Hi iamisha1:
Sorry for answering so late!
On Wednesday 09 May 2007 23:47, [EMAIL PROTECTED] wrote:
I get the following error message after using the sysfit package's function
'systemfitClassic':
Error in data[[eqnVar]] : subscript out of bounds
When I do this:
MSYS1 - cbind(Y, Num, F,
'description' has to be a filepath of a zip file. You will have to
download it first.
On Wed, 6 Jun 2007, [EMAIL PROTECTED] wrote:
Hi
Reading the help for ?unz I was wondering if I can read data into R from
within
an zipfile that is on some website, like maybe:
dtaa =
Hello!
I have a short question: Is it possible to create a
(non-existing) Access database using R (and if yes,
how)? I need to create a new database and then insert
a few tables into it.
Thank you in advance,
Moshe Olshansky
[EMAIL PROTECTED]
__
Hi
OK, quick question - I can suppress the calculation and drawing of the
column dendrogram by using Colv=FALSE and dendrogram=row, but that
leaves me with a large amount of white space at the top of the plot
where the dendrogram would have been drawn... Is there a way of getting
rid of that?
Gudday,
I am generating a series of lattice contourplots that are conditioned on a
variable (Year) that has 27 different levels. If I try and put them all on one
plot, it ends up pretty messy and you can't really read anything, so instead I
have set the layout to 3x3, thus generating three
Dear Chung-hong Chan,
Thanks! Can you recommend a text editor for splitting? I used UltraEdit
and TextPad but did not find they can split files.
Sincerely,
Alex
On 6/6/07, Chung-hong Chan [EMAIL PROTECTED] wrote:
Easy solution will be split your big txt files by text editor.
e.g. 5000 rows
Dear Michael,
It consists of 238305 rows and 50 columns including the header and row
names.
Thanks!
Alex
On 6/7/07, michael watson (IAH-C) [EMAIL PROTECTED] wrote:
Erm... Is that a typo? Are we really talking 23800 rows and 49 columns?
Because that doesn't seem that many
On Wed, 6 Jun 2007, Moshe Olshansky wrote:
Hello!
I have a short question: Is it possible to create a
(non-existing) Access database using R (and if yes,
how)? I need to create a new database and then insert
a few tables into it.
Short answer: yes, if you are using Windows (you did not
Dear Jim,
Thanks a lot! The size of the text file is 189,588,541 bytes.
It consists of 238305 rows (including the header) and
50 columns (the first column is for ID and the rest for 49 samples).
The first row looks like:
ID
AIRNS_p_Sty5_Mapping250K_Sty_A09_50156.cel
Erm... Is that a typo? Are we really talking 23800 rows and 49 columns?
Because that doesn't seem that many
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of ssls sddd
Sent: 07 June 2007 10:48
To: r-help@stat.math.ethz.ch
Subject: Re: [R] How to load a
scott flemming wrote:
Hi,
I wonder whether R can finish the following project:
I want to make a chart to represent 10 genes. Each gene has orientation and
length. Therefore, a gene can be represented by arrows.
Can R be used to draw 10 arrows in one line ?
Hi Scott,
Maybe the
Dear R-list,
I have encountered the following error message trying to update R packages:
update.packages(ask='graphics')
Warning in install.packages(update[instlib == l, Package], l,
contriburl = contriburl, :
'lib' is not writable
Error in install.packages(update[instlib == l,
This works on my Windows machine starting off at a new R session:
options(graphics.record = TRUE)
library(lattice)
xyplot(uptake ~ conc | Plant, CO2, layout = c(2,2))
Now switch focus to the graphics window and you can PgUp and PgDn
through them.
There are several variations to this:
1. use
Hello,
I have a question about interacting with MySQL from R,
I have a vector of ids and for each id I would like to query my database and
retrieve 3 values and combine the results of all the ids into a dataframe
currently I have been using RODBC for single queries, but I have not found
See the rw-FAQ, which describes this in detail.
Almost certainly you are trying to update the package 'cluster' which is
in the main library. But as you used the GUI, we can't see that.
On Thu, 7 Jun 2007, Stefan Grosse wrote:
Dear R-list,
I have encountered the following error message
I took your data and duped the data line so I had 100,000 rows and it took
40 seconds to read in when specifying colClasses
system.time(x - read.table('/tempxx.txt',
header=TRUE,colClasses=c('factor', rep('numeric',49
user system elapsed
40.980.46 42.39
str(x)
'data.frame':
Hi,
how can I use R in a pipline like this
$ ./generate-data | R --script-file=Script.R | ./further-analyse-data
result.dat
Assume a column based output of ./generate-data, e.g. something like:
1 1 1
2 4 8
3 9 27
4 16 64
The R commands that process the data should come from Script.R and
Hello,
I'm wondering if there are any packages/functions that can perform
conditional sequential gaussian simulation.
