[R] sprng 2.0 header file for Rmpi

When I try to install Rmpi, it has a dependency rsprng which, as its description says: Provides interface to SPRNG 2.0 APIs I installed it on Mepis by installing the appropriate debs with minimal drama. In the rpm world of Fedora, no such luxury. Installing rsprng fails because: checking

Re: [R] Use of R in clinical trials

I can't believe I'm saying this, but I think Peter is being a bit harsh on SAS. I prefer Greg Snow's analogy (in the fortune collection): If SPSS (or SAS) and R were vehicles, SPSS would be the bus, going on fixed routes and efficiently carrying lots of people to standard places, whereas R

[R] parsing strings between [ ] in columns

Dear all, I have a data.frame with a column like the x shown below myDF-data.frame(cbind(x=c([[1, 0, 0], [0, 1]], [[1, 1, 0], [0, 1]],[[1, 0, 0], [1, 1]], [[0, 0, 1], [0, 1]]))) myDF x 1 [[1, 0, 0], [0, 1]] 2 [[1, 1, 0], [0, 1]] 3 [[1, 0, 0], [1, 1]] 4 [[0, 0, 1], [0,

Re: [R] parsing strings between [ ] in columns

On Thu, Feb 18, 2010 at 8:29 AM, milton ruser milton.ru...@gmail.com wrote: Dear all, I have a data.frame with a column like the x shown below myDF-data.frame(cbind(x=c([[1, 0, 0], [0, 1]],   [[1, 1, 0], [0, 1]],[[1, 0, 0], [1, 1]],   [[0, 0, 1], [0, 1]]))) myDF                    x 1

Re: [R] parsing strings between [ ] in columns

On Thu, Feb 18, 2010 at 8:29 AM, milton ruser milton.ru...@gmail.com wrote: Dear all, I have a data.frame with a column like the x shown below myDF-data.frame(cbind(x=c([[1, 0, 0], [0, 1]],   [[1, 1, 0], [0, 1]],[[1, 0, 0], [1, 1]],   [[0, 0, 1], [0, 1]]))) myDF After identify the groups

Re: [R] sprng 2.0 header file for Rmpi

This is really an R-devel topic. But, - Rmpi only suggests rsprng, and you are unlikely to need it. - sprng2.0b.tar.gz builds from the sources without problem on Fedora 12, and then rsprng installs. See http://sprng.fsu.edu/Version2.0/quick-start.html . On Thu, 18 Feb 2010, Patrick Connolly

[R] Rearranging data

Hi! I have just started learning R and today only I have joined this group. This is my first mail and I wish to thank all of you for allowing me to be part of this group. I have following problem. I have an input.csv file such that corp_id      date    investment_id       rate corp1       

Re: [R] Use of R in clinical trials

On 2/18/10, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote: How amazing that SAS is still used to produce reports that reviewers hate and that requires tedious low-level programming. R + LaTeX has it all over To simplify things, R + LyX could also be a solution. Liviu

[R] R-commands for MDS

Hello I am using the following command but not able to text the values on the graph can someone please make suggestions for improvement #here is the command loc_mds - cmdscale(dist.r, k = 7, eig = TRUE) loc_mds$eig sum(abs(loc_mds$eig[1:2]))/sum(abs(loc_mds$eig))

Re: [R] Bayesian Block Kriging?

Hi Candan, As a more general remark, there is a mailing list for spatial data, including interpolation, r-sig-geo. This question would be more appropriate there. I gave some answers in-line below from what I could come up with. Reposting on r-sig-geo would be a good idea to get more

[R] how to change number of itemes appeare in right-hand-side of the rule with apriori in R(arules)?

Hi All, I use arules library, and try to create an association rules for this transaction file: a,c,f,3,4,5 b,e,1,2,4 a,c,e,f,1,3,4,5 d,5 b,c,e,f,1,2,3,4 a,c,e,f,1,3,4,5 b,c,e,f,1,3,4 b,e,1,2,4 a,c,e,f,1,3,4,5 a,b,c,e,f,1,3,4 a,c,d,f,3,4,5 I want to get the rule such: {c,e,f}= {3,4,5} I

Re: [R] Can R make an usual dotplot

On 02/18/2010 05:31 PM, Peter Ehlers wrote: I agree with Bill's advice, but if you want the easy way out, try dotplot.mtb in package plotrix. Jim Lemon's done the job for us. In fact, Barry Rowlingson and Rolf Turner did the job, I just bask in the glory of being the package maintainer. Jim

Re: [R] How to detect and exclude outliers in R?

