Re: [R] What is the difference between expression and quote whenused with eval()?
On 02/21/2010 01:45 AM, blue sky wrote: On Sat, Feb 20, 2010 at 2:40 AM, Romain Francois romain.franc...@dbmail.com wrote: On 02/19/2010 10:31 PM, William Dunlap wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of blue sky Sent: Friday, February 19, 2010 12:11 PM To: Peter Dalgaard Cc: r-h...@stat.math.ethz.ch Subject: Re: [R] What is the difference between expression and quote whenused with eval()? On Fri, Feb 19, 2010 at 12:39 PM, Peter Dalgaard p.dalga...@biostat.ku.dkwrote: blue sky wrote: I made the following example to see what are the difference between expression and quote. But I don't see any difference when they are used with eval()? Could somebody let me know what the difference is between expression and quote? Expressions are vectors of unevaluated expressions, so one difference is that expressions can have more than one element. Another difference is more subtle: objects of mode expression are better at retaining their identity as an unevaluated expression eval(substitute(2+x,list(x=expression(pi Error in 2 + expression(pi) : non-numeric argument to binary operator eval(substitute(2+x,list(x=quote(pi [1] 5.141593 The really convincing application of this escapes me for the moment, but the gist of it is that there are cases where a quoted expression may blend in a bit too seemlessly when using computing on the language. Also, expression objects are more easy to recognize programmeatically, quote() may result in objects of mode call, name, or one of the base classes. I want to see how expression(something) and quote(something) are represented in R internally. But it seems that str() doesn't go to that low level. Is there a way to show the internal representation? There is also the internal inspect function : inspect- function(x, ...) .Internal(inspect(x,...)) inspect( expression(log(1), sqrt(2), trunc(pi)) ) @9657560 20 EXPRSXP g0c2 [NAM(2)] (len=3, tl=153865256) @97ab5e8 06 LANGSXP g0c0 [] @92cf3fc 01 SYMSXP g0c0 [MARK,gp=0x4000] log @9709a28 14 REALSXP g0c1 [] (len=1, tl=0) 1 @97aa750 06 LANGSXP g0c0 [] @92cf204 01 SYMSXP g0c0 [MARK,gp=0x4000] sqrt @97099e8 14 REALSXP g0c1 [] (len=1, tl=0) 2 @97aa84c 06 LANGSXP g0c0 [] @92cf15c 01 SYMSXP g0c0 [MARK,gp=0x4000] trunc @9347c38 01 SYMSXP g0c0 [MARK,gp=0x4000] pi Where is the internal inspect documented? Would you please help explain what does '@9657560 20', 'g0c2', 'NAM(2)', 'MARK', 'tl' and 'gp' stand for? Reading R internals gives some clues, otherwise you can read the source, it is only about 200 lines in src/main/inspect.c -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/OIXN : raster images and RImageJ |- http://tr.im/OcQe : Rcpp 0.7.7 `- http://tr.im/O1wO : highlight 0.1-5 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of R in clinical trials
Looks like my message misunderstood: I tried to explain that assay validation and validation for clinical trials are mixed up by people working mainly in clinical applications, who have to make judgments about statistical applications. There is nothing wrong in using SAS, R or Excel (with caveats) in statistics. Dieter -- View this message in context: http://n4.nabble.com/Use-of-R-in-clinical-trials-tp1559402p1563402.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Time series cross-sectional regression analysis
Hi all,
Is there a package in R to perform time series cross-sectional regression
analysis (like the TSCSREG procedure in SAS)? Thanks for the info.
Thanks and Regards,
Shubha Karanth | Amba Research
Ph +91 80 3980 8283 | Mob +91 94 4886 4510
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com
This e-mail may contain confidential and/or privileged i...{{dropped:13}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] a question about the command followup.plot of epicale package
Works fine for me. Maybe you're messing up epicalc's use() procedure. It would really help if you took the trouble to read and follow the posting guide and provide *reproducible code* to illustrate your problem. It's also customary to indicate where the data can be found (Orthodont is in pkg nlme). -Peter Ehlers On 2010-02-20 19:40, 孟欣 wrote: Hi all: I have a question about the command followup.plot of epicale package. As to the demo data Orthodont, the command followup.plot works well.But if I delete some rows of data(delete Male data,and keep Female data only, for instance),the command can't work,and the warning is In attr(get(search()[2]), names) == as.character(substitute(ylab)) : Longer object length is not an integer multiples of the shorter object. If anyone can give me some guidance,I'll appreciate your help deeply. Thanks a lot. My best regards [[alternative HTML version deleted]] -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Downloading data from Reuters - second trial
Dear lists (I was not sure which list would be the better-one), I'm trying to download data from Reuters (3000 Xtra) into R with the extension written by Rory Winston (http://www.theresearchkitchen.com). I first stored the dlls into the bin directory of R, tried to load it into R with dyn.load but the extension cannot be loaded. So I hoped to find an answer in the R list and got the topic. It seems like I have the same problem as Shubha, because also on his PC dyn.load(reuters_ts.dll) fails to load. Unfortunately the topics ends with I'll email you off-list and we can work through it. Maybe anyone's also tried to download data from Reuters (even via another way than Rorys) and got it to work? Thanks for your help and have a nice weekend, Thomas Configuration: Windows 7, R 2.10.0, Reuters 3000 Xtra __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to: Compare Two dendrograms (Hierarchical Clusterings) ?
Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an hclust object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a function called as.dendrogram But I wasn't able to find an example on how to use it. 2) Assuming that I have to hclust (or dendrogram ) objects, how can I compare them ? After some searching and asking, I found this article: http://www.jstor.org/pss/2288117 And a few others that cite it, that gives ideas on how to do this. But I wasn't able to come a cross a R implementation of it. Is there ? Many thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Tutorials and scripts of Stochastic Frontier Analysis and Linear Programming.
