similar to: Re: Need help on how to list functions from a loaded pack age...

To All How does one get a list of functions from a loaded package so that one can then get the appropriate help for each of the functions. Currently my method is based on a lot of trial-and-error. Here's an example of what I mean... >From this forum I learn that an interesting package called "multtest" exists on Bioconductor. I then use R Console's "Packages" --

I have been running R CMD check for the first time on of our own packages, which otherwise builds, installs and runs just fine. The package depends on package akima and suggests package multtest; suggesting multtest is indicated because a) it loads a lot of other Bioconductor packages, very slowly, and b) it is only needed for one specific subroutine, which executes require(multtest)

Hi, I am using SAM (from siggenes_1.2.11 package) method to select genes from a microarray data set. After installing the latest R2.4.0 on my computer, to my surprise the results are totally different from that calculated using R2.1.1. Even the example code doesn't work the same way under these two versions of R. Does anybody know what is going on? Thanks for any suggestions.

Dear R users, Please help me with the following problem. I have a data set of the form ´dat´   dat <- data.frame(id = seq(1:5), trt=c(0,0,1,1,1),tid=c(0,0,0,0,0),                   ntid=c(0,0,0,0,0))   The function auto is used to generate the autoregressive model:   auto <- function(seed,delta,beta,maxt,dat){ set.seed(seed)  sp <- lapply(split(dat,dat$id),function(x){  while(x$tid <

Full_Name: Ken Kompass Version: 2.2.0 OS: winXP pro (2002 version, SP2) Submission from: (NULL) (128.252.149.244) Using R2.2.0 I get this error msg when loading certain bioconductor libraries (depending on whether the library contains file named "all.rda" in R folder of library) : > library(multtest) Error in open.connection(con, "rb") : unable to open connection In

Hi, Installing from binaries on Windows: > install.packages("multtest") Warning: dependency 'Biobase' is not available trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip' Content type 'application/zip' length 1645590 bytes (1.6 Mb) opened URL downloaded 1.6 Mb package 'multtest' successfully unpacked

Hello! I downloaded a package "multtest" (from bioconductor.org) in R, and installed it by 'R CMD <package>' (after unzipping and taring). The problem is when I say 'library(multtest)' in R, the following error is generated: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

Hi, thanks for the report - but it should have gone to the Bioconductor list, and the package maintainer, thanks. New versions of multtest and a few other packages will percolate up in the next few days to resolve the problem. Best wishes, Robert kompass at vision.wustl.edu wrote: > Full_Name: Ken Kompass > Version: 2.2.0 > OS: winXP pro (2002 version, SP2) > Submission

Dear R users, Kindly help me to look into the following problem. I have a dataset like the following dat <- data.frame(id = seq(1:5), trt=c(0,0,1,1,1),tid=c(0,0,0,0,0),                   ntid=c(0,0,0,0,0)) I want to create waiting times using   B <- rexp(1) f1 <- (1/phi)+ ntid; f2 <- abs(1+phi*delta*tid*exp(beta*trt)) f3 <- phi*delta*exp(beta*trt) wait <-

Hi, With recent versions of R-devel, "R CMD check" complains about some "Rd files with unknown sections". hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz ... ... * checking Rd files ... WARNING Rd files with unknown sections: /home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd: notes

Dear r-help, I would like to use the 'ppm' function of the 'spatstat' package to fit a Strauss inhibition model. I understand that I can specify a parametric model for the "background" trend, but how would I specify a trend which is estimated using a Kernel density smoother? In particular, I would like to use the 'kde' function of the 'ks' package to

Dear Madam or Mister, My name is Manuel Montesino and I am a PhD student at the University of Copenhagen. I am not a programmer myself, but my thesis requires the combined use of R and a model. I would be very grateful if you help me with the following issue; I am trying to combine a small piece of code written in Fortran 77 with R. The F77 code aims to select data from a library and write it

i have trouble in using spatstat package. i want to simulate a community under the Strauss process,which has a parameter gamma that controls interaction strength between points,and Strauss process is defined only for 0 ¡Ügamma ¡Ü 1 and is a model for inhibition between points. my problem is that in my data, many species's estimated gamma is larger than one.so if i still wanna simulate

Hi, I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification. For example,if I run it on a dataset, I get the following result using pamr.adaptthresh(): predicted true (1)

Hi, Sorry about the earlier formatting errors... I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification. For example,if I run it on a dataset, I get the following result using

Hi Nguyen, > Subject: [R] install "multtest" and "preprocessCore" packages in > Bioconductor library > Date: Wed, 30 Nov 2011 09:57:36 -0800 > From: UyenThao Nguyen <unguyen at tethysbio.com> > To: r-help <r-help at r-project.org> > CC: uth.nguyen at ucdavis.edu <uth.nguyen at ucdavis.edu> > > Hi All, > > I've tried to

Hi all, before I roll my own, naive implementation of a particular spatial point process, I thought I'd ask whether this has already been done. Specifically, I am looking for essentially the opposite of the Strauss and Mate'rn processes included in library(spatial) and documented in MASS. I am examining daily travel patterns, focusing on just the destinations of trips, not the

Dear All, I would like to simulate a Strauss process in 3D, but there is only 2D in R. I understand a programming which is necessary, but I don't have idea how to simulate. Thanks. Apple [[alternative HTML version deleted]]

Sorry if this is a stupid question but I tried reading, studying and finding solution but am not making it alone :) On my home lan I have a Linux (Debian sid) box (192.168.174.244) running 3.0.10 samba and cups 1.1.23. My objective is to print from this box to the other home PC which is running XP (192.168.174.242) and sharing an Epson R200 printer. Follows the troubleshooting I could do

Dear all, I want to simulate a Strauss Hard Core process in 3D. I have found that someone else tried to do the same and he recived this answer, "If you need this immediately, I suggest you follow Brian Ripley's advice. This probably involves downloading a source tar file of the R package and finding the Fortran code in library/spatial/src/. The Fortran should be edited to generate 3D