I had a similar problem. In my case, I had a large table of data and wanted to find and exclude a single huge value in one column (i.e. remove the entire row). There were thousands of rows of data, and this single value was more than 3x the next value, and at least 30x the typical value. I

Re: [R] parsing strings between [ ] in columns

Here is a solution using strapply in the gsubfn package. First we define a proto object p containing a single method, i.e. function, called fun. fun will take one [...] construct and split it into the numeric vector v using strsplit and will also assign it names. strapply has a built in

[R] Matrix in a Reverse order

Dear 'R' friends I have a sort of stupid question to ask. I have a matrix say of the order 4 X 3 as 83    98    90 21    83    84 70    39    56 65    29    38 Is there any command in R which will reverse the order i.e. I need to have same 4 X 3 matrix but as given below 65    29    38 70   

Re: [R] Matrix in a Reverse order

x[nrow(x):1,] b On Thu, Feb 18, 2010 at 11:45 AM, Amelia Livington amelia_living...@yahoo.com wrote: Dear 'R' friends I have a sort of stupid question to ask. I have a matrix say of the order 4 X 3 as 83    98    90 21    83    84 70    39    56 65    29    38 Is there any command in

Re: [R] Ordered logit in R

so, what did you expect instead as a result of an orderd logistic regression? See http://www.ats.ucla.edu/stat/R/dae/ologit.htm for interpretational help. hth. Mathew, Abraham T schrieb: I ran the follow code for an ordered logit, but don't know why two levels of my dependent variable are at

Re: [R] Use of R in clinical trials

It is easy to devolve into visceral response mode, lose objectivity and slip into intolerance. R, S, S-Plus, SAS, PASW (nee SPSS), STATA, are all tools. Each has strengths and weaknesses. No one is inherently better, or worse than the other. The quality of the results produced by anyone of them

Re: [R] Rearranging data

On Thu, Feb 18, 2010 at 9:21 AM, Anna Carter anna_carte...@yahoo.com wrote: My objective is to rearrange filtered1 as date corp1   corp2   corp11    corp17 17-Feb   65    95 30  16 16-Feb   70   135 15-Feb   69   140 14-Feb   89 13-Feb   

Re: [R] Rearranging data

On Thu, Feb 18, 2010 at 12:14 PM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote:  Ooh, so close! If you'd said 'reshaped' you'd be half way there: .. because that is all in the reshape package. So do library(reshape) first. Oops -- blog: http://geospaced.blogspot.com/ web:

[R] Sweave in PNG: driver online

Dear R addicts, Back in 2006, I posted the proposition for a tweak of the Sweave driver so that PNG figures can be produced instead of eps/pdf : https://stat.ethz.ch/pipermail/r-help/2006-March/102122.html The amount of code modified is tiny (it was designed to induce minimal changes to the

Re: [R] Rearranging data

Try this also; xtabs(rate ~ date + corp_id + investment_id, data = DF) On Thu, Feb 18, 2010 at 7:21 AM, Anna Carter anna_carte...@yahoo.com wrote: Hi! I have just started learning R and today only I have joined this group. This is my first mail and I wish to thank all of you for allowing me

Re: [R] Use of R in clinical trials

On Thu, Feb 18, 2010 at 12:12 PM, John Sorkin jsor...@grecc.umaryland.edu wrote: It is easy to devolve into visceral response mode, lose objectivity and slip into intolerance. R, S, S-Plus, SAS, PASW (nee SPSS), STATA, are all tools. Each has strengths and weaknesses. No one is inherently

[R] curve3d in emdbook package: scaling z axis?

Dear R community, Is there an option to assign minimum and maximum values for z axis in 3D graph using the function curve3d from the package emdbook? I know there are such options for x and y axes. Thanks. Julia

[R] bipartite- is the quantitative linkage density measure weighted or not?

