ?? In the example below graphisc and table are subsequent and not pair.. directory=getwd() myfile-file.path(directory,testHTML.html) HTMLoutput=file.path(directory,testHTML.html) graf=graf.png png(file.path(directory,graf)) plot(c(1:12)) dev.off() tab-as.matrix(c(1:12)) HTMLInsertGraph(graf,tab,file=HTMLoutput,caption=Esempio di grafico) browseURL(myfile) Thanks in advance Roberto Iacopetti -- View this message in context: http://www.nabble.com/R2HTML--how-to-pair-graphic.png-and-table-tf4956321.html#a14193218 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. -- Eric Lecoutre Consultant - Business Decision Business Intelligence Customer Intelligence [[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. -- View this message in context: http://www.nabble.com/R2HTML--how-to-pair-graphic.png-and-table-tf4956321.html#a14194905 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.
[R] Frequency and Phase Spectrograms
I know that there is a function, (spectro3D), that produces the Power Spectrogram. Are there R functions that produce the Frequency Spectrogram and the Phase Spectrogram? Thank you for your time. [[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] hclust in heatmap.2
Thanks Ashoka! Allen On Dec 6, 2007 12:27 AM, Ashoka Polpitiya [EMAIL PROTECTED] wrote: Check the Rowv, Colv options to heatmap.2 data(mtcars) x - as.matrix(mtcars) heatmap.2(x, Rowv=FALSE, dendrogram=column) -Ashoka Scientist - Pacific Northwest National Lab On Dec 5, 2007 4:20 PM, affy snp [EMAIL PROTECTED] wrote: Dear list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! Best, Allen [[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.
Re: [R] hclust in heatmap.2
Thanks James! Allen On Dec 6, 2007 9:21 AM, James W. MacDonald [EMAIL PROTECTED] wrote: affy snp wrote: Dear list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! From the help page: Arguments: x: numeric matrix of the values to be plotted. Rowv: determines if and how the _row_ dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and reordering is done. If a 'dendrogram', then it is used as-is, ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector. Best, Allen [[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. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 [[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] Vertical text in a plot
There is an example in the example section of library(zoo) ?plot.zoo starting at: ## plot with left and right axes On Dec 6, 2007 10:16 AM, Marcin Kozak [EMAIL PROTECTED] wrote: Hi, Consider this simple plot: plot(1:25,runif(25,0,1),ylab=First Y-axis label,xaxt=n) I want to add an additional axis as axis(4,at=seq(0.2,1,.2), labels=1:5) I have no idea how to add now the title of the new axis as Second Y-axis label. I want this text to be vertically directed from bottom to top. I can't find the function in text() to write vertically. Any ideas? Thanks, Marcin __ 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] alternatives to latex() or xtable()
An alternative solution that allows you to break it down by categories is in
the functions below. Comments/suggestions welcome and encouraged.
Note that much thanks is due to those who responded to an earlier post of
mine on a similar topic.
To use (assuming you have a data.frame falled pathDist with columns
distances (your numeric data of interest), Capacity, Surface, and SITE
(vectors of categories)):
ops=c(quote(mean),quote(median),quote(sd),quote(length))
ops.desc=list(mean=Mean,median=Median,sd=S.D.,length=N)
pathDist.indices=list
(Surface=pathDist$Surface,Capacity=pathDist$Capacity,Site=pathDist$SITE)
pathDist.bytable=bytable(pathDist$distances,pathDist.indices,ops=ops,
ops.desc=ops.desc,na.rm=TRUE)
pathDist.table=latex.table.by(pathDist.bytable,num.by.vars=length(
pathDist.indices),caption=Path Characteristics)
print(pathDist.table,
type=latex,file=E:/xdrive/projects/Ghana_air/backpack_data/plots/pathDist.table.tex,
include.rownames = FALSE, include.colnames = TRUE, sanitize.text.function =
force, tabular.environment='longtable', floating=FALSE)
# Make a table by group
# Usage:
# print(latex.table.by(test.df), include.rownames = FALSE,
include.colnames = TRUE, sanitize.text.function = force)
# then add \usepackage{multirow} to the preamble of your LaTeX document
# for longtable support, add ,tabular.environment='longtable' to the print
command (plus add in ,floating=FALSE), then \usepackage{longtable} to the
LaTeX preamble
latex.table.by = function(df,num.by.vars=1,...) {
# first num.by.vars groups must be sorted and in descending order of
priority
if(!is.numeric(num.by.vars) | length(num.by.vars)!=1) {
stop(num.by.vars must be a number)
}
# Create a by.vars vector
by.vars=1:num.by.vars
numcols=length(colnames(df))
df.original=df
# Initialize our clines variable (gives the start column of the cline
for each row)
clines = rep(num.by.vars+1,length(df[[1]]))
# - Make grouping columns multirow - #
for(b in rev(by.vars)) {
# Create a groups variable for all by.vars up to the current one
groups=rep(,length(df[[b]]))
for(by.vars.index in 1:b) {
groups = paste(groups,df.original[[by.vars.index]],sep=)
}
# Add multirow code to current column according to the groups
pattern
df[[b]] - as.character(df[[b]])
rle.lengths - rle(groups)$lengths
first - !duplicated(groups)
df[[b]][!first] -
df[[b]][first] - paste(\\multirow{, rle.lengths, }{*}{,
df[[b]][first], })
# Store this by.var's information in the clines variable
clines[first]=b
}
# Specify horizontal lines wherever all combinations of grouping
variables change
df[[1]]-paste(\\cline{,clines,-,numcols,},df[[1]],sep=)
align.by.vars = sapply(list(rep(|c, (length(by.vars)+1)
)),paste,collapse=)
align.other.vars = sapply(list(rep(r|, (length(colnames(df))-length(
by.vars)) )),paste,collapse=)
align.df = paste(|, align.by.vars , | , align.other.vars ,sep=)
xt=xtable(df, align = align.df,...)
return(xt)
}
bytable = function(datavec,indices,ops=c(quote(mean)),ops.desc=list
(mean=Mean),na.rm=TRUE,...) {
groups=as.character()
combinations.others=c()
# indices should be a list of grouping vectors, just like you would pass
to -by-, but with sensible names for each vector
if(!is.list(indices)) {
stop(indices needs to be a list)
}
# Create a selector variable from the indices given as a list
if(length(indices) 1) {
for(indexnum in length(indices):1) {
groups=paste(groups,indices[[indexnum]],sep=)
}
}
if(length(indices)==1) {
groups=indices[[1]]
}
first=!duplicated(groups)
# Initialize data frame with grouping variables (indices)
bynames=dimnames(by(datavec,indices,function(x) x=1)) # run a dummy by
statement to get the name order out...highly inefficient...could use
indices.levels=lapply(indices,function(x) x[!duplicated(x)]) instead, as
long as we're sure the ordering is the same
for(indexnum in length(indices):1) {
# get the number of combinations of other index levels after this
one (e.g. the number of replicates we need to make of each one in this
index)
others.selector=rep(TRUE,length(indices))
others.selector[length(indices):indexnum]=FALSE
numcombinations.others = prod(unlist(subset(lapply(bynames,length),
others.selector)))
# Replicate each level of this index the number of existing
combinations of other indices
newcolumn=rep(bynames[[indexnum]],each=numcombinations.others)
if(indexnum==length(indices)) { # first run
by.df=data.frame(newcolumn)
}
if(indexnum!=length(indices)) {
# newcolumn is too short by some multiple so we have to fix that
newcolumn=rep(newcolumn, length(rownames(by.df))/length(newcolumn)
)
# now attach our
Re: [R] Sweave problem in Windows
huang min wrote:
Hi,
I have searched the lists but still can not solve the problem. I am using
a
windows machine. After I sweave some Rnw file, I got a tex file. However,
the tex file can not be compiled. I know the problem is in the line
\usepackage{C:/PROGRA~1/R/R-25~1.1/share/texmf/Sweave} and I need to
modify
this line to
\usepackage{Sweave}.
I hope there can be some automatic way to do this instead of changing this
line in the tex file whenever I modify something. Thank you.
Huang
[[alternative HTML version deleted]]
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Simple workaround is to include the \usepackage{Sweave} in your .Rnw file,
after the \documentclass like this:
\documentclass[a4paper]{article}
\usepackage{Sweave}
Make sure you have all the .sty files you need in the same folder as your
.tex file.
cheers, Mike
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and provide commented, minimal, self-contained, reproducible code.
[R] Any package for deconvolution?
I want to run deconvolution of a time series by an impulse or point-spread function through Wiener filter, regularized filter, Lucy-Richardson method, or any other approaches. I searched the CRAN website and the mailing list archive, but could not find any package for such a deconvolution analysis. Does anybody know an existing R function for deconvolution? TIA, Gang __ 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 on a multi core unix box
Hi, I installed the snow package on a unix box that has multiple cores. To be able to exploit the multiple cores (on one pc) do I still need to install the rmpi package (or rpvm). Another question, if i run a bayesian simulation on the multiple core after setting them up correctly (using snow), would you think there will be a noticeable speedup gain. Thanks, Saeed --- linux centos 4 dual core processors 32 gb ram R (2.6.0) snow 0.29 [[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] Any package for deconvolution?
The RTisean package has wiener filter functions (wiener1 and wiener2).
Regards,
Richie.
Mathematical Sciences Unit
HSL
Chen, Gang (NIH/NIMH) [C] [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
06/12/2007 16:20
To
r-help@r-project.org
cc
Subject
[R] Any package for deconvolution?
I want to run deconvolution of a time series by an impulse or point-spread
function through Wiener filter, regularized filter, Lucy-Richardson
method, or any other approaches. I searched the CRAN website and the
mailing list archive, but could not find any package for such a
deconvolution analysis. Does anybody know an existing R function for
deconvolution?