Dear all, I want to program my own models about Stochastic Frontier Analysis and Linear programming (Data Envelopment Analysis). In this context, is there anyone that may help me with some simple tutorials and scripts about these issues? Thanks a lot. -- Marcus Vinicius Pereira de Souza, Prof. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] aggregating using 'with' function
Wow! Jim, this is really impressive. I can't wrap my head around how you figured this out. Thank you, AC On Sun, Feb 21, 2010 at 12:02 AM, jim holtman jholt...@gmail.com wrote: This will do it. You can see two different values for id=1: x - with(datas, aggregate(list(r = r), by = list(id = id, mod1 = mod1),mean)) x id mod1 r 1 1 1 0.980 2 4 1 0.640 3 7 1 0.490 4 10 1 0.180 5 1 2 0.295 6 5 2 0.490 7 8 2 0.330 8 11 2 0.600 9 6 3 -0.040 10 9 3 0.580 11 12 3 0.210 # choose random duplicate to use do.call(rbind, lapply(split(x, x$id), function(.data) .data[sample(nrow(.data), 1),])) id mod1 r 1 1 1 0.98 4 4 1 0.64 5 5 2 0.49 6 6 3 -0.04 7 7 1 0.49 8 8 2 0.33 9 9 3 0.58 10 10 1 0.18 11 11 2 0.60 12 12 3 0.21 # choose random duplicate to use - try to see if a different one comes up do.call(rbind, lapply(split(x, x$id), function(.data) .data[sample(nrow(.data), 1),])) id mod1 r 1 1 2 0.295 4 4 1 0.640 5 5 2 0.490 6 6 3 -0.040 7 7 1 0.490 8 8 2 0.330 9 9 3 0.580 10 10 1 0.180 11 11 2 0.600 12 12 3 0.210 On Sat, Feb 20, 2010 at 9:50 PM, AC Del Re acde...@gmail.com wrote: OK, this is great, Jim. Last question: How about if I want the 1 copy of each id to be selected randomly versus taking the first one? AC On Sat, Feb 20, 2010 at 8:37 PM, jim holtman jholt...@gmail.com wrote: I am not sure what you mean by eliminating a row. Now if you want only one copy of each 'id', and it is the first one, the you can use 'duplicated': x - with(datas, aggregate(list(r = r), by = list(id = id, mod1 = mod1),mean)) x id mod1 r 1 1 1 0.980 2 4 1 0.640 3 7 1 0.490 4 10 1 0.180 5 1 2 0.295 6 5 2 0.490 7 8 2 0.330 8 11 2 0.600 9 6 3 -0.040 10 9 3 0.580 11 12 3 0.210 subset(x, !duplicated(id)) id mod1 r 1 1 1 0.98 2 4 1 0.64 3 7 1 0.49 4 10 1 0.18 6 5 2 0.49 7 8 2 0.33 8 11 2 0.60 9 6 3 -0.04 10 9 3 0.58 11 12 3 0.21 On Sat, Feb 20, 2010 at 8:07 PM, AC Del Re de...@wisc.edu wrote: Perfect! Thanks Jim. Do you know how I could then reduce the data even further? Specifically, reducing it to 1 id per row? In this dataset, id 1 would have one row eliminated. Assume the data is much larger and cannot be deleted by visual inspection and elimination one row at a time. Thank you, AC On Sat, Feb 20, 2010 at 6:26 PM, jim holtman jholt...@gmail.com wrote: This seems to work fine (notice the missing 'c(...)'; why did you think you needed it); with(datas, aggregate(list(r = r), by = list(id = id, mod1 = mod1),mean)) id mod1 r 1 1 1 0.980 2 4 1 0.640 3 7 1 0.490 4 10 1 0.180 5 1 2 0.295 6 5 2 0.490 7 8 2 0.330 8 11 2 0.600 9 6 3 -0.040 10 9 3 0.580 11 12 3 0.210 On Sat, Feb 20, 2010 at 6:54 PM, AC Del Re de...@wisc.edu wrote: Hi All, I am interested in aggregating a data frame based on 2 categories--mean effect size (r) for each 'id's' 'mod1'. The 'with' function works well when aggregating on one category (e.g., based on 'id' below) but doesnt work if I try 2 categories. How can this be accomplished? # sample data id-c(1,1,1,rep(4:12)) n-c(10,20,13,22,28,12,12,36,19,12, 15,8) r-c(.98,.56,.03,.64,.49,-.04,.49,.33,.58,.18, .6,.21) mod1-factor(c(1,2,2, rep(c(1,2,3),3))) mod2-c(1,2,15,rep(3,9)) datas-data.frame(id,n,r,mod1,mod2) # one category works perfect: with(datas, aggregate(list(r = r), by = list(id = id),mean)) id r 1 1 0.523 2 4 0.640 3 5 0.490 4 6 -0.040 5 7 0.490 6 8 0.330 7 9 0.580 8 10 0.180 9 11 0.600 10 12 0.210 # trying with 2 categories: with(datas, aggregate(list(r = r), by = list(c(id = id, mod1 = mod1)),mean)) Error in FUN(X[[1L]], ...) : arguments must have same length Thank you, AC __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve?
[R] Intervention Analysis
Dear Sir/Madam, I am doing the intervention analysis on climate data (time series). Is there any package or methods to estimate the parameters (delta omega) by R? Thank you very much, Best, Jian Kang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 3D plot
On 18/02/2010 11:43 AM, David A.G wrote:
Dearl list,
can anyone point me to a function or library that can create a graph similar to
the one in the following powerpoint presentation?
It could be done in rgl with a lot of work. I don't know of a package
where someone has already done the work.
rgl can plot triangles and quadrilaterals in 3d, but not general
polygons. So you'd need to decompose each chromosome sequence into a
sequence of simpler shapes. For example,
n - 100
f - rnorm(n, mean=10, sd=1)
g - rnorm(n, mean=10, sd=1)
x - 1:n
fn - colorRamp(c(blue,white,red))
color - function(value) {
vals - fn(value)
rgb(vals[,1], vals[,2], vals[,3], max=255)
}
m - max(f,g)
quadx - cbind( x[-n], x[-1], x[-1], x[-n] )
quadh - cbind( 0, 0, f[-1], f[-n] )
quadcol - cbind( color(0), color(0), color(f[-1]/m), color(f[-n]/m))
quads3d( as.numeric(t(quadx)), 10, as.numeric(t(quadh)),
col=as.character(t(quadcol)))
quadh - cbind( 0, 0, g[-1], g[-n] )
quadcol - cbind( color(0), color(0), color(g[-1]/m), color(g[-n]/m))
quads3d( as.numeric(t(quadx)), 20, as.numeric(t(quadh)),
col=as.character(t(quadcol)))
This doesn't get the colours the way the presentation had them, that
would be a bit more work.
Duncan Murdoch
http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt
(pages 36-37)
In order to try to explain the graph, the way I see it in R terms is something
like this:
the p-q axis is a vector of positions (for example, seq(0,500,1))
the Chr1-Chrx is a vector of units, in this case chromosomes (so something
like seq(1,10,1))
the plotted data is observations for each unit at each position
I guess the fancy gradient on the highest peaks is tougher to get (knowing I am
not an R expert), but just plain blue would suffice.
I have checked some of the graphs in the R graph gallery but I don´t think any
of them would work
Thanks in advance,
Dave
_
Hotmail: Trusted email with powerful SPAM protection.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tutorials and scripts of Stochastic Frontier Analysis and Linear Programming.
Hi Marcus! On Sun, Feb 21, 2010 at 1:47 PM, Marcus Vinicius mvi...@gmail.com wrote: I want to program my own models about Stochastic Frontier Analysis and Linear programming (Data Envelopment Analysis). In this context, is there anyone that may help me with some simple tutorials and scripts about these issues? What do you mean with own models? Have you developed new theoretical models that are not (yet) available in current software package? Various types of Stochastic Frontier Analysis (SFA) can be performed by the frontier package [1,2] and there are (at least) three R packages for Data Envelopment Analysis: DEA [3], FEAR [4] (academic use without payments but NOT open source :-( ), and one of my colleagues has an unpublished package for DEA (I can ask him to send it to you). [1] http://cran.r-project.org/package=frontier [2] http://r-forge.r-project.org/projects/frontier/ [3] http://cran.r-project.org/package=DEA [4] http://www.clemson.edu/economics/faculty/wilson/Software/FEAR/fear.html Best wishes, Arne -- Arne Henningsen http://www.arne-henningsen.name __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot is not keeping the order of variable
Hi, I created a simple data frame with one factor and one numerical variable. The factor was actually a vector of names of techniques to trimm reaction time data. I want to create a plot that shows the value of F test for every trimming method. So the data frame has its trim factor (who has those labels mean,2500,2000,1500,1000,log,inverse,1SD,2SD) and the numerical variable of the data frame has the F values for each one of those trimming method. When I ask R to plot it, it doesn't keep the order of the trimm verctor correctly and the plot confuses the order so the most left one will be 1500 and then 1SD etc. The values are correct but it is important for me to keep it in the same order I built it. How can I do it? Thank you very much, Or D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot is not keeping the order of variable
Hi Or, I can't know for sure what your problem is without an example, but the first thing I would do is check to make sure that your labels are stored as an ordered factor (and that the order is correct). See ?factor for details. Best, Ista On Sun, Feb 21, 2010 at 10:57 AM, Or Duek ord...@gmail.com wrote: Hi, I created a simple data frame with one factor and one numerical variable. The factor was actually a vector of names of techniques to trimm reaction time data. I want to create a plot that shows the value of F test for every trimming method. So the data frame has its trim factor (who has those labels mean,2500,2000,1500,1000,log,inverse,1SD,2SD) and the numerical variable of the data frame has the F values for each one of those trimming method. When I ask R to plot it, it doesn't keep the order of the trimm verctor correctly and the plot confuses the order so the most left one will be 1500 and then 1SD etc. The values are correct but it is important for me to keep it in the same order I built it. How can I do it? Thank you very much, Or D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot is not keeping the order of variable
Ok, It seems that the problem lays in the order (as Ista mentioned), But, when I ask R to order it he chooses to order it by size and not by the specific order I mentioned when I built the vector. Is it possible to tell him to keep the order as mentioned? Thank you. On Sun, Feb 21, 2010 at 6:16 PM, Ista Zahn istaz...@gmail.com wrote: Hi Or, I can't know for sure what your problem is without an example, but the first thing I would do is check to make sure that your labels are stored as an ordered factor (and that the order is correct). See ?factor for details. Best, Ista On Sun, Feb 21, 2010 at 10:57 AM, Or Duek ord...@gmail.com wrote: Hi, I created a simple data frame with one factor and one numerical variable. The factor was actually a vector of names of techniques to trimm reaction time data. I want to create a plot that shows the value of F test for every trimming method. So the data frame has its trim factor (who has those labels mean,2500,2000,1500,1000,log,inverse,1SD,2SD) and the numerical variable of the data frame has the F values for each one of those trimming method. When I ask R to plot it, it doesn't keep the order of the trimm verctor correctly and the plot confuses the order so the most left one will be 1500 and then 1SD etc. The values are correct but it is important for me to keep it in the same order I built it. How can I do it? Thank you very much, Or D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] odfWeave - merged table cells, and adding information like totals and p-values
I'm hoping I'm missing some (probably fundamental basic process) which might
make my life easier!