Dear Carsten Dormann, I would like to know if the quantitative linkage density measure given by bipartite is weighted or not? I couldn't find this information on the package manual or on previous posts from R-help.in Tylyanakis et al 2007 (the reference provided in bipartite package manual) both

Re: [R] Trouble with optim function

You're minimizing the log likelihood, but you want to minimize the *negative* log likelihood. Also, optimize() is better than optim() if you have a function of only one argument. Replace Jon Moroney wrote: #Create the log likelihood function LL-function(x) {(trials*log(x))-(x*sumvect)}

Re: [R] AFTREG with ID argument

Göran, David, in order to adapt aftreg to my needs I wrote a little function that I would like to share with you and the community. WHAT DOES IT FIX? (1) Using the id-argument in combination with missing values on covariates wasn't easily possible before because the id-dataframe and the

Re: [R] Use of R in clinical trials

I really like both of your responses. To add to Peter's thoughts, I've found that more than half of SAS programmers can learn modern programming languages given a push. And if pharmaceutical companies ever knew the true cost of SAS in terms of their having to hire more programmers to deal

[R] Munich R Course - Parallel Computing with R

Dear R users, at March 15. 16. there will be an R course for 'Parallel Computing with R' in Munich at the super computer center. The course is part of the Munich R Course series and gives an introduction to parallel computing with R. Especially the R packages snow, snowfall, multicore, nws

Re: [R] Can R make an usual dotplot

On 2010-02-18 1:04, Jim Lemon wrote: On 02/18/2010 05:31 PM, Peter Ehlers wrote: I agree with Bill's advice, but if you want the easy way out, try dotplot.mtb in package plotrix. Jim Lemon's done the job for us. In fact, Barry Rowlingson and Rolf Turner did the job, I just bask in the glory

Re: [R] Checking the assumptions for a proper GLM model

So what I'm looking for is readily available tools/packages that could produce some of the following: 3.6 Summary of Useful Commands (STATA: Source: http://www.ats.ucla.edu/stat/Stata/webbooks/logistic/chapter3/statalog3.htm) * linktest--performs a link test for model specification, in our

[R] Shapiro-Wilk test problem

Hi everybody, Does anyone know what problem may be with this test. I am applying 5 different normality tests and use p-values for them, but for some reason S-W gives me NA, while sample size is 100. Any ideas? Thanks a lot! [[alternative HTML version deleted]]

[R] reading socket hangs

HI All I am newbie to using socket in R. I wrote the function below in R for Windows. The strange behavior is that each time I call this function R seems to hang for I don't know what reason. If I give at prompt line by line the commands below everything is fine: connection happens

[R] variable substitution

Hi I would like to write a script that reads a list of variable names. These variable names are some of the column headers in a data.frame. Then I want do a for-loop to execute various operations on the specified variables in the data.frame, but can't figure out how to do the necessary

Re: [R] Use of R in clinical trials

bill.venab...@csiro.au wrote: I can't believe I'm saying this, but I think Peter is being a bit harsh on SAS. I prefer Greg Snow's analogy (in the fortune collection): If SPSS (or SAS) and R were vehicles, SPSS would be the bus, going on fixed routes and efficiently carrying lots of

Re: [R] variable substitution

Hello, Jon Erik Ween wrote: Hi I would like to write a script that reads a list of variable names. These variable names are some of the column headers in a data.frame. Then I want do a for-loop to execute various operations on the specified variables in the data.frame, but can't figure out

Re: [R] how to change number of itemes appeare in right-hand-side of the rule with apriori in R(arules)?

Nooshin, arules currently only implements mining algorithms that produce rules with one item in the right-hand-side (RHS) (apriori, ruleInduction). If you need rules with more than one items then you can mine frequent itemsets (with eclat or apriori). Then you take each itemset, e.g., {1, 2,

[R] 'npmc output'

Hi I am new to using R and don't know understand the output of the npmc package. What is the difference between the two R values, and which one should I consider? Any advice on this would be helpful as would direction to relevant links/literature. Thank you Gráinne [[alternative HTML

[R] Error message when using error.bars(x,add=TRUE)

Hey hey, I`m analyzing a data set containing the element contentrations of various samples... I wanted to construct notched boxplots and got quite ugly results for some of the boxplots. The notches are often larger then the hinges which resulted in weird looking edges (even though I`m using a

[R] aggregate by column names

Hi, I've this dataframe: V1 V5 V6 1 MOD13Q1_249 0.1723 A1 2 MOD13Q1_249 0.1824 B1 3 MOD13Q1_249 0.1824 C1 4 MOD13Q1_249 0.1774 A2 5 MOD13Q1_249 0.1953 B2 6 MOD13Q1_249 0.1824 C2 7 MOD13Q1_265 0.1921 A1 8 MOD13Q1_265 0.1938 B1 9

