[R] RWinEdt installation problems with Vista
Hi, I was trying to install the packageRWinEdt in my computer with Vista OS. Once I finished the installation, R just cannot load this library at all, reporting some error information. I reinstalled R and Winedit and reloaded this package. RWinEdt seemed to register in the computer but never work again. I searched some related information on internet. I did try using administer privilege to install R and Winedit. Ans I also opened it by run as administrator. The problem still insisted. R always report following results. Error in getRegistryKeyValues(createRegistryPath(path, top, isValue = FALSE)) : Error in get keys: The parameter is incorrect. Error : .onAttach failed in 'attachNamespace' Error: package/namespace load failed for 'RWinEdt' If anyone can help me out on this issue? Thank you in advance. Kevin [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to auto-scale cex of y-axis labels in lattice dotplot?
When I create a dotplot in lattice, I frequently observe overplotting of the labels along the vertical axis. On my screen, this illustrates overplotting of the letters: windows() reps=6 dat=data.frame(let=rep(letters,each=reps), grp=rep(1:reps, 26), y=runif(26*reps)) dotplot(let~y|grp, dat) Is there a way to automatically scale the labels so that they are not over-plotted? I currently do something like this: Calculate or guess the number of panel rows: NumPanelRows cexLab - min(1, .9*par()$pin[2]/ (nlevels(dat$let)*NumPanelRows*strheight(A,units=in))) dotplot(..., scales=list(y=list(cex=cexLab)) Is there an easier way? Is there a function that I can call which calculates the layout of the panels that will be used in the dotplot? Any tips will be appreciated. K Wright __ R-help@stat.math.ethz.ch 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] gam function time trend splines
I've been doing a simple time-series analysis looking at the relationship between daily pneumonia hospitalizations and daily temperature. To mimic some of the literature, I've been including a time-trend to try to account for normal cyclical trends in hospitalization. So I've been using a function that looks something like this: gam(pneucount ~ temp_f + s(day,bs=cr,k=(4*totalyears)+1), day being the enumerated day in the analysis (1-365 for a 1 year analysis). This seems to work well enough. What troubles me is when I think about doing an analysis focusing on winter days using more than one year of data. If I just delete the summer days from the dataset, the time trend spline is trying to anneal counts from the end of one winter with the beginning of another, which doesn't seem right to me. What's the route to a statistically defensible result? Is it as simple as using the subset option? Or would I need to create indicator variables for each winter I'm interested and work in a by statement somehow (with an extra term for the levels of that indicator, I assume)? Thanks in advance for helping a Epi student who's being exposed to all this for the first time. Sincerely, Kevin Sorensen Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. __ R-help@stat.math.ethz.ch 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] Tools For Preparing Data For Analysis
I am posting to this thread that has been quiet for some time because I
remembered the following question.
Christophe Pallier wrote:
Hi,
Can you provide examples of data formats that are problematic to read and
clean with R ?
Today I had a data manipulation problem that I don't know how to do in R
so I solved it with perl. Since I'm always interested in learning more
about complex data manipulation in R I am posting my problem in the
hopes of receiving some hints for doing this in R.
If anyone has nothing better to do than play with other people's data,
I would be happy to send the row files off-list.
Background:
I have been given data that contains two measurements of left
ventricular ejection fraction. One of the methods is echocardiogram
which sometimes gives a true quantitative value and other times a
semi-quantitative value. The desire is to compare echo with the
other method (MUGA). In most cases, patients had either quantitative
or semi-quantitative. Same patients had both. The data came
to me in excel files with, basically, no patient identifiers to link
the both with the semi-quantitative patients (the both patients
were in multiple data sets).
What I wanted to do was extract from the semi-quantitative data file
those patients with only semi-quantitative. All I have to link with
are the semi-quantitative echo and the MUGA and these pairs of values
are not unique.
To make this more concrete, here are some portions of the raw data.
Both
ID NUM,ECHO,MUGA,Semiquant,Quant
B,12,37,10,12
D,13,13,10,13
E,13,26,10,15
F,13,31,10,13
H,15,15,10,15
I,15,21,10,15
J,15,22,10,15
K,17,22,10,17
N,17.5,4,10,17.5
P,18,25,10,18
R,19,25,10,19
Seimi-quantitative
echo,muga,quant
10,20,0 -- keep
10,20,0 -- keep
10,21,0 -- remove
10,21,0 -- keep
10,24,0 -- keep
10,25,0 -- remove
10,25,0 -- remove
10,25,0 -- keep
Here is the perl program I wrote for this.
#!/usr/bin/perl
open(BOTH, quant_qual_echo.csv) || die Can't open quant_qual_echo.csv;
# Discard first row;
$_ = BOTH;
while(BOTH) {
chomp;
($id, $e, $m, $sq, $qu) = split(/,/);
$both{$sq,$m}++;
}
close(BOTH);
open(OUT, qual_echo_only.csv) || die Can't open qual_echo_only.csv;
print OUT pid,echo,muga,quant\n;
$pid = 2001;
open(QUAL, qual_echo.csv) || die Can't open qual_echo.csv;
# Discard first row
$_ = QUAL;
while(QUAL) {
chomp;
($echo, $muga, $quant) = split(/,/);
if ($both{$echo,$muga} 0) {
$both{$echo,$muga}--;
}
else {
print OUT $pid,$echo,$muga,$quant\n;
$pid++;
}
}
close(QUAL);
close(OUT);
open(OUT, both_echo.csv) || die Can't open both_echo.csv;
print OUT pid,echo,muga,quant\n;
$pid = 3001;
open(BOTH, quant_qual_echo.csv) || die Can't open quant_qual_echo.csv;
# Discard first row;
$_ = BOTH;
while(BOTH) {
chomp;
($id, $e, $m, $sq, $qu) = split(/,/);
print OUT $pid,$sq,$m,0\n;
print OUT $pid,$qu,$m,1\n;
$pid++;
}
close(BOTH);
close(OUT);
--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057
__
R-help@stat.math.ethz.ch 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] fitCopula
I am using R 2.5.0 on windows XP and trying to fit copula. I see the following code works for some users, however my code crashes on the chol. Any suggestions? mycop - tCopula(param=0.5, dim=8, dispstr=ex, df=5) x - rcopula(mycop, 1000) myfit - fitCopula(x, mycop, c(0.6, 10), optim.control=list(trace=1), method=Nelder-Mead) Nelder-Mead direct search function minimizer function value for initial parameters = -1747.582044 Scaled convergence tolerance is 2.6041e-05 Stepsize computed as 1.00 Error in chol(x, pivot = FALSE) : the leading minor of order 2 is not positive definite Kevin D. Oden e: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] fitCopula
I am using R 2.5.0 on windows XP and trying to fit copula. I see the following code works for some users, however my code crashes on the chol. Any suggestions? mycop - tCopula(param=0.5, dim=8, dispstr=ex, df=5) x - rcopula(mycop, 1000) myfit - fitCopula(x, mycop, c(0.6, 10), optim.control=list(trace=1), method=Nelder-Mead) Nelder-Mead direct search function minimizer function value for initial parameters = -1747.582044 Scaled convergence tolerance is 2.6041e-05 Stepsize computed as 1.00 Error in chol(x, pivot = FALSE) : the leading minor of order 2 is not positive definite Kevin D. Oden e: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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
elyakhlifi mustapha wrote: hello, is it possible to merge 2 matrix or data.frame by roxnames? I checked details about the functino merge but I haven't fond this option. Can you help me please? thanks. The first paragraph of the Details section says: By default the data frames are merged on the columns with names they both have, but separate specifications of the columns can be given by by.x and by.y. Columns can be specified by name, number or by a logical vector: the name row.names or the number 0 specifies the row names. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@stat.math.ethz.ch 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] Confidence interval for coefficient of variation
This is a function I coded a few years ago to calculate a confidence
interval for a coefficient of variation. The code is based on a paper
by Mark Vangel in The American Statistician. I have not used the
function much, but it could be useful for comparing cv's from
different groups.
Kevin Wright
confint.cv - function(x,alpha=.05, method=modmckay){
# Calculate the confidence interval of the cv of the vector x
# Author: Kevin Wright
# See: Vangel, Mark. Confidence Intervals for a Normal Coefficient
# of Variation. American Statistician, Vol 15, No1, p. 21--26.
# x - c(326,302,307,299,329)
# confint.cv(x,.05,modmckay)
x - na.omit(x)
v - length(x)-1
mu - mean(x)
sigma - sqrt(var(x))
k - sigma/mu
# CV .33 may give poor results, so warn the user
if(k.33) warning(Confidence interval may be very approximate.)
method - casefold(method) # In case we see McKay
if(method==mckay){
# McKay method. See equation 15.
t1 - qchisq(1-alpha/2,v)/v
t2 - qchisq(alpha/2,v)/v
u1 - v*t1
u2 - v*t2
lower - k/sqrt(( u1/(v+1) -1)*k*k + u1/v)
upper - k/sqrt(( u2/(v+1) -1)*k*k + u2/v)
} else if (method==naive){
# Naive method. See equation 17.
t1 - qchisq(1-alpha/2,v)/v
t2 - qchisq(alpha/2,v)/v
lower - k/sqrt(t1)
upper - k/sqrt(t2)
} else {
# Modified McKay method. See equation 16.
u1 - qchisq(1-alpha/2,v)
u2 - qchisq(alpha/2,v)
lower - k/sqrt(( (u1+2)/(v+1) -1)*k*k + u1/v)
upper - k/sqrt(( (u2+2)/(v+1) -1)*k*k + u2/v)
}
ci - c(lower,upper)
attr(ci,CV) - k
attr(ci,alpha) - alpha
return(ci)
}
__
R-help@stat.math.ethz.ch 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] Sorting dataframe by different columns
On the R wiki site there is a general-purpose function (sort.data.frame) that allows you to do this: sort(df, by=~ x-z) See: http://wiki.r-project.org/rwiki/doku.php?id=tips:data-frames:sort Regards, Kevin On 6/8/07, Gunther Höning [EMAIL PROTECTED] wrote: Dear list, I have a very short question, Suggest a dataframe of four columns. df - data.frame(w,x,y,z) I want this ordered the following way: first by :x, decreasing = FALSE and secondly by: z, decreasing =TRUE How can this be done ? Thanks Gunther __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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 update R version
Yanqin Yang wrote: Hello, I am new in using Linux R. Would someone tell me what the best way to update my current R 2.3.0 to R 2.5.0? I want to keep my current library packages. Do I have to erase the older version and install the newer version? In that case, I need to re-download all the packages I need. Any short way to do the update? Thanks for your help! yanqin Since I compile from source, I simply compile the new version and install it to the same location as the old. Then I run update.packages() to update the additional packages I have installed. Of course, I may get bit by this approach one day. It is possible to have more than one directory for packages. One suggestion I've seen is to collect your user installed packages in a different directory than the base and recommended packages. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@stat.math.ethz.ch 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] Metropolis-Hastings Markov Chain Monte Carlo in Spatstat
I'm testing some different formulations of pairwise interaction point processes in Spatstat (version 1.11-6) using R 2.5.0 on a Windows platform and I wish to simulate them using the Metropolis-Hastings algorithm implemented with Spatstat. Spatstat utilizes Fortran77 code with the preprocessor RatFor to do the Metropolis-Hastings MCMC, but the Makefile is more complicated than any I have worked with. Any suggestions on how I could get started working with the Fortran code in conjunction with RatFor is appreciated. Sincerely, Kevin Kevin Packard Department of Forestry, PhD student Department of Statistics, MS student Virginia Polytechnic Institute and State University Blacksburg, Virginia, USA __ R-help@stat.math.ethz.ch 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] Logrank test
See ?survdiff in the survival package. Mbini wrote: Hi I have a problem with computing the logrank test using R, can someone give me the relavent code or help me otherwise please! Thanks -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@stat.math.ethz.ch 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] Competing Risks Analysis
I am working on a competing risks problem, specifically an analysis of cause-specific mortality. I am familiar with the cmprsk package and have used it before to create cumulative incidence plots. I also came across an old (1998) s-news post from Dr. Terry Therneau describing a way to use coxph to model competing risks. I am re-producing the post at the bottom of this message. I would like to know if this approach is still reasonable or are there other ways to go now. I did an RSiteSearch with the term competing risks and found some interesting articles but nothing as specific as the post below. - S-news Article Begins - Competing risks It's actually quite easy. Assume a data set with n subjects and 4 types of competing events. Then create a data set with 4n observations First n obs: the data set you would create for an analysis of time to event type 1, where all other event types are censored. An extra variable etype is =1. Second n obs: the data set you would create for time to event type 2, with etype=2 . . . Then fit - coxph(Surv(time,status) ~ + strata(etype), 1. Wei, Lin, and Weissfeld apply this to data sets where the competing risks are not necessarily exclusive, i.e., time to progression and time to death for cancer patients. JASA 1989, 1065-1073. If a given subject can have more than one event, then you need to use the sandwich estimate of variance, obtained by adding .. + cluster(id).. to the model statement above, where id is variable unique to each subject. (The method of fitting found in WLW, namely to do individual fits and then glue the results together, is not necessary). 2. If a given subject can have at most one event, then it is not clear that the sandwich estimate of variance is necessary. See Lunn and McNeil, Biometrics (year?) for an example. 3. The covariates can be coded any way you like. WLW put in all of the strata * covariate interactions for instance (the x coef is different for each event type), but I never seem to have a big enough sample to justify doing this. Lunn and McNeil use a certain coding of the treatment effect, so that the betas are a contrast of interest to them; I've used similar things but never that particular one. 4. etype doesn't have to be 1,2,3,... of course; etype= 'paper', 'scissors', 'stone', 'pc' would work as well. Terry M. Therneau, Ph.D. - S-news Article Ends - -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@stat.math.ethz.ch 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] Parsing data with an uneven number of delimiters
I have a list of data that is delimited by a / and, as long as there is an equal number of delimiters, I can parse the data and put it into a data frame: t1-c(a/a/a,b/bb/bbb,ccc/cc/c) t2-strsplit(t1,/) t3-data.frame(t2) t3 c..aaa.. c..bbbbbb.. c..cccccc.. 1a b ccc 2a bb cc 3a bbb c However, if I don't have an equal number of delimiters, this technique doesn't work: l1-c(a/a/a,b/bb/bbb,cc/c) l2-strsplit(l1,/) l3-data.frame(l2) Error in data.frame(c(a, a, a), c(b, bb, bbb), c(cc, c : arguments imply differing number of rows: 3, 2 Is there an easy way to get this into a data frame with NA's (or something else) where the missing data would be? Thanks in advance. Kevin Burke __ R-help@stat.math.ethz.ch 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] SweaveInput and absolute paths
The path is correct, and the file exists. Here is a transcript of the R
session:
-
sessionInfo()
R version 2.4.0 (2006-10-03)
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] methods stats graphics grDevices utils datasets
[7] base
getwd()
[1] G:/Working/Fidler-Nakamura-Periphery
dir(M:/Resources/Affymetrix)
[1] affyExample.Rnw affyExample.tex affyplots.Rnw chkMiame.Rnw
[5] fnp.Rnw libLoad.Rnw readCel.Rnwrma.Rnw
[9] rnadeg.Rnw simpleQC.Rnw
Sweave(affyExample.Rnw)
Writing to file affyExample.tex
Processing code chunks ...