Lets assume I have a 3 column table summarizing results from a trial from three
arms (Arm A, B and C).
For each arm there will be a number of pieces of information to report. The
simplest example might be to compare this to the demographic comparisons often
seen in clinical traisl where you are setting out to prove that your
randomization produced similar populations
So I might have a table like this:
---
A B C
---
Male50 50 50
Female 49 51 50
Age 6530 29 31
Age 65+ 69 72 69
---
I've got a matrix with that data in it which I'm passing to odfWeave's table
function. I just want to check a few basic things.
Here's some short code which will create the matrix:
groups = c(A,B,C)
factors = c(Male,Female, Age lt; 65, Age 65+)
mydata = matrix (c(50,49,30,69,50,51,29,72,50,50,31,69), nrow=4, dimnames =
list(factors,groups))
- Is there anyway to add a merged cell above ABC which would say Group?
- If I want to total column I can do that using:
total=as.numeric()
for (fact in 1:length(factors)) {
total[fact]=sum(mydata[fact,])
}
mydata = cbind(mydata,total)
Is there an easier way?
- Now lets say i want to do a chi-squ test between the ages differences in Gp A
and Gp B I run
chisq.test(mydata[3:4,1:2])
What I really want is the p-value and I'll want to repeat that for Gp A vs Gp
C. If I was just using R I'd simply print those and then add them to my table
by hand. But I'm trying to be smart and use odfWeave. Now I know I can put
them in my caption but I'd probably have added them as an extra row in my table
or added it in brackets similar to the SDs/ORs and CIs shown in this example
http://www.bmj.com/cgi/content-nw/full/340/feb05_1/c199/TBL2 depending which
was more appropriate.
- Is there an easy way to do anything like this? I'm thinking that we often
put crude numbers in and (%) in brackets, or CIs etc - so my exported table
would not ideally be pure numbers.
- As a p value usually links two columns I might have expected to use a merged
cell which again brings me back to my original question ;-)
Thanks
Calum Polwart BSc(Hons) MSc MRPharmS SP IP
Network Pharmacist - North of England Cancer Network and
Pharmacy Clinical Team Manager (Cancer Aseptic Services) - County Durham
Darlington NHS Foundation Trust
This message may contain confidential information. If yo...{{dropped:21}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Hotelling T-test in R - error?
Hey there, I am trying to do a series of hotelling t-tests in R. But I keep getting the following error: mat - cbind(Dataset$Ula.l.sl1A,Dataset$incisordepth.residuals,Dataset$lclhm.residuals,Dataset$lclpsl2.residuals,Dataset$llaheight.residuals,Dataset$llas.residuals,Dataset$lm3.m1,Dataset$lmheight.residuals,Dataset$ucllalia.residuals,Dataset$uclppr.residuals,Dataset$ulaah.residuals,Dataset$ulm3.residuals,Dataset$um3.m1,Dataset$umah.residuals,Dataset$uprheight.residuals) # Hotelling T2 test for grps 1 2 T2.test(mat[which(as.factor(Dataset$diet)==levels(as.factor(Dataset$diet))[1]),],mat[which(as.factor(Dataset$diet)==levels(as.factor(Dataset$diet))[2]),]) Error in drop(.Call(La_dgesv, a, as.matrix(b), tol, PACKAGE = base)) : system is computationally singular: reciprocal condition number = 5.39931e-21 I am not sure what is going on but I assume it has to do with the matrix math? I have 6 groups, and some of them will work, and others I get this error. Does this have to do with group size? I am running the t-test using 15 variables, when I run the ttest w/ 7 (despite which 7 I choose) the test will run fine for all 6 groups. What do you think could be causing this? Thanks, Stephanie -- View this message in context: http://n4.nabble.com/Hotelling-T-test-in-R-error-tp1563584p1563584.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What is your system for WorkFlow and Source Code Organizing in R ?
On 2/20/2010 9:49 AM, Tal Galili wrote:
Hello dear R users,
Recently there has been several fascinating threads on the website
stackoverflowhttp://stackoverflow.com regarding the subject of R WorkFlow
best practices:
- What best practices do you use for programming in
R?http://stackoverflow.com/questions/2258092/what-best-practices-do-you-use-for-programming-in-r
- Workflow for statistical analysis and report
writinghttp://stackoverflow.com/questions/1429907/workflow-for-statistical-analysis-and-report-writing/1434424
- How to organize large R
programs?http://stackoverflow.com/questions/1266279/how-to-organize-large-r-programs
- Organizing R Source
Codehttp://stackoverflow.com/questions/2284446/organizing-r-source-code
And although many people there gave very detailed answers, I have the
feeling that there is much more wisdom on the subject that is still only
available in this mailing list.
Thanks for this post as I was unaware of stackOverflow. Most of my work
is single user development with some projects with 2 or 3
collaborators. I'm a scientific analyst so my needs may be different
than others. To sum up my comments, I'm a big proponent of package
development for analysis and I've recently started incorporating
Sweave/Tex via Lyx into my publication/reporting.
So I'll phrase a few questions, and I hope as many people will participate
in sharing work styles tips:
1) What IDE do you use (and what features in it do you find are most
important to you. besides syntax highlighting and indentation)
I'm using Tinn-R. Until recently I've only used it for syntax
highlighting but I'm learning that the project capability is quite
useful and I'm integrating that. However, a lot more could be done to
support package development.
2) Do you use a version control system? if so which, and how do you often
use it?
Since I do all my work in packages as a single user, I simply zip up the
source directory and store in an archive directory. My own experience
using Source-Forge on a project has not left me impressed but maybe that
is my own lack of experience with it.
3) How (and when) do you document your code ?
I document each function (to some degree) as I go and then use those
comments and more in each package help file.
4) What guides you when you build/organize your folders, files (data, code
and results) for a given project (when the project is small, medium and
I develop everything as a package unless it is a very small one time
only analysis. Thus I use the package structure. I can see from the
stackOverflow discussions that some use packages the way I do but in
general I think package development is viewed by most users as something
for CRAN submission only. They are missing out on a great system for
organizing projects which enables you to document data and code for
analysis which provides a simple system for sharing your analytical
techniques and analysis with others. If the data are included in or with
the package, another researcher can repeat your analysis and look at
each component. I use the example() functionality in the package man
file for the main script for the analysis. If I understood correctly
this handles the issue of using source() rather than functions for
reading, cleaning data etc that was discussed in one of the
stackOverflow threads. The script is contained in your example and your
true functions for analysis etc are in the package along with any data
(if appropriate). I'm not a naturally organized person and this gives
me the structure I need to stay organized.
large) ?
5) Did I leave any important aspect of this subject out?
With regard to one of the comments on stackOverflow, I recently wrote a
small function to detach, build and reattach a package from within R. I
used to work on a package using a command window to build the package,
Tinn-R to edit functions and R to test. At a recent Seattle RUsers
meeting Joe Cheng suggested building the package from within Rgui, so I
wrote this function which gets rid of the need for the command window
and automates the detach and library() to reattach. I'd be interested
to know how others do this. What I'd like to see is for some way to
initiate that within Tinn-R. I understand it is possible in Eclipse.
bpkg=function(pkg=RMark,pkg.dir=C:/Users/Jeff
Laake/Desktop/MyDocuments/R Development/)
{
# Detaches package if it is loaded; installs and builds package and
reloads the package
#
# Arguments:
# pkg - name of your package
# pkg.dir - directory containing all of your package directories
# package source is assumed to be in pkg.dir/pkg/pkg
# I use this structure because this lets me keep binary
zip's and other files
# under pkg.dir/pkg. I also usually create
pkg.dir/pkg/archive and keep previous
# zipped source and binary versions in the archive
directory. If you don't want
# to
Re: [R] Unordered Factors For ggplot?