TIA,
Gang
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ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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Re: [R] creating conditional means
hi gabor, i was able to get your suggestion to work. i have been going through the R help tools to figure out what each step actually does because i have something similar but hours 2,5,8,11,14,17 and 20 are missing. i haven't had any luck. each mean value that is calculated is the same. i keep getting the following error: DF- read.table(textConnection(Lines), header = TRUE) Error in read.table(textConnection(Lines), header = TRUE) : duplicate 'row.names' are not allowed aggregate(DF[2:4], +with(DF, data.frame(Year, Qtr = (Month - 3) %/% 3 + 1, Hour)), +mean)#skip=hour[2,5,8,11,14] Error in data.frame(Year, Qtr = (Month - 3)%/%3 + 1, Hour) : object Year not found i am not clear why in aggregate(DF[#:#] that we are subsetting other variables besides co2. i have been trying to just subset co2 without success though. your original suggestion is below and a snippet of my data set is below that. if you have any ideas or if you know of a help page that i may not have found yet that would be great (i've been using the aggregate help pages mostly. thanks for your help- s.heck Lines - Year Month Hour co2 num1 num2 2006 110 383.3709 28 28 2006 111 383.3709 28 28 2006 112 383.3709 28 28 2006 113 383.3709 28 28 2006 114 383.3709 28 28 2006 115 383.3709 28 28 2006 116 383.3709 28 28 2006 117 383.3709 28 28 2006 118 383.3709 28 28 2006 119 383.3709 27 27 2006 11 10 383.3709 28 28 DF - read.table(textConnection(Lines), header = TRUE) aggregate(DF[4:6], with(DF, data.frame(Year, Qtr = (Month - 1) %/% 3 + 1, Hour)), mean)#skip=hour[2,5,8,11,14,17,20]??? Year Month Hour co2 200510386.1600708 200511386.823056 200513387.1335939 200514387.0681103 200516387.4750983 200517388.3398313 200519388.7545317 2005110388.0844451 2005112386.7929627 2005113385.5569521 2005115384.5523752 2005116385.0246721 2005118385.8646669 2005119386.2182493 2005121386.4820756 2005122386.6606276 200520386.6791667 200521386.6597544 200523386.5725303 200524387.0638611 200526387.9293508 200527388.3778991 200529388.3721947 2005210387.8324642 2005212386.8404892 2005213385.6770345 2005215384.4798484 2005216384.6214677 2005218384.3044105 2005219383.3018709 2005221382.5837339 2005222382.2658036 Gabor Grothendieck wrote: Just adjust the formula for Qtr appropriately if your quarters are not Jan/Feb/Mar, Apr/May/Jun, Jul/Aug/Sep, Oct/Nov/Dec as I assumed. On Dec 1, 2007 5:21 PM, Sherri Heck [EMAIL PROTECTED] wrote: Hi Gabor, Thank you for your help. I think I need to clarify a bit more. I am trying to say average all 2pms for months march + april + may (for example). I hope this is clearer. here's a larger subset of my data set: year, month, hour, co2(ppm), num1,num2 2006 1 0 384.2055 14 14 2006 1 1 384.0304 14 14 2006 1 2 383.9672 14 14 2006 1 3 383.8452 14 14 2006 1 4 383.8594 14 14 2006 1 5 383.7318 14 14 2006 1 6 383.6439 14 14 2006 1 7 383.7019 14 14 2006 1 8 383.7487 14 14 2006 1 9 383.8376 14 14 2006 1 10 383.8684 14 14 2006 1 11 383.8301 14 14 2006 1 12 383.8058 14 14 2006 1 13 383.9419 14 14 2006 1 14 383.7876 14 14 2006 1 15 383.7744 14 14 2006 1 16 383.8566 14 14 2006 1 17 384.1014 14 14 2006 1 18 384.1312 14 14 2006 1 19 384.1551 14 14 2006 1 20 384.099 14 14 2006 1 21 384.1408 14 14 2006 1 22 384.3637 14 14 2006 1 23 384.1491 14 14 2006 2 0 384.7082 27 27 2006 2 1 384.6139 27 27 2006 2 2 384.7453 26 26 2006 2 3 384.9224 28 28 2006 2 4 384.8581 28 28 2006 2 5 384.9208 28 28 2006 2 6 384.9086 28 28 2006 2 7 384.837 28 28 2006 2 8 384.6163 27 27 2006 2 9 384.7406 28 28 2006 2 10 384.7468 28 28 2006 2 11 384.6992 28 28 2006 2 12 384.6388 28 28 2006 2 13 384.6346 28 28 2006 2 14 384.6037 28 28 2006 2 15 384.5295 28 28 2006 2 16 384.5654 28 28 2006 2 17 384.6466 28 28 2006 2 18 384.6344 28 28 2006 2 19 384.5911 28 28 2006 2 20 384.6084 28 28 2006 2 21 384.6318 28 28 2006 2 22 384.6181 27 27 2006 2 23 384.6087 27 27 thanks you again for your assistance- s.heck Gabor Grothendieck wrote: Try aggregate: Lines - Year Month Hour co2 num1 num2 2006 110 383.3709 28 28 2006 111 383.3709 28 28 2006 112 383.3709 28 28 2006 113 383.3709 28 28 2006 114 383.3709 28 28 2006 115 383.3709 28 28 2006 116 383.3709 28 28 2006 117 383.3709 28 28 2006 118 383.3709 28 28 2006 119 383.3709
Re: [R] Using panel.densityplot with stripplot
On 12/6/07, Christopher Oezbek [EMAIL PROTECTED] wrote: But is there a technical reason for making this distinction? It seemed to me that most panel functions can deal with x and y parameters and that panel.densityplot could make use of the same mechanisms as panel.violin to subdivide based on factor y. The technical reason is a fundamental part of the Trellis design. The prepanel function determines a bounding box as part of the initial calculations. Knowing this in advance allows the panel display and the axis rendering to be completely separated. Note that the panel.violin plot cannot easily say anything about the actual heights of the densities, only their shape. The y-axis there annotates the sample groups. -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] Help rewriting looping structure?
Hey Folks,
Could somebody help me rewrite the following code?
I am looping through all records across 5 fields to calculate the cumulative
percentage of each record (relative to each individual field).
Is there a way to rewrite it so I don't have to loop through each individual
record?
# tdat is my data frame
# j is my field index
# k is my record index
# tsum is the sum of all values in field j
# tmp is a vector containing the values in field j
# tdat[k,paste(cpct,j,sep=)] creates new fields cpct1,...,cpct5
for(j in 1:5) {
tsum- sum(tdat[,j]);
for(k in 1:nrow(tdat)) {
td- tdat[k,j];
tmp-tdat[,j];
# sum values = to current value and divide by the total sum
tdat[k,paste(cpct,j,sep=)]- sum(tmp[tmp = td]) / tsum;
}
}
Thanks,
TLowe
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Re: [R] creating conditional means
The error message says you have duplicate row names and that is not allowed. Make sure you have the same number of elements on each line of data as in the header. If you have one more on each line than on the header then the first data item on each line will be regarded as the row name. See ?count.fields The rest of your message is not clear. On Dec 6, 2007 11:52 AM, Sherri Heck [EMAIL PROTECTED] wrote: hi gabor, i was able to get your suggestion to work. i have been going through the R help tools to figure out what each step actually does because i have something similar but hours 2,5,8,11,14,17 and 20 are missing. i haven't had any luck. each mean value that is calculated is the same. i keep getting the following error: DF- read.table(textConnection(Lines), header = TRUE) Error in read.table(textConnection(Lines), header = TRUE) : duplicate 'row.names' are not allowed aggregate(DF[2:4], +with(DF, data.frame(Year, Qtr = (Month - 3) %/% 3 + 1, Hour)), +mean)#skip=hour[2,5,8,11,14] Error in data.frame(Year, Qtr = (Month - 3)%/%3 + 1, Hour) : object Year not found i am not clear why in aggregate(DF[#:#] that we are subsetting other variables besides co2. i have been trying to just subset co2 without success though. your original suggestion is below and a snippet of my data set is below that. if you have any ideas or if you know of a help page that i may not have found yet that would be great (i've been using the aggregate help pages mostly. thanks for your help- s.heck Lines - Year Month Hour co2 num1 num2 2006 110 383.3709 28 28 2006 111 383.3709 28 28 2006 112 383.3709 28 28 2006 113 383.3709 28 28 2006 114 383.3709 28 28 2006 115 383.3709 28 28 2006 116 383.3709 28 28 2006 117 383.3709 28 28 2006 118 383.3709 28 28 2006 119 383.3709 27 27 2006 11 10 383.3709 28 28 DF - read.table(textConnection(Lines), header = TRUE) aggregate(DF[4:6], with(DF, data.frame(Year, Qtr = (Month - 1) %/% 3 + 1, Hour)), mean)#skip=hour[2,5,8,11,14,17,20]??? Year Month Hour co2 200510386.1600708 200511386.823056 200513387.1335939 200514387.0681103 200516387.4750983 200517388.3398313 200519388.7545317 2005110388.0844451 2005112386.7929627 2005113385.5569521 2005115384.5523752 2005116385.0246721 2005118385.8646669 2005119386.2182493 2005121386.4820756 2005122386.6606276 200520386.6791667 200521386.6597544 200523386.5725303 200524387.0638611 200526387.9293508 200527388.3778991 200529388.3721947 2005210387.8324642 2005212386.8404892 2005213385.6770345 2005215384.4798484 2005216384.6214677 2005218384.3044105 2005219383.3018709 2005221382.5837339 2005222382.2658036 Gabor Grothendieck wrote: Just adjust the formula for Qtr appropriately if your quarters are not Jan/Feb/Mar, Apr/May/Jun, Jul/Aug/Sep, Oct/Nov/Dec as I assumed. On Dec 1, 2007 5:21 PM, Sherri Heck [EMAIL PROTECTED] wrote: Hi Gabor, Thank you for your help. I think I need to clarify a bit more. I am trying to say average all 2pms for months march + april + may (for example). I hope this is clearer. here's a larger subset of my data set: year, month, hour, co2(ppm), num1,num2 2006 1 0 384.2055 14 14 2006 1 1 384.0304 14 14 2006 1 2 383.9672 14 14 2006 1 3 383.8452 14 14 2006 1 4 383.8594 14 14 2006 1 5 383.7318 14 14 2006 1 6 383.6439 14 14 2006 1 7 383.7019 14 14 2006 1 8 383.7487 14 14 2006 1 9 383.8376 14 14 2006 1 10 383.8684 14 14 2006 1 11 383.8301 14 14 2006 1 12 383.8058 14 14 2006 1 13 383.9419 14 14 2006 1 14 383.7876 14 14 2006 1 15 383.7744 14 14 2006 1 16 383.8566 14 14 2006 1 17 384.1014 14 14 2006 1 18 384.1312 14 14 2006 1 19 384.1551 14 14 2006 1 20 384.099 14 14 2006 1 21 384.1408 14 14 2006 1 22 384.3637 14 14 2006 1 23 384.1491 14 14 2006 2 0 384.7082 27 27 2006 2 1 384.6139 27 27 2006 2 2 384.7453 26 26 2006 2 3 384.9224 28 28 2006 2 4 384.8581 28 28 2006 2 5 384.9208 28 28 2006 2 6 384.9086 28 28 2006 2 7 384.837 28 28 2006 2 8 384.6163 27 27 2006 2 9 384.7406 28 28 2006 2 10 384.7468 28 28 2006 2 11 384.6992 28 28 2006 2 12 384.6388 28 28 2006 2 13 384.6346 28 28 2006 2 14 384.6037 28 28 2006 2 15 384.5295 28 28 2006 2 16 384.5654 28 28 2006 2 17 384.6466 28 28 2006 2 18 384.6344 28 28 2006 2 19 384.5911 28 28 2006 2 20 384.6084 28 28 2006 2 21 384.6318 28 28 2006 2
Re: [R] Bootstrap Correlation Coefficient with Moving Block Bootstrap
It sounds like you should sample x and y together using the block bootstrap. If you have the usual situation, x and y in columns and observations in rows, then sample blocks of rows. Even though observations in y are independent, you would take advantage of that only for bootstrapping statistics that depend only on y. The answer to your second question is the same as the first - sample blocks of observations, keeping x and y together. Tim Hesterberg Hello. I have got two problems in bootstrapping from dependent data sets. Given two time-series x and y. Both consisting of n observations with x consisting of dependent and y consisting of independent observations over time. Also assume, that the optimal block-length l is given. To obtain my bootstrap sample, I have to draw pairwise, but there is the problem of dependence of the x-observations and so if I draw the third observation of y, I cannot simply draw the third observation of x (to retain the serial correlation structure between x and y), because I devided x into blocks of length l and I have to draw blocks, then I draw from x. 1. How can I compute a bootstrap sample of the correlation coefficient between x and y with respect to the dependence in time-series of x? 2. How does it look like, if x and y both consist of dependent observations? I hope you can help me. I got really stuck with this problem. Sincerly Klein. __ 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] coxme frailty model standard errors?
