similar to: Strange error

I am making the question clear. Please help. > Dear R experts > > I was using kinship package to fit mixed model with kinship matrix. > The package looks like lme4, but I could find a way to extract p-value > out of it. I need to extract is as I need to analyse large number of > variables (> 10000). > > Please help me: > > require(kinship) > > #Generating

Hi,I use the 'lmekin' model of the 'kinship' package of R in order to estimate heritability. I want to estimate the confidence interval of the variance coefficient and so I should use a bootstrap simulation. The pedigree file has 1386 subjects so I create a kinship matrix [1386*1386].This is the code of R I use: kfit2 <- lmekin(IT~1+AGE +(1|ID), dati1,

Dear R experts I was using kinship package to fit mixed model with kinship matrix. The package looks like lme4, but I could find a way to extract p-value out of it. I need to extract is as I need to analyse large number of variables (> 10000). Please help me: require(kinship) Generating random example data id <- 1:100 dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7,

I was looking at how the model.frame method for lm works and comparing it to my own for coxph. The big difference is that I try to retain xlevels and predvars information for a new model frame, and lm does not. I use a call to model.frame in predict.coxph, which is why I went that route, but never noted the difference till now (preparing for my course in Nashville). Could someone shed light

Version 2.2 of coxme has been posted to CRAN, Windows versions and mirrors should appear in due course. This is a major update with three features of note: 1. A non-upwardly compatable change: Extractor functions: beta= fixed effects, b=random effects nlme lme4 coxme <2.2 coxme 2.2 lmekin 2.2 ------------------------------------------------------ beta

Hi, I had a problem with the lmekin() in kinship package: lmekin() can not be wrapped into another function library(kinship) #creat an example dataset xx<-rnorm(100) yy<-rnorm(100) id<-1:100 test.dat<-as.data.frame(cbind(xx,yy,id)) rm(xx,yy,id) a<-bdsmatrix(rep(10,10),rep(block,10),dimnames=list(c(1:100),c(1:100))) #100x100 block (n=10) diagonal matrix to indicate the

On 09/06/2012 05:00 AM, r-help-request at r-project.org wrote: > Hi, R experts > > I am currently using lmekin() function in coxme package to fit a > mixed effect model for family based genetic data. How can I extract the p > value from a lmekin object? When I print the object in R console, I can > see the p value and Z value are just over there. But I can not extract

Hi, R experts I am currently using lmekin() function in coxme package to fit a mixed effect model for family based genetic data. How can I extract the p value from a lmekin object? When I print the object in R console, I can see the p value and Z value are just over there. But I can not extract them by the coef() function. kinfit$coefficient$fixed (kinfit is the name of the lmekin object)

Hi All. I'd like to send some control arguments to the nls function when performing a nlsList analysis. I'm fitting a power model to some grouped data and would like to impose lower bounds on the estimates using the "port" algorithm. Obtaining the lower bound constraint works fine with a direct call to nls for a single level of the grouping variable. ?However, the bounds

Take a look at lmekin() in the coxme package. The motivating data set for my development of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families. The random effect is an intercept per subject with sigma^2 K as its variance where K is the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice, etc). lmekin is a linear models front

I have library in development with a function that works when called from the top level, but fails under R CMD check. The paricular line of failure is rsum <- rowSums(kmat>0) where kmat is a dsCMatrix object. I'm currently stumped and looking for some ideas. I've created a stripped down library "ktest" that has only 3 functions: pedigree.R to create a pedigree or

Hi Rick Thanks to Dieter Menne I did manage to solve the problem of imposing bounds on the parameter space duirng an nlsList fit. He suggested using optim to optimize the parameters prior to each fit. This worked well for me as I had a customized selfStart function that then optimized the parameters for each individual separately. if you rewrote your selfStart function as: powrDpltInit <-

I'm having a problem rebuilding a package, new to me in R 2.15.0 (Linux) It hits all that contain the line \usepackage[pdftex]{graphics} and leads to the following when running R CMD check on the directory. (I do this often; a final run on the tar.gz file will happen before submission.) Since I float and resize my figures, removing the line is fatal in other ways.

Thanks for the feedback Dirk. I sent my follow-up before I saw it. Looking at the source code, it appears that there is no options() call to turn this on. Nor does "R --help" reveal a command line option. How then does a user turn this on outside of the R CMD check envirionment, so as to chase things like this down? The fact that 1. renaming my function makes the error go away, 2.

Hello, All, GWAF 1.2 R.Version() is below. system(lme.batch.imputed( phenfile = 'phenfile.csv', genfile = 'CARe_imputed_release.0.fhsR.gz', pedfile='pedfile.csv', phen='phen1', covar=c('covar1','covar2'), kinmat='imputed_fhs.kinship.RData', outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt' )) Gives the error messages: Error in

Hi, I'm using kinship2 to calculate heritabilty, but I would like calculate in GenABEL too. I trying the code: > require(kinship2) > require(GenABEL) > pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX, famid=FID, missid=0)) > kmat = kinship(pedig) > (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat)) Erro em intI(i, n = d[1],

On 13 January 2020 at 10:02, Therneau, Terry M., Ph.D. via R-devel wrote: | Where can I find out (and replicate) what options as-cran turns on? See the file src/library/tools/R/check.R in the R sources, and grep for as_cran which is the internal variable controlled by the --as-cran option [...] | The check log contains multiple instances of the lines below: | | < Warning message: | < In

From R NEWS (changes in 3.6.0) Experimentally, setting environment variable _R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the variable is set to a ?true? value) when && or || encounter and use arguments of length more than one. On 2020-01-13 11:46 a.m., Therneau, Terry M., Ph.D. via R-devel wrote: > Thanks for the feedback Dirk.?? I sent my follow-up before I saw it.

On 13/01/2020 11:02 a.m., Therneau, Terry M., Ph.D. via R-devel wrote: > Where can I find out (and replicate) what options as-cran turns on? > > The issue: the following lines generate an error in R CMD check --as-cran? for coxme.? But > there is no error without as-cran nor is there one when I run the code in a terminal window. > > ismat <- function(x)? inherits(x,

Where can I find out (and replicate) what options as-cran turns on? The issue: the following lines generate an error in R CMD check --as-cran? for coxme.? But there is no error without as-cran nor is there one when I run the code in a terminal window. ismat <- function(x)? inherits(x, "matrix") || inherits(x, "bdsmatrix") || inherits(x, "Matrix") if