[R] ffload "unzip not found"

Dear all, I do have zipped data and want to use the package "ff". Unfortunately I am not able to load the date: When I try to use "ffload" I always get: Error in system(cmd, intern = TRUE) : 'unzip' not found Conferring to other R-help posts I already downloaded a software for zipping/unzipping

[R] Event-triggered change in value with a time-delay

Hello, I am solving a set of ODEs using deSolve and have run into a problem I would appreciate some advice on. One of the parameters (m) in the ODEs changes between two states when one of the variables (D) crosses a threshold (D_T) for the first time in either direction. Additionally, when the var

Re: [R] Event-triggered change in value with a time-delay

Hi David, Thank you for your suggestion- I will look into it some more. Thanks again, Hannah On Wed, Apr 18, 2018 at 5:09 PM, David Winsemius wrote: > > > On Apr 18, 2018, at 1:04 AM, Hannah Meredith > wrote: > > > > Hello, > > > > I am solving a set of OD

[R] GAMM - error when using spline smoother, only allowed to use tensor product

better when I don't treat the sin covariate as cyclic, but that doesn't seem appropriate to me, because a sin is naturally cyclic. Any help is much appreciate, thank-you for your time! Hannah [[alternative HTML version deleted]] _

[R] Ancestral state problem (length of phylogenetic and phenotypic data don't match)

Dear All, I am trying to do an ancestral state reconstruction in R using the package 'ape'. I have tried trimming my tree in BayesTraits and in R itself, and the resulting tree reports as having 573 species tips, which is the same as my dataset. As far as I can tell everything is loading prop

[R] graphs for pretest data

Is there an easy way to make graphs for the following data. I have pretest and posttest scores for men and women. I would like to form a 'titlted segment' plot for the data. That is, make segments joining the scores, with different types of segments for men and women. Example data: menpre <- c(43

Re: [R] xyplot and subscripts

I'm not sure how to do this in lattice, but here is an option with ggplot2. library(ggplot2) set.seed(123) # Make sure the data has a variable that indicates # which group is red and which one is black DF <- data.frame(x = rnorm(10), y = rnorm(10), gr = rep(1:5, 2),endpoint = c(rep("Red_Group",5)

Re: [R] Strange package installation error

Hi Janet, Were you able to install the package? I just installed it without problems. I don't think there should be any issues installing it. If it has not worked yet, make sure your R is updated, and if it is, maybe reinstall it. Best, Juliet On Mon, Aug 17, 2009 at 8:43 PM, Janet Rosenbaum wr

Re: [R] How can I do a generic specification in multiple logistic regression

Is multinom the function you are looking for? library(nnet) library(MASS) ?multinom indicates that this fits multinomial log-linear models. If you are looking for multiple logistic regression you may want to read up on glm or lrm from the Design package. Could you elaborate on what you mean by a

Re: [R] Within factor & random factor

Let's say that location defined a group, and observations may be more similar in a group. You could account for this similarity with the following model. model1 <-lme(X~CorP,random=~1|location,data=mydata,method="ML") This fits a random intercept model grouped by location. This would assume that

Re: [R] Logistic Politomic Regression in R

Check out Chapter 7 of Laura Thompson's R Companion to Agresti (you can find it online). It will show you how to fit proportional odds models (polr in MASS, and lrm in the Design library) and multinomial regression models. __ R-help@r-project.org mailin

Re: [R] permutation test - query

You may find the multtest package helpful. It implements methods from Westfall and Young (Resampling based multiple testing). On Mon, Aug 31, 2009 at 5:37 AM, Yonatan Nissenbaum wrote: > Hi, > > My query is regarding permutation test and reshuffling of genotype/phenotype > data > I have been usi

Re: [R] using an array of strings with strsplit, issue when including a space in split criteria

I get a different result: txt <- c("sales to 23 August 2008 published 29 August","sales to 6 September 2008 published 11 September") strsplit(txt, 'published ', fixed=TRUE) [[1]] [1] "sales to 23 August 2008 " "29 August" [[2]] [1] "sales to 6 September 2008 " "11 September" > sessionInfo() R ve