--- begin included message
I am running R 2.6.1 on windows xp
I am trying to fit a cox proportional hazard model with a shared
Gaussian frailty term using coxme My model is specified as:
nofit1-coxme(Surv(Age,cen1new)~ Sex+bo2+bo3,random=~1|isl,data=mydat)
With x1-x3 being dummy variables, and isl being the community level
variable with 4 levels.
Does anyone know if there is a way to get the standard error for the
random effect, like in nofit1$var? I would like to know if my random
effect is worth writing home about.
-- end included message
Computation of the se of the random effect turns out to be very hard, and
worse it isn't worth much when you have done so. For both these reasons coxme
doesn't even try (and it's not on the list of things to add).
First, you can do a likelihood ratio test by comparing the fit to a coxph
model that does not have the random effect. Make sure that the null
loglikelihood for the two fits are the same though! (For instance, one obs was
missing the isl variable above, so the two fits have differnt n).
fit1- coxme(Surv(Age,cen1new)~ Sex+bo2+bo3,random=~1|isl, data=mydat)
fit2- coxph(Surv(Age,cen1new)~ Sex+bo2+bo3, data=mydat)
fit1$loglik[1:2] - fit2$loglik
The first number printed should be 0, twice the second is distributed as a
chisq
on number of random effects degrees of freedom. (Not quite. The chisq test
is actually conservative since the random effect is constrained to be =0. But
it is close, and I'll let someone else work out the details)
Second, you can print a profile likelihood confidence interval. You had a
random effects variance of about .4, so make a guess that the confidence
interval is somewhere between 0 and 2.
vtemp - seq(0.0001, 2, length=20)
ltemp - 0*vtemp
for (i in 1:length(vtemp)) {
tfit - coxme(Surv(Age,cen1new)~ Sex+bo2+bo3,random=~1|isl, data=mydat,
variance= vtemp[i])
ltemp - 2 * diff(tfit$loglik[1:2])
}
plot(vtemp, ltemp, xlab='Variance', ylab=LR test)
abline(h= 2*diff(fit1$loglik[1:2]) - 3.84)
The sequence of fits each have a fixed value for the variance of the random
effect; the plot shows the profile likelihood. The profile is often very
asymmetric (which is why the se of the random effect isn't worth much). The
intersection of the profile with a line 3.84 units down (chisq on 1df) is the
profile based 95% confidence interval.
Terry Therneau
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[R] using eval(parse(text)) , gsub(pattern, replacement, x) , to process code within a loop/custom function
R-help users,
Thanks in advance for any assistance ... I truly appreciate your expertise.
I searched help and could not figure this out, and think you can probably offer
some helpful tips. I apologize if I missed something, which I'm sure I probably
did.
I have data for many samples. (e.g. 1950, 1951, 1952, etc.)
For each sample, I have many data-frames. (e.g. temp.1952, births.1952,
gdp.1952, etc.)
(Because the data is rather large (and for other reasons), I have chosen to
store the data as individual files, as opposed to a list of data frames.)
I wish to write a function that enables me to run any of many custom
functions/processes on each sample of data.
I currently accomplish this by using a custom function that uses:
eval(parse(t=text.i2)) , and gsub(pat, rep, x) (this changes the sample
number for each line of text I submit to eval(parse(t=text.i2)) ).
Is there a better/preferred/more flexible way to do this?
One issue/obstacle that I have encountered: Some of the custom functions I
use need to take as input the value of d in the loop below.
(Please see the sample function fn.mn.d below.)
#creates sample data
temp.1951 - c(11,13,15)
births.1951 - c(123, 156, 178)
temp.1952 - c(21,23,25)
births.1952 - c(223, 256, 278)
###
#function that looks for a a pattern pat.i within x, and replaces it with
rep
recurse - function(x, pat.i,rep.i) {
f - function(x,pat,rep) if (mode(x) == character) gsub(pat, rep, x) else x
if (length(x) == 0) return(x)
if (is.list(x)) for(i in seq_along(x)) x[[i]] - recurse(x[[i]], pat.i,rep.i)
else x - f(x,pat.i,rep.i)
x
#f - function(x) if (mode(x) == character) gsub(a, green, x) else x
}# end recurse end
###
###
#function that processes code submitted as text.i for each date in dates.i
fn.dateloop - function(text.i, dates.i ) {
for(d in 1: length(dates.i) ) {
tempdate - dates.i[d]
text.i2 - recurse(text.i, pat.i='#', rep.i=tempdate)
temp0=eval(parse(t=text.i2))
tempname - paste(names(temp0)[1], tempdate, sep='.')
save(list='temp0', file = tempname)
} # next d
} # end fn.dateloop
###
#
#a sample custom function that I want to run on each sample of data
fn.mn - function(x, y) {
res = x - y
names(res) = 'mn'
res
}
#
#
#example of function that takes d as input...
#I have not been able to get this to work with the custom function
fn.dateloop above
#I request assistance in learning how to accomplish this
fn.mn.d - function(x, y, d) {x[d] - y[d]}
#
#
setwd('c:/') #specifies location where sample data will be saved
getwd() #checks location
fn.mn(x=temp.1951, y=births.1951)
fn.mn(x=temp.1952, y=births.1952)
#
fn.dateloop(text.i = fn.mn(x=get('temp.#'), y=get('births.#') ) ,
dates.i=c('1951','1952') )
get(load('mn.1951'))
get(load('mn.1952'))
-
[[alternative HTML version deleted]]
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Re: [R] Using expression in Hmisc Key()
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Michael Kubovy Sent: Thursday, December 06, 2007 2:12 AM To: Dieter Menne Cc: [EMAIL PROTECTED] Subject: Re: [R] Using expression in Hmisc Key() [snip] This is one of the cases where I wish there were a function that exercised all the arguments of a graphics function by visualizing the effect of changing two or three levels of each argument (one by one, of course). This might have the side effect of allowing authors to shorten documentation. I have in mind adding a method to each graphics function, and having the author specify the two or three instructive levels of each argument. See the exhaustive exploration by J.R. Lobry, A.B. Dufour D. Chessel of the graphical parameters accessible by par(), at http://pbil.univ-lyon1.fr/R/fichestd/tdr75.pdf There are some tools that already exist to help with creating these types of visualization tools. The playwith package appears to be one such set of tools (I have not played with it much, so don't expect details from me). The tkrplot package is another one (I am more familiar with this one). The slider function (relax and TeachingDemos package) and sliderv function (TeachingDemos) also help here. Try running the example for the sliderv function and move the sliders around to see the effects. (one of these days I am going to rewrite many of the demos in TeachingDemos to use tkrplot) Yes, it would be nice to have a general function that could look at the arguments of a function, but this is not an easy task, for example, how many arguments can you pass to the plot function? Also which arguments should use slider bars and which text widgets? (radio buttons are a bit easier). One option (that I think you are possibly suggesting above) is to have each writer of a function include some type of metadata that a general function could query and use to make decisions about what type of control to use for that option including possible ranges of values. I'll think some more about this approach. I have plans to add some more graphical demos to the TeachingDemos package that would do what you want with subsets of the par arguments (there are too many to do all at once, but one function could let you modify plotting type, cex, lwd, lty, col, and similar options, it gets tricky when mar and mai both modify the same thing in different ways and both take vectors rather than a single number). Some functions have arguments that depend on each other, making the GUI for these cases is a bit more dificult in that you need to build in those relationships (see the vis.gamma function in TeachingDemos for one example, the rate and scale arguments are 2 different ways of specifying the same thing). One option (I would be willing to put this into TeachingDemos, or it may want its own package at some point) is to write a general function that takes a plotting expression/function as the first argument and a list as the 2nd argument. The list would include information on which type of widget (slider, radio buttons, entry, ...) to use, what the range of values are, and which argument to the plotting function they correspond to. The function would then create a gui (using tkrplot would be my preference) that would modify those values. Any function author that wants users to be able to use this with their function just needs to provide the list and possibly a not run example in the docs (and we can create several predone lists in the package for common plotting functions and subsets of par arguments). I'm adding this to my list of bus projects to think about. Any other thoughts, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 __ 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] Any package for deconvolution?