Error in SweaveReadFile(c(ifile, file), syntax) :
no Sweave file with name
'./M:/Resources/Affymetrix/libLoad.Rnw' found
In addition: Warning message:
list.files: './M:/Resources/Affymetrix' is not a readable directory
-
Dieter Menne writes:
Kevin R. Coombes krc at mdacc.tmc.edu writes:
Is there a way to turn off the automatic inclusion of ./ at the
beginning of a path specified in an \SweaveInput{} instruction?
Giving a full file path name works for me (Windows, R 2.4.1)
\SweaveInput{C:/tmp/MyTitle.rnw}
Note the if the path does not exist, e.g
\SweaveInput{C:/tmpnotexist/MyTitle.rnw},
the error message refert to ./C:/tmpnotexist/MyTitle.rnw, so it
could be that the path you chose had been incorrectly entered.
Dieter
__
R-help@stat.math.ethz.ch 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] SweaveInput and absolute paths
Hi,
Is there a way to turn off the automatic inclusion of ./ at the
beginning of a path specified in an \SweaveInput{} instruction?
I'd like to create some reusable template modules of Sweave code and
put them in a standard directory like
/Resources/Affymetrix
Then the corresponding file that uses one of these would include a
command like
\SweaveInput{/Resources/Affymetrix/libload.Rnw}
If I try that (in R 2.4.0 on either Windows or UNIX), however, I get an
error message to the following effect:
Writing to file affyExample.tex
Processing code chunks ...
Error in SweaveReadFile(c(ifile, file), syntax) :
no Sweave file with name './/Resources/Affymetrix/libload.Rnw' found
In addition: Warning message:
list.files: './/Resources/Affymetrix' is not a readable directory
Of course it cannot find the files if it insists on looking in the wrong
place
On a related note, where is SweaveInput documented besides in the R help
archives?
Thanks,
Kevin
__
R-help@stat.math.ethz.ch 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] sorting data in R
Now that sort is a generic function, I have modified my original
sort.data.frame function to be s 'data.frame' method to sort. (You
now have to specify the formula as the 'by' argument).
See the R Wiki:
http://wiki.r-project.org/rwiki/doku.php?id=tips:data-frames:sorts=sort%20data
There are also some other tips on that page for sorting.
Kevin Wright
On 4/20/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi
Best function for sorting which i have used and many in the community :-)
HTH Cheers
sort.data.frame(Oats, ~ -nitro + Variety)
Feedback and improvements are welcome.
sort.data.frame - function(form,dat){
# Author: Kevin Wright
# Some ideas from Andy Liaw
# http://tolstoy.newcastle.edu.au/R/help/04/07/1076.html
# Use + for ascending, - for decending.
# Sorting is left to right in the formula
# Useage is either of the following:
# library(nlme); data(Oats)
# sort.data.frame(~-Variety+Block,Oats) # Note: levels(Oats$Block)
# sort.data.frame(Oats,~nitro-Variety)
# If dat is the formula, then switch form and dat
if(inherits(dat,formula)){
f=dat
dat=form
form=f
}
if(form[[1]] != ~)
stop(Formula must be one-sided.)
# Make the formula into character and remove spaces
formc - as.character(form[2])
formc - gsub( ,,formc)
# If the first character is not + or -, add +
if(!is.element(substring(formc,1,1),c(+,-)))
formc - paste(+,formc,sep=)
# Extract the variables from the formula
if(exists(is.R) is.R()){
vars - unlist(strsplit(formc, [\\+\\-]))
}
else{
vars - unlist(lapply(unpaste(formc,-),unpaste,+))
}
vars - vars[vars!=] # Remove spurious terms
# Build a list of arguments to pass to order function
calllist - list()
pos=1 # Position of + or -
for(i in 1:length(vars)){
varsign - substring(formc,pos,pos)
pos - pos+1+nchar(vars[i])
if(is.factor(dat[,vars[i]])){
if(varsign==-)
calllist[[i]] - -rank(dat[,vars[i]])
else
calllist[[i]] - rank(dat[,vars[i]])
}
else {
if(varsign==-)
calllist[[i]] - -dat[,vars[i]]
else
calllist[[i]] - dat[,vars[i]]
}
}
dat[do.call(order,calllist),]
}
elyakhlifi mustapha [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
20-04-07 03:30 PM
To
R-help@stat.math.ethz.ch
cc
Subject
[R] sorting data in R
hello,
I'd like know how to sort a data frame in R for example how I should do
to sort by Catholic with swiss data frame like below
thanks
Fertility Agriculture Examination Education Catholic
Infant.Mortality
Courtelary80.217.0 1512 9.9622.2
Delemont 83.145.1 6 984.8422.2
Franches-Mnt 92.539.7 5 593.4020.2
Moutier 85.836.5 12 733.7720.3
Neuveville76.943.5 1715 5.1620.6
Porrentruy76.135.3 9 790.5726.6
Broye 83.870.2 16 792.8523.6
Glane 92.467.8 14 897.1624.9
Gruyere 82.453.3 12 797.6721.0
Sarine82.945.2 161391.3824.4
Veveyse 87.164.5 14 698.6124.5
Aigle 64.162.0 2112 8.5216.5
Aubonne 66.967.5 14 7 2.2719.1
Avenches 68.960.7 1912 4.4322.7
Cossonay 61.769.3 22 5 2.8218.7
Echallens 68.372.6 18 224.2021.2
Grandson 71.734.0 17 8 3.3020.0
Lausanne 55.719.4 262812.1120.2
La Vallee 54.315.2 3120 2.1510.8
Lavaux65.173.0 19 9 2.8420.0
Morges65.559.8 2210 5.2318.0
Moudon65.055.1 14 3 4.5222.4
Nyone 56.650.9 221215.1416.7
Orbe 57.454.1 20 6 4.2015.3
Oron 72.571.2 12 1 2.4021.0
Payerne 74.258.1 14 8 5.2323.8
Paysd'enhaut 72.063.5 6 3 2.5618.0
Rolle 60.560.8 1610 7.7216.3
Vevey 58.326.8 251918.4620.9
Yverdon 65.449.5 15 8 6.1022.5
Conthey 75.585.9 3 299.7115.1
Entremont 69.3
[R] Problem saving xYplot graph to file
Hello. I am having a problem directing the results of xYplot in the Hmisc package to a file. First I'll give you my sessionInfo and then my data and code, afterwhich I'll describe my problem. sessionInfo() R version 2.4.1 Patched (2007-02-26 r40806) i686-pc-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_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets [7] methods base other attached packages: lattice Hmisc acepack 0.14-16 3.3-1 1.3-2.2 `pcs.means.sd` - structure(list(group = structure(as.integer(c(1, 2, 1, 2, 1, 2, 1, 2)), .Label = c(Strength, Aerobic), class = factor), vis = c(0, 0, 2, 2, 6, 6, 18, 18), pcs = c(39.0334828308696, 36.9953199347826, 41.8490848139535, 39.0470522655814, 44.9146868080952, 41.04989196775, 46.4435591345946, 39.928985488), sd = c(8.6865669448865, 8.133546159086, 8.73403314236636, 8.34564558942182, 9.95941054193798, 10.7706814575657, 8.88934684511587, 10.9269199038043)), .Names = c(group, vis, pcs, sd), row.names = c(1, 2, 3, 4, 5, 6, 7, 8), class = data.frame) Ylim - c(pcs.means.sd$pcs-pcs.means.sd$sd-1, pcs.means.sd$pcs+pcs.means.sd$sd+1) trellis.device(postscript,color=FALSE,file=pcs.ps) xYplot(Cbind(pcs,pcs-sd,pcs+sd)~vis,data=pcs.means.sd,groups=group,type='b', method=bands,scales=list(x=list(at=c(0,2,6,18))), ylim=Ylim,xlab=Months,ylab=PCS) dev.off() Now, when I call xYplot without the trellis.device() and dev.off() the graph I want displays on the screen. When I try this with the trellis.device() the plot is only partially created. The axes are drawn but the actual plot area is empty except for the curve labels, although these are plotted on to of each other in the wrong place. I also tried putting my xYplot() inside a print() which gave the same results. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ [EMAIL PROTECTED] 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 alpha transparency for lines in levelplot - SUMMARY
I reported a similar issue with Adobe Reader in a thread starting here: http://tolstoy.newcastle.edu.au/R/e2/devel/06/10/0706.html K Wright On 3/27/07, Michael Sumner [EMAIL PROTECTED] wrote: Hello, thanks to Deepayan Sarkar for sorting me out on this one. The problem with transparent lines affecting region colour in lattice plot appears when using Adobe Reader (v 8 in my case). I've only viewed the file on Windows XP. I've tried using Foxit Reader to view the file and there's no problem. Cheers, Mike. __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Implementing trees in R
Hi all, I am rather new to R. Recently I have been trying to implement some tree algorithms in R. I used lists to model tree nodes. I thought something like this would work: parent - list(); child - list(); parent$child1 - child; child$parent - parent; When I tried to check whether a node is its parent's first child using if (node$parent$child1 == node), it always returned false. Then I realized that it does not really work because parent$child1 - child actually makes a copy of child instead of referencing it. I think one possible fix is to keep a list of node objects, and make references using the positions in the list. For example, I think the following would work: parent - list(); child - list(); nodes - list(parent, child); parent$child1 - 2; child$parent - 1; Then the first child test can be rewritten as if (nodes[[nodes[[nodeId]]$parent]]$child1 == nodeId). However, I would prefer not to implement trees in this way, as it requires the inconvenient and error-prone manipulations of node IDs. May I know if there is a way to make object references to lists? Or are there other ways to implement tree data structures in R? BTW, I checked how hclust was implemented, and noticed that it calls an external Fortran program. I would want a solution not involving any external programs. Thanks. -- God bless. Kevin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Implementing trees in R
Hi Gabor, Thanks for the suggestions. I tried to look for the proto vignette document but could not find it, could you tell me how to reach it? Besides, is it possible to define my own node object type with a default behavior for the - operator of its member variables being referencing rather than copying? Any good reference material/ similar code examples? Thanks. Gabor Grothendieck wrote: Lists are not good for this. There is an example in section 3.3 of the proto vignette of using proto objects for this. That section also references an S4 example although its pretty messy with S4. You might want to look at the graph, RBGL and graphviz packages in Bioconductor and the dynamicgraph, mathgraph and sna packages on CRAN. On 3/16/07, Yuk Lap Yip (Kevin) [EMAIL PROTECTED] wrote: Hi all, I am rather new to R. Recently I have been trying to implement some tree algorithms in R. I used lists to model tree nodes. I thought something like this would work: parent - list(); child - list(); parent$child1 - child; child$parent - parent; When I tried to check whether a node is its parent's first child using if (node$parent$child1 == node), it always returned false. Then I realized that it does not really work because parent$child1 - child actually makes a copy of child instead of referencing it. I think one possible fix is to keep a list of node objects, and make references using the positions in the list. For example, I think the following would work: parent - list(); child - list(); nodes - list(parent, child); parent$child1 - 2; child$parent - 1; Then the first child test can be rewritten as if (nodes[[nodes[[nodeId]]$parent]]$child1 == nodeId). However, I would prefer not to implement trees in this way, as it requires the inconvenient and error-prone manipulations of node IDs. May I know if there is a way to make object references to lists? Or are there other ways to implement tree data structures in R? BTW, I checked how hclust was implemented, and noticed that it calls an external Fortran program. I would want a solution not involving any external programs. Thanks. -- God bless. Kevin __ R-help@stat.math.ethz.ch 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. -- God bless. Kevin __ R-help@stat.math.ethz.ch 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] Implementing trees in R
Gabor,
Thanks. That helps a lot.
Gabor Grothendieck wrote:
On 3/16/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
1. Here is your example redone using proto:
library(proto)
parent - proto()
child - proto(a = 1)
parent$child1 - child
child$parent.env - parent
This last line should have been:
parent.env(child) - parent
# also just for illustration lets change a
parent$child1$a # 1
child$a - 2
parent$child1$a # 2
2. To redefine $- use S3 or S4 but it can be done
in conjunction with proto like this:
# constructor
node - function(. = parent.frame(), ...)
structure(proto(...), class = c(node, proto))
$-.node - function(this, s, value) {
if (s == .super)
parent.env(this) - value
if (is.function(value))
environment(value) - this
if (inherits(value, node))
parent.env(value) - this
this[[as.character(substitute(s))]] - value
this
}
p - node(a = 1)
p$child - node(b = 2)
p$child$parent.env()
p # same
On 3/16/07, Yuk Lap Yip (Kevin) [EMAIL PROTECTED] wrote:
Hi Gabor,
Thanks for the suggestions. I tried to look for the proto vignette
document but could not find it, could you tell me how to reach it?
Besides, is it possible to define my own node object type with a
default behavior for the - operator of its member variables being
referencing rather than copying? Any good reference material/ similar
code examples?
Thanks.
Gabor Grothendieck wrote:
Lists are not good for this. There is an example in section 3.3 of
the proto vignette of using proto objects for this. That section
also references an S4 example although its pretty messy with S4.
You might want to look at the graph, RBGL and graphviz packages
in Bioconductor and the dynamicgraph, mathgraph and sna packages
on CRAN.
On 3/16/07, Yuk Lap Yip (Kevin) [EMAIL PROTECTED] wrote:
Hi all,
I am rather new to R. Recently I have been trying to
implement some
tree algorithms in R. I used lists to model tree nodes. I thought
something like this would work:
parent - list();
child - list();
parent$child1 - child;
child$parent - parent;
When I tried to check whether a node is its parent's first child
using if (node$parent$child1 == node), it always returned
false. Then
I realized that it does not really work because parent$child1
- child
actually makes a copy of child instead of referencing it. I
think one
possible fix is to keep a list of node objects, and make references
using the positions in the list. For example, I think the following
would work:
parent - list();
child - list();
nodes - list(parent, child);
parent$child1 - 2;
child$parent - 1;
Then the first child test can be rewritten as if
(nodes[[nodes[[nodeId]]$parent]]$child1 == nodeId). However, I
would
prefer not to implement trees in this way, as it requires the
inconvenient and error-prone manipulations of node IDs.
May I know if there is a way to make object references to
lists? Or
are there other ways to implement tree data structures in R?