It would be easier with some example data. Make sure the data is represented by factors and check the levels and relevel if needed. Something like: df$day - factor(df$day, levels = c(30, 29, 20)) Also search the ggplot2 mailing list for factor and order. I think similar questions are asked often (although I may not be interpreting your question correctly). On Wed, Feb 17, 2010 at 1:50 PM, Ryan Garner ryan.steven.gar...@gmail.com wrote: I have data that comes into R already ordered. When I use ggplot, it orders them which I don't want. How do I fix this without changing options(contrast)? The data I have is number of days: 30 29 ... 20 19 ... 10 9 ... 1 When I plot with ggplot, it orders them by the first number only. So 3 ends up coming before 29. -- View this message in context: http://n4.nabble.com/Unordered-Factors-For-ggplot-tp1559146p1559146.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] error in using sample( )
On 2010-02-18 8:48, j...@math.ucdavis.edu wrote: Hi, I am using the command sample(c(0,1,2),1,prob=c(0.2,0.3,0.5)) and I have this error notification Error in sample(c(0,1,2),1,prob=c(0.2,0.3,0.5)): unused argument(s)(1,prob=c(0.2,0.3,0.5)) I don't know what is going wrong. Please give me some suggestions. Try this: rm(sample) sample(c(0,1,2),1,prob=c(0.2,0.3,0.5)) -Peter Ehlers Thank you Best, Jing __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Exporting Graphs
I am a beginner to R, and am working on exporting graphs. Even when I reduce the quality, it takes 30 or 40 minutes to export the graph. Does anyone have suggestions on how to make it faster? Thank you! Karthik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
Hi Karthik, Please give a sample code of what it is that you are doing that is causing this. Also, have a look at: ?pdf Or ?png Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sun, Feb 21, 2010 at 9:27 PM, Karthik kwr...@gmail.com wrote: I am a beginner to R, and am working on exporting graphs. Even when I reduce the quality, it takes 30 or 40 minutes to export the graph. Does anyone have suggestions on how to make it faster? Thank you! Karthik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] machine precision problem
Dear all, I am analysising a set of gene expression data using multiplicative Gaussian Kernel function. I calculated the kernels between two gene sets with 2 genes for each set. The kernels are less than 1, therefore the product of the kernels is out of the minimum precision in R. I wonder if there is a way to lowering the minimum double precision in R. I am using R version 2.10.1. Thank you in advance. Wendy -- View this message in context: http://n4.nabble.com/machine-precision-problem-tp1563732p1563732.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] PostgreSQL under Snow Leopard
Hi, I have nicely used RdbiPgSQL under 10.5 but now that I run 10.6 I can't get this to work. I am quite sure I will not be the first to have this problem, so can someone please point me somewhere where this has been described or let me have a cookbook? greetings, el __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
Hello Tal, This is the code. hist(rnorm(100)) jpeg(histogram.jpeg) --- Even when I decrease the quality, I still have the same problem. hist(rnorm(100)) jpeg(histogram.jpeg,quality=30) Thank you for taking a look. Karthik On Sun, Feb 21, 2010 at 11:32 AM, Tal Galili tal.gal...@gmail.com wrote: Hi Karthik, Please give a sample code of what it is that you are doing that is causing this. Also, have a look at: ?pdf Or ?png Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sun, Feb 21, 2010 at 9:27 PM, Karthik kwr...@gmail.com wrote: I am a beginner to R, and am working on exporting graphs. Even when I reduce the quality, it takes 30 or 40 minutes to export the graph. Does anyone have suggestions on how to make it faster? Thank you! Karthik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
Hi, just to make sure, you didn't forget to close the device with dev.off() ? baptiste On 21 February 2010 20:48, Karthik kwr...@gmail.com wrote: Hello Tal, This is the code. hist(rnorm(100)) jpeg(histogram.jpeg) --- Even when I decrease the quality, I still have the same problem. hist(rnorm(100)) jpeg(histogram.jpeg,quality=30) Thank you for taking a look. Karthik On Sun, Feb 21, 2010 at 11:32 AM, Tal Galili tal.gal...@gmail.com wrote: Hi Karthik, Please give a sample code of what it is that you are doing that is causing this. Also, have a look at: ?pdf Or ?png Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sun, Feb 21, 2010 at 9:27 PM, Karthik kwr...@gmail.com wrote: I am a beginner to R, and am working on exporting graphs. Even when I reduce the quality, it takes 30 or 40 minutes to export the graph. Does anyone have suggestions on how to make it faster? Thank you! Karthik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
Hi Karthik, I think you will need to do something like jpeg(histograms.jpg) hist(rnorm(100)) dev.off() HTH Stephan Karthik schrieb: Hello Tal, This is the code. hist(rnorm(100)) jpeg(histogram.jpeg) --- Even when I decrease the quality, I still have the same problem. hist(rnorm(100)) jpeg(histogram.jpeg,quality=30) Thank you for taking a look. Karthik On Sun, Feb 21, 2010 at 11:32 AM, Tal Galili tal.gal...@gmail.com wrote: Hi Karthik, Please give a sample code of what it is that you are doing that is causing this. Also, have a look at: ?pdf Or ?png Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sun, Feb 21, 2010 at 9:27 PM, Karthik kwr...@gmail.com wrote: I am a beginner to R, and am working on exporting graphs. Even when I reduce the quality, it takes 30 or 40 minutes to export the graph. Does anyone have suggestions on how to make it faster? Thank you! Karthik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
Karthik wrote: Hello Tal, This is the code. hist(rnorm(100)) jpeg(histogram.jpeg) --- Even when I decrease the quality, I still have the same problem. hist(rnorm(100)) jpeg(histogram.jpeg,quality=30) Thank you for taking a look. Karthik Hi Karthic, You have things a little mixed around there-- use plotting commands after you open an output device. Like so: jpeg( histogram.jpeg ) hist( rnorm(100) ) And when you're done, don't forget to call dev.off(). As you mentioned that you are a beginner, I would strongly suggest flipping through the Introduction to R manual. A copy can be accessed online at: http://cran.r-project.org/doc/manuals/R-intro.html Section 12 provides a good overview of graphics in R. Good luck! -Charlie -- View this message in context: http://n4.nabble.com/Exporting-Graphs-tp1563718p1563753.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] PostgreSQL under Snow Leopard
On Feb 21, 2010, at 1:47 PM, Dr Eberhard W Lisse wrote: Hi, I have nicely used RdbiPgSQL under 10.5 but now that I run 10.6 I can't get this to work. I am quite sure I will not be the first to have this problem, so can someone please point me somewhere where this has been described or let me have a cookbook? You should check the R-Mac-SIG archives: http://dir.gmane.org/gmane.comp.lang.r.mac http://markmail.org/browse/org.r-project.r-sig-mac And if not found, then post on that list. David. greetings, el __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How get the single bar x coordinate in barchart when groups is used?
On 2010-02-20 6:22, Walmes Marques Zeviani wrote:
Hi all,
I am using barchart() to plot values above the bars. When using groups argument
we get bars grouped arround a given x level. By placing values above this bars
we need to know the respective x coordinates. How can I get it?
require(lattice)
da- expand.grid(x=1:5, z=1:3, w=1:2)
da$y- rpois(da$x, lambda=23)
barchart(y~x|w, groups=z, data=da, horizontal=FALSE,
panel=function(x, y, subscripts, groups, ...){
panel.barchart(x, y, subscripts=subscripts, groups=groups, ...)
d- 0.22 #-- how obtain d or coordinates?
panel.text(x+c(-d,0,d), y, label=y, pos=3)
})
The width of each bar is 'd';
the width of the space between bars is 's';
the distance from the start of one group to the start of the
next group is 3*d + s = 1 unit on the x-scale;
Now we need to know the relationship of 's' to 'd': 3*d/s = 2;
Hence 3*d + 3*d/2 = 1 = d = 2/9 (so your 0.22 was spot-on).