Thanks a lot for the quick pointer, Richie. I will take a close look of the
RTisean package.
Gang
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Thu 12/6/2007 11:46 AM
To: Chen, Gang (NIH/NIMH) [C]
Cc: r-help@r-project.org
Subject: Re: [R] Any package for deconvolution?
The RTisean package has wiener filter functions (wiener1 and wiener2).
Regards,
Richie.
Mathematical Sciences Unit
HSL
Chen, Gang (NIH/NIMH) [C] [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
06/12/2007 16:20
To
r-help@r-project.org
cc
Subject
[R] Any package for deconvolution?
I want to run deconvolution of a time series by an impulse or point-spread
function through Wiener filter, regularized filter, Lucy-Richardson
method, or any other approaches. I searched the CRAN website and the
mailing list archive, but could not find any package for such a
deconvolution analysis. Does anybody know an existing R function for
deconvolution?
TIA,
Gang
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and provide commented, minimal, self-contained, reproducible code.
ATTENTION:
This message contains privileged and confidential inform...{{dropped:21}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] logistic regression using glm,which y is set to be 1
On Wed, 2007-12-05 at 22:33 -0800, Bin Yue wrote: Dear all: By comparing glmresult$y and model.response(model.frame(glmresult)), I have found out which one is set to be TRUE and which FALSE.But it seems that to fit a logistic regression , logit (or logistic) transformation has to be done before regression. Does anybody know how to obtain the transformation result ? It is hard to settle down before knowing the actual process R works . I have read some books and the ?glm help file , but what they told me was not sufficient. Best wishes , Bin Yue Bin, I may be mis-interpreting your follow up query, but here goes: You have presumably created a logistic regression model. The resultant model object is called 'glmresult'. If you use: fitted(glmresult) it will return the fitted predicted values on a probability scale (0 - 1) for the original set of data that you used. You can also use: predict(glmresult, type = response) The advantage of using predict.glm() is that you can apply the model against new data. If you want the linear predicted values on a log-odds scale, you can use: glmresult$linear.predictors or more easily: predict(glmresult) See ?fitted and ?predict.glm for more information. Let's use an example from ?infert: model1 - glm(case ~ spontaneous+induced, data=infert,family=binomial()) # Summary of fitted values on a probability scale summary(fitted(model1)) Min. 1st Qu. MedianMean 3rd Qu.Max. 0.1534 0.1534 0.2949 0.3347 0.3750 0.7511 # Same summary(predict(model1, type = response)) Min. 1st Qu. MedianMean 3rd Qu.Max. 0.1534 0.1534 0.2949 0.3347 0.3750 0.7511 # Get log-odds scale values summary(model1$linear.predictors) Min. 1st Qu. MedianMean 3rd Qu.Max. -1.7080 -1.7080 -0.8716 -0.7781 -0.5107 1.1050 # Same summary(predict(model1)) Min. 1st Qu. MedianMean 3rd Qu.Max. -1.7080 -1.7080 -0.8716 -0.7781 -0.5107 1.1050 If we wanted to do the log-odds scale to probability scale transform manually, we could do: summary(exp(predict(model1)) / (1 + exp(predict(model1 Min. 1st Qu. MedianMean 3rd Qu.Max. 0.1534 0.1534 0.2949 0.3347 0.3750 0.7511 Look familiar? I would urge you to read through An Introduction To R, which is available with your R installation or via the R web site under Documentation. In addition, there are various books listed on the R web site regarding model building and related subject matter. Which you choose can be a matter of taste, but two I recommend would be: William N. Venables and Brian D. Ripley. Modern Applied Statistics with S. Fourth Edition. Springer, New York, 2002. ISBN 0-387-95457-0 Frank E. Harrell. Regression Modeling Strategies, with Applications to Linear Models, Survival Analysis and Logistic Regression. Springer, 2001. ISBN 0-387-95232-2 HTH, Marc Schwartz __ 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] Help rewriting looping structure?
How about this example?
## sample data frame with two columns
df - data.frame(x = abs(rnorm(20)), y=abs(rnorm(20,2)))
## create new variables in df with an lapply call
df[c(cpctx,cptcty)] - lapply(df, function(x) cumsum(x)/sum(x))
A possible improvement would be to construct the new column names in
the data frame automatically.
Best,
Erik
TLowe wrote:
Hey Folks,
Could somebody help me rewrite the following code?
I am looping through all records across 5 fields to calculate the cumulative
percentage of each record (relative to each individual field).
Is there a way to rewrite it so I don't have to loop through each individual
record?
# tdat is my data frame
# j is my field index
# k is my record index
# tsum is the sum of all values in field j
# tmp is a vector containing the values in field j
# tdat[k,paste(cpct,j,sep=)] creates new fields cpct1,...,cpct5
for(j in 1:5) {
tsum- sum(tdat[,j]);
for(k in 1:nrow(tdat)) {
td- tdat[k,j];
tmp-tdat[,j];
# sum values = to current value and divide by the total sum
tdat[k,paste(cpct,j,sep=)]- sum(tmp[tmp = td]) / tsum;
}
}
Thanks,
TLowe
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Re: [R] Help rewriting looping structure?
Is this basically what you want to do? (Please include commented,
minimal, self-contained, reproducible code so we don't have to guess
at what you want)
x - data.frame(a=runif(10), b=runif(10))
# do for one column
cumsum(x$a)/sum(x$a)
[1] 0.05892073 0.08129611 0.11067218 0.28640268 0.28969826 0.44477544
0.55195101 0.76500220 0.85234025
[10] 1.
If this is the case, you can extend it.
On Dec 6, 2007 9:02 AM, TLowe [EMAIL PROTECTED] wrote:
Hey Folks,
Could somebody help me rewrite the following code?
I am looping through all records across 5 fields to calculate the cumulative
percentage of each record (relative to each individual field).
Is there a way to rewrite it so I don't have to loop through each individual
record?
# tdat is my data frame
# j is my field index
# k is my record index
# tsum is the sum of all values in field j
# tmp is a vector containing the values in field j
# tdat[k,paste(cpct,j,sep=)] creates new fields cpct1,...,cpct5
for(j in 1:5) {
tsum- sum(tdat[,j]);
for(k in 1:nrow(tdat)) {
td- tdat[k,j];
tmp-tdat[,j];
# sum values = to current value and divide by the total sum
tdat[k,paste(cpct,j,sep=)]- sum(tmp[tmp = td]) / tsum;
}
}
Thanks,
TLowe
--
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and provide commented, minimal, self-contained, reproducible code.
--
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Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] Help rewriting looping structure?
Thank you all. That's exactly what I was looking for.
TLowe wrote:
Hey Folks,
Could somebody help me rewrite the following code?
I am looping through all records across 5 fields to calculate the
cumulative
percentage of each record (relative to each individual field).
Is there a way to rewrite it so I don't have to loop through each
individual
record?
# tdat is my data frame
# j is my field index
# k is my record index
# tsum is the sum of all values in field j
# tmp is a vector containing the values in field j
# tdat[k,paste(cpct,j,sep=)] creates new fields cpct1,...,cpct5
for(j in 1:5) {
tsum- sum(tdat[,j]);
for(k in 1:nrow(tdat)) {
td- tdat[k,j];
tmp-tdat[,j];
# sum values = to current value and divide by the total sum
tdat[k,paste(cpct,j,sep=)]- sum(tmp[tmp = td]) / tsum;
}
}
Thanks,
TLowe
--
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http://www.nabble.com/Help-rewriting-looping-structure--tf4957267.html#a14198294
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and provide commented, minimal, self-contained, reproducible code.
[R] a question on stepAIC
Hi, I am trying to use stepAIC to do forward stepwise selection for a logistic model. I did hi - glm(melanoma ~ ., family = binomial, data=data) lo - glm(melanoma ~ 1, family = binomial, data=data) stepAIC(lo, scope=list(upper = hi , lower = lo), direction = forward ) But the full model hi did not converge since I have many many candidate covariates: Warning message: algorithm did not converge in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, Question: Can I do the forward selection without specifying a maximal model hi? Thanks, Minya Pu [[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] Displaying numerics to full double precision
Thanks Ben, that fixed the display within R. However, even after changing
the display settings, the matrix elements still appear to be exported in
single precision. The matrix object is being passed into my C routines as
an SEXP Numeric type, and somewhere along the way, some of the digits are
getting lost.
Here's the relevant bit of my C code:
SEXP
divideMatrix(SEXP matrix_in, SEXP sub_height, SEXP sub_width, SEXP fileS)
...
if ( isMatrix(matrix_in) isNumeric(matrix_in) )
{
/* Use R macros to convert from SEXP to C types */
matrix = REAL(matrix_in);
height = INTEGER(GET_DIM(matrix_in))[0];
width = INTEGER(GET_DIM(matrix_in))[1];
subW = INTEGER_VALUE(sub_width);
subH = INTEGER_VALUE(sub_height);
...
}
Am I using the wrong macro to convert into a double in C? Any ideas?
Thanks,
Jeff Delmerico
Ben Bolker wrote:
Jeff Delmerico wrote:
I'm working on a shared library of C functions for use with R, and I want
to create a matrix in R and pass it to the C routines. I know R computes
and supposedly stores numerics in double precision, but when I create a
matrix of random numerics using rnorm(), the values are displayed in
single precision, and also exported in single precision when I pass them
out to my C routines. An example is below:
a - matrix(rnorm(16, mean=10, sd=4), nrow=4)
a
[,1] [,2] [,3] [,4]
[1,] 14.907606 17.572872 19.708977 9.809943
[2,] 9.322041 13.624452 7.745254 7.596176
[3,] 10.642408 6.151546 9.937434 6.913875
[4,] 14.617647 5.577073 8.217559 12.115465
storage.mode(a)
[1] double
Does anyone know if there is a way to change the display or storage
settings so that the values will be displayed to their full precision?