I'm following an article written by Grunwald, Reddy, Prenger and Fisher
2007. Modeling of the spatial variability of biogeochemical soil
properties in a freshwater
This is one of the things that 'Rscript' is for: see 'An Introduction to
R' (section B.4 in the HTML version,
http://cran.r-project.org/doc/manuals/R-intro.html#Scripting-with-R).
You haven't even told us your version of R or OS (see the posting guide):
you need R = 2.5.0 for this. But your
David and Ted,
since David asked about wavelets, there are some examples
at the packages Wavethresh and Waveslim that could be useful.
Waveslim deals with time series that are or are not a power of 2,
but must be regularly spaced.
Wavethresh 3 (http://www.maths.bris.ac.uk/~wavethresh/)
has
Actually the packages R wants to update are: VR, cluster, lattice, mgcv,
nlme and rcompgen. I did how described in the R-Win-FAQ create a
.Renviron File containing the path to the win-library that R already
created (R_LIBS=C: ... ). I also tried to add R_LIBS= as Rgui parameter
from within Tinn-R.
Hi there,
i tried to run an ordered logistic regression with polr. so far it
worked after i turned my data into factors.
but here´s my problem:
my output is like this:
Call:
polr(formula = factor(fulltest[, 1]) ~ factor(fulltest[, 2]) +
factor(fulltest[, 10]), method = logistic)
Hi,
The silverman's paper introduction offer how to find a mode for one
dimensional data based
on software
http://www.stanford.edu/~kasparr/software/silverman.r,
for two dimensional data I use kde2d to smooth it out first, then I get a
matrix of densities for all the X(one dimension) cross
Dear list members!
Could you help me?
I would like to compare two models: a) logistic regression model, 3
factors as independents b) logistic regression model, 3 factors and one
random effect as independents (function glmmPQL). AIC are not available
with PQL and model comparison using ANOVA is
Hello R-list,
I have released an update version (0.3-1) of Rdonlp2.
Some (fatal) bugs which may kill interpreter should be fixed.
In addition, user-visible changes are:
* *.mes, *.pro files are not created if name=NULL(this is default) in donlp2().
* use machine-epsilons defined in R for
You could use lmer in the lme4 package to fit the logistic regression
with random effect as it does report the AIC.
On 07/06/07, Anna-Maria Tyriseva [EMAIL PROTECTED] wrote:
Dear list members!
Could you help me?
I would like to compare two models: a) logistic regression model, 3
factors as
Not sure what you are going to get. Can you shorten your functions and
specify some example data? Then please tell us what your expected result is.
Best,
Uwe Ligges
david dav wrote:
Dear all,
I 'd like to keep the names of variables when calling them in a function.
An example might help
ramakanth reddy wrote:
Hi
I am using the pamr.plotsurvival fucntion to plot the KM curves,how can I
change the x axis and y axis labels according to my interest.
If we are talking about the most recent version of package pamr (you
forgot to tell us these details):
In R, type
Dear Fellow Rers,
I have a table looks like this:
ca, la, 12
ca, sd, 22
ca, la, 33
nm, al, 9
ma, lx, 18
ma, bs, 90
ma, lx, 22
I want to sum the 3rd column grouped by the first and
the second column, so the result look like this table:
ca, la, 45
ca, sd, 22
nm, al, 9
ma, lx, 40
ma, bs, 90
This seems to work fine:
x - ca, la, 12
+ ca, sd, 22
+ ca, la, 33
+ nm, al, 9
+ ma, lx, 18
+ ma, bs, 90
+ ma, lx, 22
+
table - read.csv(textConnection(x), header=FALSE)
aggregate(table$V3,list(table$V1,table$V2),mean)
Group.1 Group.2x
1 nm al 9.0
2 ma bs 90.0
3
Hello
I am trying to fit a GARCH model, but continue to get error messages.
Here is what I am trying and the error message I get
garchmodel-garchFit(~arma(0,1), ~garch(0,1),series=junk)
Error in as.data.frame.default(data) : cannot coerce class formula into a
data.frame
junk is a time series.
On 07/06/07, alison weir [EMAIL PROTECTED] wrote:
Hello
I am trying to fit a GARCH model, but continue to get error messages.