How do we know that 3*d/s = 2? That's the default box.ratio value.
See what happens if you add box.ratio=3 (or whatever) to your call.
-Peter Ehlers
Thanks in advance.
Walmes Zeviani, Lavras - MG, Brasil.
_
os.
dium=Taglineutm_campaign=InfuseSocial
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Peter Ehlers
University of Calgary
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
Thank you everyone. Your advice helped. Right now I am working through Introductory Statistics with R (Dalgaard) and will also take a look at the R Manual. --Karthik [:-)]+|=0='' On Sun, Feb 21, 2010 at 12:01 PM, Sharpie ch...@sharpsteen.net wrote: Karthik wrote: Hello Tal, This is the code. hist(rnorm(100)) jpeg(histogram.jpeg) --- Even when I decrease the quality, I still have the same problem. hist(rnorm(100)) jpeg(histogram.jpeg,quality=30) Thank you for taking a look. Karthik Hi Karthic, You have things a little mixed around there-- use plotting commands after you open an output device. Like so: jpeg( histogram.jpeg ) hist( rnorm(100) ) And when you're done, don't forget to call dev.off(). As you mentioned that you are a beginner, I would strongly suggest flipping through the Introduction to R manual. A copy can be accessed online at: http://cran.r-project.org/doc/manuals/R-intro.html Section 12 provides a good overview of graphics in R. Good luck! -Charlie -- View this message in context: http://n4.nabble.com/Exporting-Graphs-tp1563718p1563753.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Exporting Graphs
BTW - if you are using an image with little color (but many lines), I remember reading that png is better to use then jpeg. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sun, Feb 21, 2010 at 10:07 PM, Karthik kwr...@gmail.com wrote: Thank you everyone. Your advice helped. Right now I am working through Introductory Statistics with R (Dalgaard) and will also take a look at the R Manual. --Karthik [:-)]+|=0='' On Sun, Feb 21, 2010 at 12:01 PM, Sharpie ch...@sharpsteen.net wrote: Karthik wrote: Hello Tal, This is the code. hist(rnorm(100)) jpeg(histogram.jpeg) --- Even when I decrease the quality, I still have the same problem. hist(rnorm(100)) jpeg(histogram.jpeg,quality=30) Thank you for taking a look. Karthik Hi Karthic, You have things a little mixed around there-- use plotting commands after you open an output device. Like so: jpeg( histogram.jpeg ) hist( rnorm(100) ) And when you're done, don't forget to call dev.off(). As you mentioned that you are a beginner, I would strongly suggest flipping through the Introduction to R manual. A copy can be accessed online at: http://cran.r-project.org/doc/manuals/R-intro.html Section 12 provides a good overview of graphics in R. Good luck! -Charlie -- View this message in context: http://n4.nabble.com/Exporting-Graphs-tp1563718p1563753.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Comparing two date columns
Hi everyone, I have another fairly simple question. I want to take the earliest of two dates from these two date columns. I've tried converting the dates to numbers and just get a vector full of NA's. I've also tried using the chron function to compare the two and have been unsuccessful. I then tried to use:temp.2 - as.POSIXct(strptime(temp, '%d/%m/%Y')) where temp is character vector of one of the date columns this did not work either. I'm not sure what to do now. date_1 date_2 2005-11-25 NA 2007-10-23 NA NA 1999-12-13 2006-01-25 NA 2006-06-12 NA 2005-08-08 NA 2007-12-12 NA 2008-04-29 NA 2005-03-28 NA 2004-11-18 2000-11-02 2006-03-16 NA 2007-01-17 NA Thanks for your help, Natalie -- View this message in context: http://n4.nabble.com/Comparing-two-date-columns-tp1563776p1563776.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparing two date columns
On Feb 21, 2010, at 2:19 PM, Newbie19_02 wrote: Hi everyone, I have another fairly simple question. I want to take the earliest of two dates from these two date columns. I've tried converting the dates to numbers and just get a vector full of NA's. I've also tried using the chron function to compare the two and have been unsuccessful. I then tried to use:temp.2 - as.POSIXct(strptime(temp, '%d/%m/%Y')) where temp is character vector of one of the date columns this did not work either. I'm not sure what to do now. date_1 date_2 2005-11-25 NA 2007-10-23 NA NA 1999-12-13 2006-01-25 NA 2006-06-12 NA 2005-08-08 NA 2007-12-12 NA 2008-04-29 NA 2005-03-28 NA 2004-11-18 2000-11-02 2006-03-16 NA 2007-01-17 NA We cannot tell from that output what data type you are working with. You may not be working with Dates at all. You also have not offered the code that is not working. If they are dates, then pmin should work well. pmin(as.Date(2004-11-18), as.Date(2000-11-02)) [1] 2000-11-02 Next time use dput to allow unambiguous communication. (The fact that you are not using either dput or dump suggests you have not yet spent enough effort at reading the Posting Guide.) -- David Thanks for your help, Natalie -- View this message in context: http://n4.nabble.com/Comparing-two-date-columns-tp1563776p1563776.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] cross-validation in plsr package
Dear readers, can anyone give an example how to use cross-validation in the plsr package. I miss to find the number of factors proposed by cross-validation as optimum. Thank you Peter -- View this message in context: http://n4.nabble.com/cross-validation-in-plsr-package-tp1563815p1563815.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparing two date columns
Dear David and Mark, Thanks very much for your help. THey were actually in date format so pmin works really well. I didn't realise that you could use it on dates that is why I was trying to coerce the date into a numeric. Thanks for both suggestions and I will remember to use a working example next time. Thanks again, Natalie -- View this message in context: http://n4.nabble.com/Comparing-two-date-columns-tp1563776p1563829.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] PostgreSQL under Snow Leopard
Thank you, last post 2007. el On 2010-02-21 22:05 , David Winsemius wrote: You should check the R-Mac-SIG archives: http://dir.gmane.org/gmane.comp.lang.r.mac http://markmail.org/browse/org.r-project.r-sig-mac And if not found, then post on that list. David. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Newbie woes with par:mar
I have a simple barchart with horizontal bars and horizontal tick labels, produced with barplot(x, horiz = T, names.arg = c, las = 1) The labels are longish strings, truncated on the plot. I wish to leave more space for the left margin, and experiment with mar parameter, barplot(x, horiz = T, names.arg = c, las = 1, mar = c(5, 15, 4, 2)) trying various values for the second vector element, but do not notice any change. Consulting this nice tutorial http://research.stowers-institute.org/efg/R/Graphics/Basics/mar-oma/index.htm has not helped. Can anyone point me in the right direction? Thank you. -- View this message in context: http://n4.nabble.com/Newbie-woes-with-par-mar-tp1563745p1563745.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with write.table
I was trying to save a data frame to an excel file using the following command: write.table(myData, file=myData.csv,sep=,, row.names=F) The command works for some data frames, but for other data frames, I get the following error: Error in if (inherits(X[[j]], data.frame) ncol(xj) 1L) X[[j]] - as.matrix(X[[j]]) : missing value where TRUE/FALSE needed I got an identical error message when instead of combining two data frames (a,b) with a method such as: a - cbind.data.frame(a,b) I embedded a data.frame in another, e.g., a$b - b In the latter example, I have a column (a$b) that consists of a data frame onto itself, which write.table apparently can't handle. Jesse Gray Neurobiology Harvard Medical School Here's my precise error message: Error in if (inherits(X[[j]], data.frame) ncol(xj) 1L) X[[j]] - as.matrix(X[[j]]) : missing value where TRUE/FALSE needed -- View this message in context: http://n4.nabble.com/Error-with-write-table-tp1460198p1563869.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Newbie woes with par:mar
On 2010-02-21 12:51, Dimitri Shvorob wrote: I have a simple barchart with horizontal bars and horizontal tick labels, produced with barplot(x, horiz = T, names.arg = c, las = 1) The labels are longish strings, truncated on the plot. I wish to leave more space for the left margin, and experiment with mar parameter, barplot(x, horiz = T, names.arg = c, las = 1, mar = c(5, 15, 4, 2)) par(mar = c(5, 15, 4, 2)) barplot(x, .) I always find it best to set my graphics pars first instead of overloading the plot call (where, as you've discovered, some of the par settings don't work). -Peter Ehlers trying various values for the second vector element, but do not notice any change. Consulting this nice tutorial http://research.stowers-institute.org/efg/R/Graphics/Basics/mar-oma/index.htm has not helped. Can anyone point me in the right direction? Thank you. -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot is not keeping the order of variable
Perhaps this example will help.
x - factor(c('b','a','d'), levels=c('a','d','b'))
y - 1:3
plot(x,y)
And compare with
z - factor(c('b','a','d'))
plot(z,y)
In the first, the plot is in the order that I chose. In the second it
is in the order that R chose -- and R chose it according to a
built-in and reasonable rule.