Or does rnorm only produce values to single precision?
Any assistance would be greatly appreciated.
Thanks,
Jeff Delmerico
options(digits) # 7
options(digits=x)
I may be mistaken, but I think the values are indeed exported
as double precision -- the issue here is just a display setting.
Ben Bolker
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Re: [R] Frequency and Phase Spectrograms
Todd Remund tkremund98 at hotmail.com writes: I know that there is a function, (spectro3D), that produces the Power Spectrogram. Are there R functions that produce the Frequency Spectrogram and the Phase Spectrogram? Thank you for your time. fft in stats gives you all you need, possibly combined with some time window in package signal, which also has some higher level stuff. Do you really want to interpret the frequency spectrum (whatever it is) with real, imaginary part and signs? The docs of spectro3D gives makes me cringe: Following Heisenberg uncertainty principle, the short-term Fourier transform cannot be precised in both time and frequency. I know that's written in quite a few books, but that upside-down thinking has been a source of confusion for generations of students and professors (of biology, to say). Dieter __ 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] relationship between two factors
I have a dataset with two variables that are factors: 1) Decision Making Satisfaction (DMS), values = A - Completely, B - Mostly, C - Partly, D - Not at all 2) IT Satisfaction values (ITS), values = A - Completely, B - Mostly, C - Partly, D - Not at all I would like to produce a table (matrix) and a chart of the factors, with counts at the cross sections: A B C D A B counts C D How can I do this in R? Many thanks, Chris -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ 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] generalized linear model with mixed effects
Hi, I need to fit a general generalized linear model, for observations on a response Y which is Gamma-distributed and observed in clusters. So, if E(Y) = mu, then for a suitable link function f, f(mu) is a (linear) function of both fixed and random effects. Are there R packages or functions which fit these models, using either MLE or estimating-equation approaches? Many thanks, Sam -- Professor Samuel D. Oman Department of Statistics Hebrew University Mount Scopus Jerusalem 91905 Israel tel:+ 972 2 5883 442 fax:+ 972 2 5883 549 __ 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] Help rewriting looping structure?
This will give you the percents in the same order as your original data (as
this is what your original code did)
apply(tdat, 2,
function(x) {
o - order(x)
oldo - order(o)
prc - cumsum(x[o]) / sum(x)
prc[oldo]
})
Jason Law
Statistician
City of Portland, Bureau of Environmental Services
Water Pollution Control Laboratory
6543 N Burlington Avenue
Portland, OR 97203 -5452
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of TLowe
Sent: Thursday, December 06, 2007 10:28 AM
To: r-help@r-project.org
Subject: Re: [R] Help rewriting looping structure?
Thank you all. That's exactly what I was looking for.
TLowe wrote:
Hey Folks,
Could somebody help me rewrite the following code?
I am looping through all records across 5 fields to calculate the
cumulative
percentage of each record (relative to each individual field).
Is there a way to rewrite it so I don't have to loop through each
individual
record?
# tdat is my data frame
# j is my field index
# k is my record index
# tsum is the sum of all values in field j
# tmp is a vector containing the values in field j
# tdat[k,paste(cpct,j,sep=)] creates new fields cpct1,...,cpct5
for(j in 1:5) {
tsum- sum(tdat[,j]);
for(k in 1:nrow(tdat)) {
td- tdat[k,j];
tmp-tdat[,j];
# sum values = to current value and divide by the total sum
tdat[k,paste(cpct,j,sep=)]- sum(tmp[tmp = td]) / tsum;
}
}
Thanks,
TLowe
--
View this message in context:
http://www.nabble.com/Help-rewriting-looping-structure--tf4957267.html#a1419
8294
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting large titles in a plot
Try inserting \n into the title where you would like it to start on a new line, e.g.: plot(A,main=This is my really long title\nand it's so long\nthat I can see just about half of it.) You may need to give yourself more room in the margin for multi-line titles (see ?par and the mar entry) and using the title function (rather than in the plot) will let you specify the position of the title (line argument). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Svempa Sent: Thursday, December 06, 2007 8:16 AM To: r-help@r-project.org Subject: [R] Fitting large titles in a plot I want to fit a fairly long main title for a plot, supposedly by changing row after a while. As for now it starts way outside the picture margin at the left and continues way out right passed the right margins. plot(A,main=This is my really long title and it's so long that I can see just about half of it.) Any suggestions? Shouldn't be that hard. -- View this message in context: http://www.nabble.com/Fitting-large-titles-in-a-plot-tf4956510 .html#a14193900 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. __ 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] Fitting large titles in a plot
On Thu, 2007-12-06 at 07:16 -0800, Svempa wrote:
I want to fit a fairly long main title for a plot, supposedly by changing row
after a while. As for now it starts way outside the picture margin at the
left and continues way out right passed the right margins.
plot(A,main=This is my really long title and it's so long that I can see
just about half of it.)
Any suggestions? Shouldn't be that hard.
You can insert newline characters ('\n') in the title:
plot(A, main = This is my really long title\nand it's so long that I
can see\njust about half of it.)
The likelihood is that you will need to alter the vertical position of
the title to accommodate the line wrapping.
To do that, you can either use mtext() in lieu of the 'main' argument,
or consider adjusting par(mgp), the first value of which is the
position of the plot title. See ?mtext and ?par.
You might also want to look at ?strwrap for a more general way of
wrapping long lines of text.
HTH,
Marc Schwartz
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Re: [R] differences in using source() or console
On 12/6/2007 8:01 AM, vito muggeo wrote: Dear all, Is there *any* reason explaining what I describe below? Probably, but you're unlikely to get a correct explanation if you don't give us code to reproduce the problem. From the look of things, your real example is quite complex, which is probably why you didn't post it. But the very act of simplifying it to something that is reasonable to post is quite likely to reveal to you what the problem is. Duncan Murdoch I have the following line myfun(x) If I type them directly in R (or copy/past), it works.. However if I type in R 2.6.1 source(code.R) ##code.R includes the above line Error in inherits(x, data.frame) : object d not found namely myfun() does not work correctly. In particular the non-working line inside myfun() is update(eval(x$call$obj), data=d) #d is created in myfun() My question is: why the problem occurs just via source()ing??? many thanks, vito Vito M.R. Muggeo Dip.to Sc Statist e Matem `Vianelli' Università di Palermo viale delle Scienze, edificio 13 90128 Palermo - ITALY tel: 091 6626240 fax: 091 485726/485612 __ 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] Fitting large titles in a plot
try this: plot(0, main=paste(strwrap(This is my really long title and it's so long that I can see just about half of it., width=50), collapse=\n)) On Dec 6, 2007 7:16 AM, Svempa [EMAIL PROTECTED] wrote: I want to fit a fairly long main title for a plot, supposedly by changing row after a while. As for now it starts way outside the picture margin at the left and continues way out right passed the right margins. plot(A,main=This is my really long title and it's so long that I can see just about half of it.) Any suggestions? Shouldn't be that hard. -- View this message in context: http://www.nabble.com/Fitting-large-titles-in-a-plot-tf4956510.html#a14193900 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ 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] merge in function
On Thu, 2007-12-06 at 09:27 -0800, qian z wrote:
I used merge() in a function, but it doesn't return correct data frame.
add.name - function(data, x)
{
...
...
newfile - merge(data, resid, by =0, all.x=TRUE, all.y= FALSE)
newfile
}
You are going to need to give us more information.
It is not clear what you mean by not returning the correct data frame.
Why is it not correct?
Where and what is 'resid'?
What is 'x' and how is it used in the function?
What is 'by = 0'? The 'by' argument values need to be quoted.
Please provide a small reproducible example as per the Posting Guide.
HTH,
Marc Schwartz
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Re: [R] Fitting large titles in a plot
I wrote a little utility function for exactly this reason, which I use with
long titles. You may want to add calls to par to adjust the upper margin if
you are using raw graphical functionality (plot et al) - but lattice adjusts
the upper margin automatically so you wouldn't need to add anything else.
PrettyString - function(theString, maxLength, collapse = \n)
{
words - unlist(strsplit(theString, ))
wordLengths - unlist(lapply(strsplit(words, ), length))
if(max(wordLengths) maxLength)
stop(maxChar must be increased due to string length)
count = wordLengths[1]
results = vector()
currentLine = words[1]
for(i in 2:length(words))
{
if((count + wordLengths[i] + 1) maxLength)
{
results = c(results, currentLine)
currentLine = words[i]
count = wordLengths[i]
}
else
{
currentLine = paste(currentLine, words[i])
count = count + wordLengths[i] + 1
}
}
if(length(currentLine))
results - c(results, currentLine)
paste(results, collapse = collapse)
}
Knowing the R list, someone can probably reduce this function to 2 lines of
code.
Jim
Svempa wrote:
I want to fit a fairly long main title for a plot, supposedly by changing
row after a while. As for now it starts way outside the picture margin at
the left and continues way out right passed the right margins.
plot(A,main=This is my really long title and it's so long that I can see
just about half of it.)
Any suggestions? Shouldn't be that hard.