Re: [R] Scan and read.table

Do you run into problems if you use something like: cc <- rep("numeric",9) mydata <- read.table("yourdata",header=TRUE,colClasses=cc,skip=1,nrows=numRows) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read t

Re: [R] Compare a group of line slopes

The test that a slope differs by group is a test that the variable*group interaction equals zero (overall test). Maybe searching post-hoc comparisons in regression will give you some leads. On Tue, Sep 15, 2009 at 10:57 AM, Jun Shen wrote: > Hi, all, > > I am thinking to compare a group of slopes

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

Re: [R] Problem with installing "genetics" package

I just installed it, and it worked fine. > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached ba

Re: [R] How to do: Correlation with "blocks" (or - "repeated measures" ?!) ?

I didn't follow your question completely. But do a search for intraclass correlation with nlme or lmer and see if those results relate to the question you are asking. If so, I would suggest following up on the mixed model list. I know you wanted to avoid mixed models, but if I have understood your

Re: [R] Three most useful R package

I use rms, lme4, ggplot2 frequently (also lattice and MASS). On Tue, Mar 2, 2010 at 3:13 PM, Ralf B wrote: > Hi R-fans, > > I would like put out a question to all R users on this list and hope > it will create some feedback and discussion. > > 1) What are your 3 most useful R package? and > > 2)

Re: [R] Help with multtest (rawp2adjp)

Some code to cut and paste would be helpful. The following may help out. library(multtest) # create some p-values p <- runif(100) p <- sort(p) p_adj <- mt.rawp2adjp(p, proc="BH", alpha = 0.05) > str(p_adj) List of 4 $ adjp : num [1:100, 1:2] 0.0142 0.0174 0.0254 0.0258 0.0736 ... ..- attr(*

Re: [R] skip the error to continue the logistic regression in a loop

Here are two things to try. First check the data. There may be a factor that does not have variation in the sample. For example, if you had a predictor such as 'present'/'absent', in the current sample, all of them may be 'present'. Second, you can put a 'try' statement in your function. try(

[R] correct way to subset a vector

Hi, #make example data dat <- data.frame(matrix(rnorm(15),ncol=5)) colnames(dat) <- c("ab","cd","ef","gh","ij") If I want to get a subset of the data for the middle 3 columns, and I know the names of the start column and the end column, I can do this: mysub <- subset(dat,select=c(cd:gh)) If I w

[R] strategy to iterate over repeated measures/longitudinal data

Hi Group, Create some example data. set.seed(1) wide_data <- data.frame( id=c(1:10), predictor1 = sample(c("a","b"),10,replace=TRUE), predictor2 = sample(c("a","b"),10,replace=TRUE), predictor3 = sample(c("a","b"),10,replace=TRUE), measurement1=rnorm(10), measurement2=rnorm

[R] c-index validation from Design library

Hi Group, I have a question about obtaining the bias-corrected c-index using validate from the Design library. As an example, consider the example from help page: library(Design) ?validate.lrm n <- 1000 age<- rnorm(n, 50, 10) blood.pressure <- rnorm(n, 120, 15) cholesterol<- rno

Re: [R] Simulate residuals with different properties for a linear model (regression)

Here are a couple of examples. # residuals not normal n <- 100; x = seq(n) y = 10 + 10 *x + 20 * rchisq(n,df=2) non_normal_lm = lm(y~x) #non-constant variance n <- 100; x = seq(n) y = 100 + 3 * x + rnorm(n,0,3) * x; het_var_lm = lm(y~x) #For each of these try: plot(non_normal_lm) plot(het_var_lm

Re: [R] suggestion for paired t-tests

Hi Jack, Maybe this helps. # make some data set.seed(123) condition <- factor(rep(c("a","b"), each = 5)) score <- rnorm(10); lg <- data.frame(condition, score) # Carry out commands a <- subset(lg,condition=="a")["score"] b <- subset(lg,condition=="b")["score"] t.test(a,b,paired=TRUE) #Error