Re: [R] Shapiro-Wilk test problem

Trafim, Could you please provide an example of the data? I don't believe the sample size to be the driver of the issue you are having. For example, set.seed(20) x - rnorm(100) shapiro.test(x) returns no error and a p value of 0.5519. Sample (or actual) data would be helpful in diagnosing

[R] Trouble with optim function

optim really isn't intended for [1D] functions. And if you have a constrained search area, it pays to use it. The result you are getting is like the second root of a quadratic that you are not interested in. You may want to be rather careful about the problem to make sure you have the function

[R] non-linear contrained optimization

If the data is fairly small, send it and the objective function to me off-list and I'll give it a quick try. However, this looks very much like the kind of distance-constrained type of problem like the largest small polygon i.e., what is the maximum area hexagon where no vertex is more than 1

Re: [R] aggregate by column names

Try this: xtabs(V5 ~ V1 + V6, data = DF) On Thu, Feb 18, 2010 at 1:50 PM, Alfredo Alessandrini alfreal...@gmail.com wrote: Hi, I've this dataframe:                 V1     V5 V6 1   MOD13Q1_249 0.1723 A1 2   MOD13Q1_249 0.1824 B1 3   MOD13Q1_249 0.1824 C1 4   MOD13Q1_249

[R] row indexes from logical statment

Is there any easy way to pull out the row indexes for a logical matching statment? #example code# foo - data.frame(name=c(rep(A, 25), rep(B, 25), rep(C, 25), rep(A, 25)), stuff=rnorm(100), and=rnorm(100), things=rnorm(100)) #this is what I

[R] Extract p-value from aftreg object

Dear all, does anyone know how I can extract specific p-values for covariates from an aftreg object? After fitting a model with aftreg I can find all different variables by using str(), but there's no place where p-values are kept. The odd thing is that print() displays them correctly.

Re: [R] row indexes from logical statment

Hi Stephen, See below. On Thursday 18 February 2010 11:01:25 am stephen sefick wrote: Is there any easy way to pull out the row indexes for a logical matching statment? #example code# foo - data.frame(name=c(rep(A, 25), rep(B, 25),

Re: [R] row indexes from logical statment

If I understand your question, you can try this: which(foo$name %in% c(A, B)) On Thu, Feb 18, 2010 at 2:01 PM, stephen sefick ssef...@gmail.com wrote: Is there any easy way to pull out the row indexes for a logical matching statment? #example

Re: [R] row indexes from logical statment

Hi: You might also want to consider the use of subset, as in subset(foo, name == A)or subset(foo, name %in% c(A, B)) HTH, Dennis On Thu, Feb 18, 2010 at 8:01 AM, stephen sefick ssef...@gmail.com wrote: Is there any easy way to pull out the row indexes for a logical matching statment?

[R] svm regression

Hi, I am trying to use svm for regression data. this is how my data looks like: dataTrain x y z 1 4 6 2 5 4 3 7 5 classTrain a 2 3 4 dataTest x y z 1 7 2 2 8 3 classTest a 3 4 5 building the model model-svm(dataTrain,classTrain,type=nu-regression) pred - predict(model,

Re: [R] AFTREG with ID argument

Göran, no worries - your help advice is already invaluable! Göran Broström wrote: 2010/2/18 Philipp Rappold philipp.rapp...@gmail.com: Göran, David, in order to adapt aftreg to my needs I wrote a little function that I would like to share with you and the community. I once promised to fix

Re: [R] Checking the assumptions for a proper GLM model

At one time the answer would have been to buy a copy of Venables and Ripley's Modern Applied Statistics with S (and R), and that would still be a sensible strategy. There are now quite a few other R- centric texts that have been published in the last few years. Search Amazon if needed. You

Re: [R] Use of R in clinical trials

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

Re: [R] Use of R in clinical trials

Bert, I have to disagree with just part of what you said. The ultimate savings by using R is astronomical. Up front it would definitely cost more, as you so eloquently stated. So it boils down to short-term vs. long-term thinking. More importantly, the statistical/graphical reports

[R] problem with multiple plots (mfrow, mar)