Here is what I am trying and the error message I get
garchmodel-garchFit(~arma(0,1), ~garch(0,1),series=junk)
Error in as.data.frame.default(data) : cannot
On Thu, 7 Jun 2007, David Barron wrote:
You could use lmer in the lme4 package to fit the logistic regression
with random effect as it does report the AIC.
Indeed you could (lmer reports _an approximation_ to the AIC), but AIC
comparison between these two models is not valid as whereas they
I realize that this question has been asked before (2003);
From: Yi-Xiong Zhou
Date: Sat 22 Nov 2003 - 10:57:35 EST
but I am hoping that the answer has changed. Namely, I would
rather read the BMP (or TIFF) files directly instead of putting
them though a separate utility for conversion
Hi everybody,
i am like to do a ordered logistic model, but cant figure out which
syntax / library fits best.
i´ve answer possibilites in a matrix (-1 0 1 2 3), these are saved as
factors.
i guess i need something pretty basic. i tried VGAM, polr but
received not what i wanted.
Whicht
I am using the Akima interpolation package to generate an interpolated
color contour plot. It is working very well, except for one problem.
The data that I have represents real-time readings from a thermistor
string vs. time, so the data points are often very nearly in a
rectangular array,
Hello everybody, i wish to input data from the keyboard. In C++ it would seem
like this:
printf(Input parameter Alpha= );
scanf(%d, alpha);
how would be in R?
Thanks for your help.
Bye
Miguel.
--
View this message in context:
I have a data frame with three columns, one coded as a factor. I would like
to separate my data out into separate data frames according to the factor
level. Below is a simple example to illustrate. I can get R to return the
data in the correct format but cannot work out how to get separate data
Please do your homework:
help.search(input)
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Miguel Caro
Sent: Thursday, June 07, 2007 11:01 AM
To: r-help@stat.math.ethz.ch
Subject: [R] how to input data
Hi Emily,
Emily Broccoli wrote:
I have a data frame with three columns, one coded as a factor. I would like
to separate my data out into separate data frames according to the factor
level. Below is a simple example to illustrate. I can get R to return the
data in the correct format but
On 6/7/07, Bob Meglen [EMAIL PROTECTED] wrote:
I realize that this question has been asked before (2003);
From: Yi-Xiong Zhou
Date: Sat 22 Nov 2003 - 10:57:35 EST
but I am hoping that the answer has changed. Namely, I would
rather read the BMP (or TIFF) files directly instead of putting
I use Windows, R version 2.4.1.
I have a dataset in which columns 1-3 are replicates, 4-6, are replicates,
etc. I need to calculate an average for every set of replicates (columns
1-3, 4-6, 7-9, etc.) AND each set of replicates should be averaged every 14
rows (for more detail, to measure fruit
R-users helpers:
I am using Amelia, mitools and cmprsk to fit cumulative incidence curves
to multiply imputed datasets. The error message that I get
Error in eval(expr, envir, enclos) : invalid 'envir' argument
occurs when I try to fit models to the 50 imputed datasets using the
On 6/7/07, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Gudday,
I am generating a series of lattice contourplots that are conditioned on a
variable (Year) that has 27 different levels. If I try and put them all on
one plot, it ends up pretty messy and you can't really read anything, so
Thank you everyone for all of your suggestions!!
I am going to try compiling R from the source- it should be the best exercise
to broaden my understanding of Linux.
Best.
Jonathan.
Roland Rau [EMAIL PROTECTED] wrote: Hi Jonathan,
Jonathan Morse wrote:
I am new to Linux (not to R) and
Check out rowMeans to average over replicate columns first, ie:
means - data.frame(t1=rowMeans(a[,1:3]),
t2=rowMeans(a[,4:6]),
etc)
Then, if you want to aggregate every 14 rows:
aggregate(means, by=list(rows=rep(1:(nrow(means)/14), each=14)), mean)
Or
michael watson (IAH-C) wrote:
Check out rowMeans to average over replicate columns first, ie:
means - data.frame(t1=rowMeans(a[,1:3]),
t2=rowMeans(a[,4:6]),
etc)
Then, if you want to aggregate every 14 rows:
aggregate(means,
If R is installed within Program Files, one of Vista's security
settings may interfere with the -update- process.
The setting may be disabled globally by choosing:
Windows (Start) menu, Control Panels, User Accounts and Family
Safety (green title), User Accounts (green title), and
Turn User
I am trying to clean up some dates and I am clearly
doing something wrong. I have laid out an example
that seems to show what is happening with the real
data. The coding is lousy but it looks like it
should have worked.