Re: [R] plotting points in random but different colors based on condition

Maybe this is helpful. Install ggplot2. #Create a small example x <- seq(1:20) y <- (2*x) + rnorm(length(x),0,1) id <- rep(1:5,each=4) dat <- data.frame(x,y,id) library(ggplot2) p <- ggplot(dat,aes(x=x,y=y,colour=factor(id))) p <- p + geom_point() p If this is not the correct structure, maybe i

[R] uninstalling and installing on linux

Hi List, I have a question about uninstalling and installing R on linux, which I am new to. > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C

Re: [R] uninstalling and installing on linux

>> >> This has not worked for me, meaning I can still use R, so instead I >> removed the directory >> >> rm -fR R-2.10.1 >> >> Is one method preferable to another. And what am I doing incorrectly >> with "make uninstall"? > > Don't know, probably not many are using it and it may be fairly untested.

[R] doBy and Hmisc on R version 2.11.0

I installed R 2.11.0, and I don't think I can load the doBy package now. Any suggestions? > library("doBy") Loading required package: survival Loading required package: splines Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'Hmisc' Error: package/namespace

Re: [R] doBy and Hmisc on R version 2.11.0

I should have mentioned that I also tried: > install.packages("Hmisc") Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘Hmisc’ is not available On Fri, Apr 23, 2010 at 3:15 PM, David Winsemius wrote: > > On Apr 23, 2010, at 3:09 PM,

Re: [R] Error in make.names when trying to read.table in if statement

Does this work for you? data_list <- list() filepattern="modrate*" all_files <- list.files(pattern=filepattern) data_list <- lapply(all_files, read.table,header=TRUE,sep=",") __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-h

Re: [R] QQ plotting of various distributions...

I think it's helpful to show the sampling variability in a QQ plot under repeated sampling. An example is given in Venables, Ripley pg 86. The variance is higher at the tails. Even when the distributions are the same, the QQ plot does not have to resemble a straight line because of sampling. I don'

Re: [R] when vectorising does not work: silent function fail?

> > Also, you probably get less data copying by using a for() or while() loop > than by using apply() in this context. Why may there be less data copying with "for" and "while" compared to apply? > > Finally, the overhead of formula parsing and model matrix construction > repeated thousands of

Re: [R] Need help for graphical representation

Check out examples in the lattice package and ggplot2 package. For example let's say you plot points and confidence intervals. These packages will then allow you to plot these values by group and by combinations of groups. Look up conditioning and faceting in these packages. On Wed, Nov 18, 2009 a

Re: [R] Sampling dataframe

Here are some options that may help you out. First, let's put the data in a format that can be cut-and-pasted into R. myData <- read.table(textConnection("var1 var2 var3 1 111 2 312 3 813 4 614 51015 6 221 7 422 8

Re: [R] Partial correlations and p-values

Your R code looks correct. Because this is a straightforward calculation, I would be surprised if there were any differences with SPSS. It may be worthwhile to check if SPSS gives partial correlations or semipartial correlations. For example, if you take the correlation between py <- resid(lm(y

[R] data manipulation/subsetting and relation matrix

Hi List, Here is some example data. myDat <- read.table(textConnection("group id 1 101 1 201 1 301 2 401 2 501 2 601 3 701 3 801 3 901"),header=TRUE) closeAllConnections() corr_mat <-read.table(textConnection("1 1 .5 0 0 0 0 0 0 0 2 .5 1 0 0 0 0 0 0 0 3 00 1.0

Re: [R] How to set a filter during reading tables

One can use colClasses to set which columns get read in. For the columns you don't want you can set those to NULL. For example, cc <- c("NULL",rep("numeric",9)) myData <- read.table("myFile.txt",header=TRUE,colClasses=cc,nrow=numRows). On Wed, May 27, 2009 at 12:27 PM, wrote: > We are reading