-Don
At 6:30 PM +0200 2/21/10, Or Duek wrote:
Ok,
It seems that the problem lays in the order (as Ista mentioned),
But, when I ask R to order it he chooses to order it by size and not by the
specific order I mentioned when I built the vector.
Is it possible to tell him to keep the order as mentioned?
Thank you.
On Sun, Feb 21, 2010 at 6:16 PM, Ista Zahn istaz...@gmail.com wrote:
Hi Or,
I can't know for sure what your problem is without an example, but the
first thing I would do is check to make sure that your labels are
stored as an ordered factor (and that the order is correct). See
?factor for details.
Best,
Ista
On Sun, Feb 21, 2010 at 10:57 AM, Or Duek ord...@gmail.com wrote:
Hi,
I created a simple data frame with one factor and one numerical variable.
The factor was actually a vector of names of techniques to trimm reaction
time data.
I want to create a plot that shows the value of F test for every trimming
method.
So the data frame has its trim factor (who has those labels
mean,2500,2000,1500,1000,log,inverse,1SD,2SD)
and the numerical variable of the data frame has the F values for each
one
of those trimming method.
When I ask R to plot it, it doesn't keep the order of the trimm verctor
correctly and the plot confuses the order so the most left one will be
1500
and then 1SD etc.
The values are correct but it is important for me to keep it in the same
order I built it.
How can I do it?
Thank you very much,
Or D.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://*yourpsyche.org
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with write.table
On 2010-02-21 15:06, jmgray wrote: I was trying to save a data frame to an excel file using the following command: write.table(myData, file=myData.csv,sep=,, row.names=F) The command works for some data frames, but for other data frames, I get the following error: Error in if (inherits(X[[j]], data.frame) ncol(xj) 1L) X[[j]]- as.matrix(X[[j]]) : missing value where TRUE/FALSE needed I got an identical error message when instead of combining two data frames (a,b) with a method such as: a- cbind.data.frame(a,b) I embedded a data.frame in another, e.g., a$b- b In the latter example, I have a column (a$b) that consists of a data frame onto itself, which write.table apparently can't handle. Jesse Gray Neurobiology Harvard Medical School Here's my precise error message: Error in if (inherits(X[[j]], data.frame) ncol(xj) 1L) X[[j]]- as.matrix(X[[j]]) : missing value where TRUE/FALSE needed This is one reason why I'm not fond of the '$' way of accessing dataframe components. I like neither of your methods for combining two dataframes. Try instead: a - data.frame(a, b) ## no problem (assuming same number of rows) or a[, b] - b ## R tells you that you're trying to do something you shouldn't. -Peter Ehlers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R on 64-Bit…
Dear R users, I know this issue came up in the list several times. Im currently running R on 32-bit on Windows and due to memory limitation problems would like to move to a 64-bit environment. Im exploring my options and would appreciate your expertise: 1) Windows 64-bit: Prof. Brian Ripley recently posted the experimental built of R for win 64-bit. Ill appreciate any feedback on anyone who has been testing this. He also mentioned that for now, ...this as only being of interest for those who only use a few relatively simple packages. But if one uses packages beyond those relatively simple, how possible is today to have those installed? 2) MacOS or Unix. Sorry for my ignorance on this but if I use any of these environments on 64-bit and installed R on any of those, this is all I need to have R working on 64-bit. How about installing specialized packages? Are the packages on the CRAN repositories ready tho use on these systems or do I have to do any additional work to get them going? Thanks in advance for your help! Axel. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot is not keeping the order of variable
Or Duek wrote: Ok, It seems that the problem lays in the order (as Ista mentioned), But, when I ask R to order it he chooses to order it by size and not by the specific order I mentioned when I built the vector. Is it possible to tell him to keep the order as mentioned? Thank you. You're still not completely clear about how you built the factor, but I venture a guess: Notice that factors tend to get their levels in alphabetical order, unless special tricks are used. d - data.frame(f=c(rare, medium,well-done)) d$f [1] rare mediumwell-done Levels: medium rare well-done To get the cast in order of appearance, this can be used: d$f - factor(d$f, levels=unique(d$f)) d$f [1] rare mediumwell-done Levels: rare medium well-done On Sun, Feb 21, 2010 at 6:16 PM, Ista Zahn istaz...@gmail.com wrote: Hi Or, I can't know for sure what your problem is without an example, but the first thing I would do is check to make sure that your labels are stored as an ordered factor (and that the order is correct). See ?factor for details. Best, Ista On Sun, Feb 21, 2010 at 10:57 AM, Or Duek ord...@gmail.com wrote: Hi, I created a simple data frame with one factor and one numerical variable. The factor was actually a vector of names of techniques to trimm reaction time data. I want to create a plot that shows the value of F test for every trimming method. So the data frame has its trim factor (who has those labels mean,2500,2000,1500,1000,log,inverse,1SD,2SD) and the numerical variable of the data frame has the F values for each one of those trimming method. When I ask R to plot it, it doesn't keep the order of the trimm verctor correctly and the plot confuses the order so the most left one will be 1500 and then 1SD etc. The values are correct but it is important for me to keep it in the same order I built it. How can I do it? Thank you very much, Or D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on 64-Bit…
On Sun, Feb 21, 2010 at 2:43 PM, Axel Urbiz axel.ur...@gmail.com wrote: Dear R users, I know this issue came up in the list several times. I’m currently running R on 32-bit on Windows and due to memory limitation problems would like to move to a 64-bit environment. I’m exploring my options and would appreciate your expertise: 1) Windows 64-bit: Prof. Brian Ripley recently posted the experimental built of R for win 64-bit. I’ll appreciate any feedback on anyone who has been testing this. He also mentioned that for now, “...this as only being of interest for those who only use a few relatively simple packages”. But if one uses packages beyond those “relatively simple”, how possible is today to have those installed? 2) MacOS or Unix. Sorry for my ignorance on this…but if I use any of these environments on 64-bit and installed R on any of those, this is all I need to have R working on 64-bit. How about installing specialized packages? Are the packages on the CRAN repositories “ready tho use” on these systems or do I have to do any additional work to get them going? Thanks in advance for your help! Axel. I can certainly report the R is functional on Gentoo 64-bit Linux. I wouldn't know how to test whether it's stuck with any form of 32-bit limitations as my use of R is very remedial, but it's certainly working. R is supported in Gentoo portage. R-2.9.2 is marked stable, 2.10.0 and 2.10.1 are marked testing. If you're not a Linux guy already then Gentoo might not be where you'd want to start but the R programming language is here, alive and well. Cheers, Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Newbie woes with par:mar
Thanks a lot, Peter! -- View this message in context: http://n4.nabble.com/Newbie-woes-with-par-mar-tp1563745p1563905.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on 64-Bit…
I'm using R for x64bit on my Windows machine and I haven't had any problems. I've installed a number of packages for data analysis and they all seem to work. -- View this message in context: http://n4.nabble.com/R-on-64-Bit-tp1563895p1563910.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on 64-Bit…
On Feb 21, 2010, at 4:43 PM, Axel Urbiz wrote: Dear R users, I know this issue came up in the list several times. Im currently running R on 32-bit on Windows and due to memory limitation problems would like to move to a 64-bit environment. Im exploring my options and would appreciate your expertise: 1) Windows 64-bit: Prof. Brian Ripley recently posted the experimental built of R for win 64-bit. Ill appreciate any feedback on anyone who has been testing this. He also mentioned that for now, ...this as only being of interest for those who only use a few relatively simple packages. But if one uses packages beyond those relatively simple, how possible is today to have those installed? 2) MacOS or Unix. Sorry for my ignorance on this but if I use any of these environments on 64-bit and installed R on any of those, this is all I need to have R working on 64-bit. How about installing specialized packages? Are the packages on the CRAN repositories ready tho use on these systems or do I have to do any additional work to get them going? MacOS version of R from the att.research site can be run 64 bit as either a Terminal launched console or from the R64.app GUI. My experience is with the 64-bit GUI. Most packages are available as binaries on CRAN these days. The GUI offers a Package Installer so it really quite intuitive. It used to be that you often needed to compile from source, which wass still pretty easy if you have the necessary Apple and other tools from the att.research site. The source compilation generally proceeds automagically. My work machine uses its 16GB very well. Occasionally it maxes out and paging to disk slows down computation for a bit, but eventually the garbage collection kicks in and cleans things up. Overall a very capable environment. Thanks in advance for your help! Axel. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] tests for measures of influence in regression
