similar to: how to pass a command variable in DOS to R program in R CMD BATCH

Hi all, How can I have a dynamic list for different combinations of grouping factors in the following example? Thanks. dat <- data.frame(x=rnorm(100), a=sample(letters[1:5], replace = T), b=sample(letters[1:5], replace = T), c=sample(letters[1:5], replace = T), d=sample(letters[1:5], replace = T)) ## define grouping

Hi all, While dat['a1',] and dat['a10',] produce the same results in the following example, I'd like dat['a1',] to return NAs. dat <- data.frame(x1 = paste(letters[1:5],10, sep=''), x2=rnorm(5)) rownames(dat) <- dat$x1 dat['a1',] dat['a10',] > sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale:

Dear R users,   I am trying to use "wgaim" package for QTL analysis using mixed model approach. But i am stuck with "asreml" function while using "wgaim" package. Do i need a separate package to activate "asreml" function beside "wgaim" package ?   If so, i tried to download "Asreml-R" package (i guess this is right package

Estimados, Les tengo una pequeña consulta. Estoy trabajando con ASReml en Rstudio, me encuentro corriendo un modelo (CHL) para obtener el ANOVA de la interacción de los factores gen x env CHL<- asreml(fixed= MS~geno:env, random = ~rep, data = index) (interacción) Sin embargo, cuando ejecuto el modelo, R indica que siguiente mensaje: Current workspace: 128.000000Mb Warning message: Abnormal

Hi Everyone, I am using ASReml to fit a spatial model. I do not have all the components of ASReml when I call; names(summary()) e.g. names(summary(fcov.asr2)) [1] "call" "loglik" "nedf" "sigma" "varcomp" I am trying to get the coefs but I get "NULL". Does anybody know the reason? Any help would be much appreciated. Regards

Dear All: I want to do association study based on mixed linear model, My model not only includes serval fixed effects and random effects but also incorporates some covariates such as "birth weight". Otherwise, the size of the data are about 180 individuals and 12 variables and 60000 Fixed effect estimates As asreml-R is not free ,is there any packages for my study? I heard nlme or

Dear R gurus, I have the following code, but I still not know how to estimate and extract confidence intervals (95%CI) from resampling. Thanks! ~Adriana #data penta<-c(770,729,640,486,450,410,400,340,306,283,278,260,253,242,240,229,201,198,190,186,180,170,168,151,150,148,147,125,117,110,107,104,85,83,80,74,70,66,54,46,45,43,40,38,10) x<-log(penta+1) plot(ecdf(x),

Good day, I need to subset a data by removing several rows. I know the %in% operator, i.e. sub <- mydata[group %in% c("A","B","E","G"), ] What I need is the opposite, that is remove rows and/or columns. What is the operator for "NOT IN"? I tried (i)! %in% and (ii) ^%in% and both resulted in a "could not find function" error.

Using R-2.8.0 and R-2.8.1, I get behaviour like this: R version 2.8.0 (2008-10-20) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [....] > Sys.getenv("LD_LIBRARY_PATH") LD_LIBRARY_PATH

Hi, I am looking to do some quantitative genetic analyses using animal models and was wondering if someone could suggest an appropriate package in R. It would help if it was similar to the ASReml genetic analyses software. Thanks, Deepa Senapathi Deepa Senapathi Centre for Agri-Environmental Research (CAER) School of Agriculture, Policy & Developement. University of Reading

I am using R (version 2.13.0; 2011-04-13). Platform: x86_64-pc-mingw32/x64 (64-bit). The messages that I see is “This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information” I am using the following libraries: > library(package="gmodels") > library(package="gtools")

Hi! I have fitted two glms assuming a poisson distribution which are: fit1 <- glm(Aids ~ Year, data=aids, family=poisson()) fit2 <- glm(Aids ~ Year+I(Year^2), data=aids, family=poisson()) I am trying to work out how to represent the fitted regression curves of fit1 and fit2 on the one graph. I have tried: graphics.off() plot(Aids ~ Year, data = aids) line(glm(Aids ~ Year,

Dear Sirs I would like to make you aware of the following training taking place in Chicago next month. Analysis of experiments using ASReml-R, Chicago, 24/25th April This workshop is aimed at scientist/practitioners that are interested in analyzing complex datasets by fitting linear mixed models, particularly users with experience in breeding programs and design and analysis of experiments.

Dear all, I imagine that this is a trival question, but it has perplexed for most of the day. Any help would be greatly appreciated. Below is an example of what I'm trying to do. Essentially I want to produce all unique 1 x 1 combinations of certain columns from a dataframe, and join these to other columns from the same dataframe. I'm having problems with the nested loop as I can only

The coxme package has a ranef() method, as does lme4. I'm having trouble getting them to play together, as shown below. (The particular model in the example isn't defensible, but uses a standard data set.) The problem is that most of the time only one of lme4 or coxme will be loaded, so each needs to define the basic ranef function as well as a method for it. But when loaded together

First, a big thanks to all of the developers and users that have worked to make R such useful software. It is only because I find the software so useful that I have the following opinions. A recent post to R-devel listed the 'Top 10 Features' for one person. I found it to be quite an interesting read. Over the past couple of years I have assembled my own lists. Retrospective. Some of

Hi, I am trying to manipulate a gls regression model output to adjust for use of two-stage least squares. Basically, I want to estimate a model, then feed in a new set of residuals, then re-calculate all of the model output (i.e. the standard errors of the estimators, etc.). I have found some documentation on doing this in stata, which is below: http://www.stata.com/help.cgi?ereturn I am

First, a disclaimer. I am not affiliatied with the SAMM package. I am only a user of the package, but I have been contacted (off list) by people requesting information about SAMM and so I am posting this information here. SAMM is software for fitting mixed models. Versions are available for both S-Plus and R. More information and downloads of the software (and manual) are available here:

Great, thanks, Dirk. Nice example :-) On Wed, Oct 28, 2015 at 10:05 PM, Dirk Eddelbuettel <edd at debian.org> wrote: > > On 28 October 2015 at 21:39, Marius Hofert wrote: > | Out of laziness I just used "R CMD batch" instead of "R CMD BATCH". I > | didn't get an error so didn't think about the consequences... One > | consequence is (at least on

On 29 Oct 2015, at 10:44 , Rainer M Krug <Rainer at krugs.de> wrote: > Out of interest: What is the magic ~R CMD~ is doing? Is it documented > anywhere? R is open source.... (and shell scripts are considered self-documenting by some) On Unix-alikes, R is a shell script which, if called with 1st argument CMD, calls ${R_HOME}/bin/Rcmd, which is another shell script that ends with