similar to: specifying x-axis scale on random forest variable importance plot

I am trying to plot survival curves using the following code as an example: >rs1799964.coxph<-(coxph(Surv(sassurvmonths,status)~age+stage+rs1799964_TNFA,method="efron")) >plot(rs1799964.coxph,lyt=c(1,3),xlab="Survival in Months",ylab="Proportion Surviving") I am gettingthe following error message: >Error in xy.coords(x, y, xlabel, ylabel, log) :

I am new to using R. Currently, I am using the logistf package to run logistic regression analysis. When I run the following line of code: attach(snpriskdata) logisticpaper<-logistf(sascasecon~saspackyrs+newsbmi+EDUCATION+sasagedx+sasflung+condobst+sasadultasprev) I get the following error message: Error in sum(y) : invalid 'type' (character) of argument What does this error

Hello, I am using the R randomForest package to classify variable stars. I have a training set of 1755 stars described by (too) many variables. Some of these variables are highly correlated. I believe that I understand how randomForest works and how the variable importance are evaluated (through variable permutations). Here are my questions. 1) variable importance error? Is there any ways

Hi everyone, I have another "Random Forest" package question: - my (presumably incorrect) understanding of the varImpPlot is that it should plot the "% increase in MSE" and "IncNodePurity" exactly as can be found from the "importance" section of the model results. - However, the plot does not, in fact, match the "importance"

Hi, I'm using package "caret" to rank predictors using random forest model and draw predictors importance plot. I used below commands: rf.fit<-randomForest(x,y,ntree=500,importance=TRUE) ## "x" is matrix whose columns are predictors, "y" is a binary resonse vector ## Then I got the ranked predictors by ranking

I'm calculating nodes using Random Forest in R but i only get nodes for a fraction of the compounds i want to calculate, the rest is ommited and is not printed in the output file, (i'm working with 3012 compounds). What can i do to have nodes printed for all the compounds. Thanks Gon?alo

Hi, I have a table with data, as below: dput(table): structure(list(Adrian.Cole = c(0L, 0L, 0L, 0L, 0L, 0L), Alison.Wong = c(0L, 0L, 0L, 0L, 0L, 0L), Andrei.Savu = c(0L, 0L, 0L, 0L, 0L, 0L), Bruno.Dumon = c(0L, 0L, 0L, 0L, 0L, 0L), Edward.J..Yoon = c(0L, 0L, 0L, 0L, 0L, 0L), Eugene.Koontz = c(0L, 0L, 0L, 0L, 0L, 0L), Jakob.Homan = c(0L, 0L, 0L, 0L, 0L, 0L), Kelvin.Kakugawa = c(0L, 0L,

Dear Debian persons I would like enquire about whether the repository deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ I tried to follow the instructions and I cannot get R3.5.1 - I get R3.4.4??? I have been able to install R3.5.1 on Ubuntu 16.02 using the xenial-cran35/ repository & so not sure if the bionic link is up to date? thanks in advance Regards Alison

Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward

CVS HEAD from about 1 week ago. TDM30P and call through Nufone. I was talking and wanted to park the call and move to another phone to pick it up. I hit #701 instead of #700 though -- after a pause, I got a fast busy and the call was gone. When I called the person back, she said that Alison told HER that 701 was an invalid extension. I should have heard that though, not her. If I dial

Hi folks, With thanks to Alison Keenan (another Alison!) for the voice, Chris Bagnal for converting from 44k wav to sln and finally Terje Elde for debugging my HTML code, the British English files are now ready for download. They can be got from http://www.enicomms.com/cutglassivr/ Thanks and don't forget to practice safe IAX ;-} Mark -- Mark Phillips <g7ltt@g7ltt.com>

Full_Name: Daniel Normolle Version: 2.0.1 OS: Linux/Fedora Core 3 Submission from: (NULL) (141.214.17.5) varImpPlot in Random Forests 4.5-10 produces the error "incorrect number of subscripts on matrix" (and no plot) when applied to a randomForest object. This error did not occur with 4.5-4 or earlier versions.

Hello all, I am trying to use the micEcon 'insertRow' function inside a function I have written. For example: insert_row_test <- function(m){ insertRow(m,nrow(m)+1,v=0,rName="test") } However, when I try to call the 'insert_row_test' function (after loading the micEcon package), it does not insert a row into the matrix I pass in. When I call the insertRow

Hello all, I am trying to use cbind to add a named empty column to a Matrix: outputmatrix <- cbind(outputmatrix,kog_id = seq(0,0,0)) The problem I have is that kog_id is a variable that has a value e.g. "KOG1234", but I when I try to use this to name the added column, it is named literally "kog_id" instead of "KOG1234". How can I name a column by passing in a

Hi all, I'm having problems installing plotrix. I tried installing it through install.packages, and from the unix command line, but each time it seems to stall when it is installing the help indices. has anyone had this same problem, is this package still maintained ? any help? thanks > install.packages("plotrix") > > I also tried using the source package > R CMD

Hi all, I have 6 datasets(dataframes Assem_ContigsLen7 through all_ContigsLen12) containing 3 columns (contig_id, contig_length, read_count). Each dataset is composed of 3 types of contigs (assemblies of genomic fragments), 1- all Bacterial fragments, 2 - all Viral fragments, 3 - mixed fragments. I identified the type of contig through a merge with another table with just contig_id and

If I want to create a heat map where I have a graphic of a US State with county borders, how do I import and work with the graphic image? The reason I would like to use R is so I can then define color parameters and quickly produce heat maps that correspond to various data in dataframes.   Thanks. Alison [[alternative HTML version deleted]]

I'd like to increase the speed of the Asterisk sound files. Miss Alison talks a bit slow. I can use sox to increase the speed, but then the pitch changes and she starts to sound like a chipmunk. Any audio experts out there know how I can increase the speed a little bit, and change the pitch accordingly so that she sounds ... normal? Thanks Doug.

Dear all, I want to use string split to parse column names, however, I am having some errors that I don't understand. I see a problem when I try to rbind the output from strsplit. please let me know if I'm missing something obvious, thanks, alison here are my commands: >strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\\.") >

Hi, I''m trying to setup my mongrel clusters to start on boot. I have followed the instructions under the "On Boot Initialization Setup" section at http://mongrel.rubyforge.org/docs/mongrel_cluster.html. When I try to start it up, I get the following error: me at mybox.com: sudo /etc/init.d/mongrel_cluster start Starting all mongrel_clusters... !!! Path to log file not