Re: [R] How to set a filter during reading tables

There are several things you can tell read.table to make it faster. First, as mentioned, setting colClasses helps. I think telling read.table how many rows and columns there are also helps. When this was not sufficient, I've had to do the data processing using Python, Perl, or awk. If that had

[R] learning about panel functions in lattice

Hi All, I am trying to understand panel functions. Let's use this example. library(lattice) time<-c(rep(1:10,5)) y <-time+rnorm(50,5,2) group<-c(rep('A',30),rep('B',20)) subject<-c(rep('a',10),rep('b',10),rep('c',10),rep('d',10),rep('e',10)) myData <-data.frame(subject,group,time,y) head(myData)

Re: [R] [Repost][Off Topic] Pointers needed for breakthrough in statistics

You may find the following two books useful: Lehmann, Reminiscences of a Statistician (Springer). David Salsburg, The lady testing tea. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide h

[R] png with ggplot on windows xp

Hi Group, I posted this question on the ggplot list and was advised to try here also. The code below produces a plot as a png and pdf. The pdf looks great, and I cannot make the png look this way. I've tried various combinations of height, width, and dpi, but it has not worked out so far. Any sug

[R] using more plotting area for a lattice plot

Hi Group, For the plot below, are there other ways I can use more of the plotting space. I've tweaked the parameters I know of. I could also put the plot titles inside the plot if there is a way to do that. Thanks for your input. Regards, Juliet p1 <- runif(1000) # sample data qp1 <- qqmath(~ -l

[R] looking for one-liner for strsplit and regex

Hi, I have a line such as: myline <- "0.10 1.5000 0.6000 538 0.369404" and I would like to put the numbers into a vector. Some combination of tabs and spaces occur between the numbers. I tried: try1 <- strsplit(myline,"[[:blank:]]+") > try1 [[1]] [1] ""

[R] what is R best for; what should one learn in addition to R

Hi, I've been working with R for a couple of years, and I've been able to get most of the things done that I needed (sometimes in a roundabout way). A few experienced statisticians told me that R is best for interactive data analysis, but for large-scale computations, one needs something else. I

Re: [R] Eigenvectors and values in R and SAS

Here is an example that may be helpful. A <- matrix(c(-3,5,4,-2),nrow=2,byrow=TRUE) eigs <- eigen(A) eigs $values [1] -7 2 $vectors [,1] [,2] [1,] -0.7808688 -0.7071068 [2,] 0.6246950 -0.7071068 The eigenvectors may be scaled differently because they are not unique (or have

Re: [R] simulation of binary data

Check out the help page of the lrm function in the rms library. To show how lrm is used, the examples simulate data for logistic regression. This may give you some ideas. On Wed, Jan 20, 2010 at 10:41 AM, omar kairan wrote: > Hi, > > could someone help me with dilemma on the simulation of logisti

[R] convert data frame of values into correlation matrix

Hi Group, Consider a data frame like this: mylabel1 <- rep(c("A","B","C"),each=3) mylabel2 <- rep(c("A","B","C"),3) corrs <- c(1,.8,.7,.8,1,.7,.7,.7,1) myData <- data.frame(mylabel1,mylabel2,corrs) myData mylabel1 mylabel2 corrs 1AA 1.0 2AB 0.8 3A

Re: [R] Hierarchical data sets: which software to use?

Check out the book Linear Mixed Models: A Practical Guide Using Statistical Software by Brady West. It sets up analyses, similar to ones you described, in SPSS, R, and others as well. In general, I think it is good to know a couple of different packages, especially if you plan on doing a lot of

Re: [R] mgcv: how select significant predictor vars when using gam(...select=TRUE) using automatic optimization

Hi Jan and Simon, If possible, could you attach the diagnostic plots. I would be curious to see them. Thanks, Juliet On Fri, Apr 19, 2013 at 4:39 AM, jholstei wrote: > Simon, > > that was very instructive—very special thanks to you. > I already noticed that the model was bad, but it was not

Re: [R] Apply acf to data frame containing 'NA'