Can anyone suggest a) why I am getting that NA
appearing after the
Perhaps you want one of these:
sort(as.Date(aa$times, %d/%m/%Y))
[1] 1995-03-02 2001-05-12 2007-02-14
sort(as.Date(aa$times, %d/%m/%Y), na.last = TRUE)
[1] 1995-03-02 2001-05-12 2007-02-14 NA NA
[6] NA
On 6/7/07, John Kane [EMAIL PROTECTED] wrote:
I am trying to clean up some
Hi All,
This is not directly related to R but I post the questions here since
there are a lot of experts on statistics. I want to calculate power
of logistic regression using likelihood ratio test in unmatched case
control design. The paper I have read is power calculations for
likelihood
I'm just curious if anyone else has had problems with this
configuration. I added the CRAN repository to apt and installed 2.5.0
with apt-get. I then did an install.packages(Rmpi) on cluster nodes.
Rmpi loads and lamhosts() shows the nodes, but mpi.spawn.Rslaves()
fails (something to do with temp
Hi John,
a) The NA appears because '30/02/1995' is not a valid date.
strptime('30/02/1995' , %d/%m/%Y)
[1] NA
b) dates which has the following classes uses sort.POSIXlt which in
turns sets na.last to NA. ?order details how NA's are handled in
ordering data via na.last.
As noted on the R-project web site itself ( www.r-project.org -
Manuals - R Data Import/Export ), it can be cumbersome to prepare
messy and dirty data for analysis with the R tool itself. I've also
seen at least one S programming book (one of the yellow Springer ones)
that says, more briefly, the
Hello
I followed the example in page 59, chapter 11 of the 'Introduction to R'
manual. I entered my own x,y data. I used the least squares. My function has
5 parameters: p[1], p[2], p[3], p[4], p[5]. I plotted the x-y data. Then I
used lines(spline(xfit,yfit)) to overlay best curves on the data
See the EBImage package on Bioconductor. /Henrik
On 6/7/07, Bob Meglen [EMAIL PROTECTED] wrote:
I realize that this question has been asked before (2003);
From: Yi-Xiong Zhou
Date: Sat 22 Nov 2003 - 10:57:35 EST
but I am hoping that the answer has changed. Namely, I would
rather read the
An additional option for Windows users is Micro Osiris
http://www.microsiris.com/
best
robert
On 6/7/07, Robert Wilkins [EMAIL PROTECTED] wrote:
As noted on the R-project web site itself ( www.r-project.org -
Manuals - R Data Import/Export ), it can be cumbersome to prepare
messy and dirty
Dear List,
I have another question to bother you about how to do clustering.
My data consists of 49 columns (49 variables) and 238804 rows.
I would like to do hierarchical clustering (unsupervised clustering
and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/*pvclust*
/)
but I
Dear Jim,
It works great. I appreciate your help.
Sincerely,
Alex
On 6/7/07, jim holtman [EMAIL PROTECTED] wrote:
I took your data and duped the data line so I had 100,000 rows and it took
40 seconds to read in when specifying colClasses
system.time(x - read.table('/tempxx.txt',
sorry, I hit send before finishing my thoughts...
and as for clustering microarray data, you might want to consider the
bioconductor mailing list...
[EMAIL PROTECTED]
b
On Jun 7, 2007, at 10:42 PM, ssls sddd wrote:
Dear List,
I have another question to bother you about how to do
Hi Alex,
just in case you're trying to get genotypes from the Affymetrix 500K
set, you might want to check the oligo package available on
BioConductor.
best,
b
On Jun 7, 2007, at 10:42 PM, ssls sddd wrote:
Dear List,
I have another question to bother you about how to do clustering.
My
Robert Wilkins wrote:
As noted on the R-project web site itself ( www.r-project.org -
Manuals - R Data Import/Export ), it can be cumbersome to prepare
messy and dirty data for analysis with the R tool itself. I've also
seen at least one S programming book (one of the yellow Springer ones)
Given
D = data.frame(o=gl(2,1,4))
this works as I expected:
evalq(o, D)
[1] 1 2 1 2
Levels: 1 2
but neither of these does:
f - function(x, dat) evalq(x, dat)
f(o, D)
Error in eval(expr, envir, enclos) : object o not found
g - function(x, dat) eval(x, dat)
g(o, D)
Error in eval(x, dat) :
This is my first post requesting help to this mailing list. I am new
to R. My apologies for any breach in posting etiquette. I am new to
this language and just learning my way around. I am attempting to run
some sample code and and am confused by the error message:
Loading required package: rrcov
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