Dear R-users, I often stack plots that have the same x-axis. To save space and have the plots themselves as large as possible I like to minimize the margins between the plots to zero. I use the mfrow and mar parameters to achieve this. However, the different margin settings for the individual

[R] an error about return some vectors from some functions within a function

Dear all, When I try to return some vectors from some functions within a function, it indicate an error, Error in rbind(ck1, ck2, ck3) : object 'ck1' not found, in one of the iterations and stop.  Since I am not experienced in programming, can anyone give me a suggestion to inspect this

Re: [R] Extract p-value from aftreg object

I don't seem to have the unnamed package loaded that has aftreg(), but in general you ought to be able to get what you want by looking not just at the aftreg-object but also at the print(aftreg)-object using str(). On Feb 18, 2010, at 11:07 AM, Philipp Rappold wrote: Dear all, does

Re: [R] AFTREG with ID argument

2010/2/18 Philipp Rappold philipp.rapp...@gmail.com: Göran, David, in order to adapt aftreg to my needs I wrote a little function that I would like to share with you and the community. I once promised to fix this 'asap'. Now I promise to do it tonight. OK? Göran WHAT DOES IT FIX? (1)

Re: [R] Extract p-value from aftreg object

2010/2/18 Philipp Rappold philipp.rapp...@gmail.com: Dear all, does anyone know how I can extract specific p-values for covariates from an aftreg object? After fitting a model with aftreg I can find all different variables by using str(), but there's no place where p-values are kept. The odd

[R] subset() for multiple values

This code works: subset(NativeDominant.df,!ID==37-R17) This code does not: Tree.df-subset(NativeDominant.df,!ID==c(37-R17,37-R18,10-R1,37-R21,37-R24,R7A-R1,3-R1,37-R16)) how do i get subset() to work on a range of values? -- View this message in context:

Re: [R] subset() for multiple values

Use ' %in%': Tree.df-subset(NativeDominant.df,!ID %in% c(37-R17,37-R18,10-R1,37-R21,37-R24,R7A-R1,3-R1,37-R16)) On Thu, Feb 18, 2010 at 3:59 PM, chipmaney chipma...@hotmail.com wrote: This code works: subset(NativeDominant.df,!ID==37-R17) This code does not:

Re: [R] subset() for multiple values

subset(df, x %in% c(...)) chipmaney wrote: This code works: subset(NativeDominant.df,!ID==37-R17) This code does not: Tree.df-subset(NativeDominant.df,!ID==c(37-R17,37-R18,10-R1,37-R21,37-R24,R7A-R1,3-R1,37-R16)) how do i get subset() to work on a range of values?

[R] Funny result from rep(...) procedure

I'm observing odd behavior of the rep(...) procedure when using variables as parameters in a loop. Here's a simple loop on a vector 'branches' that is c(5,6,5,5,5). The statement in question is print(c(ni,rep(i,times=ni))) that works properly first time through the loop but the second

[R] Hmisc summary.formula.reverse

Hello, Can summary.formula.reverse be customized to allow other summary statistics to be reported rather than the quartiles and mean +/- sd? The fun option apparently doesn't apply when method='reverse' Thanks -- Abhijit Dasgupta, PhD Statistician | Clinical Sciences Section | NIAMS/NIH

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

Re: [R] an error about return some vectors from some functions within a function

Might be the case that the 'while' loop was not executed and therefore 'ck1' was not defined. You might put a check to see if that was happening. Also you are incrementing 'count1' in the functions and it is not being passed in as a parameter. What are you expecting it to do? Is it defined in

Re: [R] Funny result from rep(...) procedure

Cannot reproduce, what is branches? If you can narrow it down to a commented, minimal, self-contained, reproducible example, you're far more likely to get help from the list. dkStevens wrote: I'm observing odd behavior of the rep(...) procedure when using variables as parameters in a loop.

Re: [R] Funny result from rep(...) procedure

Erik Iverson wrote: Cannot reproduce, what is branches? If you can narrow it down to a commented, minimal, self-contained, reproducible example, you're far more likely to get help from the list. My blinded guess though, is something to do with FAQ 7.31.