Hi, The acf function requires that you specify how to deal with NAs in your data. By default, it uses na.fail ("Error in *na.fail.default*(as.ts(x)) : missing values in object). Try using na.action=na.pass as an argument. While this will pass over your NAs, make sure that you understand how that w

Re: [R] Speeding reading of a large file

All, Can someone describe what x[] <- lapply(x, as.numeric) I see that it is putting the list elements into a data frame. The results for lapply are a list, so how does this become a data frame. Thanks, Juliet On Mon, Dec 3, 2012 at 5:49 PM, Fisher Dennis wrote: > Colleagues, >

Re: [R] Speeding reading of a large file

Because x[] keeps the dimensions, unlike just x. > > Hope this helps, > > Rui Barradas > Em 06-12-2012 16:24, Juliet Hannah escreveu: > >> All, >> >> Can someone describe what >> >> x[] <- lapply(x, as.numeric) >> >> I see th

[R] [] and escaping in regular expressions

Is it correct that one does not need to escape special characters such as "*" (are these properly called metacharacters) inside []. If so, what is the logic to this? mytest <- "he*llo" sub("[*]","",mytest) sub("\\*","",mytest) [] is easier to read for me than \\. Is this what people tend to use?

Re: [R] reg: R genetics problem

I've used this package before, and it always gives me the message: NOTE: THIS PACKAGE IS NOW OBSOLETE. So I stopped using it. I just tried installing it and it gave me some new errors (below). Maybe you should also post your sessionInfo(). > library("genetics") Loading required package: combinat

Re: [R] logistic regression - glm() - example in Dalgaard's book ISwR

You may find both of Alan Agresti's books on categorcial data analysis useful. Try googling both books and then search the word "grouped" within each book. Agresti refers to the difference you describe as grouped versus ungrouped data. The likelihoods differ and all summaries based on the likelihoo

[R] long to wide on larger data set

I have a data set that has 4 columns and 53860858 rows. I was able to read this into R with: cc <- rep("character",4) myData <- read.table("myData.csv",header=FALSE,skip=1,colClasses=cc,nrow=53860858,sep=",") I need to reshape this data from long to wide. On a small data set the following lines

Re: [R] long to wide on larger data set

> 'str' of it.  If it is numeric, then the size of the object is > probably about 1.8GB.  Doing the long to wide you will probably need > at least that much additional memory to hold the copy, if not more. > This would be impossible on a 32-bit version of R. > > On Mo

Re: [R] long to wide on larger data set

.table() fails with out of memory.  That is not >> data.table >> but unique. There is a change in unique.c in R 2.12 which makes unique >> more >> efficient and since factor calls unique, it may be necessary to use R >> 2.12. >> >> If that still doesn't

[R] replace negative numbers by smallest positive value in matrix

Hi Group, I have a matrix, and I would like to replace numbers less than 0 by the smallest minimum number. Below is an small matrix, and the loop I used. I would like to get suggestions on the "R way" to do this. Thanks, Juliet # example data set mymat <- structure(c(-0.503183609420937, 0.1790

Re: [R] replace negative numbers by smallest positive value in matrix

erkeley.edu > > > > On Thu, 15 Jul 2010, Juliet Hannah wrote: > >> Hi Group, >> >> I have a matrix, and I would like to replace numbers less than 0 by >> the smallest minimum number. Below is an >> small matrix, and the loop I used. I would like to get s

Re: [R] R Founding

Hi Group, I have a possibly naive question, but it seems like it fits into this discussion. I have observed that when researchers publish findings that are deemed to be high-impact, generous funding often follows. R is used everywhere, and, of course, for many of these projects. So my naive que

Re: [R] post

See if rowttests is any faster. library(genefilter) ?rowttests You have to install Bioconductor. I've used this on large datasets, but I haven't compared timings. On Mon, Sep 13, 2010 at 4:26 PM, Alexey Ush wrote: > Hello, > > I have a question regarding how to speed up the t.test on large dat

Re: [R] Ordered logit with polr won't match SPSS output

I think the most common reason to see different parameter estimates with ordinal regression is that programs set up the model differently. For example, check out library(MASS) ?polr We see polr uses: logit P(Y <= k | x) = zeta_k - eta and notes that other software packages may use the opposite

Re: [R] Number above the bar?