BTW, I checked how hclust was implemented, and noticed that
it calls
an external Fortran program. I would want a solution not
involving any
external programs.
Thanks.
--
God bless.
Kevin
__
R-help@stat.math.ethz.ch 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.
--
God bless.
Kevin
--
God bless.
Kevin
__
R-help@stat.math.ethz.ch 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] Sweave question: prevent expansion of unevaluated reused code chunk
Hi, I don't know of a standard way to indicate this; I would have suggested combined,expand=FALSE (with expand=TRUE the default), except for the fact that Seth Falcon already suggested the same notation in his response...so I can only second the motion. Kevin Duncan Murdoch wrote: On 3/13/2007 7:02 PM, Kevin R. Coombes wrote: Hi, Consider the following (much simplified) Sweave example: -- First, we set the value of $x$: chunk1,eval=FALSE= x - 1 @ Then we set the value of $y$: chunk2,eval=FALSE= y - 2 @ Thus, the overall algorithm has this structure: combined,eval=FALSE= chunk1 chunk2 @ justDoIt,echo=FALSE= combined @ --- I'd like to be able to do something like this, where the combined chunk prints out in the final LaTeX document essentially verbatim. In particular, I want to see the chunk1 unexpanded in that block, since this gives me a nice conceptual overview of the algorithm. (Of courser, this is more useful when chunk1 and chunk2 are much longer than they are in this example) Is there an option that allows me to get this behavior? As others have said, the answer is currently no, but in R 2.5.0 this should be a relatively easy modification (because it has the ability to echo your input, rather than a deparsed version of it). In the other platforms you've used, is there a standard syntax to indicate whether or not you want the chunks expanded? I can see either behaviour as being desirable in different circumstances. Sometimes you want the reader to know about your chunk names, and sometimes you don't. Duncan Murdoch __ R-help@stat.math.ethz.ch 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] Sweave question: prevent expansion of unevaluated reused code chunk
Hi, Consider the following (much simplified) Sweave example: -- First, we set the value of $x$: chunk1,eval=FALSE= x - 1 @ Then we set the value of $y$: chunk2,eval=FALSE= y - 2 @ Thus, the overall algorithm has this structure: combined,eval=FALSE= chunk1 chunk2 @ justDoIt,echo=FALSE= combined @ --- I'd like to be able to do something like this, where the combined chunk prints out in the final LaTeX document essentially verbatim. In particular, I want to see the chunk1 unexpanded in that block, since this gives me a nice conceptual overview of the algorithm. (Of courser, this is more useful when chunk1 and chunk2 are much longer than they are in this example) Is there an option that allows me to get this behavior? Thanks, Kevin __ R-help@stat.math.ethz.ch 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] Sweave question: prevent expansion of unevaluated reused code chunk
[1] In the example I presented, you're right; I can just use a verbatim
environment. In the following more complicated example
combined,eval=FALSE
if (some.condition) {
chunk1
} else {
chunk2
}
@
I would still want to be able to see the outline of what is going on,
and a verbatim environment wouldn't work.
[2] You are also correct that there is no advantage if I just call them
chunk1 and chunk2. But if I call them something more interesting,
like perform.quantile.normalization or truncate.and.log.transform,
then I can use this structure to explain the algorithm at a higher
level. If you go back to Knuth's original literate programming
examples, this is exactly how he presents his examples. For instance, on
page 104 of the Literate Programming book, he has
Program to print the first thousand prime numbers 2 =
program print_primes(output);
const m = 1000; other constants of the program 5
var Variables of the program 4
begin Print the first m prime numbers 3;
end.
Of course, he's writing pascal instead of R. But the stuff between
are the program chunks, and he is displaying them without expanding the
chunks. And, as a result, You get to see a high-level picture of the
algorithm, keeping the details somewhere else.
Since I'm looking at the results of weave in Knuth's example, I don't
know if he is using a verbatim environment or is automatically
generating this using his implementation of weave for teX and pascal
But that's the idea.
Kevin
Seth Falcon wrote:
Kevin R. Coombes [EMAIL PROTECTED] writes:
Hi,
Consider the following (much simplified) Sweave example:
--
First, we set the value of $x$:
chunk1,eval=FALSE=
x - 1
@
Then we set the value of $y$:
chunk2,eval=FALSE=
y - 2
@
Thus, the overall algorithm has this structure:
combined,eval=FALSE=
chunk1
chunk2
@
justDoIt,echo=FALSE=
combined
@
---
I'd like to be able to do something like this, where the combined
chunk prints out in the final LaTeX document essentially verbatim. In
particular, I want to see the chunk1 unexpanded in that block,
since this gives me a nice conceptual overview of the algorithm. (Of
courser, this is more useful when chunk1 and chunk2 are much longer than
they are in this example)
Is there an option that allows me to get this behavior?
Maybe I'm not understanding what it is you want, but why not:
\begin{verbatim}
chunk1
chunk2
\end{verbatim}
What does putting this in an unevaluated chunk buy you? The
chunkName markers are an internal detail of the document and so
must of the time these never appear in the rendered output. Even in
your example, won't it be confusing that chunk1 and chunk2
won't have appeared in labels earlier in the rendered document?
+ seth
__
R-help@stat.math.ethz.ch 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] Another newbie book recommandation question
I hope this question is sufficiently different from the other requests for book recommendations that it's not repetitious. If not, I apologize in advance. I'm curious what standard reference books working statisticians, or biostatisticians, have within easy reach of their desk. I'm a computer systems administrator, and have a two-foot bookshelf directory under my monitor that contains 13 paperback manuals that I refer to frequently, some once or twice a day. Are there standard reference works for statisticians that are used the same way? From reading this list, I'm guessing that one might be W. N. Venables and B. D. Ripley (2002), Modern Applied Statistics with S. Fourth Edition, Springer, ISBN 0-387-95457-0. However, I'm not limiting this to books pertaining to R. On the other hand, maybe Google and other on-line sources, as well as interactive programs like R that can spit out numbers previously looked up in tables, have completely replaced the need for reference books. Is this the case today? I'm particularly interested in reference books that may be helpful in my organization's work. We typically deal with datasets from international Demographic and Health Surveys (DHS) similar to those available at http://www.measuredhs.com/aboutsurveys/search/search_survey_main.cfm?Srv yTp=typelisttypes=1. These typically contain 10,000+ respondents and can have up to 800 fields. We currently analyze these datasets using Stata. Thanks for taking the time to think about and respond to this question. I'll summarize the answers in a later post for the archive. -Kevin Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@stat.math.ethz.ch 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 using Sweave with wireframe or cloud
Matthieu Cornec wrote: Hi, I used the sweave package to get a 3D plot echo=F,fig=F= wireframe(volcano, shade = TRUE, aspect = c(61/87, 0.4), light.source = c(10,0,10)) @ but it gives an error message for the pdf file of this picture. Any one could help ? Try this. echo=FALSE,fig=TRUE= library(lattice) print(wireframe(volcano, shade = TRUE, aspect = c(61/87, 0.4), light.source = c(10,0,10))) @ Thanks in advance, Matthieu -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@stat.math.ethz.ch 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] NEWBIE: @BOOK help?
In Henric's recent post, he included this output:
@BOOK{R:Harrell:2001,
AUTHOR = {Frank E. Harrell},
TITLE = {Regression Modeling Strategies, with Applications to
Linear Models, Survival Analysis and Logistic
Regression},
PUBLISHER = {Springer},
YEAR = 2001,
NOTE = {ISBN 0-387-95232-2},
URL = {http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RmS}
}
Can someone tell me how this is generated? I've noticed this in a few
recent posts. I attempted:
RSiteSearch(@BOOK)
?BOOK
?book
but it didn't return anything useful.
Thanks.
-Kevin
Kevin Zembower
Internet Services Group manager
Center for Communication Programs
Bloomberg School of Public Health
Johns Hopkins University
111 Market Place, Suite 310
Baltimore, Maryland 21202
410-659-6139
__
R-help@stat.math.ethz.ch 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] Sweave, Xfig, pdflatex and \setkeys
David Lindelöf wrote:
Dear useRs,
How does one include graphics created with Xfig with LaTeX fonts into
Sweave?
If I create a graphic with Xfig with some Computer Modern fonts, I
choose to export it as combined PDF and LaTeX. So I get two files, one
foo.pdf with the drawings without the text and foo.pdftex with some
LaTeX code that ensures the text lands in the right place together with
the drawing. I'm supposed to \input{} this file in my LaTeX document.
Trouble is that Sweave defines (with \setkeys) the default width of
\includegraphics to be 0.8 times the \textwidth. The result is that the
graphic is scaled, but not the text.
I was looking for a way to temporarily undefine the default width of
included graphics, but without success. Does anyone know how to undo a
definition that has been set with \setkeys?
Or does anyone has another workaround for including xfig graphics with
LaTeX text in Sweave?
Looking forward to your help,
If you knew what setting you needed, you could try
\setkeys{Gin}{width=whatever}
before your include, and set it back to the default afterward with
\setkeys{Gin}{width=0.8\textwidth}
I have run into this myself, but since I was also using beamer, it
wasn't at all obvious what I should try for the setting, so I don't
know if this will work. I have used this to rescale the imported
graphics from R. Fortunately, the graphic I created in xfig could
be completely specified in LaTeX, and so I exported it in that format
and imported it with \scalebox{0.5}{\input{xfigfile.latex}}
--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057
__
R-help@stat.math.ethz.ch 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 and LaTeX
Hi David, You can export the graphs in (encapsulated) postscript format, or in PDF/PNG/JPEG format. The following functions may be helpful: postscript() png() pdf() You may also want to check out Sweave (http://www.ci.tuwien.ac.at/~leisch/Sweave/), it allows you to integrate LaTeX and R neatly. Cheers, Kevin David Kaplan wrote: Hi all, I have started using LaTeX for writing papers and I have heard that R works well with LaTeX. I'm specifically interested in how I can have LaTeX read in R generated graphics - for example graphs formed by matplot, or other such processes. Does anyone out there use LaTeX and can point me in the right direction? Thanks David -- Ko-Kang Kevin Wang Ph (H): +61-2-612 57471 Ph (M): +61-40-4518301 http://wwwmaths.anu.edu.au/~wangk/personal/ __ R-help@stat.math.ethz.ch 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] cat not evaluated before file.choose
As part of a larger function I have code similar to the reduced
example below. The user is instructed to choose a file, which gets
read using read.csv. In this example, I just have the name of the
file print out.
When I call this function with choosefile(), the file dialog box
appears before the first cat line is printed. After I choose a file,
both cat lines are printed.
choosefile - function (){
cat(Choose the data file.\n)
filename - file.choose(new = FALSE)
cat(You chose: , filename, sep = )
}
Is there a way to force the first cat line to print before the call
to file.choose? I'm using R 2.4.0 Patched (2006-11-24 r39989) on OS
X. Session info below.
Any suggestions would be greatly appreciated.
Kevin Middleton
---
sessionInfo()
R version 2.4.0 Patched (2006-11-24 r39989)
powerpc-apple-darwin8.8.0
locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets
methods base
__
R-help@stat.math.ethz.ch 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] confige error:X11 headres/libs
Prof Brian Ripley wrote: Please do as the file INSTALL asks and read the R-admin.html file. It says Remember that some package management systems (such as RPM and deb) make a distinction between the user version of a package and the development version. The latter usually has the same name but with the extension `-devel' or `-dev': you need both versions installed. Unless you do not want to view graphs on-screen you need `X11' installed, including its headers and client libraries. (On Fedora Core Linux this means the `xorg-x11-devel' and `xorg-x11-libs' RPMs, for example. Older Linuxen used `XFree86-'. Some Debian derivatives apparently also require `libxt-dev'.) If you really do not want these you will need to explicitly configure R without X11, using --with-x=no. They have the same names on my SuSE 9.2 installation as Prof. Ripley indicated for a Fedora Core system. On SuSE, you need to install these packages with YaST (assuming that's what you are using for system admin). On Tue, 14 Nov 2006, thomas phillipson wrote: Can someone who uses SuSe Linux (I currently use 9.3) please tell me what I need toto to avoid the message configure: error: --with-x=yes (default) and X11 headers/libs are not available without setting --with-x=no currently my /usr/lib/X11 directory looks like this ls /usr/lib/X11 app-defaults fvwm2 nlstwm XErrorDB Xmodmap Cards getconfig Optionswmmount xinit Xmodmap.remote etc icons proxymngr x11perfcomp xkbXresources fonts lbxproxy rgb.txtxdm XKeysymDB xserver fslocale rstart xeditxman.help xsm thanks tom -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch 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] Next useR conference date/location
Are there any tentative plans for the next useR conference? I ask because I will soon need to develop an expense budget for 2007 and wondered if the conference is switching to an annual meeting or will continue every two years. Thanks for any information K Wright __ R-help@stat.math.ethz.ch 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] Unexpected behavior of predict and interval=confidence
Based on some recent r-help discussions, I have been trying out plotting confidence intervals using predict and matplot. Matplot appeared to not be plotting the linear regression when using the default column names generated by read.table (V1, V2, etc). On further inspection, the error seemed to be with predict and vector names (V1, V2) rather than with matplot. I was using some textbook data sets that were read with read.table, so my data.frame columns were named by default. The problem seems to be related to the name of the vector only (though I may be wrong). The example below, based on that in ?predict.lm, better describes the problem. Using predict with V2~V1 y~x produces identical output (when x-V1 and y-V2). However, using predict with interval=confidence results in different output from the same data. That with y~x is correct, and V2~V1 is incorrect. This may be related to a previous post on r-help: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/56982.html I can't figure out why there would be a difference in predict when only the vector name seemingly changes. Granted, I could just read the data.frame is as x and y. Thanks Kevin ## set.seed(10) # For example purposes, plot side by side par(mfrow=c(1,2)) V1 - rnorm(15) V2 - V1 + rnorm(15) new - data.frame(x = seq(min(V1), max(V1), length.out = length(V1))) pred.w.clim - predict(lm(V2 ~ V1), new, interval=confidence) matplot(new$x, pred.w.clim, lty=c(1,2,2), type=l, col=c(black, red, red), ylab=predicted y) points(V1,V2) # Create x y equal to V1 V2 x - V1 y - V2 pred.w.clim2 - predict(lm(y ~ x), new, interval=confidence) matplot(new$x, pred.w.clim2, lty=c(1,2,2), type=l, col=c(black, red, red), ylab=predicted y) points(x,y) # Test if V1=x, V2=y all.equal(x,V1) all.equal(y,V2) # Same output with predict predict(lm(V2 ~ V1)) predict(lm(y ~ x)) all.equal(predict(lm(V2 ~ V1)), predict(lm(y ~ x))) # Different output with interval=confidence pred.w.clim pred.w.clim2 all.equal(pred.w.clim, pred.w.clim2) __ R-help@stat.math.ethz.ch 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] Newbie: Better way to do compound conditionals in subset?