influence.measures gives several measures of influence for each observation (Cook's Distance, etc) and actually flags observations that it determines are influential by any of the measures. Looks good! But how does it discriminate between the influential and non- influential observations by each of the measures? Like does it do a Bonferroni-corrected t on the residuals identified by the influence measures or some other test? Cheers, Frank Tamborello, PhD W. M. Keck Postdoctoral Fellow School of Health Information Sciences University of Texas Health Science Center, Houston [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on 64-Bit…
On 2/21/10, Axel Urbiz axel.ur...@gmail.com wrote: 2) MacOS or Unix. Sorry for my ignorance on this…but if I use any of these environments on 64-bit and installed R on any of those, this is all I need to have R working on 64-bit. How about installing specialized packages? Are the packages on the CRAN repositories “ready tho use” on these systems or do I have to do any additional work to get them going? I am using R on Debian testing 64-bit. Debian has good support for R, and provides most CRAN packages as binaries, via cran2deb (a rarity on Linux). With a slight effort Debian can be good for a novice in Linux. Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] vloopkup or search function
Hi, Does R has something similar to vlookup function in excel? Thank you for the info. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] vloopkup or search function
?match and several other ways depending on exactly what you are trying to do. On Sun, Feb 21, 2010 at 9:15 PM, Roslina Zakaria zrosl...@yahoo.com wrote: Hi, Does R has something similar to vlookup function in excel? Thank you for the info. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] vloopkup or search function
Tena koe Roslina ?merge HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Roslina Zakaria Sent: Monday, 22 February 2010 3:15 p.m. To: r-help@r-project.org Subject: [R] vloopkup or search function Hi, Does R has something similar to vlookup function in excel? Thank you for the info. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (Somewhat) broken EPS files produced
Hello. I'm writing some simple text using sweave, and faced a strange problem with eps files produced for my plots (one example attached). Individual eps files are interpreted by ghostscript just fine, and show up without errors. But once I try to include them into main LaTeX/Sweave document (using regular \includegraphics, produced by Sweave), ghostscript gives me this error on those files: Error: /undefinedresult in --stringwidth-- Operand stack: (600) 0.5 Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1878 1 3 %oparray_pop 1877 1 3 %oparray_pop 1861 1 3 %oparray_pop 1755 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- Dictionary stack: --dict:1157/1684(ro)(G)-- --dict:0/20(G)-- --dict:82/200(L)-- --dict:178/300(L)-- --dict:91/200(L)-- Current allocation mode is local Current file position is 207944 GPL Ghostscript 8.71: Unrecoverable error, exit code 1 What might be the problem? P.S. I get exactly the same behavior on Debian/sid and OS X. -- Regards, Wartan. Report-fig1.eps Description: PostScript document __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of R in clinical trials
A John Chambers article (published back when S was but a twinkle in
his eye) provides an interesting snapshop of pre-SAS statistical
computing:
@article{chambers67,
title={Some general aspects of statistical computing},
author={Chambers, J.M.},
journal={Journal of the Royal Statistical Society. Series C (Applied
Statistics)},
volume={16},
number={2},
pages={124--132},
year={1967},
publisher={Blackwell Publishing; Royal Statistical Society}
}
BMD and P-stat are discussed in some detail, while the following get
mention in the reference section: TISER, BOMM, ASCOP, AARDVARK,
TARSIER, ZORILLA, GENSTAT, and STORM, among others.
best,
Kingsford Jones
On Thu, Feb 18, 2010 at 9:05 PM, myrm...@earthlink.net wrote:
I am old enough to have lived through this particular transition.
Prior to the advent of SAS, trials were analyzed by in-house written
programs (usually in Fortran maybe with the help of IMSL). These
programs were huge card decks. Having the card reader eat a card
half way through reading the deck was a not unusual occurrence.
I was responsible for deploying the first version of SAS. This meant
compiling PL/I code stored on a magnetic tape and storing it on limited
and expensive disk drives. It was several years before the transition
from using in-house programs to SAS was completed. Yes there was a
great deal of angst and I spent a lot of time convincing people that
in the end there would be a cost advantage and overcoming institutional
inertia.
By the way, this was all done on computers that you will probably find
only in a museum, if at all. These systems filled whole rooms and required
a staff just to keep them running.
Murray M Cooper, PhD
Richland Statistics
9800 North 24th St
Richland, MI 49083
-Original Message-
From: Christopher W. Ryan cr...@binghamton.edu
Sent: Feb 18, 2010 1:08 PM
To: r-help@r-project.org
Cc: p.dalga...@biostat.ku.dk
Subject: Re: [R] Use of R in clinical trials
Pure Food and Drug Act: 1906
FDA: 1930s
founding of SAS: early 1970s
(from the history websites of SAS and FDA)
What did pharmaceutical companies use for data analysis before there was
SAS? And was there much angst over the change to SAS from whatever was
in use before?
Or was there not such emphasis on and need for thorough data analysis
back then?
--Chris
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY 13904
cryanatbinghamtondotedu
If you want to build a ship, don't drum up the men to gather wood,
divide the work and give orders. Instead, teach them to yearn for the
vast and endless sea. [Antoine de St. Exupery]
Bert Gunter wrote:
DISCLAIMER: This represents my personal view and in no way reflects that of
my company.
Warning: This is a long harangue that contains no useful information on R.
May be wise to delete without reading.
--
Sorry folks, I still don't understand your comments. As Cody's original
post
pointed out, there are a host of factors other than ease of programmability
or even quality of results that weigh against any change. To reiterate, all
companies have a huge infrastructure of **validated SAS code** that would
have to be replaced. This, in itself, would take years and cost tens of
millions of dollars at least. Also to reiterate, it's not only
statistical/reporting functionality but even more the integration into the
existing clinical database systems that would have to be rewritten **and
validated**. All this would have to be done while continuing full steam on
existing submissions. It is therefore not surprising to me that no pharma
company in its right mind even contemplates undertaking such an effort.
To put these things into perspective. Let's say Pfizer has 200 SAS
programmers (it's probably more, as they are a large Pharma, but I dunno).
If each programmer costs, conservatively, $200K U.S. per year fully loaded,
that's $40 million U.S. for SAS Programmers. And this is probably a severe
underestimate. So the $14M quoted below is chicken feed -- it doesn't even
make the radar.
To add further perspective, a single (large) pivotal clinical trial can
easily cost $250M . A delay in approval due to fooling around trying to
shift to a whole new software system could easily cause hundreds of million
to billions if it means a competitor gets to the marketplace first. So, to
repeat, SAS costs are chicken feed.
Yes, I suppose that the present system institutionalizes mediocrity. How
could it be otherwise in any such large scale enterprise? Continuity,
reliability, and robustness are all orders of magnitude more important for
both the FDA and Pharma to get safe and efficacious drugs to the public.
Constantly hopping onto the latest and greatest craze (yes, I exaggerate
here!) would be dangerous, unacceptable, and would probably delay drug
approvals.