Check out ggplot2, specifically geom_bar and geom_text. http://had.co.nz/ggplot2/ You have to get used to its syntax, which can take some time, but after that it can make things a lot easier. Here is an example. library(ggplot2) df <- data.frame(xvar = factor(c(1, 2)), yvar = c(1, 5)) p <- ggp

Re: [R] how to add frequencies to barplot

Also check out the following post: http://permalink.gmane.org/gmane.comp.lang.r.general/210897 On Sat, Nov 20, 2010 at 4:32 PM, casperyc wrote: > > Hi, > > I have count data > > x2=rep(c(0:3),c(13,80,60,27)) > > x2 >  0  1  2  3 > 13 80 60 27 > > I want to graph to be ploted as > > barplot(table

Re: [R] Heat map in R

Make sure your data is a matrix. There are many examples of expression heatmaps available on the bioconductor list. After checking out these examples, I would post to the bioconductor list if you are still having problems. Also consider a small example to get you a working heatpmap. You have to ins

[R] partial match of one column in data frame to another character vector

Here is some data (dput output below) > myData id group 1 D599 A 2 002-0004 B 3 F01932

Re: [R] Lattice xyplots plots with multiple lines per cell

You may want to check out examples in lattice and ggplot2. Both of these make plotting subsets much easier. I can't remember the lattice syntax off the top of my head, but if you post some example data – either by creating it or using dput – people will be able to help out easier. Here is some exa

Re: [R] reading a text file, one line at a time

Hi Jim, I was trying to use your template without success. With the toy data below, could you explain how to use this template to change all "b"s to "z"s -- just as an exercise, reading in 3 lines at a time. I need to use this strategy for a larger problem, but I haven't been able to get the basic

[R] error possibly related to sweave, path, and spaces on windows

I have downloaded a file that I don't know how to describe correctly. It contains R code and Latex, and I should be able to reproduce an analysis by running an R script in this folder. There is a line in the R script: junk <- system(paste("/usr/texbin/pdflatex ",latexFiles[i1]),

Re: [R] error possibly related to sweave, path, and spaces on windows

Wow, it works! Thanks Erik. Your suggestion worked. MikTek is indeed in the path, so I just modified the lines to: junk <- system(paste("pdflatex ",latexFiles[i1]), intern=TRUE) On Sat, Aug 21, 2010 at 12:07 PM, Erik Iverson wrote: > On 08/21/2010 11:02 A

[R] average columns of data frame corresponding to replicates

Hi Group, I have a data frame below. Within this data frame there are samples (columns) that are measured more than once. Samples are indicated by "idx". So "id1" is present in columns 1, 3, and 5. Not every id is repeated. I would like to create a new data frame so that the repeated ids are av

Re: [R] Subsetting a data frame by dropping correlated variables

The 'findCorrelation' function in the caret package may be helpful. On Tue, Apr 19, 2011 at 3:10 PM, Rita Carreira wrote: > > Hello R Users! > I have a data frame that has many variables, some with missing observations, > and some that are correlated with each other. I would like to subset the

Re: [R] Help on selecting genes showing highest variance

# Let's say your expression data is in a matrix # named expression in which the rows are genes # and the columns are samples myvars <- apply(expression,1, var,na.rm=TRUE) myvars <- sort(myvars,decreasing=TRUE) myvars <- myvars[1:200] expression <- expression[names(myvars),] dim(expression) Also

Re: [R] Questions about ggplot2

I started with the summarized data, and there are different ways to do this. For this example, let there be four columns and a corresponding sum of 1s. library("ggplot2") mydf <- data.frame(colname = c("A","B","C","D"),mycolsum=c(1:4)) p <- ggplot(mydf,aes(x=colname,y=mycolsum)) p <- p + geom_bar