There must be a better way to select the rows after 22-Apr-2004 and before 01-Sep-2004 with a temperature below 65 than this: before2sw1 - subset(energy.data, as.Date(start, format=%d-%b-%y) as.Date(01-Sep-04, format = %d-%b-%y)) before2sw2 - subset(before2sw1, as.Date(start, format=%d-%b-%y) = as.Date(22-Apr-04, format = %d-%b-%y), select=c(therms,temp,days)) before2sw - subset(before2sw2, temp 65) Is it also possible to combine in this step: attach(before2sw) before2sw.HDD - therms / (65 - temp) * days My data looks like this: head(energy.data) start therms gas KWHs elect temp days 1 10-Jun-98 9 16.84 613 63.80 75 40 2 20-Jul-98 6 15.29 721 74.21 76 29 3 18-Aug-98 7 15.73 597 62.22 76 29 4 16-Sep-98 42 35.81 460 43.98 70 33 5 19-Oct-98105 77.28 314 31.45 57 29 6 17-Nov-98106 77.01 342 33.86 48 30 Thanks for your suggestions and advice. I'm continuing to enjoy learning R. -Kevin Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@stat.math.ethz.ch 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] Dataset on Baltimore home energy costs
Sorry, dumb typo. Should be 18-Dec-2005. -Kevin From: Richard M. Heiberger [mailto:[EMAIL PROTECTED] Sent: Fri 10/20/2006 5:43 PM To: Zembower, Kevin Subject: Re: [R] Dataset on Baltimore home energy costs Thanks for the data. Can you clarify the date here. 18-Dec-2006: Brought home son; spouse and son home during the day, setback thermostat no longer used. Interesting question: What's the cost of adding a child? It's still October, so I am not at all sure which year this should be. Rich [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] I really don't understand functions in R :-)
Is this what you want? f - function(x,n=3) x^n f(2) [1] 8 n - 2 f(2) [1] 8 f(2,2) [1] 4 Alberto Monteiro wrote: An example: n - 3 f - function(x) x^n f(2) # [1] 8 n - 2 f(2) # [1] 4 f # function(x) x^n Ok, I know this is trivial, because function f is foverer bound to the variable n. But how can I _fix_ n when I define _f_, so that changing _n_ won't change the function f? Alberto Monteiro -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch 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] Dataset on Baltimore home energy costs
I received a private request for my complete dataset from my previous questions. In gratitude to the developers of R, and especially to the helpful members of r-help, I'm happy to attach it. Anyone is free to use this dataset in any manner they wish, including published books. Attribution is not required, or even desired. Explanatory notes on dataset: This data is collected from monthly utility bills for my 80 year old house in northern Baltimore City, Maryland, USA. The fields are: start: date of start of billing period therms: integer number of therms used in this billing period gas: Total cost of gas (including delivery and commodity charges) for natural gas KWHs: integer number of KWH used in this billing period elect: Total cost of electricity (including delivery and commodity charges) temp: average daily outdoor temperature in degrees Fahrenheit, as printed on the bill days: number of days in billing period. Heating system is a 10-15 year old natural gas steam boiler supplying iron radiators. Hot water heater, clothes dryer and stove and oven are also natural gas. Air conditioning is by various numbers of window units. If surface area of house is desired, I can add this at a later time. Some interesting points in time: 22-Apr-04: Date when I upgraded 2 failed, older storm windows to more modern ones. 1-Sep-04: Date when I upgraded 4 failed, older storm windows to more modern ones. Interesting question: Did upgrading the windows significantly change the heat loss? last week of July 1999: Spouse moved in; both adults absent during the work day, setback thermostat used. Interesting question: Is there a discernable difference in the energy costs for heating between a single person and a couple? What's the heating cost of adding a spouse or roommate? 18-Dec-2006: Brought home son; spouse and son home during the day, setback thermostat no longer used. Interesting question: What's the cost of adding a child? If I could supply any more information that would make this dataset more useful or interesting, please let me know. I'm having fun 'playing' with these data; I hope you and your students do, too. -Kevin start therms gas KWHselect tempdays 10-Jun-98 9 16.84 613 63.80 75 40 20-Jul-98 6 15.29 721 74.21 76 29 18-Aug-98 7 15.73 597 62.22 76 29 16-Sep-98 42 35.81 460 43.98 70 33 19-Oct-98 105 77.28 314 31.45 57 29 17-Nov-98 106 77.01 342 33.86 48 30 17-Dec-98 200 136.66 298 30.08 40 33 19-Jan-99 144 107.28 278 28.37 37 30 18-Feb-99 179 122.80 253 26.21 39 29 16-Apr-99 57 49.81 315 31.56 54 32 18-May-99 8 17.11 373 40.57 64 30 17-Jun-99 6 15.77 596 62.12 73 33 20-Jul-99 6 15.88 723 74.41 77 29 18-Aug-99 7 16.69 532 55.94 76 30 17-Sep-99 45 42.20 551 50.81 66 32 19-Oct-99 107 82.87 367 36.00 55 29 16-Dec-99 245 166.94 490 46.56 42 33 18-Jan-00 267 183.35 395 38.40 33 30 17-Feb-00 147 99.77 448 42.95 38 32 20-Mar-00 94 72.39 395 38.40 49 29 18-Apr-00 50 46.87 363 35.65 56 29 17-May-00 25 28.63 457 48.68 64 33 19-Jun-00 5 16.53 525 55.26 70 31 20-Jul-00 7 18.23 511 51.64 74 28 17-Aug-00 8 19.22 538 53.95 72 33 19-Sep-00 51 60.78 390 34.98 65 30 19-Oct-00 91 94.72 364 33.18 56 28 16-Nov-00 241 226.93 465 40.19 44 33 19-Dec-00 289 287.52 423 37.28 33 31 19-Jan-01 174 197.69 348 32.07 33 28 16-Feb-01 145 163.59 338 31.38 39 32 20-Mar-01 121 122.53 346 31.93 45 29 18-Apr-01 47 50.94 370 33.60 55 29 17-May-01 16 23.99 460 48.11 65 34 20-Jun-01 7 17.25 447 46.98 71 29 19-Jul-01 6 15.81 589 59.40 75 32 20-Aug-01 6 15.66 433 45.76 74 29 18-Sep-01 44 39.27 419 36.24 66 31 19-Oct-01 97 74.58 356 31.98 56 27 15-Nov-01 120 91.27 484 40.65 51 33 18-Dec-01 183 154.37 393 34.45 43 30 17-Jan-02 170 134.35 394 34.52 38 33 19-Feb-02 142 120.94 331 30.27 43 28 19-Mar-02 88 71.53 393 34.45 48 30 18-Apr-02 47 48.19 389 34.18 57 29 20-Jun-02 5 15.92 625 61.40 78 32 22-Jul-02 5 15.90 656 64.04 80 25 19-Aug-02 6
Re: [R] binom.test
See also the binconf function in the Hmisc package. Ethan Johnsons wrote: R-experts: A quick question, please. From a lab exp, I got 12 positives out of 50. To get 90% CI for this , I think binom.test might be the one to be used. Is there a better way or function to calculate this? binom.test(x=12, n=50, p=12/50, conf.level = 0.90) Exact binomial test data: 12 and 50 number of successes = 12, number of trials = 50, p-value = 1 alternative hypothesis: true probability of success is not equal to 0.24 90 percent confidence interval: 0.1447182 0.3596557 sample estimates: probability of success 0.24 thx much ej -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch 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] Newbie: Selecting data
I've been working with R for all of about 8 hours, so anyone with more experience than this should be able to help me. General comments about my methods of work are also welcomed. I have a table that I've imported thusly: w - read.table(woodford.data, header=T) w start thermsgas KWHs elect temp days 1 10-Jun-98 9 16.84 613 63.80 75 40 2 20-Jul-98 6 15.29 721 74.21 76 29 3 18-Aug-98 7 15.73 597 62.22 76 29 4 16-Sep-98 42 35.81 460 43.98 70 33 5 19-Oct-98105 77.28 314 31.45 57 29 6 17-Nov-98106 77.01 342 33.86 48 30 snip [This is real data on my house.] 'days' is number of days in bill, 'temp' is average temperature in Fahrenheit. I'd like to see if there is a relationship between the gas burned (therms) and the number of heating degree days. I compute therms per day and heating degree days like this: thermsperday - w[,2]/w[,7] hdd - (w[,6] -65)*w[,7] However, I only want the data for the months in which the average temperature is less than 65 (otherwise, it's a cooling degree day). I tried ifelse, but couldn't get it to work. What simple technique am I overlooking? Thanks so much for your help and suggestions, especially for your patience with a newbie. -Kevin Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@stat.math.ethz.ch 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] Book recommendation for newbie to stats and R?
I'm trying to learn statistics and R at the same time. I have an undergraduate science degree and one year of calculus (30 years ago), but never took a stats course. I hope to take some stats courses in the next year, but thought I would start to see how much I could teach myself. I work for an organization that analyses behavior change communication programs regarding HIV/AIDS and reproductive health. A typical question we're trying to answer is, Watching which television programs in South Africa is related to an increased use of condoms? All of our work is in the social sciences, I'd say. I'd like to help analyze our data using R. I found these titles that may teach me both stats and R: --Data Analysis and Graphics Using R by John Maindonald, John Braun --Introductory Statistics with R by Peter Dalgaard --Statistics: An Introduction using R by Michael J. Crawley --Using R for Introductory Statistics by John Verzani I recognize some of the authors by their postings here. Can anyone recommend any of these books over the others? I'm interested in a book that I can learn statistics by reading the chapters and working out the exercises and problems, therefore having access to many or all of the problem solutions is important. Do you have any other recommendations for me in learning both R and stats? Is it an impossible quest to learn enough stats by myself to be useful in analyzing real data sets? Thanks so much for your advice and suggestions. Kevin Zembower Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University www.jhuccp.org __ R-help@stat.math.ethz.ch 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] Creating SAS transport files
Bill Knebel wrote: Is there any package in R to create a SAS transport file? I checked the help archive and did not find any references to creating SAS transport files in R, only reading them. Bill I have used write.foreign in the foreign package. This produces a text data file and a SAS program to read the data into SAS. It has worked well for my uses. As for exporting to a transport file directly, I do not know. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch 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] lme4 and lmeSplines
I'm trying to use the lmeSplines package together with lme4. Below is (1) an example of lmeSplines together with nlme (2) an attempt to use lmeSplines with lme4 (3) then a comparison of the random effects from the two different methods. (1) require(lmeSplines) data(smSplineEx1) dat - smSplineEx1 dat.lo - loess(y~time, data=dat) plot(dat.lo) dat$all - rep(1,nrow(dat)) times20 - seq(1,100,length=20) Zt20 - smspline(times20) dat$Zt20 - approx.Z(Zt20, times20, dat$time) fit1.20 - lme(y~time, data=dat, random=list(all=pdIdent(~Zt20-1))) # Loess model dat.lo - loess(y~time, data=dat) plot(dat.lo) # Spline model with(dat, lines(fitted(fit1.20)~time, col=red)) # Save random effects for later ranef.nlme - unlist(ranef(fit1.20)) (2) Now an attempt to use lme4: library(lmeSplines) detach(package:nlme) library(lme4) data(smSplineEx1) # Use 20 spline in lme4 dat - smSplineEx1 times20 - seq(1,100,length=20) Zt20 - smspline(times20) dat - cbind(dat, approx.Z(Zt20, times20, dat$time)) names(dat)[4:21] - paste(Zt,names(dat)[4:21],sep=) dat$all - rep(1, nrow(dat)) fit1.20 - lmer(y~time +(-1+Zt1|all)+(-1+Zt2|all)+(-1+Zt3|all)+(-1+Zt4|all)+(-1+Zt5|all)+(-1+Zt6|all) +(-1+Zt7|all)+(-1+Zt8|all)+(-1+Zt9|all)+(-1+Zt10|all)+(-1+Zt11|all)+(-1+Zt12|all) +(-1+Zt13|all)+(-1+Zt14|all)+(-1+Zt15|all)+(-1+Zt16|all)+(-1+Zt17|all)+(-1+Zt18|all), data=dat) #summary(fit1) # Plot the data and loess fit dat.lo - loess(y~time, data=dat) plot(dat.lo) # Fitting with splines with(dat, lines(fitted(fit1.20)~time, col=red)) ranef.lme4 - unlist(ranef(fit1.20)) (3) Compare nlme lme4 random effects plot(ranef.nlme~ranef.lme4) The plot of fitted values from lme4 is visually appealing, but the random effects from lme4 are peculiar--three are non-zero and the rest are essentially zero. Any help in getting lme4 + lmeSplines working would be appreciated. It is not unlikely that I have the lmer syntax wrong. Kevin Wright __ R-help@stat.math.ethz.ch 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] grouping by consecutive integers
Hello R-helpers! I have a question concerning extracting sequence information from a vector. I have a vector (representing the bins of a time series where the frequency of occurrences is greater than some threshold) where I would like to extract the min, median and max of each group of consecutive numbers. For Example: tmp - c(24,25,29,35,36,37,38,39,40,41,42,43,44,45,46,47,68,69,70,71) I would like to have the max,min,median of the following groups: 24,25 29 35,36,37,38,39,40,41,42,43,44,45,46,47, 68,69,70,71 I would like to be able to perform this for many time series so an automated process would be nice. I am hoping to use this as a peak detection protocol. Any advice would be greatly appreciated, Kevin - - Kevin J Emerson Center for Ecology and Evolutionary Biology 1210 University of Oregon Eugene, OR 97403 USA [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] grouping by consecutive integers
Let me clarify one thing that I dont think I made clear in my posting. I am looking for the max, min and median of the indicies, not of the time series frequency counts. I am looking to find the max, min, and median time of peaks in a time series, so i am looking for the information concerning that. so mostly my question is how to extract the information of max, min, and median of sequential numbers in a vector. I will reword my original posting below. Hello R-helpers! I have a question concerning extracting sequence information from a vector. I have a vector (representing the bins of a time series where the frequency of occurrences is greater than some threshold) where I would like to extract the min, median and max of each group of consecutive numbers in the index vector.. For Example: tmp - c(24,25,29,35,36,37,38,39,40,41,42,43,44,45,46,47,68,69,70,71) I would like to have the max,min,median of the following groups: 24,25 - max = 25, min = 24 median = 24.5 29 max=min=median = 29 35,36,37,38,39,40,41,42,43,44,45,46,47, max = 45 min = 35 etc... 68,69,70,71 I would like to be able to perform this for many time series so an automated process would be nice. I am hoping to use this as a peak detection protocol. Any advice would be greatly appreciated, Kevin - - Kevin J Emerson Center for Ecology and Evolutionary Biology 1210 University of Oregon Eugene, OR 97403 USA [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] throwaway() function
John Wiedenhoeft wrote: Dear all, I apologize if this is a FAQ (seems a bit like one, but I didn't find anything). I'm looking for an easy way to cut one value out of a vector and shorten the vector accordingly. Something like: x - c(1, 1, 0, 6, 2) throwaway(x[3]) which will return x = 1 1 6 2, with length(x) = 4. I know one could do this by hand, but then one would have to create a second vector y in a loop which has to be 1 shorter then x and then assign x - y, as there is no anti-c() function which shortens a vector (at least to my knowledge). Is there some kind of a throwaway() function in R? Best regards, John x[-3] works. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch 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] Getting rid of for loops
Hello R-users!