--
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http://www.nabble.com/Fitting-large-titles-in-a-plot-tf4956510.html#a14196971
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[R] Randomizing one column in the dataMatrix
I have huge data file, and I would like randomize just one column at a time , is there any easy way? Thanks a lot. -- View this message in context: http://www.nabble.com/Randomizing-one-column-in-the-dataMatrix-tf4957535.html#a14197423 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] Using expression in Hmisc Key()
Michael Kubovy kubovy at virginia.edu writes: This is one of the cases where I wish there were a function that exercised all the arguments of a graphics function by visualizing the effect of changing two or three levels of each argument (one by one, of course). This might have the side effect of allowing authors to shorten documentation. I have in mind adding a method to each graphics function, and having the author specify the two or three instructive levels of each argument. See the exhaustive exploration by J.R. Lobry, A.B. Dufour D. Chessel of the graphical parameters accessible by par(), at http://pbil.univ-lyon1.fr/R/fichestd/tdr75.pdf That looks like a nice source for classical graphics, but I fear that it will have a limited readience because of the language (Disclaimer: I am not working for Time Magazine, my French is acceptable, and we drink their wine. ). Even reading such stuff in German is difficult for me, because of the required switching between computer terms and translation. For lattice, show.settings() is a good starter. Too bad it's miles from showing the complete set of options. No student around looking for the first steps to fame? Dieter __ 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] Vertical text in a plot
op - par(mar=(c(5, 4, 4, 4) + 0.1)) plot(1:25,runif(25,0,1),ylab=First Y-axis label,xaxt=n) axis(4,at=seq(0.2,1,.2), labels=1:5) mtext(Second Y-axis label,side=4, line=2) par(op) --- Marcin Kozak [EMAIL PROTECTED] wrote: Hi, Consider this simple plot: plot(1:25,runif(25,0,1),ylab=First Y-axis label,xaxt=n) I want to add an additional axis as axis(4,at=seq(0.2,1,.2), labels=1:5) I have no idea how to add now the title of the new axis as Second Y-axis label. I want this text to be vertically directed from bottom to top. I can't find the function in text() to write vertically. Any ideas? Thanks, Marcin __ 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] relationship between two factors
Try this: df - data.frame(DMS=factor(rep(LETTERS[1:4], 10)), ITS=factor(rep(LETTERS[1:4], 10))) table(df) plot(table(df)) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 06/12/2007, christopher snow [EMAIL PROTECTED] wrote: I have a dataset with two variables that are factors: 1) Decision Making Satisfaction (DMS), values = A - Completely, B - Mostly, C - Partly, D - Not at all 2) IT Satisfaction values (ITS), values = A - Completely, B - Mostly, C - Partly, D - Not at all I would like to produce a table (matrix) and a chart of the factors, with counts at the cross sections: A B C D A B counts C D How can I do this in R? Many thanks, Chris -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ 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] finding most highly transcribed genes - ranking, sorting and subsets?
Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward way to do this, or a valuable function, but I've been using my own methods and going around in circles. So far I've normalized within and between arrays, then returned the RG values using RG-RG.MA, then I ranked each R and G values for each array as below. rankRG-RG rankRG$R[,1]-rank(rankRG$R[,1]) rankRG$R[,2]-rank(rankRG$R[,2]) .. and so on for 6 columns(ie. arrays, as well as the G's) then I thought I could pull out a subset of rankRG using something like; topRG-rankRG topRG$R-subset(topRG$R,topRG$R[,1]500topRG$R[,2]500topRG$R[,5]500) However, this just returned me a matrix with one row of $R (the ranks were 500 for columns 1,2, and 5 and greater than 500 for 3,4,and 6). However, I can't believe that there is only one gene that is in the top 500 for R intensitiy among those three arrays. Am I doing something wrong? Can someone think of a better way of doing this? Thanks Alison ** Alison S. Waller M.A.Sc. Doctoral Candidate [EMAIL PROTECTED] 416-978-4222 (lab) Department of Chemical Engineering Wallberg Building 200 College st. Toronto, ON M5S 3E5 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting large titles in a plot
Try This: plot(A,main=paste(This is my really long title and,\n,it's so long that I can see just about half of it., sep = )) -- Bert Gunter Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lm.influence under R2.6.1
Greetings! Recently when I tried to use lm.influence I get the following error: Error in .Fortran(lminfl, model$qr$qr, n, n, k, as.integer(do.coef), : Fortran symbol name lminfl not in DLL for package base This occurs on both Linux and Windows platforms (details below). Searching the mail lists and other sources indicates that the fortran code for lminfluence (lminfl.f) was moved in the source code tree suggesting it should be found in package stats. Not clear to me why the hardcoded path is package base. The offending line in the R code for lm.influence is: res - .Fortran(lminfl, model$qr$qr, n, n, k, as.integer(do.coef), There were no other messages from people experiencing errors with lm.influence on the mailing list. Can someone else confirm that they are experiencing the same problem? Also, as a workaround, is there a way of forcing R to look in stats for the fortran symbol (similar to using the double and triple colon for addressing specific namespaces)? On Linux platform: = sessionInfo() R version 2.6.1 (2007-11-26) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8 ;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAM E=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION =C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SMPracticals_1.1-1 ellipse_0.3-5 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.1 On Windows platform: === R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SMPracticals_1.1-1 ellipse_0.3-5 loaded via a namespace (and not attached): [1] tools_2.6.1 Gerard % Gerard Tromp, Ph.D Center for Molecular Medicine and Genetics Vox: 313.577.8773 Department of Neurologyfax: 313.577.5218 Wayne State University School of Medicine 3309 Scott Hall 540 East Canfield Ave. Detroit, MI 48201 e-mail: [EMAIL PROTECTED] web: http://www.genetics.wayne.edu/gtromp/gtromp-home.html __ 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] relationship between two factors
The 'table' function will give you the simple counts. Plotting a table with the 'plot' function gives common charts for this. The 'CrossTable' function in the gmodels package creates the table along with additional information. There are a lot of other functions for creating/working with tables depending on what you are trying to do. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of christopher snow Sent: Thursday, December 06, 2007 5:51 AM To: r-help@r-project.org Subject: [R] relationship between two factors I have a dataset with two variables that are factors: 1) Decision Making Satisfaction (DMS), values = A - Completely, B - Mostly, C - Partly, D - Not at all 2) IT Satisfaction values (ITS), values = A - Completely, B - Mostly, C - Partly, D - Not at all I would like to produce a table (matrix) and a chart of the factors, with counts at the cross sections: A B C D A B counts C D How can I do this in R? Many thanks, Chris -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ 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] S3 and S4 clash
Hello:
How can I work around the conflict between the S3 and S4
illustrated in the example below? I'm developing a package that
requires a function in 'stats4', but when 'stats4' is attached, it
breaks my AIC function. I could give my AIC function another name so it
no longer uses the generic dispatch, but I wonder if there is another way.
Thanks,
Spencer Graves
bar.tmp - structure(1, class = bar)
AIC.bar - function(object, ..., k=2) {
3
}
AIC(bar.tmp)
[1] 3
library(stats4)
AIC(bar.tmp)
Error in UseMethod(logLik) : no applicable method for logLik
detach(package:stats4)
AIC(bar.tmp)
[1] 3
objects()
[1] AIC.bar bar.tmp
sessionInfo()
R version 2.6.1 (2007-11-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] stats4_2.6.1
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Re: [R] relationship between two factors
On Thu, 2007-12-06 at 12:51 +, christopher snow wrote: I have a dataset with two variables that are factors: 1) Decision Making Satisfaction (DMS), values = A - Completely, B - Mostly, C - Partly, D - Not at all 2) IT Satisfaction values (ITS), values = A - Completely, B - Mostly, C - Partly, D - Not at all I would like to produce a table (matrix) and a chart of the factors, with counts at the cross sections: A B C D A B counts C D How can I do this in R? Many thanks, Chris See ?table, for example: table(DMS, ITS) You did not indicate the type of chart you want to create, but some possibilities, using base graphics, would be barplot(), dotchart() and mosaicplot(). The latter is in the vcd package on CRAN. HTH, Marc Schwartz __ 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] Java parser for R data file?
On 12/5/07 12:15 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Wed, 5 Dec 2007, David Coppit wrote:
Or, given that I'm dealing with just a single array, would it be better to
roll my own I/O using write.table or write.matrix from the MASS package?
It would be much easier. The save() format is far more complex than you
need. However, I would use writeBin() to write a binary file and read
that in in Java, avoiding the binary - ASCII - binary conversion.
Thanks for the suggestion-writeBin works quite well. For posterity, here's what
I did:
On the R side:
# Assumes that there are no special values in the tofList, such as NA_REAL,
# R_PosInf, R_NegInf, ISNAN, R_FINITE. See the R Data Import/Export manual.
saveListAsBinary - function( tofList, filename )
{
outConn - file( filename, wb );
for (m in 1:length(tofList)) {
writeBin(names(tofList)[[m]], outConn);
writeBin(length(tofList[[m]]), outConn, size = 4, endian = big);
writeBin(tofList[[m]], outConn, size = 4, endian = big);
}
close(outConn);
}
saveListAsBinary(myList, outfile.RDat);
On the Java side:
public static void read_R_Output(String filename, ArrayListString names,
ArrayListArrayListFloat data)
{
try {
DataInputStream dataInputStream = new DataInputStream(
new BufferedInputStream(new FileInputStream(filename)));
boolean endOfFile = false;
while (!endOfFile) {
try {
StringBuffer sb = new StringBuffer();
byte c;
while ((c = dataInputStream.readByte()) != 0)
sb.append((char)c);
names.add(new String(sb));
int cols = dataInputStream.readInt();
ArrayListFloat row = new ArrayListFloat(cols);
for (int i = 0; i cols; i++)
row.add(dataInputStream.readFloat());
data.add(row);
} catch (EOFException e) {
endOfFile = true;
}
}
dataInputStream.close();
} catch (Exception e) {
e.printStackTrace();
}
}
Regards,
David
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[R] simple problems
Hello R users, I have been looking through Help files and Nabble list for the answers for these simple questions, but it seems to be fruitless. 1- in a data frame with two columns, x and y, how do I get the corresponding value of x to, let's say, the minimum value of the y column (min (data$y)) ? 2- how do I solve a simple equation? Considering the equation y= exp(-x)^12, I would like to find the values of x for, for example, y=0.01, so exp(-x)^12=0.01. How do I do that using R? I know those a probably very, very simple questions, but for which I do not seem to find the answer. Thank you very much, Marcia -- View this message in context: http://www.nabble.com/simple-problems-tf4958407.html#a14200401 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] relationship between two factors
?table should work table (DMS, ITS) I am not clear on what kind of chart you want. will plot(DMS, ITS) do what you want? --- christopher snow [EMAIL PROTECTED] wrote: I have a dataset with two variables that are factors: 1) Decision Making Satisfaction (DMS), values = A - Completely, B - Mostly, C - Partly, D - Not at all 2) IT Satisfaction values (ITS), values = A - Completely, B - Mostly, C - Partly, D - Not at all I would like to produce a table (matrix) and a chart of the factors, with counts at the cross sections: A B C D A B counts C D How can I do this in R? Many thanks, Chris Looking for the perfect gift? Give the gift of Flickr! __ 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] Fitting large titles in a plot
On Thu, 2007-12-06 at 09:28 -0800, Jim Price wrote:
I wrote a little utility function for exactly this reason, which I use with
long titles. You may want to add calls to par to adjust the upper margin if
you are using raw graphical functionality (plot et al) - but lattice adjusts
the upper margin automatically so you wouldn't need to add anything else.