Re: [R] Extract p-value from aftreg object

On Feb 18, 2010, at 12:33 PM, David Winsemius wrote: I don't seem to have the unnamed package loaded that has aftreg(), but in general you ought to be able to get what you want by looking not just at the aftreg-object but also at the print(aftreg)-object using str(). Trying that

Re: [R] Procedure not working for actual data

Even though it may work for a small subset, it can still break on larger sets. Your code was doing a number of 'unlist' and tearing apart the data and it is possible that some of the transformations were not aligned with the data in the way you thought them to be. What you need to do in that case

Re: [R] Funny result from rep(...) procedure

Sorry, not reproducible. This works for me (as expected): branches-c(5,6) iInd = 1 for(i in 1:length(branches)) { print((1:branches[i])+iInd-1) # iInd is a position shift of the index ni = branches[i] print(i) print(ni) print(c(ni,rep(i,times=ni))) # ... some interesting other

[R] survey package question

Should the svyby function be able to work with svyquantile? I get the error below ... data(api) dclus1-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) svyby(~api00, design=dclus1, by = ~stype, quantiles=c(.25,.5,.75), FUN=svyquantile,

[R] 3D plot

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? 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

[R] Changed results in analyses run in sem and nlme ??

I'm uncertain how helpful it will be to give example code, but last week, this model gave an error message to the tune of failed to converge after about 5 minutes of run-time : library(nlme) model.A- lme (fixed = avbranch~ wk*trt*pop , random = ~wk|ID/fam/pop, data=branch) It seemed

Re: [R] skip lapply item for conditions(RAM, execution time)

Thank you, but: - How do I create a condition object watching for memory overflow? Or, alternatively, excess time? - How do I tell R to end the current lapply item, clean up memory and proceed to the next item? (I know I can write a wrapper function including gc() and direct lapply to that

Re: [R] Checking the assumptions for a proper GLM model

Well, yes and no. Obviously I was not asking for the complete recap of a all the theory on the subject. My main concern is finding readily available CRAN functions and packages that would help me in the process. I've found the UCLA site to be very informative and spent a lot of time ther the last

Re: [R] Procedure not working for actual data

Hey Jim, That appears to work properly with my larger data set. That's really strange to me though, why would my procedure not work even though the test works correctly? I have always coded under the assumption that the code doesn't do anything the user doesn't tell it too but I cant see a

[R] Plot spatial location by using azimuth and distance?

Hey, I have one data like this: tree azimuth distance 1 312 200 2 322 201 3 304 173 4 294 154 5 313 95 The azimuth stands for the azimuth of tree from plot center, and the distance is the distance of tree from plot center. I want

[R] error in using sample( )

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. Thank you Best, Jing

Re: [R] Use of R in clinical trials

The key dates are 1938 and 1962. The FDC act of 1938 essentially mandated (demonstration of) safety. The tox testing infrastructure grew from that.At that time, there were no computers, little data, little statistics methodology. Statistics played little role -- as is still mainly the case today

Re: [R] Funny result from rep(...) procedure

On Thu, Feb 18, 2010 at 7:15 PM, Erik Iverson er...@ccbr.umn.edu wrote: Erik Iverson wrote: Cannot reproduce, what is branches?  If you can narrow it down to a commented, minimal, self-contained, reproducible example, you're far more likely to get help from the list. My blinded guess

Re: [R] Procedure not working for actual data

?traceback may be useful. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of jim holtman Sent: Thursday, February 18, 2010 10:17 AM To: ROLL Josh F Cc: r-help@r-project.org Subject:

Re: [R] Hmisc summary.formula.reverse

Abhijit Dasgupta wrote: Hello, Can summary.formula.reverse be customized to allow other summary statistics to be reported rather than the quartiles and mean +/- sd? The Not easily. I'm not sure which other statistics would be descriptive however; certainly not the min and max or standard

Re: [R] error in using sample( )

Works for me: sample(c(0,1,2),1,prob=c(0.2,0.3,0.5)) [1] 2 On Thu, Feb 18, 2010 at 7:48 AM, 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

[R] svm regression

Hi, I am having trouble with svm regression.it is not giving the right results. example model - svm(dataTrain,classTrain,type=eps-regression) predict(model, dataTest) 36 37 38 39 40 41 42 -13.838257 -1.475401 10.502739 -3.047656 -8.713697

Re: [R] Funny result from rep(...) procedure

That's what I did. 'branches' was shown at the top. branches = c(5,6,5,5,5) I tested this. When I copy and paste into R 10.0 I get the result in the post. Perhaps I should reinstall R. I guess I don't see how much more narrow I can get than this. i iInd = 1 for(i in

Re: [R] Funny result from rep(...) procedure

I could send the entire bit of code but I was hoping that someone would recognize the issue from past experience. I may be an artifact of other parts of the code. I observed the problem in a larger context and cut out all that you see below. The comments were next to the results to clarify.