I have a style question. I know that for loops are somewhat frowned upon in
R, and I was trying to figure out a nice way to do something without using
loops, but figured that i could get it done quickly using them. I am now
looking to see what kind of tricks I can use to make this code a bit more
aesthetically appealing to other R users (and learn something about R along
the way...).
Here's the problem. I have a data.frame with 4 columns of dependent
variables and then ~35 columns of predictor variables (factors) [for those
interested, it is a qtl problem, where the predictors are genotypes at DNA
markers and the dependent variable is a biological trait]. I want to go
through all pairwise combinations of predictor variables and perform an
anova with two predictors and their interaction on a given dependent
variable. I then want to store the p.value of the interaction term, along
with the predictor variable information. So I want to end up with a
dataframe at the end with the two variable names and the interaction p value
in each row, for all pairwise combinations of predictors. I used the
following code:
# qtl is the original data.frame, and my dependent var in this case is
# qtl$CPP.
marker1 - NULL
marker2 - NULL
p.interaction - NULL
for ( i in 5:40) { # cols 5 - 41 are the predictor factors
for (j in (i+1):41) {
marker1 - rbind(marker1,names(qtl)[i])
marker2 - rbind(marker2,names(qtl)[j])
tmp2 - summary(aov(tmp$CPP ~ tmp[,i] * tmp[,j]))[[1]]
p.interaction - rbind(p.interaction, tmp2$Pr(F)[3])
}
}
I have two questions:
(1) is there a nicer way to do this without having to invoke for loops?
(2) my other dependent variables are categorical in nature. I need
basically the same information - I am looking for information regarding the
interaction of predictors on a categorical variable. Any ideas on what
tests to use? (I am new to analysis of all-categorical data).
Thanks in advance!
Kevin
--
--
Kevin Emerson
Center for Ecology and Evolutionary Biology
1210 University of Oregon
Eugene, OR 97403
USA
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Mixing grid and base graphics--need help understanding this quirk
My setup: Windows 2000, R 2.3.1 When I start a brand new session of R and paste the code below into R, the graphic device shows Some text in the lower left corner. If I paste the code into the command window again, then Some text does not appear in the lower left corner. Why is this? require(grid) par(mfrow=c(1,2)) plot(1:10) plot(-10:1) par(mfrow=c(1,1)) pushViewport(viewport(.04, .04, width=stringWidth(Some text), height=unit(2,lines), name=pagenum, gp=gpar(fontsize=10))) grid.text(Some text, gp=gpar(col=gray30), just=c(left,bottom)) popViewport() Kevin Wright __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] modeling logit(y/n) using lrm
Hamilton, Cody wrote: I have a dataset at a hospital level (as opposed to the patient level) that contains number of patients experiencing events (call this number y), and the number of patients eligible for such events (call this number n). I am trying to model logit(y/n) = XBeta. In SAS this can be done in PROC LOGISTIC or GENMOD with a model statement such as: model y/n = predictors;. Can this be done using lrm from the Hmisc library without restructuring the dataset so that for each hospital there is one row with y = 1 and one row with y = 0 and then using the weight option in lrm to weight these two responses by the number of 'successes' and 'failures' for that hospital, respectively? I would like to avoid the restructuring, and I understand that the use of the weight function is not compatible with a lot of the validation functions available in Hmisc (validate, bootcov, etc.). I don't know about lrm, but for glm you can do glm(cbind(y,m)~ ...) where y is number of successes and m is the number of failures. So, you might try that. Cody Hamilton, Ph.D Institute for Health Care Research and Improvement Baylor Health Care System (214) 265-3618 -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] xyplot problem
Marc Bernard wrote:
Dear all,
I have created the following data (that you can run) in order to explain
my problem:
y - rep(c(1,2), 8)
id - rep(1:8,each=2)
x1 - rep(c(-a,+a), each = 8)
x2 - rep(c(-b,+b), each = 2, times = 4)
x3 - rep(c(-c, +c), each = 4,2)
df - data.frame(cbind(id,y,x1,x2,x3))
If I do:
xyplot(y~ x3|x1*x2,data=df,groups=id,type = b)
then my id's are joined by lines which is what I want. However when I
wanted to add an horizontal line for each panel by using panel.abline the
lines disapears, i.e.
xyplot(y~ x3|x1*x2,data=df,groups=id,type = b,panel=function(x,y)
{
panel.xyplot(x,y)
panel.abline(h=1.5)
}
)
I would be grateful if someone can tell me how can I correct the second
statement in order to have horizontal lines for each panel and each id are
joined by lines.
Thank you,
Bernard,
This appears to work for me.
xyplot(y~ x3|x1*x2,data=df,groups=id,type = b,
panel=function(x,y,groups,...) {
panel.superpose(x,y,groups,...)
panel.abline(h=1.5)})
--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] DSC 2005 proceedings?
This page: http://depts.washington.edu/dsc2005/ says the proceedings for DSC 2005 will be published online and that the papers were due in final form by September 2005. Anyone know if the proceedings have been published yet or when (if?) they will be published? Thanks. Kevin Wright __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] text plots?
This may not help, but if you have S-Plus on the machine you're connecting to, it has a printer() device for this sort of thing. Robert Citek wrote: Is there a way to do text plots in R? I'd like to do some simple XY plots in R with the output in text (ascii). For example, with gnuplot I can do the following: echo 'set terminal dumb ; plot sin(x)' | gnuplot To generate a simple sin wave. Since I connect to a remote Linux machine using SSH, being able to generate a rough idea of what a plot will look like in text would be of benefit. I've looked at ?plot, ? par, and ?plot.default but didn't see anything obvious. Regards, - Robert -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] text plots?
François Pinard wrote: [Robert Citek] Is there a way to do text plots in R? I'd like to do some simple XY plots in R with the output in text (ascii). Since I connect to a remote Linux machine using SSH, being able to generate a rough idea of what a plot will look like in text would be of benefit. Note that it is easy with SSH to open a graphics connection, you may use ssh -X to force it. Than, R will show you nice graphics even if run remotely. I had forgotton about that. I just did a quick test. I SSHd into my home PC from my office (it's a 455 MHz PII), started the X11() device and ran example(xyplot). I was suprised by the speed. It was faster than I expected it to be. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] there is no xls reader in R?
Have a look at the read.xls() in gdata package. HTH, Kevin Michael wrote: Currently I have to convert all my xls into csv before I can read it in and process the excel data in R... Is there a way to directly read in xls data? Thanks a lot! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ko-Kang Kevin Wang Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7471 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Why is transform=km the default for cox.zph?
At the suggestion of Thomas Lumley, I posted this to s-news. Dr. Therneau replied and I have posted (with permission) his answer below the original question. Kevin E. Thorpe wrote: To enhance my understanding, and that of my students, I have a question about cox.zph in the survival package. If I have correctly gleaned the high-level point from the 1994 Biometrika paper of Grambsch and Therneau, it looks to me like cox.zph provides a mechanism to test for a simple trend in plots of a function of time, g(t) versus the scaled schoenfeld residuals and it also provides some built-in ones and the capability to provide your own. It also appears to me that different forms look at different departures from proportionality. So, my question is what are the advantages and disadvantages of the default transform=km compared to say, identity or log? Thank you. Kevin === Begin Dr. Therneau's Reply === There are 2 reasons for making the KM the default: 1. Safety: The test for PH is essentially a least-squares fit of line to a plot of f(time) vs residual. If the plot contains an extreme oulier in x, then the test is basically worthless. This sometimes happens with transform= identity or transform =log. It doesn't with transform='KM'. As a default value for naive users, I chose the safe course. 2. A secondary reason is efficiency. In DY Lin, JASA 1991 Dan-Yu argues that this is a good test statistic under various assumptions about censoring. (His measure has the same score statistics as the KM option). But #1 is the big one. Terry T. === End Dr. Therneau's Reply === -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Why is transform=km the default for cox.zph?
To enhance my understanding, and that of my students, I have a question about cox.zph in the survival package. If I have correctly gleaned the high-level point from the 1994 Biometrika paper of Grambsch and Therneau, it looks to me like cox.zph provides a mechanism to test for a simple trend in plots of a function of time, g(t) versus the scaled schoenfeld residuals and it also provides some built-in ones and the capability to provide your own. It also appears to me that different forms look at different departures from proportionality. So, my question is what are the advantages and disadvantages of the default transform=km compared to say, identity or log? Thank you. Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problem compiling R-Patched
I downloaded R-Patched today (to see if another problem I want to ask about is still present or if its just me - as per the posting guide). I ran tools/rsync-recommended successfully. I then ran configure --enable-R-shlib successfully. Then make stops with the following error. gcc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o -L../../../../lib -lR mkdir -p -- ../../../../library/tools/libs make[5]: Leaving directory `/home/src/R-patched/src/library/tools/src' make[4]: Leaving directory `/home/src/R-patched/src/library/tools/src' Error in file(datafile, wb) : unable to open connection In addition: Warning message: cannot open file '/usr/local/lib/R/library/tools/R/tools.rdb', reason 'Permission denied' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/src/R-patched/src/library/tools' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/src/R-patched/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/src/R-patched/src' make: *** [R] Error 1 The tools.rdb file is on my system from a previous build -rw-r--r-- 1 root root 90486 2005-08-04 18:54 /usr/local/.../tools.rdb As you can see from the output above, I am not trying to build in /usr/local/... at all so I am puzzled as to why anything is being done in /usr/local/ before the make install. Can anyone suggest what I should try? I am compiling on SuSE Linux version 9.2. Thank you. Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem compiling R-Patched
Liaw, Andy wrote: Could it be that you have the environment variable R_HOME (or something like that) defined somewhere? Just a wild guess... No, R_HOME is not defined in the shell I was compiling in, but R_LIBS was! Brilliant wild guess. Thanks, Kevin Andy From: Kevin E. Thorpe I downloaded R-Patched today (to see if another problem I want to ask about is still present or if its just me - as per the posting guide). I ran tools/rsync-recommended successfully. I then ran configure --enable-R-shlib successfully. Then make stops with the following error. gcc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o -L../../../../lib -lR mkdir -p -- ../../../../library/tools/libs make[5]: Leaving directory `/home/src/R-patched/src/library/tools/src' make[4]: Leaving directory `/home/src/R-patched/src/library/tools/src' Error in file(datafile, wb) : unable to open connection In addition: Warning message: cannot open file '/usr/local/lib/R/library/tools/R/tools.rdb', reason 'Permission denied' Execution halted make[3]: *** [all] Error 1 make[3]: Leaving directory `/home/src/R-patched/src/library/tools' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/src/R-patched/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/src/R-patched/src' make: *** [R] Error 1 The tools.rdb file is on my system from a previous build -rw-r--r-- 1 root root 90486 2005-08-04 18:54 /usr/local/.../tools.rdb As you can see from the output above, I am not trying to build in /usr/local/... at all so I am puzzled as to why anything is being done in /usr/local/ before the make install. Can anyone suggest what I should try? I am compiling on SuSE Linux version 9.2. Thank you. Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Having trouble with plot.survfit and fun=cloglog
I'm having trouble getting fun=cloglog to work with plot on a survfit object. Here are the data I used for the commands that follow. days status 2 0 2 0 5 1 9 0 14 1 16 0 16 0 17 0 29 1 30 0 37 1 37 0 39 1 44 0 44 0 58 0 60 1 67 1 68 1 82 1 82 1 86 0 86 0 89 1 93 0 97 1 100 0 100 0 100 0 library(survival) Loading required package: splines eg1.km - survfit(Surv(days,status),data=eg1) plot(eg1.km,mark.time=FALSE,conf.int=FALSE) # Works plot(eg1.km,mark.time=FALSE,conf.int=FALSE,fun=cumhaz) # Works plot(eg1.km,mark.time=FALSE,conf.int=FALSE,fun=cloglog) # Error Error in rep.default(2, n2 - 1) : invalid number of copies in rep() In addition: Warning message: 2 x values = 0 omitted from logarithmic plot in: xy.coords(x, y, xlabel, ylabel , log) The axes are set and drawn up but nothing else is plotted. plot(eg1.km,mark.time=FALSE,conf.int=FALSE,fun=cumhaz,log=xy) # OK Warning messages: 1: 2 x values = 0 omitted from logarithmic plot in: xy.coords(x, y, xlabel, yla bel, log) 2: 1 y value = 0 omitted from logarithmic plot in: xy.coords(x, y, xlabel, ylab el, log) This does display the right plot but I am confused about how the xaxis is computed. The first tick mark is labeled with 100, the next with 200 right up to 600, but the entire plot is drawn between 0 and 100. Please elighten me as to what I'm not understanding about fun=cloglog and log scales. R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major2 minor2.1 year 2006 month03 day 13 svn rev 37540 language R The survival package is version 2.21 Thank you, Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ESS, transcripts, and such
A.J. Rossini wrote: SNIP One nice thing about ESS/Emacs is that it will cean a transcript buffer. So if you are working in the inferior process buffer (where you shouldn't be, but that's for another day), then you can write it to disk as a transcript file, and clean it into a script. Okay, I'll bite. Could you ellaborate a bit on your parenthetical comment? best, -tony Thanks, Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ESS, transcripts, and such
A.J. Rossini wrote: Work in an inferior R session M-x write-buffer to TonyIsSilly.Rt So now your buffer is associated with a file, TonyIsSilly.Rt M-x R-transcript-mode M-x ess-transcript-clean-buffer and you should be left with a script file, not a transcript file. Enjoy. I'll be talking about such things at useR if enough people show up for the tutorial... Those are useful to know. I was more interested in why you advise not working directly in the inferior process buffer. Sorry for not being more clear. Kevin On 3/13/06, Kevin E. Thorpe [EMAIL PROTECTED] wrote: A.J. Rossini wrote: SNIP One nice thing about ESS/Emacs is that it will cean a transcript buffer. So if you are working in the inferior process buffer (where you shouldn't be, but that's for another day), then you can write it to disk as a transcript file, and clean it into a script. Okay, I'll bite. Could you ellaborate a bit on your parenthetical comment? -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] To improve my understanding of workspaces
Hello. I have grown accustomed to the .Data directory in S-Plus and so when I came to R I continued that behaviour by saving my workspaces at the end of each R session. So, I have saved workspaces in various directories where I have used R just as I would have had various .Data directories where I had used S-Plus. I have seen comments on the list, most recently from Prof. Ripley that they don't routinely save their workspaces in this way. So my questions are: 1. What do people do instead to manage projects? 2. Is there an official recommendation? From my reading I have learned that you can save data frames (and other objects?) to disk and then attach them. Does this save memory? If I have read correctly, I understand that everything in the workspace is in memory, but haven't been able to determine if objects in the search path are as well. Kind Regards, Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] To improve my understanding of workspaces
Thanks Adai. A couple questions/comments about this. Adaikalavan Ramasamy wrote: I use emacs and ESS to develop the scripts. The new releases of R has the script function already in built. I use emacs and ESS too (in Linux). I do not know about the script function you mention. It's not in my version (2.1.1) and I couldn't find it in an RSiteSearch either. Typically I keep all the data and scripts related to a project in its own folder, so I have minimal worry about paths. I do the same. To save large and associated objects, I use save(x, y, z, file=lala.rda, compress=TRUE) and then to load x, y, z in another session or workspace I use load(lala.rda) To save small dataframes and matrices, I use write.table(mat, file=lala.txt, sep=\t) and to read it back I use mat - read.delim(file=lala.txt, row.names=1) Am I correct that load() or read.whatever() or even data() will bring the objects into the current workspace while attach() can attach a save() data frame to the search path? Is one approach better than the other in general? The problem with .RData (via quit or save.image), is that it keeps all intermediate objects which can be unnecessarily bloated and confusing. Further you will have difficulty distinguishing one .RData from the other by looking at the filename alone. If you don't save the workspace on q(), do you also lose the history for that session (although when working in emacs, this is rarely a problem)? Regards, Adai Thanks again, Kevin On Fri, 2006-03-10 at 06:58 -0500, Kevin E. Thorpe wrote: Hello. I have grown accustomed to the .Data directory in S-Plus and so when I came to R I continued that behaviour by saving my workspaces at the end of each R session. So, I have saved workspaces in various directories where I have used R just as I would have had various .Data directories where I had used S-Plus. I have seen comments on the list, most recently from Prof. Ripley that they don't routinely save their workspaces in this way. So my questions are: 1. What do people do instead to manage projects? 2. Is there an official recommendation? From my reading I have learned that you can save data frames (and other objects?) to disk and then attach them. Does this save memory? If I have read correctly, I understand that everything in the workspace is in memory, but haven't been able to determine if objects in the search path are as well. Kind Regards, Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] To improve my understanding of workspaces
Sean Davis wrote: On 3/10/06 8:33 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: Other than Emacs, I use the same work habits as Adai. An advantage of this workflow is that almost everything is stored in text format, so it is easy to compare different versions to see what has changed, and it works very well with version control (I use Subversion). The only thing I'd add to his recommendation is that you be sure to save the scripts that produced the objects in the binary images (his lala.rda), so that they can be reconstructed if necessary. As long as the reconstruction isn't too difficult, this means I don't need to bother to save them in Subversion. Version control sounds like a good idea Duncan, but I've always been a bit intimidated by it. How cumbersome is Subversion and what are the advantages of version control? I would add a bit of detail here that I do. ESS/xemacs allows one to create a transcript file that you can then step through, executing each command as it was originally executed. I make one of these transcript files for each project and save it with the data and any scripts that I have for the project. So, in the end, I have a set of Rda files, one or more transcript files, and a Src directory that contains any function code (and ESS supports saving scripts to this directory automatically). Do you save your functions in Rda files to be loaded/attached or are they sourced every time? How do you tell ESS/emacs to save in ./src or is that only possible with xemacs (I can use emacs to do what I need to but don't know lisp so the config files and terminology are a bit cryptic to me)? Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Read SAS .sd2 file into R?
