similar to: array manipulation simple questions

  Hi there,   I am beginner in R and I have some basic question. Suppose I run a common procedure such as a t test or cox model like below:   out<-coxph( Surv(tstart,tstop, death1) ~ x1+x1:log(tstop+1) , test1,method=c("breslow"))    Which yields the following result:   Call: coxph(formula = Surv(tstart, tstop, death1) ~ x1 + x1:log(tstop +     1), data = test1, method =

Hi there, Can anyone please help me because I am going to get crazy with the pbc data set. I just want to apply simple cox regression in the data set. I am a beginner in R but I don't think I am doing anything wrong. I have the book of Fleming and Harrington 1990. I perform cox regression by typing: out<- coxph(Surv(times/365,status)~log(bili)+log(proth)+edema+log(albumin)+age) out

Hello. I have run the command imp<-mice(mydata, im=c("","pmm","logreg","logreg"),m=5)  for a variable with no missing data, a numeric one and two variables with binary data. I got the following message: There were 37 warnings (use warnings() to see them) > warnings() Warning messages: 1: In any(predictorMatrix[j, ]) ... : coercing argument of

Hi there, I have a rather large data set and perform the following cox model: test1 <- list(tstart,tstop,death1,chemo1,radio1,horm1) out1<-coxph( Surv(tstart,tstop, death1) ~ chemo1+chemo1:log(tstop+1)+horm1+horm1:log(tstop+1)+age1+grade1+grade1:log(tstop+1)+positive1+positive1:log(tstop+1)+size1+size1:log(tstop+1), test1) out1 Up to here everything works fine (with each covariate

Hi there, I perform a stratified cox and then I need the strata as a  numeric array "straft.ln" ft.ln <- coxph(Surv(times,deaths)~ages+chemos+chemos:f1+chemos:f2+horms+horms:f1+horms:f2+grades+grades:f1+grades:f2+positives+positives:f1+positives:f2+sizes+sizes:f1+sizes:f2+strata(stra),data=ddd) basehazzft.ln=basehaz(ft.ln,centered=FALSE) H0ft.ln=c(basehazzft.ln[,1])

Dear R-helpers, i have a question on how to vectorize this problem: i have a dataframe: tester <- data.frame(groups=c("A","A","B","B","C","C"), one=c(1,1,2,2,3,3), two=c(6,6,7,7,8,8)) # i split it into a list tester.L <- split(tester, tester$groups) # And want to keep only the first item in each: lapply(tester.L, function(x) x

I am trying to reshape a data set. Could someone please help me with the reshape, cast, and melt functions? I am new to R and I have tried reading up on how to use the reshape package, but I am very confused. Here is an example of what I am trying to do: subject coder score time [1,] 1 1 20 5 [2,] 1 2 30 4 [3,] 2 3 10 10 [4,] 2 2

I am trying to construct a graph of 6 box plots of blood pressures. I want them to be on a single set of axis and I want the SBP to be ontop of the DBP. I have an array bp with the data in it and I tried a[1,]<-c(145,60,147,62,140,57) a[2,]<-c(160,75,160,74,160,70) a[3,]<-c(140,55,140,65,142,55) boxplot(data.frame(a), main = "Blood Pressures", at=c(1,1,2,2,3,3),

Hi. I searched the list and didn't found nothing similar to this. I simplified my example like below: #I need calculate correlation (for example) between 2 columns classified by a third one at a data.frame, like below: #number of rows nr = 10 #the third column is to enforce that I need correlation on two variables only dataf =

I'm interested in a version of tapply() that operates with shingles instead of factors. For instance: x <- c(1,1,2,2,3,3) y <- c(1,1,1,0,0,0) s <- shingle(x,intervals=cbind(c(0.5,1.5),c(2.5,3.5))) # the following function should exist! tapply.shingle(x,s,mean) # returns the vector c(0.75,0.25) I've written such a function as follows: tapply.shingle <-

Hi, I have the following function that i use to plot graphs. plot_mi_time = function(mdata, miname) { mdata2 = mdata[row.names(mir_test3) == miname, ] # print(mdata2) xcoords <- c(1,1,2,2,3,3) plot(xcoords, mdata2, xaxt="n", ylab="Expression", xlab="Time(h)", , main=miname) axis(1, at=xcoords,

> > > I am new to this group - joined today. I am in because i have an assignment to do using R => microarray analysis using affy (bioconductor). > > while reading some tutorials, i came across this and i am stuck. i want to understand it and would appreciate if anyone can tell me. > > design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) > > can someone break

Hello, I can't find a package which calculates Kendall's tau-c. There is the package Kendall, but it only calcuates Kendall's tau-b. Here is the example from ttp://www2.chass.ncsu.edu/garson/pa765/assocordinal.htm. cityriots <- data.frame(citysize=c(1,1,2,2,3,3), riotsize=c(1,2,1,2,1,2), weight=c(4,2,2,3,0,4)) cityriots <- data.frame(lapply(cityriots,function(x)

Hi, I want to add error bars to a plot generated with xyplot. I've tried both errbar() and plotCI(), but in both cases the points are not in the same place. It's as if the two functions are using a different frame of reference for the plotting area. for example: means <- c(92.5, 92.25, 90.9, 91.0, 94.15, 90.05) #means time <- c(1,1,2,2,3,3) #occasion variable group <-

Dear guRus, I am starting to work with the ggplot2 package and have two very dumb questions: 1) deterministic position_jitter - the jittering is stochastic; is there any way to get a deterministic jittering? For instance: example.data <- data.frame(group=c("foo","bar","foo","bar","foo","bar"),x=c(1,1,2,2,3,3),y=c(1,1,0,2,1,1))

Hi folks, I have a question about how to efficiently produce random numbers from Beta and Binomial distributions. For Beta distribution, suppose we have two shape vectors shape1 and shape2. I hope to generate a 10000 x 2 matrix X whose i th rwo is a sample from reta(2,shape1[i]mshape2[i]). Of course this can be done via loops: for(i in 1:10000) { X[i,]=rbeta(2,shape1[i],shape2[i]) } However,

hello folks, i am learning R and microarray analysis from scratch using different sites. today i am doing an exercise from http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_functions the section i am at is 2. Affymetrix data analysis. I understand the syntax given in this section up until: design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) # Creates appropriate design

Hello all, One of the buildings I have an asterisk box deployed in is used by two small companies on two floors. They have an agreement between them whereby they'll answer each other's incoming calls and take messages if the office is empty / everyone is on the phone. Each of them has an ISDN BRI delivered to asterisk via zaphfc, then dropped into a context as follows: exten =>

Hello, I am almost a total novice, and I am sure there must be an easy (and basic) way to turn a variable of 1's and 2's into a variable of zeros and ones. This is in a data frame, but if I could do it with vectors, that's all I need. Can someone tell me how? Thanks so much, Jen

Hello, I have simulated 30 observations from a binomial(5,0.1) distribution. Now I need to make frequency table( that means I need to tally how many 0's , 1's 2's....... 5's) I know that the simple R function table() will do this, but I am afraid that some times I may get zero frequency for some particular values (for example in the above there are 5-0's 10-1's ,