Re: [R] Building R from source

On 17.02.2010 15:38, rkevinbur...@charter.net wrote: Thank you for the tip. I was used to inserting write statements and was surpised when it didn't work and reading this section I see that I shouldn't have been doing this anyway. One more question. Is there another call that I can use to

Re: [R] Funny result from rep(...) procedure

What does print(as.integer(branches)) give? That is what rep() uses. /H On Thu, Feb 18, 2010 at 7:49 PM, dkStevens david.stev...@usu.edu wrote: I could send the entire bit of code but I was hoping that someone would recognize the issue from past experience. I may be an artifact of other

[R] logistic regression - what is being predicted when using predict - probabilities or odds?

Dear gurus, I've analyzed a (fake) data set (data) using logistic regression (glm): logreg1 - glm(z ~ x1 + x2 + y, data=data, family=binomial(logit), na.action=na.pass) Then, I created a data frame with 2 fixed levels (0 and 1) for each predictor: attach(data) x1-c(0,1) x2-c(0,1) y-c(0,1)

[R] Natural Language Processing of R help archives

Hi useRs, This is not so much a help request as it is a request for feedback about the possibilities of using Natural Language Processing (NLP) techniques on the r-help archives for a more 'effective' retrieval of answers. A few points that may capture what I'm trying to get at: 1) R has an

Re: [R] svm regression

On 18.02.2010 17:54, madhu sankar wrote: Hi, I am trying to use svm for regression data. this is how my data looks like: dataTrain x y z 1 4 6 2 5 4 3 7 5 classTrain a 2 3 4 dataTest x y z 1 7 2 2 8 3 classTest a 3 4 5 building the model

Re: [R] svm regression

On 18.02.2010 19:43, madhu sankar wrote: Hi, I am having trouble with svm regression.it is not giving the right results. example model- svm(dataTrain,classTrain,type=eps-regression) predict(model, dataTest) 36 37 38 39 40 41 42 -13.838257

Re: [R] Use of R in clinical trials

On 19/02/2010, at 1:12 AM, John Sorkin wrote: It is easy to devolve into visceral response mode, lose objectivity and slip into intolerance. R, S, S-Plus, SAS, PASW (nee SPSS), STATA, are all tools. Each has strengths and weaknesses. No one is inherently better, or worse than the other.

Re: [R] Use of R in clinical trials

On Thu, Feb 18, 2010 at 12:36 PM, Bert Gunter gunter.ber...@gene.com wrote: The key dates are 1938 and 1962. The FDC act of 1938 essentially mandated (demonstration of) safety. The tox testing infrastructure grew from that.At that time, there were no computers, little data, little statistics

Re: [R] Use of R in clinical trials

Christopher W. Ryan wrote: 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

Re: [R] Use of R in clinical trials

Points regarding the advantages of LaTex are very well taken. If I were fortunate enough to have complete ownership of the document (as might be the case with a DSMB report produced by the Biostat group), then LaTex would be a wonderful choice.  Though I am not a LaTex user, I can easily

[R] Extracting values from a list

I have run a kruskal.test() using the by() function, which returns a list of results like the following (subset of results): Herb.df$ID: 4-2 Kruskal-Wallis chi-squared = 18.93, df = 7, p-value = 0.00841 Herb.df$ID: 44-1

Re: [R] Use of R in clinical trials

I am old enough. Memory isn't always reliable but Doug Bates recounting is what I remember and a quick search has BMDP developed in 1961 and SAS in 1966. To my surprise, the search produced a site that offered BMDP for sale. On 2/18/2010 11:15 AM, Peter Dalgaard wrote: Christopher W. Ryan

Re: [R] logistic regression - what is being predicted when using

On 18-Feb-10 18:58:57, Dimitri Liakhovitski wrote: Dear gurus, I've analyzed a (fake) data set (data) using logistic regression (glm): logreg1 - glm(z ~ x1 + x2 + y, data=data, family=binomial(logit), na.action=na.pass) Then, I created a data frame with 2 fixed levels (0 and 1) for each

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