Peter Dalgaard wrote: mtb954 mtb954 [EMAIL PROTECTED] writes: Does anyone know how to import a SAS .sd2 file into R? I can't see anything in library(foreign). The SAS dataset file formats are not publicly available. You need either SAS itself (on a Windows machine) or a specialized tool like DBMS/Copy to converti it. Peter, There may be another way, though I have yet to explore it. The SAS System Viewer is free and you may distribute it royalty free: http://www.sas.com/apps/demosdownloads/sassysview_PROD_8.2_sysdep.jsp?packageID=000176 Files Supported by the SAS System Viewer The SAS System Viewer lets you view the following types of SAS files: Read Only * 7.00 Data Sets created under the windows environment (sas7bdat, sd7, sd2, ssd, ssd0x, saseb$data) * 6.06 - 6.12 Catalogs - Directory Information Only (sc2, sct, sct0x, saseb$catalog) * 3.2.2 JMP(r) Data Sets - Macintosh and Windows (jmp) * 6.12 MDDB - Multi-dimensional Data Base Files (sm2) * SAS Transport Files (stx, xpt) * SAS Log Files (log) * SAS List Files (lst) Read and Write Enabled * Comma Delimited Files (csv) * Space Delimited Files (prn) * Text Based Files (sas, dat, cfg, html) Whether you can copy and paste will be key. Regards, Kevin -- Kevin Viel Department of Genetics e-mail: [EMAIL PROTECTED] Southwest Foundationphone: (210)258-9884 P.O. Box 760549 fax:(210)258-9444 San Antonio, TX 78245-0549 Kevin Viel PhD Candidate Department of Epidemiology Rollins School of Public Health Emory University Atlanta, GA 30322 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] OT Futility Analysis
Thank you Spencer and Steve for your helpful comments. If I may, I would like to elaborate on some of the points you raise. Stephen A Roberts wrote: I would take the line that if they hadn't pre-specified any stopping rules, the only reason to stop is safety or new external data. I would be very suspicious of requests from the steering committee to stop for futility - they should be blinded so why are they thinking futility unless results have leaked? I would argue that they are obliged to finish the trial once they start. In general I agree with this. In this case the request for a futility analysis came from the sponsor (a drug company). It is a classic case of company B buys company A and wnats to stop RD on company A's drugs. Therefore the company was looking for a reason to stop. Now that they will stop producing the drug used in the trial, recruitment will end before reaching its target. Now the Steering Committee's point of view is that if there is any reasonable hope, they would find some other way to continue recruitment. I am confident that results have not leaked. I am well aquainted with the data management and blinding procedures in place for the trial. This is an example of the need to sort out these things in advance - look up the stuff from the UK DAMOCLES project. The recent book edited by DeMets et al (Data Monitoring in Clinical Trials: A Case Studies Approach) is a good read on these sorts of issues and I think there is a more statistical book from the same group of authors. Thanks for the reference. My library has it, so will give it a look. As far as software is concerned, futility analysis and conditional power are simply standard analyses with made up data and more-or-less justifiable assumptions. I am also interested if there are good alternatives to conditional power for this type of scenario. Steve. What does this particular Steering Committee think a futility analysis is? Do they have any particular reference(s)? What do you find in your own literature review? If it were my problem, I think I'd start with questions like that. Your comments suggested to me a confounding of technical and political problems. The politics suggests the language you need to use in your response. Beyond that, I've never heard before of a futility analysis, but I think I could do one by just trying to be clear about the options the Steering Committee might consider plausible and then comparing them with appropriate simulations -- summarized as confidence intervals, as you suggest. I did ask REPEATEDLY for guidelines from the steering committee, but none came or are likely to come. In fact, they wanted me to come up with the recommendation, which I find entirely inappropriate, but here I am. So, I don't think I'm confounded between techincal and political. Basically, they want to stop if there is a low chance of rejecting the null hypothesis. This is often referred to as conditional power or stochastic curtailment. I recently saw a paper by Scott Emerson pointing out some problems (interpretation, relation to unconditional power). As far as references, I have used a book by Jennisen and Turnbull in the past, but, as I recall, with the exception of stochastic curtailment, it assumes the trial was designed with group sequential methods. I have also just found a 1988 Biometrics paper by Lan and Wittes on the B-value which I will read. And I hope that someone else will enlighten us both if there are better options available. Best Wishes, spencer graves p.s. For any attorneys who may read these comments, the suggestions are obviously warranteed up to the amount you paid for it, which is nothing. If you follow them and they turn out to be inappropriate, you will pay the price. I encourage you to share the problems with me, so I can learn from the experience. However, the limits of my liability are as already stated. Kevin E. Thorpe wrote: I beg your pardon if this is too off topic. I am posting here since I hope to find an R solution to my problem. Please indulge me while I give a little background about what I'm trying to do. I'm on a DSMB for a clinical trial. The Steering Committee for the trial has asked us to perform a futility analysis on their primary outcome which is a time-to-event endpoint. The trial was not designed with group sequential methods, nor was any futility analysis spelled out in the protocol. Another thing which may be relevant is that due to circumstances beyond the investigators' control, the trial will stop recruitment prematurely unless there is some compelling reason for them to find a way to continue the trial. Lastly, the trial has accrued not quite half of the planned sample size. Admittedly, I don't have a vast amount of experience implementing stopping rules. In other protocols I have seen where futility analyses have been planned but a group sequential
[R] Using string vectors as for loop arguments
Is there a mechanism to interate through a vector of strings? Say I
have a data frame of 50 variables (VAR1 to VAR50), each with 100
measurements along with some coding factors (EXP and DOSE). I want to
calculate the mean of a subset of each of VAR1 to VAR 50 (selecting
by EXP and DOSE). Rather than just copy/pasting the same code 50
times, I thought of using a for loop to go through a vector of VAR1
to VAR50 (VAR.LIST below). Each iteration would be the variable name
for which the mean would be calculated.
Trying this, I get an error that the argument is not numeric or
logical. So I assume that for loops with vectors of strings are
disallowed. What I am wondering is whether there a way to mimic this
sort of procedure?
The code looked something like this:
VAR.LIST-paste(c(VAR), 1:50, sep=)
for (i in VAR.LIST){
mean(i[EXP==1 DOSE==1], na.rm=T)
}
Thanks
Kevin Middleton
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installation of R on Linux
Daniel Nordlund wrote: -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Friday, January 27, 2006 11:49 PM To: Daniel Nordlund Cc: r-help@stat.math.ethz.ch Subject: Re: [R] installation of R on Linux On Fri, 27 Jan 2006, Daniel Nordlund wrote: R-users, I am new user of Linux (have been using Win XP Pro) and wanted to install R. Since I am just beginning to learn Linux I was wondering, where in the directory structure do users of Linux usually install R? Most of the instructions I have read simply say to untar the tarball where you want to install the program. Any suggestions would be welcome as to an appropriate place. I know I could get an rpm, but wanted to use this as a learning process for a variety of skills. Currently working with SuSE 9.1 There is a definitive set of instructions, in the file INSTALL in the tarball and at https://svn.r-project.org/R/trunk/INSTALL Unpacking and installing are separate operations. There is more information in the R-admin manual (which you already have in a Windows version of R, and is also in the tarball). What most of us do is to untar in any convenient place (I use ~/R), use configure, make, and then use 'make install' to install R. This installs in /usr/local in the conventional subdirectories (and conventionally needs su to access). Having installed, you can wipe out the unpacked version of the tarball. So, in my example cd ~/R tar zxf R-2.2.1.tar.gz cd R-2.2.1 configure make make info pdf su make install install-info install-pdf [leave su shell] cd .. rm -rf R-2.2.1 Rehash and start R. -- 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 Prof. Ripley, Thanks for the example and the pointers to various locations for documentation. As a new user of Linux (with minimal experience in using Unix-like systems), I am somewhat uncomfortable putting programs just anywhere since there seem to be default locations for where many system programs reside. Your concrete example is very helpful. Thanks again, Daniel Nordlund Bothell, WA USA One additional point. I have often found it preferable to run configure and make as a regular user and only run 'make install' as root. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R Commenting Style
I don't know if this is what you're referring to, but in ESS the number of octothorpes (#) affects the indentation in the emacs buffer. If I remember right, ### puts it at the beginning of the line, ## the current indentation level (eg. in a function) and # further right. Paul Roebuck wrote: I seem to remember reading somewhere about some style guide regarding R the number of comment characters (#) prior to the comment meaning something. Anyone know to what I'm referring? Where? -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Wikis etc.
Kris over at Wiki That! has a post today about what makes for a good wiki: http://www.wikithat.com/wiki_that/2006/01/wiki_of_the_wee_1.html Most wikis I’ve looked at are in danger of facing the same fate as most websites and CMS - death by boredom. They are focused on content that is used as reference for some off-line activity OR as the end-result of an off-line activity. Collaboration and participation is more than just sharing information and making it accessible. It’s all about the PROCESS of planning and executing events, projects, tasks, and deliverables. Content is boring - action is engaging. Make your wiki activity- centric, not just data-centric (content). If the wiki is a place where people just go to look things up -- we're toast. It needs to be made into an active learning environment, a place where experts and beginners alike come to interact. Some to share their knowledge, and others to learn from the masters. It's the same dynamic that makes the mailing list so active, and yet also what exposes its weakness (i.e. it doesn't scale well). Kevin Kevin J. Gamble. Ph.D. Associate Director eXtension Initiative Box 7647 NCSU Raleigh, NC 27694-7641 v: 919.515.8447 c: 919.605.5815 AIM: k1v1n Web: intranet.extension.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Wikis etc.
Frank makes an intersting point. For those interested, A site I spend quite a bit of time on for Linux related stuff is IMHO really well done. There are fora for many different linux distrubtions. There is a wiki, a collection of tutorials, etc. If you want to take a look, the url is http://www.linuxquestions.org/ Kevin Frank E Harrell Jr wrote: I feel that as long as people continue to provide help on r-help wikis will not be successful. I think we need to move to a central wiki or discussion board and to move away from e-mail. People are extremely helpful but e-mail seems to be to always be memory-less and messages get too long without factorization of old text. R-help is now too active and too many new users are asking questions asked dozens of times for e-mail to be effective. The wiki also needs to collect and organize example code, especially for data manipulation. I think that new users would profit immensely from a compendium of examples. Just my .02 Euros Frank -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Maintaining factors when copying from one data frame to another
Does newDF - oldDF[,c(A,C,D)] work? Kurt Wollenberg wrote: Greetings all: OK, this is bugging the @[EMAIL PROTECTED] out of me. I know the answer is simple and straightforward but for the life of me I cannot find it in the documentation, in the archives, or in my notes (because I know I've encountered this in the past). My problem is: I have a data frame with columns A, B, C, D, and E. A, B, and E are factors and C and D are numeric. I need a new data frame with just A, C, and D. When I copy these columns to a new data frame newDF - data.frame(cbind(oldDF$A, oldDF$C, oldDF$D)) all the factor data comes out as levels rather than the original factors. How do I preserve the factors when I copy from one data frame to another? Thanks vary much, Kurt Wollenberg, Ph.D. Tufts Center for Vision Research Tufts-New England Medical Center 750 Washington St #450 Boston, MA 02111 Office: 617-636-9028 Fax: 617-636-8945 email: kurt.wollenberg at gmail dot com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Really supress output from Sweave
Fredrik Karlsson wrote:
Hi,
I am using Sweave for chapters in my thesis that contain results.