PrettyString - function(theString, maxLength, collapse = \n)
{
words - unlist(strsplit(theString, ))
wordLengths - unlist(lapply(strsplit(words, ), length))
if(max(wordLengths) maxLength)
stop(maxChar must be increased due to string length)
count = wordLengths[1]
results = vector()
currentLine = words[1]
for(i in 2:length(words))
{
if((count + wordLengths[i] + 1) maxLength)
{
results = c(results, currentLine)
currentLine = words[i]
count = wordLengths[i]
}
else
{
currentLine = paste(currentLine, words[i])
count = count + wordLengths[i] + 1
}
}
if(length(currentLine))
results - c(results, currentLine)
paste(results, collapse = collapse)
}
Knowing the R list, someone can probably reduce this function to 2 lines of
code.
Jim
Would you believe one line?
paste(strwrap(theString, width = maxLength), collapse = \n)
;-)
See ?strwrap as I noted previously.
HTH,
Marc Schwartz
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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] lm.influence under R2.6.1
On Thu, 2007-12-06 at 14:00 -0500, Gerard Tromp wrote: Greetings! Recently when I tried to use lm.influence I get the following error: Error in .Fortran(lminfl, model$qr$qr, n, n, k, as.integer(do.coef), : Fortran symbol name lminfl not in DLL for package base This occurs on both Linux and Windows platforms (details below). I presume that the Linux message does not refer to DLLs? :-) Searching the mail lists and other sources indicates that the fortran code for lminfluence (lminfl.f) was moved in the source code tree suggesting it should be found in package stats. Not clear to me why the hardcoded path is package base. The offending line in the R code for lm.influence is: res - .Fortran(lminfl, model$qr$qr, n, n, k, as.integer(do.coef), There were no other messages from people experiencing errors with lm.influence on the mailing list. Can someone else confirm that they are experiencing the same problem? Also, as a workaround, is there a way of forcing R to look in stats for the fortran symbol (similar to using the double and triple colon for addressing specific namespaces)? snip I can run example(lm.influence) and example(influence.measures) without issue on: R version 2.6.1 Patched (2007-11-26 r43541) on an F8 Linux system. I don't see anything immediately obvious in the NEWS file for 2.6.1 patched to suggest that something has changed here. Can you provide a reproducible example here and/or try to upgrade to patched? I would also try to run: R --vanilla from the command line to provide a clean environment to be sure that none of the other packages that you are loading are causing conflicts. HTH, Marc Schwartz __ 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] Course***January 2008 *** San Francisco New York City *** R/S-Plus Advanced Programming by XLSolutions Corp
Happy Holidays Folks! XLSolutions Corporation has scheduled 2 great R/Splus Advanced programming courses. More course can be viewed on our website. R/Splus Advanced Programming* San Francisco January 21-22, 2008 R/Splus Advanced Programming* New York City January 24-25, 2008 Please email for earlybird rates: Payments due after the class. R/Splus Advanced Programming Course Outline: Day 1 - Overview of R/S fundamentals: Syntax and Semantics - Class and Inheritance - Concepts, Construction and good use of Language Objects - Coercion and Efficiency - Object-oriented Programming in R and S-Plus - Taking advantage of fast objects and fast functions - Advanced Manipulation tools: Parse, Deparse, Substitute, etc. - How to fully take advantage of Vectorization - Generic and Method Functions; S4 (S-Plus 6), etc. - Search path, Databases and Frames Visibility (S-plus) Day 2 - Working with Large Objects - Handling Properly Recursion and Iterative Calculations - Managing loops; For (S-Plus) and for() loops - Consequences of Lazy Evaluation - Efficient Code Practices for Large Computations - Memory Management and Resource Monitoring - Writing R and S-plus Functions to call Compiled Code - Writing and Debugging Compiled Code for S-plus and R system - Connecting R to External Data Sources - Macros in R - Understanding the Structure of Model fitting Functions in R and S-plus - Designing and Packaging Efficiently a new model Function Payment due AFTER the class Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Phone: 206-686-1578 Visit us: www.xlsolutions-corp.com/courselist.htm Please let us know if you and your colleagues are interested in this class to take advantage of group discount. Register now to secure your seat! Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.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] Fitting large titles in a plot
I have learned something new - thanks for the strwrap info.
The problem with posting from Nabble is that by the time your post actually
gets to the list (2 hours after you posted it in this case) and you've
written some line like Knowing the R list, someone can probably reduce this
function to 2 lines of code half a dozen people have already shown exactly
how you can do that, making me look totally incompetent.
Ah well, such is life :)
Jim.
Marc Schwartz wrote:
On Thu, 2007-12-06 at 09:28 -0800, Jim Price wrote:
I wrote a little utility function for exactly this reason, which I use
with
long titles. You may want to add calls to par to adjust the upper margin
if
you are using raw graphical functionality (plot et al) - but lattice
adjusts
the upper margin automatically so you wouldn't need to add anything else.
PrettyString - function(theString, maxLength, collapse = \n)
{
words - unlist(strsplit(theString, ))
wordLengths - unlist(lapply(strsplit(words, ), length))
if(max(wordLengths) maxLength)
stop(maxChar must be increased due to string length)
count = wordLengths[1]
results = vector()
currentLine = words[1]
for(i in 2:length(words))
{
if((count + wordLengths[i] + 1) maxLength)
{
results = c(results, currentLine)
currentLine = words[i]
count = wordLengths[i]
}
else
{
currentLine = paste(currentLine, words[i])
count = count + wordLengths[i] + 1
}
}
if(length(currentLine))
results - c(results, currentLine)
paste(results, collapse = collapse)
}
Knowing the R list, someone can probably reduce this function to 2 lines
of
code.
Jim
Would you believe one line?
paste(strwrap(theString, width = maxLength), collapse = \n)
;-)
See ?strwrap as I noted previously.
HTH,
Marc Schwartz
__
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--
View this message in context:
http://www.nabble.com/Fitting-large-titles-in-a-plot-tf4956510.html#a14201050
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] S3 and S4 clash
I'd say that was pretty clearly a bug in stats4 (which as I recall was
needed to get around the scoping awkwardnesses of S4).
But could you not write a logLik method for your class? E.g.
logLik.bar - function(object, ...) structure(pi, class=logLik, df=1)
AIC(bar.tmp)
[1] -4.283185
library(stats4)
AIC(bar.tmp)
[1] -4.283185
On Thu, 6 Dec 2007, Spencer Graves wrote:
Hello:
How can I work around the conflict between the S3 and S4
illustrated in the example below? I'm developing a package that
requires a function in 'stats4', but when 'stats4' is attached, it
breaks my AIC function. I could give my AIC function another name so it
no longer uses the generic dispatch, but I wonder if there is another way.
Thanks,
Spencer Graves
bar.tmp - structure(1, class = bar)
AIC.bar - function(object, ..., k=2) {
3
}
AIC(bar.tmp)
[1] 3
library(stats4)
AIC(bar.tmp)
Error in UseMethod(logLik) : no applicable method for logLik
detach(package:stats4)
AIC(bar.tmp)
[1] 3
objects()
[1] AIC.bar bar.tmp
sessionInfo()
R version 2.6.1 (2007-11-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] stats4_2.6.1
__
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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.
--
Brian D. Ripley, [EMAIL PROTECTED]
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
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Re: [R] Java parser for R data file?
Dear David,
You may also consider using the biocep project' tools and frameworks. they
provide an advanced bridge that allow you to exchange between R and Java
any standard R Object and any mapped S4 object.
the object extracted to Java (an RList for you data) can be serialized to
a file (saved as a java object). you can then read the serialized object
very easily from java and this is obviously much faster than parsing and
more elegant than a proprietary serialization/deserialization .
the easiest way to achieve this is to create the Serialized RList via the
Virtual R Workbench (Universal IDE for R).
you can run the R workbench on any kind of OS via the biocep sources:
http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt
or just use this link to get the software installed on your machine if you
are using Mac OS or windows
http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp
create your data via the workbench R Console (you may also use the script
editor or just read your list from a file)
go to the menu Java, choose Save R/Java Object to local file
select the name you've given to your list and choose a file name.
to retrieve your list in java, all you need is to add the RJB.jar to your
class path and use this simple code:
RList l=(RList)new ObjectInputStream(new
FileInputStream(J:/list.ser)).readObject();
and that's it.
this works for much more complex R objects (ExpressionSet..)
best wishes,
Karim
On 12/5/07 12:15 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Wed, 5 Dec 2007, David Coppit wrote:
Or, given that I'm dealing with just a single array, would it be better
to
roll my own I/O using write.table or write.matrix from the MASS package?
It would be much easier. The save() format is far more complex than you
need. However, I would use writeBin() to write a binary file and read
that in in Java, avoiding the binary - ASCII - binary conversion.