[R] suggestions/improvements for recoding strategy

I am recoding some data. Many values that should be 1.5 are recorded as 1-2. Some example data and my solution is below. I am curious about better approaches or any other suggestions. Thanks! # example input data myData <- read.table(textConnection("id, v1, v2, v3 a,1,2,3 b,1-2,,3-4 c,,3,4"),head

Re: [R] how to extract the 1st field from a vector of strings

What is the meaning of "\\1" here? Thanks. desc <- c("hsa-let-7a MIMAT062 Homo sapiens let-7a","hsa-let-7a* MIMAT0004481 Homo sapiens let-7a*","hsa-let-7a-2* MIMAT0010195 Homo sapiens let-7a-2*") I'm missing something: > gsub(" MIMA.*", "\\1", desc) [1] "hsa-let-7a""hsa-let-7a*" "hsa-l

Re: [R] Problem with factor analysis

It looks like the text didn't show assigning the results of factanal to an object. Try: pgdata<-read.table("pgfull.txt",header=T) names(pgdata) pgd<-pgdata[,1:54] #missing line model <- factanal(pgd,8) par(mfrow=c(2,2)) plot(loadings(model)[,1],loadings(model)[,2],pch=16,xlab="Factor 1",ylab="Fac

Re: [R] GWAF package: lme.batch.imputed(): object 'kmat' not found

GWAF uses the kinship package. The documentation is pretty good for it, and I've used it successfully. It may be helpful to get that working before trying automate some tasks using GWAF. On Fri, Feb 4, 2011 at 2:20 PM, Jim Moon wrote: > Hello, All, > > GWAF 1.2 > R.Version() is below. > > system(

Re: [R] series of boxplots

If you could provide a small example of an actual data set (using dput), you may get some suggestions specific to your goals. Here are a few examples of boxplots. If these look along the lines of what you are looking for, you may want to search the ggplot2 mailing list for more examples. library(

Re: [R] covar

Relatedness if often defined in terms of the kinship matrix. It may be helpful to search for this. Several packages in R use this matrix including the kinship package. On Wed, Feb 16, 2011 at 3:14 PM, Val wrote: > Hi all, > > I want to construct relatedness among individuals and have a look at th

Re: [R] About proportional odds ratio model with LASSO in ordinal regression

If you can work with a different penalty check out the lrm function from the rms package, which uses penalized likelihood to fit proportional odds. 2011/3/24 Jheng-Jhong Wang : > Dear R-users, > >         I try to fit proportional odds ratio model "with LASSO" in > ordinal regression. >  But I jus

Re: [R] converting affybatch object to matrix

Use exprs on the output from RMA (or another method you like) library("affy") myData <-ReadAffy() myRMA <- rma(myData) e = exprs(myRMA) Also, check out the Bioconductor mailing list where Bioconductor-related topics are discussed. On Fri, Apr 1, 2011 at 9:54 AM, Landes, Ezekiel wrote: > I hav

Re: [R] no solution yet, please help: extract p-value from mixed model in kinship package

Maybe the pedigree is not set up correctly. If this is the case, the kinship matrix will not be constructed correctly. I see that in this example, the diagonal terms differ. diag(kmat) lmekin runs fine for me, and I can extract p-values with: lmekinfit <- lmekin(...) pval <- lmekinfit$ctab

Re: [R] GLM output for deviance and loglikelihood

As you mentioned, the deviance does not always reduce to: D = -2(loglikelihood(model)) It does for ungrouped data, such as for binary logistic regression. So let's stick with the original definition. In this case, we need the log-likelihood for the saturated model. x = rnorm(10) y = rpois(10,l

[R] improve formatting of HTML table

I am trying to improve the look of an HTML table for a report (that needs to be pasted into Word). Here is an example. table2 <- structure(c(26L, 0L, 40L, 0L, 10L, 0L, 0L, 188L, 0L, 281L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 4L), .Dim = c(6L, 3L), .Dimnames = structure(list( myvar = c("Don't know", "S