In the beginning of each chapter, I use this to load libraries I need.
init,echo=FALSE,quiet=TRUE=
Have you tried init,echo=FALSE,quiet=TRUE,results=hide=
library(gplots)
library(Hmisc)
library(e1071)
@
What I want is, of course, to supress messages written by this code,
but what I get in the end is X-init.tex with this the contents below.
How do I really supress it?
/Fredrik
Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
to see overall documentation.
NOTE:Hmisc no longer redefines [.factor to drop unused levels when
subsetting. To get the old behavior of Hmisc type dropUnusedLevels().
Attaching package: 'Hmisc'
The following object(s) are masked from package:gdata :
reorder.factor
The following object(s) are masked from package:car :
recode
The following object(s) are masked from package:stats :
ecdf
\end{Soutput}
\begin{Soutput}
Loading required package: class
Attaching package: 'e1071'
The following object(s) are masked from package:Hmisc :
impute
The following object(s) are masked from package:gtools :
permutations
The following object(s) are masked from package:foreign :
read.octave
\end{Soutput}
\begin{Soutput}
Attaching package: 'xtable'
The following object(s) are masked _by_ .GlobalEnv :
digits
The following object(s) are masked from package:Hmisc :
label label-
\end{Soutput}
\end{Schunk}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] new article on R at oreillynet.com
An article I wrote that provides a basic introduction to R has been published on Oreillynet.com. The article is titled Analyzing Statistics with GNU/R. Here is the link: http://www.onlamp.com/pub/a/onlamp/2005/11/17/r_for_statistics.html Please feel free to post comments or interesting basic R scripts at the end of the article. Kevin Farnham __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RODBC and Excel: Wrong Data Type Assumed on Import
From my experience (somewhat of a guess): 1. Excel uses the first 16 rows of data to determine if a column is numeric or character. The data type which is most common in the first 16 rows will then be used for the whole column. If you sort the data so that at least the first 9 rows have character data, you may find this allows the data to be interpreted as character. There is supposedly a registy setting that can control how many lines to use (instead of 16), but I have not had success with the setting. I suspect that ODBC uses JET4, which may be the real source of the problem. See more here: http://www.dicks-blog.com/archives/2004/06/03/external-data-mixed-data-types/ 2. The gregmisc bundle has a different read.xls function that uses a Perl script (xls2csv) and seems to be safer with mixed-type columns. Requires a working version of Perl. Best, Kevin Wright The first column in my Excel sheet has mostly numbers but I need to treat it as character data: library(RODBC) http://tolstoy.newcastle.edu.au/R/help/05/09/11324.html#14938qlink1 * channel - odbcConnectExcel(U:/efg/lab/R/Plasmid/construct list.xls) * * plasmid - sqlFetch(channel,Sheet1, as.is=TRUE) * * odbcClose(channel) * names(plasmid) [1] Plasmid Number Plasmid Concentration Comments Lost # How is the type decided? I need a character type. class(plasmid$Plasmid Number) [1] numeric typeof(plasmid$Plasmid Number) [1] double plasmid$Plasmid Number[273:276] [1] 274 NA NA 276 The two NAs are supposed to be 275a and 275b. I tried the as.is=TRUE but that didn't help. I consulted Section 4, Relational databases, in the R Data Import/Export document (for Version 2.2.0). Section 4.2.2, Data types, was not helpful. In particular, this did not seem helpful: The more comprehensive of the R interface packages hide the type conversion issues from the user. Section 4.3.2, Package RODBC, provided a simple example of using ODBC .. with a(sic) Excel spreadsheet but is silent on how to control the data type on import. Could the documentation be expanded to address this issue? I really need to show Plasmid 275a and Plasmid 275b instead of Plasmid NA. Thanks for any help with this. efg -- Earl F. Glynn Scientific Programmer Bioinformatics Department [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to create a new data.frame with all possible observations
I would like to use something like expand.grid to get a data.frame with all
possible combinations of model terms from a formula. For example:
R dat=data.frame(y=rnorm(8),
+ trt=rep(c(A,B),4),
+ state=c(rep(c('IA','NE'),each=4)),
+ county=c('P','P','S','S','J','J','N','N'))
R dat=dat[-1,]
R dat
y trt state county
2 0.36 B IA P
3 0.44 A IA S
4 2.26 B IA S
5 -0.12 A NE J
6 0.84 B NE J
7 -2.11 A NE N
8 -0.69 B NE N
If my model is
model=formula(y~trt+state + county%in%state)
Then I would like to create a data.frame that includes the missing
observation for
A + IA + P %in IA (trt + state + county %in% state)
I currently use expand.grid to get all possible combinations of variables,
then delete impossible combinations like J %in IA. This works, but is a
bit clumsy and I wonder if there is a more general solution.
Ideas welcome.
Kevin Wright
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] simple question
Hi, Korbinian von Blanckenburg wrote: Its just a simple question I guess: I have a vector with missing information like x-c(0,1,31,131,NA,133,NA,310,NA,112,3,1,2,93) How can I make a vector like this no missing in it. I used the x[x0] commabd and tried some more, with no success. Try na.omit() HTH, Kevin -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7488 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem whit a piece of program
Arturo Coral Alamo wrote:
Hi friends, I'm beginning in R and I have simple question.
I have this piece of my program and how you see, that's ok (whit num-
0.002)
num-0.002 # ok, but not when I change whit num-0... ?
factor1-1;
while(1)
{
if (num*factor11)
factor1-factor1*10
else
{
print(out ok!!);
break;
}
}
[1] out ok!!
but when I change (whit num-0) R show this:
Since num==0, num*factor1 is always 0 and so the loop never terminates
and factor1 grows without bound becoming Inf.
Error in if (num * factor1 1) factor1 - factor1 * 10 else { :
missing value where TRUE/FALSE needed
I can't understand that error, can somebody help me, please
thanks in advance
Jac
--
Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Binary Logit Regression with R
Hi, Johann Park wrote: Let say, my Y is war occurence (occur=1, otherwise 0). And my independent variables (Xs) are trade, democracy, military poweretc. Take a look at ?glm. HTH, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7488 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] graphics guide?
Hi, Karin Lagesen wrote: I am trying to create some graphs with R and it seems to be able to do what I need. However, I have so far not been able to find any sort of explanation of how the graphics system works. I am for instance trying to create a multiple figure, and I seem to have to call plot.new() before every new plot command, I have however not found any Do you mean several graphs in the same window? If so, you want something like, e.g.: par(mfrow = c(2, 2)) Take a look at ?par and the mfrow or mfcol options. Cheers and HTH, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7488 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Transform variable number of rows per subject to column variables?
Hey Bing, Reshape's the ticker -- ?reshape. For example, reshape(myFrame, idvar = ID, timevar = TEST.A) should do most of the trick. Kevin -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bing Ho Sent: Monday, September 19, 2005 10:04 PM To: r-help@stat.math.ethz.ch Subject: [R] Transform variable number of rows per subject to column variables? Hello, I am very new to R, but I am having trouble with my dataset. I have a data frame where a subject has a variable number of multiple observations for each row, which I wish the transform these observations to column variables. An example of the data frame ID TEST.A TEST.B 1 10 1 1 13 2 1 11 1 2 15 2 2 17 3 And I wish to transform it to the following: ID TEST.A1 TEST.A2 TEST.A3 TEST.B1 TEST.B2 TEST.B3 1 10 13 11 1 2 1 2 15 17 NA 2 3 NA In other words, for the variable number of repeated follow up studies, a new column variable for each subject, but they are grouped by the original test. Thank you for any help - I'm realizing that I am a terrible programmer! Bing Ho __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] pairwise comparisons among treatments
Hello R listing, I did two-way anova on lm. Further question the investigator interested in is what two treatments are different? I am looking for a command which could do pairwise comparison for every treatment. Could anyone help me out? Thanks a bunch Kevin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] pairwise comparisons among treatments
Hello Bert,
Thanks for your response. I don't know why I am getting following
error messages. I use version of R version 2.1.1, 2005-06-20,
powerpc-apple-darwin7.9.0 in Mac OS X version 10.3.8.
I did try to load following packages before, but it failed.
help.search(pairwise comparison)
Error in help.search(pairwise comparison) :
could not find package 'arrayQuality.1'
In addition: Warning messages:
1: no Rd contents for package 'R2HTML' in
'/Library/Frameworks/R.framework/Resources/library' in:
help.search(pairwise comparison)
2: no Rd contents for package 'affylmGUI' in
'/Library/Frameworks/R.framework/Resources/library' in:
help.search(pairwise comparison)
Thanks.
Kevin
help.search('pairwise comparison')
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [handling] Missing [values in randomForest]
Hi Jan-Paul, You definitely want to be careful with na.omit in randomForest -- that wipes out any row with even one NA. If NAs are sprawled throughout your dataset, na.omit might end up killing a lot of rows. Here's my usual MO for missing values: 1) impute in Hmisc fills in gaps with the mean, median, most common value, etc. 2) rfImpute: fits a forest on the rows available and uses it to predict the missing values. 3) aregImpute: similar to rfImpute, but using a linear model. 4) You may want to consider using a single tree (rpart package) in this case instead of a forest. Single trees deal with missing values cleanly through surrogate splits. Good luck! Kevin -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Uwe Ligges Sent: Sunday, September 11, 2005 3:44 AM To: Jan-Paul Roodbol Cc: r-help@stat.math.ethz.ch Subject: Re: [R] [handling] Missing [values in randomForest] Jan-Paul Roodbol wrote: Does anyone know if randomForest in R can handle dataset with missings? See ?randomForest, you can omit observations including NAs by specifying na.action=na.omit Please do not cross-post! Please specify a sensible subject! Uwe Ligges Thank you Kind regards Jan-Paul __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] TeX distribution on Windows
Hi, Göran Broström wrote: So, what is suggested? TUG (tug.org) recommends something called proTeXt, which is said to be based on MiKTeX, for Windows users. Since MikTeX could be used with R, that sounds like a good alternative. Any comments to that? I've been using MikTeX on Windows for years and have never had any problems. Its Update Wizard also has a nice and intuitive user interface. I've never had any problems using it with R. Cheers, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7488 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] TeX distribution on Windows
Thomas Petzoldt wrote: Miktex can be used with WinEDT, Emacs, Texniccenter and others as editor. Slightly off topic, if you want to get MikTeX working with Emacs and ESS, the Claus Dethlefsen has a wonderful web site (in fact, best website on this topic IMHO) http://www.math.auc.dk/~dethlef/Tips/ Cheers, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7488 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] preprocessing data
Some time ago, Doug Bates wrote a useful paper called Data manipulatation in perl. It is a very concise intoduction and introduces the unpack function which is one way to deal with fixed format data. Just google for data manipulation in perl bates and you should be able to find a copy. Jean Eid wrote: Dear all, My question is concerning the line This is adequate for small files, but for anything more complicated we recommend using the facilities of a language like perl to pre-process the file. in the import/export manual. I have a large fixed-width file that I would like to preprocess in Perl or awk. The problem is that I do not know where to start. Does anyone have a simple example on how to turn a fixed-width file in any of these facilities into csv or tab delimited file. I guess I am looking for somewhat a perl for dummies or awk for dummies that does this. any pointers for website will be greatly appreciated Thank you Jean Eid __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem configuring R-patched
Martin Maechler wrote: Duncan I believe there are two kinds of tar files. The daily Duncan snapshots don't include the recommended packages, the Duncan releases do. eeehm, no: The daily snapshots do contain the recommended packages, and have for quite a while now. Duncan Or perhaps the test is a recent addition. only for a pretty generous definition of recent. To be honest, I don't know what Kevin's problem could be. The daily snapshots are really produced here at ETH Zurich and daily mirrored from here to CRAN. I can see that the R-patched_2005-08-04.tar.gz does contain the recommended packages. Maybe your download wasn't completed; your disk full; or you have a gnome in your computer who occasionally deletes some of your files? I've had similar feelings a few times in the past... Kevin Both versions were R-patched.tar.gz as opposed to the Kevin devel sets which looks like it's actually a link to Kevin the most recent. Maybe I incorrectly assumed that Kevin Maybe I incorrectly assumed that the patched tarballs Kevin contained the recommended packages. actually that was a correct assumption. Martin Maechler, ETH Zurich I still don't know why it didn't work observe (sorry for the wrapping): [EMAIL PROTECTED]:/home/src tar tvzf R-patched.tar.gz | grep Recommended drwxr-xr-x local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/ -rw-r--r-- local/local2394 2005-04-18 08:51:32 R-patched/src/library/Recommended/Makefile.in -rw-r--r-- local/local 20 2005-04-18 08:51:32 R-patched/src/library/Recommended/.cvsignore -rw-r--r-- local/local 25656 2005-04-18 08:58:17 R-patched/src/library/Recommended/KernSmooth_2.22-15.tar.gz -rw-r--r-- local/local 465529 2005-07-28 11:45:14 R-patched/src/library/Recommended/VR_7.2-17.tar.gz -rw-r--r-- local/local 179895 2005-07-28 11:45:14 R-patched/src/library/Recommended/boot_1.2-23.tar.gz -rw-r--r-- local/local 190975 2005-07-03 11:45:11 R-patched/src/library/Recommended/cluster_1.10.1.tar.gz -rw-r--r-- local/local 273520 2005-07-14 11:45:08 R-patched/src/library/Recommended/foreign_0.8-9.tar.gz -rw-r--r-- local/local 205131 2005-07-27 11:45:14 R-patched/src/library/Recommended/lattice_0.12-1.tar.gz -rw-r--r-- local/local 240276 2005-07-12 11:46:13 R-patched/src/library/Recommended/mgcv_1.3-4.tar.gz -rw-r--r-- local/local 662143 2005-07-26 11:45:13 R-patched/src/library/Recommended/nlme_3.1-62.tar.gz -rw-r--r-- local/local 110072 2005-04-19 11:45:20 R-patched/src/library/Recommended/rpart_3.1-23.tar.gz -rw-r--r-- local/local 846737 2005-06-10 11:45:23 R-patched/src/library/Recommended/survival_2.18.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/VR.tgz - VR_7.2-17.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/boot.tgz - boot_1.2-23.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/cluster.tgz - cluster_1.10.1.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/foreign.tgz - foreign_0.8-9.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/KernSmooth.tgz - KernSmooth_2.22-15.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/lattice.tgz - lattice_0.12-1.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/nlme.tgz - nlme_3.1-62.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/mgcv.tgz - mgcv_1.3-4.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/rpart.tgz - rpart_3.1-23.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/survival.tgz - survival_2.18.tar.gz It appears to me that the recommended packages were in the tarball. I suppose it is largely immaterial now given I have successfully re-built R. Thanks your help. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problem configuring R-patched