Thanks for the suggestion-writeBin works quite well. For posterity, here's
what I did:
On the R side:
# Assumes that there are no special values in the tofList, such as
NA_REAL,
# R_PosInf, R_NegInf, ISNAN, R_FINITE. See the R Data Import/Export
manual.
saveListAsBinary - function( tofList, filename )
{
outConn - file( filename, wb );
for (m in 1:length(tofList)) {
writeBin(names(tofList)[[m]], outConn);
writeBin(length(tofList[[m]]), outConn, size = 4, endian = big);
writeBin(tofList[[m]], outConn, size = 4, endian = big);
}
close(outConn);
}
saveListAsBinary(myList, outfile.RDat);
On the Java side:
public static void read_R_Output(String filename, ArrayListString
names,
ArrayListArrayListFloat data)
{
try {
DataInputStream dataInputStream = new DataInputStream(
new BufferedInputStream(new FileInputStream(filename)));
boolean endOfFile = false;
while (!endOfFile) {
try {
StringBuffer sb = new StringBuffer();
byte c;
while ((c = dataInputStream.readByte()) != 0)
sb.append((char)c);
names.add(new String(sb));
int cols = dataInputStream.readInt();
ArrayListFloat row = new ArrayListFloat(cols);
for (int i = 0; i cols; i++)
row.add(dataInputStream.readFloat());
data.add(row);
} catch (EOFException e) {
endOfFile = true;
}
}
dataInputStream.close();
} catch (Exception e) {
e.printStackTrace();
}
}
Regards,
David
[[alternative HTML version deleted]]
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[R] Integral implicit function
Hi,
Could somebody help me with the following. I want to calculate the integral
over an implicit function. I thought to integrate over a function depending on
uniroot. In previous topics I found a thread about finding the root of an
integral. And that works. But the other way around, does not work. Does R
support this?
I included the following example. The function in the example is very easy and
can be solved explicitly, but when it does not work for such an easy function
it will certainly not work for a more difficult function. First the root of an
integral (which works) and then the integral of a function dependent on uniroot:
# Calculating the root of an integral
a- function(x,y)
{x-y}
b- function(y)
{integrate(a,lower=1,upper=2,y=y)$value}
d- uniroot(b,c(0,10))$root
print(d)
# Calculating the integral of a function dependent on uniroot
e- function(u,v)
{u-v}
f- function(v)
{uniroot(e,c(0,10),v=v)$root}
g- integrate(f,lower=1,upper=2)$value
print(g)
Does anyone have suggestions how to proceed? By the way, the implicit function
I am targeting does have a unique solution, it is only not explicitly solvable,
i.e. in the example above, you cannot solve u as a function of v explicitly, so
as to substitute it in the integrand.
Thanks a lot in advance for your help,
Best regards,
Eddy Bekkers
Department of Economics
Erasmus University Rotterdam
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[R] coxme() random effect syntax
Hello: I would like to run a Cox proportional hazards regression on crayfish dislodgement at different water velocities by crayfish size class and substrate (rock) type. Additionally, there is a covariate variable, rock movement that may be influencing crayfish dislodgment. So... I have crayfish size class (CFSZCL) and substrate type (SUBSZ) as fixed factors influencing the dislodgment of crayfish at different water velocities (SLIPVEL). Thus, I am currently using the call: coxph(Surv(SLIPVEL, FREEDOM) ~ CFSZCL + SUBSZ + CFSZCL:SUBSZ, data = data.table) However, I would like to add rock movement (BEDLOAD) as a random co-variate, which is not possible with the coxph() function. Is it possible to do so with coxme() in the kinship package? If so, what is the proper syntax? Thanks for any help. Justin Montemarano __ 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 problems
marciarr wrote: Hello R users, I have been looking through Help files and Nabble list for the answers for these simple questions, but it seems to be fruitless. 1- in a data frame with two columns, x and y, how do I get the corresponding value of x to, let's say, the minimum value of the y column (min (data$y)) ? data$x2[data$x1==min(data$x1)] 2- how do I solve a simple equation? Considering the equation y= exp(-x)^12, I would like to find the values of x for, for example, y=0.01, so exp(-x)^12=0.01. How do I do that using R? I know there is solve for linear equations, but I do not know if there is a generic solver for other equations. You could implement it using a numerical approach (perhaps it is yet in some package). domenico __ 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] row lables in heatmap.2()
Dear list, I am wondering if there are any parameters in heatmap.2 to be able to adjust the size of row labels. Or the size of the plot can be made smaller. The plot I got is big and cannot see the full row labels completely. And what is the maximum of rows which could allow row labels visible in the plot? Last time, I tried a matrix of 2900 rows, but apparently the row labels are too dense to see it clearly. Any suggestions? Allen [[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] Testing Two Categorical Variable
The chi-square does not need your two categorical variables to have equal levels, nor limitation for the number of levels. The Chi-square procedure is as follow: χ^2=∑_(All Cells)▒〖(Observed-Expected)〗^2/Expected Expected Cell= E_ij=n((i^th RowTotal)/n)((j^th RowTotal)/n) Degree of Freedom=df= (row-1)(Col-1) This way should not give you any errors if your calculations are all correct. I usually use SAS for calculations like this. Below is a sample code I wrote to test whether US_State and Blood type are independent. You can modify it for your data and should give you no error. data bloodtype; input bloodtype$ state$ count@@; datalines; A FL 122 B FL 117 AB FL 19 O FL 244 A IA 1781 B IA 351 AB IA 289 O IA 3301 A MO 353 B MO 269 AB MO 60 O MO 713 ; proc freq data=bloodtype; tables bloodtype*state / cellchi2 chisq expected norow nocol nopercent; weight count; quit; Best Ramin __ 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] Testing Two Categorical Variable
The chi-square does not need your two categorical variables to have equal levels, nor limitation for the number of levels. The Chi-square procedure is as follow: χ^2=∑_(All Cells)▒〖(Observed-Expected)〗^2/Expected Expected Cell= E_ij=n((i^th RowTotal)/n)((j^th RowTotal)/n) Degree of Freedom=df= (row-1)(Col-1) This way should not give you any errors if your calculations are all correct. I usually use SAS for calculations like this. Below is a sample code I wrote to test whether US_State and Blood type are independent. You can modify it for your data and should give you no error. data bloodtype; input bloodtype$ state$ count@@; datalines; A FL 122 B FL 117 AB FL 19 O FL 244 A IA 1781 B IA 351 AB IA 289 O IA 3301 A MO 353 B MO 269 AB MO 60 O MO 713 ; proc freq data=bloodtype; tables bloodtype*state / cellchi2 chisq expected norow nocol nopercent; weight count; quit; Best Ramin __ 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] updating a helper function in a R package
Hi list,
Sorry for the vague title, but here is the scenario.
I’m writing an R package, let’s say, ‘pkg1’, which contains 3 functions: f1,
f2, f3. f2 and f3 are helper functions for f1, i.e. f1 calls f2 which in turn
calls f3.
f1 - function(…) {
….
f2()
…
}
f2 - function(…){
…
f3(…)
…
}
f3 - function(...){
}
Then, I wrote a new version of f3 and I want to test it. With the old version
of ‘pkg1’ already loaded into my R session, I tried just copy-and-paste the new
‘f3’ to R console and hope f1 will pick the new ‘f3’ up. It obviously didn’t
work. I know it’s b/c the new f3 and old f3 are in different environments and
when f1 is called, only old f3 is used. Then I tried to change the environment
of new f3 to the same as the old f3's by calling:
environment(f3) - environment(pkg1:::f3)
but it wasn't working either.
So,
1) Could somebody help me to put all these into perspectives?
2) Is there an easier way to update f3 without rebuilding the package? (by
that I mean, writing the new version of f3 in a way that I only need to
copy-and-paste to R console and I’m good to go. I know it’s kind of stupid but
I’m curious to know)
I'm using R-2.5.1, on WinXP.
Many thanks,
…Tao
_
07
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] simple problems
On Dec 6, 2007 3:26 PM, marciarr [EMAIL PROTECTED] wrote: Hello R users, I have been looking through Help files and Nabble list for the answers for these simple questions, but it seems to be fruitless. 1- in a data frame with two columns, x and y, how do I get the corresponding value of x to, let's say, the minimum value of the y column (min (data$y)) ? In the builtin Formaldehyde data frame find the value of carb (first column) which corresponds to the least value of optden (second column): with(Formaldehyde, carb[which.min(optden)]) 2- how do I solve a simple equation? Considering the equation y= exp(-x)^12, I would like to find the values of x for, for example, y=0.01, so exp(-x)^12=0.01. How do I do that using R? I know those a probably very, very simple questions, but for which I do not seem to find the answer. Search between 0 and 1 for the root of the indicated function: uniroot(function(x) 0.1 - exp(-x)^12, 0:1) __ 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] updating a helper function in a R package
If you are using namespaces see:
?assignInNamespace
On Dec 6, 2007 5:38 PM, Tao Shi [EMAIL PROTECTED] wrote:
Hi list,
Sorry for the vague title, but here is the scenario.
I'm writing an R package, let's say, 'pkg1', which contains 3 functions: f1,
f2, f3. f2 and f3 are helper functions for f1, i.e. f1 calls f2 which in
turn calls f3.
f1 - function(…) {
….
f2()
…
}
f2 - function(…){
…
f3(…)
…
}
f3 - function(...){
}
Then, I wrote a new version of f3 and I want to test it. With the old
version of 'pkg1' already loaded into my R session, I tried just
copy-and-paste the new 'f3' to R console and hope f1 will pick the new 'f3'
up. It obviously didn't work. I know it's b/c the new f3 and old f3 are in
different environments and when f1 is called, only old f3 is used. Then I
tried to change the environment of new f3 to the same as the old f3's by
calling:
environment(f3) - environment(pkg1:::f3)
but it wasn't working either.
So,
1) Could somebody help me to put all these into perspectives?
2) Is there an easier way to update f3 without rebuilding the package?
(by that I mean, writing the new version of f3 in a way that I only need to
copy-and-paste to R console and I'm good to go. I know it's kind of stupid
but I'm curious to know)
I'm using R-2.5.1, on WinXP.
Many thanks,
…Tao
_
07
__
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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.
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[R] How can I plot this graph
Hi, I am having trouble plotting the graph I need given the follow kind of data xxx - data.frame( x=c(1,2,3,4,5), y1=c(2,4,3,5,6), y2=c(3,4,6,3,1), y3=c(1,3,5,7,3), z1=c(1,NA,3,5,NA), z2=c(2,NA,4,6,NA) ) xxx x y1 y2 y3 z1 z2 1 1 2 3 1 1 2 2 2 4 4 3 NA NA 3 3 3 6 5 3 4 4 4 5 3 7 5 6 5 5 6 1 3 NA NA What I need is the following - One graph - y1, y2, y3 plotted as seperate lines vs x - z1, z2 give the range of the value of z, and need to be plotted as error bars or confidence intervals vs x Many thanks for any help, Regards, David - [[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.
