similar to: It is time to say thank you.

R 2.7.2 Windows XP I am using apply to compute a series of Student's t-test from two matrices, sample1 and sample2. boo<-apply(sample1,1,t.test,sample2) I want to pick of the p-values from the tests, but can't seem to get it to work. I have tried several methods to get the values including: boo<-apply(sample1,1,t.test$t.test,sample2) boo<-apply(sample1,1,t.test,sample2)$t.test

Can anyone suggest a good non-parametric test, and an R implementation of the test, that allows for two or more factors? Wilcoxon signed rank allows for only one. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC and University of Maryland School of Medicine Claude Pepper OAIC University of Maryland School of Medicine Division of

Is there any way to load a package using R code rather than the Load Package command in the Package menu? I would like to load the boot package. R.2.1.0 Patched Win 2k. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC and University of Maryland School of Medicine Claude Pepper OAIC University of Maryland School of Medicine Division of

I am having trouble with apply. Could someone suggest changes to the code below that will eliminate the for loops? R 2.1.1 patched Windows 2k Thanks, John function () { NaCon<-array(dim=c(10,10)) for (i in 1:10) {NaCon[i,]<-rnorm(10,10.77,0.02)} MeanNaCon<-vector(mode="numeric",length=10) for (j in 1:10) {MeanNaCon[j]<-mean(NaCon[j,1:10])} print(MeanNaCon)

I am trying to fit lme using R 2.1.1 under Windows 2k. I am getting the following message noted below. Any suggestions that would help me correct my error would be greatly appreciated. Thanks, John > fit1lme<-lme(Velocity~time,data=gate) Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics

R 2.3.1 Windows XP Question: How can I obtain the values of BIAS and STD. ERROR from a bootstrap. Background: I am running a bootstrap: result2<-boot(1:400,regSEvssample,R=5000) and obtain the following results: Bootstrap Statistics : original bias std. error t1* 1.876602 -0.0001368616 0.1630380 I would like to get the values of ORIGINAL and BIAS. I can get the value of

R 2.1.1 on Windows 2K I hope one and all will allow both an R question and a general stats question: (1) Is there any function that will perform non-parametric tests such as a sign test or a signed rank test? I know I could program both but I would prefer not re-inventing the wheel. (2) When performing a sign test, the usual practice is to drop zero values. Is there any theoretical reason

Given a square matrix of variables X, is there any way to compute a multivariable correlation among all the variables in the array? It is possible to calculate the correlation of all pairs of variables in the array, but I want to know the correlation of all the variables taken together, i.e. for the matrix X=x1 x2 x3 x4 x5 x6 x7 x8 x9 I don't want the pair-wise correlations

R2.1.1 Win 2k I have a function, B, within a function, A. I would like to have B print the name of the argument passed to it (not the value of the arguments). i.e., A<-function() { B<-function(x,y) { fit1<-lm(y~x,data=jo) print(summary(fit1) I want B to print the string "age" and the string "height". } B(age,height) }

Windows Vista R 2.9.1 When trying to install Rcmdr I get the message shown below. What does it mean, do I need to do anything? The downloaded packages are in C:\Users\John Sorkin\AppData\Local\Temp\RtmpRCLbhe\downloaded_packages updating HTML package descriptions Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-29~1.1/doc/html/packages.html', reason

I am trying to run a Cox regression (coxph) to predict survival after surgery and xray therapy. The model violates the proportionality assumption (tested using time-dependent covariates). I have tried to use strata to solve the problem but the stratified model still violates the assumption. Does the violation of proportionality preclude use of a Kaplan-Meier analysis? Is there any other possible

R 2.2.0 windows XP I am beginning to explore the mitools package contributed by Thomas Lumley (thank you Thomas) and I have a few questions: (1) In the examples given in the mitools documentation, the only family argument used is family=binomial. Does the package support family=gaussian and other link functions? I ran the with function with family=gaussian and I obtained results, but I am not

I know that mvrnorm from MASS (generously provided by Profs. Venables and Ripley) can be used to generate multivariable normal data that can be used in a linear regression with certain desired characteristics (e.g. a given mean for each variable as well as a given variance-covariance pattern). Is there any similar facility that can be used to generate data for (1) a logistic regression and (2) a

Can someone direct me to an R function that properly computes standard errors of data obtained from a complex survery design, i.e. perform alnalyses similiar to those that can be performed with SUDAAN, particularly for a non-parametric one-way ANOVA, e.g. signed rank test? Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of

R 2.8.1 windows XP I don't understand the output from x[iS+1:iE] produced by the code below: x = c(1,2,3,4,5) x [1] 1 2 3 4 5 iS=2 # start position iE=4 # end position [iS:iE] [1] 2 3 4 # I don't understand the results of the command below. I would expect to see 3, 4, not 3, 4, 5, NA x[iS+1:iE] [1] 3 4 5 NA Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and

I am trying to install R.2.1.1 under Linux FC4 using RPM. During the installation I get the following message: The following package could not be found on your system. Installation cannot continue until it is installed. The package in question of libblas.so.3. Does anyone know where I can get the package? Can I use RPM to intall the package? Thanks, John John Sorkin M.D., Ph.D. Chief,

Can someone tell me why apply (and apply) are faster in performing repeated operations than a for (or do) loop? I am looking for a technical explanation. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC and University of Maryland School of Medicine Claude Pepper OAIC University of Maryland School of Medicine Division of Gerontology

Timothy, I believe you are mistaken. Fisher's exact test give the correct answer even in the face of small expected values for the cell counts. Pearson's Chi-square approximates Fisher's exact test and can give the wrong answer when expected cell counts are low. Chi-square was developed because it is computationally "simple". Fisher's exact test, particularly with tables

R 2.0.1 Linux I am using rlm() to fit a model, e.g. fit1<-rlm(y~x). My model is more complex than the one shown. When I enter summary(fit1) I get estimates for the model's coefficients along with their SEs, and t values, but no p values. The p value column is blank. Similarly, when I enter anova(fit1) I get DF, Sum Sq, Mean Sq, but the column for F value and Pr(>F) are blank. Any

I am using read.csv to read a CSV file (produced by saving an Excel file as a CSV file). The columns containing dates are being read as factors. Because of this, I can not compute follow-up time, i.e. Followup<-postDate-preDate. I would appreciate any suggestion that would help me read the dates as dates and thus allow me to calculate follow-up time. Thanks John John Sorkin M.D., Ph.D. Chief,