I downloaded R-patched (2005-08-04) from CRAN today. I ran ./configure --enable-R-shlib I received the error message: checking for recommended packages... no configure: error: Some of the recommended packages are missing Use --without-recommended-packages if this was intentional I built a previous version of R-patched successfully on my system which is running the SuSE 9,2 Pro Linux distribution. I untarred the tar ball into the same directory I did my last build on in case that's important. The only other differences between this attempt and my successful build are: 1. I did not use --enable-R-shlib last time. 2. I found and installed the blas libraries for this build. Have I messed up or made an erroneous assumption along the way? Thanks -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem configuring R-patched
Gavin Simpson wrote: On Thu, 2005-08-04 at 14:57 -0400, Kevin E. Thorpe wrote: I downloaded R-patched (2005-08-04) from CRAN today. I ran ./configure --enable-R-shlib I received the error message: checking for recommended packages... no configure: error: Some of the recommended packages are missing Use --without-recommended-packages if this was intentional ^^ So was this intentional? No, it wasn't. I built a previous version of R-patched successfully on my system which is running the SuSE 9,2 Pro Linux distribution. I untarred the tar ball into the same directory I did my last build on in case that's important. The only other differences between this attempt and my successful build are: 1. I did not use --enable-R-shlib last time. 2. I found and installed the blas libraries for this build. Have I messed up or made an erroneous assumption along the way? Yes and No. You obviously haven't compiled R recently. If you haven't got the recommended packages in the source you are compiling, configure now gives an error, which quite clearly states (and you've quoted it in your email!) that it cannot find (some of) the recommended packages. Actually, I compiled it about a week ago. Here is my current version. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major2 minor1.1 year 2005 month07 day 28 language R When I compiled that version, I did my tar xzf to a clean directory and did not receive that error. A solution - again given by the error message you quote! - is: ./configure --enable-R-shlib --without-recommended-packages ^ That should clear things up. I realise that would clear it up. I was puzzled why I got this message in the first place, given I didn't get it last week. Other wise you need to cd to the R directory (where you have the source code), and then execute ./tools/rsync-recommended and then run your configure command. HTH G Thanks for the rsync tip. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem configuring R-patched
Duncan Murdoch wrote: Kevin E. Thorpe wrote: Gavin Simpson wrote: On Thu, 2005-08-04 at 14:57 -0400, Kevin E. Thorpe wrote: I downloaded R-patched (2005-08-04) from CRAN today. I ran ./configure --enable-R-shlib I received the error message: checking for recommended packages... no configure: error: Some of the recommended packages are missing Use --without-recommended-packages if this was intentional ^^ So was this intentional? No, it wasn't. I built a previous version of R-patched successfully on my system which is running the SuSE 9,2 Pro Linux distribution. I untarred the tar ball into the same directory I did my last build on in case that's important. The only other differences between this attempt and my successful build are: 1. I did not use --enable-R-shlib last time. 2. I found and installed the blas libraries for this build. Have I messed up or made an erroneous assumption along the way? Yes and No. You obviously haven't compiled R recently. If you haven't got the recommended packages in the source you are compiling, configure now gives an error, which quite clearly states (and you've quoted it in your email!) that it cannot find (some of) the recommended packages. Actually, I compiled it about a week ago. Here is my current version. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major2 minor1.1 year 2005 month07 day 28 language R When I compiled that version, I did my tar xzf to a clean directory and did not receive that error. A solution - again given by the error message you quote! - is: ./configure --enable-R-shlib --without-recommended-packages ^ That should clear things up. I realise that would clear it up. I was puzzled why I got this message in the first place, given I didn't get it last week. I believe there are two kinds of tar files. The daily snapshots don't include the recommended packages, the releases do. Or perhaps the test is a recent addition. Both versions were R-patched.tar.gz as opposed to the devel sets which looks like it's actually a link to the most recent. Maybe I incorrectly assumed that the patched tarballs contained the recommended packages. Duncan Murdoch Other wise you need to cd to the R directory (where you have the source code), and then execute ./tools/rsync-recommended and then run your configure command. HTH G Thanks for the rsync tip. Anyway, running rsync-recommended did the trick. Thanks -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R: regression data set
Clark Allan wrote: i would like to give the class a practical assignment as well. could you suggest a good problem and the location of the data set/s? it would be good if the data set has been analysed by a number of other people so that students can see the different ways of tackling a regression problem. If you want some textbook examples I'd recommend Ripley and Venables's Modern Applied Statistics With S (VR bundle); Maindonald and Braun's Data Analysis and Graphics using R (DAAG package) Cheers, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error with scan
Can you show us the first line of the file? The error means that in one of the values you specified as numeric (first, second, third, fourth, fifth, seventh, eighth, ninth), it found the character value it displayed. Otherwise, this looks like a good use of scan. Kevin -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jean-Pierre Gattuso Sent: Tuesday, July 26, 2005 11:52 AM To: r-help@stat.math.ethz.ch Cc: Jean-Pierre Gattuso Subject: [R] error with scan Hi: I am trying to read a large (50+ lines) with scan() as read.table is unable to read it. I get a strange error (below) which says that 'a real' was expected and '5' was read. Can someone help? Thanks, jp type=list(a=0,b=0,c=0,d=0,e=0,f=,g=0,h=0,i=0) tmp2 - scan(file=tmp2.txt, what=type, sep=,, quote=\, dec=., skip=1, nmax=541502) Erreur dans scan(file = tmp2.txt, what = type, sep = ,, quote = \, : scan() attendait 'a real' et a reçu '5 ' __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
Prof Brian Ripley wrote: On Wed, 20 Jul 2005, Kevin E. Thorpe wrote: Thank you for the information. I have contacted the RPM maintainer and am awaiting a response. It occurs to me that my problem could also be fixed by putting ATLAS on my system. Are there advantages to doing that or any reasons not to? It is a good idea unless you share R systems between different architectures (even down to the vintage of P4 or Xeon chips). We do and so tend to avoid ATLAS (which gets statically compiled in by default). After following the discussion between you and Uwe, and thinking a bit, I've decided to give it a try. My system is basically stand-alone so different architectures are not an issue. Now my question (recognising this may be the wrong list). I successfully compiled ATLAS, but it isn't clear to me from the install instructions that came with it how to make the libraries seen by gcc and g77 and therefore, presumably by the configure script with the R source. How do I make the libraries available? I've looked at the ATLAS project page and done a couple RSiteSearch's but have not yet recognised the answer to my question. Prof Brian Ripley wrote: -lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS installed. lme4 needs a compatible Matrix installed. I do think installing from the sources would solve this, but probably you need to discuss this with the RPM maintainer as a dependency appears to be missing. On Fri, 15 Jul 2005, Kevin E. Thorpe wrote: I just upgraded to version 2.1.1 (from 2.0.1) today. R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 1.1 year 2005 month 06 day 20 language R I am using SuSE 9.2 and did the upgrade using rpm -U with the RPM available on CRAN. After upgrading r-base, I ran update.packages(). Four previously installed packages failed to update: Matrix (0.95-5 to 0.97-4) gam (0.93 to 0.94) lme4 (0.95-3 to 0.96-1) mgcv (1.3-1 to 1.3-4) In the case of Matrix, gam and mgcv I get the message: [long path]/ld: cannot find -lf77blas In the case of lme4 the messages are: ** preparing package for lazy loading Error in setMethod(coef, signature(object = lmList), function(object, : no existing definition for function 'coef' Error: unable to load R code in package 'lme4' Execution halted ERROR: lazy loading failed for package 'lme4' I have searched the SuSE repository for any package that provides f77blas but came up empty. I also could not identify any relevant messages in the mailing list archives. Is R looking for that library because it was present on the machine the RPM was built on? Would building R myself solve the missing library problem or did I do something wrong? -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Cannot update some packages after upgrade to 2.1.1
Thank you for the information. I have contacted the RPM maintainer and am awaiting a response. It occurs to me that my problem could also be fixed by putting ATLAS on my system. Are there advantages to doing that or any reasons not to? Prof Brian Ripley wrote: -lf77blas is part of ATLAS, so I do suspect the RPM builder had ATLAS installed. lme4 needs a compatible Matrix installed. I do think installing from the sources would solve this, but probably you need to discuss this with the RPM maintainer as a dependency appears to be missing. On Fri, 15 Jul 2005, Kevin E. Thorpe wrote: I just upgraded to version 2.1.1 (from 2.0.1) today. R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 1.1 year 2005 month 06 day 20 language R I am using SuSE 9.2 and did the upgrade using rpm -U with the RPM available on CRAN. After upgrading r-base, I ran update.packages(). Four previously installed packages failed to update: Matrix (0.95-5 to 0.97-4) gam (0.93 to 0.94) lme4 (0.95-3 to 0.96-1) mgcv (1.3-1 to 1.3-4) In the case of Matrix, gam and mgcv I get the message: [long path]/ld: cannot find -lf77blas In the case of lme4 the messages are: ** preparing package for lazy loading Error in setMethod(coef, signature(object = lmList), function(object, : no existing definition for function 'coef' Error: unable to load R code in package 'lme4' Execution halted ERROR: lazy loading failed for package 'lme4' I have searched the SuSE repository for any package that provides f77blas but came up empty. I also could not identify any relevant messages in the mailing list archives. Is R looking for that library because it was present on the machine the RPM was built on? Would building R myself solve the missing library problem or did I do something wrong? -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Cannot update some packages after upgrade to 2.1.1
I just upgraded to version 2.1.1 (from 2.0.1) today. R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R I am using SuSE 9.2 and did the upgrade using rpm -U with the RPM available on CRAN. After upgrading r-base, I ran update.packages(). Four previously installed packages failed to update: Matrix (0.95-5 to 0.97-4) gam (0.93 to 0.94) lme4 (0.95-3 to 0.96-1) mgcv (1.3-1 to 1.3-4) In the case of Matrix, gam and mgcv I get the message: [long path]/ld: cannot find -lf77blas In the case of lme4 the messages are: ** preparing package for lazy loading Error in setMethod(coef, signature(object = lmList), function(object, : no existing definition for function 'coef' Error: unable to load R code in package 'lme4' Execution halted ERROR: lazy loading failed for package 'lme4' I have searched the SuSE repository for any package that provides f77blas but came up empty. I also could not identify any relevant messages in the mailing list archives. Is R looking for that library because it was present on the machine the RPM was built on? Would building R myself solve the missing library problem or did I do something wrong? -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] logistic regression asymptote problem
R-helpers, I have a question about logistic regressions. Consider a case where you have binary data that reaches an asymptote that is not 1, maybe its 0.5. Can I still use a logistic regression to fit a curve to this data? If so, how can I do this in R. As far as I can figure out, using a logit link function assumes that the asymptote is at y = 1. An example. Consider the following data: tmp - structure(list(x = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14), yes = c(0, 0, 0, 2, 1, 14, 24, 15, 23, 18, 22, 20, 14, 17 ), no = c(94, 101, 95, 80, 81, 63, 51, 56, 30, 38, 31, 18, 21, 20)), .Names = c(x, yes, no), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14), class = data.frame) where x is the independent variable, and yes and no are counts of events. plotting the data you can see that the data seem to reach an asymptote at around y=0.5. using glm to fit a logistic regression it is easily seen that it does not fit well. tmp.glm - glm(cbind(yes,no) ~ x, data = tmp, family = binomial(link = logit)) plot(tmp.glm$fitted, type = l, ylim = c(0,1)) par(new=T) plot(tmp$yes / (tmp$yes + tmp$no), ylim = c(0,1)) Any suggestions would be greatly appreciated. Cheers, Kevin -- Kevin J Emerson Center for Ecology and Evolutionary Biology 1210 University of Oregon University of Oregon Eugene, OR 97403 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Finding out collinearity in regression
Hi, Young Cho wrote: fit - aov( Y ~ . , data = dat) Error in contrasts-(`*tmp*`, value = contr.treatment) : contrasts can be applied only to factors with 2 or more levels I think there is a dependency in explanatory variables. So, I wanted to use alias to find out a dependency in design matrix but I can't because I cannot create fit in the first place. The error message actually looks like you have got (at least) a variable that only has 1 level, e.g. a factor with only one level. Cheers, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] frequency tables
R-masters, I have a problem that I have been working on for a while and it seems that there may be a simple solution that I have yet to figure out, so I thought that I would venture to post to the help list. Let's say there was a data.frame with three vectors, two that are factors identifying the data, and one that holds the frequency of occurrence (the events are binary, yes or no). I would like to perform logistic regression on this data, and it seems that I need a vector of 0s and 1s for input into lrm. How might I convert between a frequency table and a vector of binary data while still maintaining all identifier information? I have thought about using the rep command over and over again and basically building the data.frame by hand but that seems long and tedious. Is there a quick and dirty way of doing this? Thanks in advance! Kevin -- Kevin J Emerson Center for Ecology and Evolutionary Biology 1210 University of Oregon University of Oregon Eugene, OR 97403 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vectorization
These two lines worked for me:
rst - tapply(mydata$income, mydata$education, median)
mydata$md - rst[mydata$education]
Here's my cheesy example:
mydata - data.frame(income= round(rnorm(3, 55000, 1)),
+ education = letters[rbinom(3, 4, 1/2)+1])
rst - tapply(mydata$income, mydata$education, median)
mydata$md - rst[mydata$education]
head(mydata)
income education md
1 66223 e 55094.5
2 56830 c 54966.0
3 58035 b 54937.5
4 74045 a 55213.5
5 61327 b 54937.5
6 64150 b 54937.5
Is this what you wanted?
Kevin
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dimitri Joe
Sent: Friday, June 17, 2005 10:01 AM
To: R-Help
Subject: [R] vectorization
Hi there,
I have a data frame (mydata) with 1 numeric variable (income) and 1
factor (education). I want a new column in this data with the median
income for each education level. A obviously inneficient way to do this
is
for ( k in 1: nrow(mydata) ){
l - mydata$education[k]
mydata$md[k] - median(mydata$income[mydata$education==l],na.rm=T)
}
Since mydata has nearly 30.000 rows, this will be done not untill the
end of this month. I thus need some help for vectorizing this, please.
Thanks,
Dimitri
[[alternative HTML version deleted]]
___
Instale o discador agora! http://br.acesso.yahoo.com/
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