[R] getting names of dimnames of xtabs into xtable latex output

In R, the output of xtabs displays the names of the dimnames. In the example below, these are "change_diet" and "mydiet". Is there a way to have xtable incorporate these names directly into the latex output. Thanks for your help. table2 <- structure(c(26, 0, 40, 0, 10, 0, 188, 0, 281, 0), .Dim =

Re: [R] getting names of dimnames of xtabs into xtable latex output

Thanks for the suggestion, Duncan. However, I was trying to maintain the contingency table/cross-classification structure of the original table. My use of xtable on this table, maintains the structure I want, but the labels for the rownames and colum names is lost. On Tue, Aug 16, 2011 at 11:0

Re: [R] getting names of dimnames of xtabs into xtable latex output

Thanks to Duncan Mackay and Dennis Murphy for help. The following solution seems to give me what I need. library(memisc) toLatex(ftable(cyl ~ am,data=mtcars)) For this to work, we have to use: \documentclass{article} \usepackage{booktabs} \usepackage{dcolumn} \begin{document} at the beginning

[R] data manipulation and summaries with few million rows

I have a data set with about 6 million rows and 50 columns. It is a mixture of dates, factors, and numerics. What I am trying to accomplish can be seen with the following simplified data, which is given as dput output below. > head(myData) mydate gender mygroup id 1 2012-03-25 F

Re: [R] data manipulation and summaries with few million rows

;- function(d) length(rle(d$mygroup)$lengths) - 1 > ddply(myData, .(id), g)    # gives the same answer as above > myDT[, list(nswitch = length(rle(mygroup)$lengths) - 1), by = 'id']   # ditto > > > HTH, > Dennis > > On Wed, Aug 24, 2011 at 9:48 AM, Juliet Hannah

[R] formatting a 6 million row data set; creating a censoring variable

List, Consider the following data. gender mygroup id 1 F A 1 2 F B 2 3 F B 2 4 F B 2 5 F C 2 6 F C 2 7 F C 2 8 F D 2 9 F D 2 10 F D 2 11 F D 2 12 F

Re: [R] error building package: packaging into .tar.gz failed

Help Workshop was at the beginning. With this, my attempts at package creation worked. On Thu, Jun 30, 2011 at 12:51 PM, Juliet Hannah wrote: > I am trying to build a package using windows xp. Here is the error I am > getting: > > R CMD build myfunctions > > * checkin

[R] indexing with which, logical indexing, and missing values

I have a data frame in which missing values exist, and I need to recode the string "missing" to a missing value. For the example, let's assume I cannot do this while reading it in. Even though this has been discussed extensively, I'm still a little confused about when to index with "which" and when

[R] error building package: packaging into .tar.gz failed

I am trying to build a package using windows xp. Here is the error I am getting: R CMD build myfunctions * checking for file 'myfunctions/DESCRIPTION' ... OK * preparing 'myfunctions': * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files * checkin

Re: [R] deming regresion to make 2 variables comparable

See if the following thread http://www.mail-archive.com/r-help@r-project.org/msg85070.html and the paper cited in it are helpful. Terry Therneau provides code for a Deming regression. On Thu, Jul 7, 2011 at 12:58 PM, devon woodcomb wrote: > Hi, > > I have a dataset which has var1 from 1 sours

[R] suggestions regarding reading in a messy file

I have a file in stata format, which I have read in, and I am trying to create a text file. I have exported the data using various delimiters, but I'm unable to read it back in. I originally read in the file with: library(foreign) myData <- read.dta("mydata.dta") I then exported it with write.tab

Re: [R] suggestions regarding reading in a messy file

ius wrote: > > On Jul 12, 2011, at 4:37 PM, Juliet Hannah wrote: > >> I have a file in stata format, which I have read in, and I am trying >> to create a text file. I have exported the data using various >> delimiters, but I'm unable to read it back in. I original

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