Re: [R] R on 64-Bit…
Axel Urbiz wrote: Dear R users, I know this issue came up in the list several times. Im currently running R on 32-bit on Windows and due to memory limitation problems would like to move to a 64-bit environment. Im exploring my options and would appreciate your expertise: 1) Windows 64-bit: Prof. Brian Ripley recently posted the experimental built of R for win 64-bit. Ill appreciate any feedback on anyone who has been testing this. He also mentioned that for now, ...this as only being of interest for those who only use a few relatively simple packages. But if one uses packages beyond those relatively simple, how possible is today to have those installed? As far as I know, the problems with running 64-bit R on windows are due to the lack of a well-developed, 64 bit minGW compiler. Therefore I would imagine that the packages that may have trouble installing under the experimental 64 bit build are those that include either C or Fortran source code that needs to be compiled. You may also find that you need to compile packages yourself-- prebuilt 64 bit versions for windows may not be available on CRAN. Axel Urbiz wrote: 2) MacOS or Unix. Sorry for my ignorance on this but if I use any of these environments on 64-bit and installed R on any of those, this is all I need to have R working on 64-bit. How about installing specialized packages? Are the packages on the CRAN repositories ready tho use on these systems or do I have to do any additional work to get them going? Thanks in advance for your help! Axel. MacOS/Unix/Linux shouldn't have a problem with running 64 bit R and building 64 bit R packages-- this is because the GNU project provides a very mature set of 64 bit compilers that these systems can use. I personally use 64 bit R on Mac OS and have had no problems developing and installing packages for the 64 bit system. -Charlie -- View this message in context: http://n4.nabble.com/R-on-64-Bit-tp1563895p1564056.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] retrieve from function
Hi
r-help-boun...@r-project.org napsal dne 19.02.2010 19:06:52:
Thank you for response. The problem is that using return(y1) in my
function
formula always returns y1, but what I want is to return it only when I
wish,
like p.value in
t.test(rnorm(100),rnorm(100))$p.value
Put results in your function to list.
x=function(nbr){list(y-rnorm(nbr), y1 - mean(y);plot(y))}
x(whatever)$y
x(whatever)$y1
and when you do not want results immediately printed consult
?invisible
Regards
Petr
robert
--
View this message in context:
http://n4.nabble.com/retrieve-from-function-
tp1561972p1562012.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on 64-Bit…
Let's not speculate when doing basic research is so easy. I guess the thread about 64-bit Windows referred to was https://stat.ethz.ch/pipermail/r-devel/2010-January/056301.html https://stat.ethz.ch/pipermail/r-devel/2010-January/056411.html (note the update). The CRAN daily check http://cran.r-project.org/web/checks/check_summary.html shows that 106/2170 packages are currently giving errors, and 20 or so of those are available from CRANextras. See http://cran.r-project.org/bin/windows64/contrib/2.11/@ReadMe for more details. Note that the x64 Windows builds are for the unreleased R pre-2.11.0: they will become more visible on CRAN once that is released. For MacOS X: the CRAN build of 2.10.x for 10.5/6 includes the 64-bit x86_64 architecture, and many packages are available (about the same proportion as on x64 Windows). For Unix-alikes (including Linux), 64-bit R has been available for about a decade and some of us have been running 64-bit R exclusively for years. Again, the CRAN Daily Check page shows a high rate of success on x86_64 Linux. Installation of packages without compiled code is done entirely in R and so is the same on any platform. The difficulties in installing packages arise either with compiled code or with dependencies: for example as we do not yet have rgdal working on x64 Windows, none of the dozen or so packages which depend on it are available. On Sun, 21 Feb 2010, Sharpie wrote: Axel Urbiz wrote: Dear R users, I know this issue came up in the list several times. I?m currently running R on 32-bit on Windows and due to memory limitation problems would like to move to a 64-bit environment. I?m exploring my options and would appreciate your expertise: 1) Windows 64-bit: Prof. Brian Ripley recently posted the experimental built of R for win 64-bit. I?ll appreciate any feedback on anyone who has been testing this. He also mentioned that for now, ?...this as only being of interest for those who only use a few relatively simple packages?. But if one uses packages beyond those ?relatively simple?, how possible is today to have those installed? As far as I know, the problems with running 64-bit R on windows are due to the lack of a well-developed, 64 bit minGW compiler. Therefore I would imagine that the packages that may have trouble installing under the experimental 64 bit build are those that include either C or Fortran source code that needs to be compiled. You may also find that you need to compile packages yourself-- prebuilt 64 bit versions for windows may not be available on CRAN. Axel Urbiz wrote: 2) MacOS or Unix. Sorry for my ignorance on this?but if I use any of these environments on 64-bit and installed R on any of those, this is all I need to have R working on 64-bit. How about installing specialized packages? Are the packages on the CRAN repositories ?ready tho use? on these systems or do I have to do any additional work to get them going? Thanks in advance for your help! Axel. MacOS/Unix/Linux shouldn't have a problem with running 64 bit R and building 64 bit R packages-- this is because the GNU project provides a very mature set of 64 bit compilers that these systems can use. I personally use 64 bit R on Mac OS and have had no problems developing and installing packages for the 64 bit system. -Charlie -- View this message in context: http://n4.nabble.com/R-on-64-Bit-tp1563895p1564056.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot is not keeping the order of variable
Peter Dalgaard wrote: d - data.frame(f=c(rare, medium,well-done)) #To get the cast in order of appearance, this can be used: d$f - factor(d$f, levels=unique(d$f)) d$f [1] rare mediumwell-done Levels: rare medium well-done .. which caused some head-scratching from me, because it made me believe there was some hidden Kopenhagen-factor conserving the original order. To protect the innocent: for the more general case, unique() does not help. Dieter levs = c(rare, medium,well-done) set.seed(4711) d - data.frame(f=sample(levs,10,TRUE)) unique(d$f) d$f = factor(d$f, levels=unique(d$f)) levels(d$f) d$f = factor(d$f, levels = levs) levels(d$f) -- View this message in context: http://n4.nabble.com/plot-is-not-keeping-the-order-of-variable-tp1563553p1564087.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to generate graph from dataframe?
I connected to database and i am accessing the tables but i dont know how to generate graphs from the database tables. can anyone please help me i am new to R project -- View this message in context: http://n4.nabble.com/how-to-generate-graph-from-dataframe-tp1564099p1564099.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] new to R Project
hi everyone, i am new to R project can anyone please help me by providing documents my goal is using R i have to connect to the database and i have to generate reports. Thanks in advance chinna. -- View this message in context: http://n4.nabble.com/new-to-R-Project-tp1564104p1564104.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot is not keeping the order of variable
Thank you very much, You solved my problem. On Mon, Feb 22, 2010 at 12:42 AM, Peter Dalgaard p.dalga...@biostat.ku.dkwrote: Or Duek wrote: Ok, It seems that the problem lays in the order (as Ista mentioned), But, when I ask R to order it he chooses to order it by size and not by the specific order I mentioned when I built the vector. Is it possible to tell him to keep the order as mentioned? Thank you. You're still not completely clear about how you built the factor, but I venture a guess: Notice that factors tend to get their levels in alphabetical order, unless special tricks are used. d - data.frame(f=c(rare, medium,well-done)) d$f [1] rare mediumwell-done Levels: medium rare well-done To get the cast in order of appearance, this can be used: d$f - factor(d$f, levels=unique(d$f)) d$f [1] rare mediumwell-done Levels: rare medium well-done On Sun, Feb 21, 2010 at 6:16 PM, Ista Zahn istaz...@gmail.com wrote: Hi Or, I can't know for sure what your problem is without an example, but the first thing I would do is check to make sure that your labels are stored as an ordered factor (and that the order is correct). See ?factor for details. Best, Ista On Sun, Feb 21, 2010 at 10:57 AM, Or Duek ord...@gmail.com wrote: Hi, I created a simple data frame with one factor and one numerical variable. The factor was actually a vector of names of techniques to trimm reaction time data. I want to create a plot that shows the value of F test for every trimming method. So the data frame has its trim factor (who has those labels mean,2500,2000,1500,1000,log,inverse,1SD,2SD) and the numerical variable of the data frame has the F values for each one of those trimming method. When I ask R to plot it, it doesn't keep the order of the trimm verctor correctly and the plot confuses the order so the most left one will be 1500 and then 1SD etc. The values are correct but it is important for me to keep it in the same order I built it. How can I do it? Thank you very much, Or D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
