similar to: GWAF package: lme.batch.imputed(): object 'kmat' not found

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

Hello all I have what seems like a simple question but have not been able to find an answer on the forum. I'm trying to define a function which involves regression models and a large number of covariates. I would like the function to accept any number of covariates and, ideally, I would like to be able to enter the covariates in a group (e.g. as a list) rather than individually. Is there any

Hi, Im using geoR and I'm trying to do some predictions, based on an external trend. I'm having some problems specifying my model.control, specifically how do I define my model, and also the source of the covariate data at the prediction locations? I am assuming that the covariate data at the prediction locations should be imported to a geodata object along with the prediction location

How can I delete both rows and columns that do not meet a particular cut off value. Example: > d <- rbind(c(0, 1, 6, 4), + c(2, 5, 7, 5), + c(3, 6, 1, 6), + c(4, 4, 4, 4)) > f <- as.matrix(d) > f [,1] [,2] [,3] [,4] [1,] 0 1 6 4 [2,] 2 5 7 5 [3,] 3 6 1 6 [4,] 4 4 4 4 I would like to delete all

I have a few questions about GenABEL, gwaa data. 1) is there a universal way that most GenABEL people use to add more individuals into a 'gwaa' data? For example, I have a 'gwaa' data, but I need to add some dummy parents, for 'gwaa at phdata', it's easy to add these rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0 0.....'

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 developers: I am a PHD candidate student in the school of public health of Peking University and my major is genetic epidemiology. I am learning the FAM-MDR algorithm, which is used to detect the gene-gene and gene-environment interactions in the data of pedigree. The codes were written by Tom Cattaert of the University of Liege. The algorithms and the sample datasets are available at

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

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

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.

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,

>>>>> Ben Bolker >>>>> on Mon, 13 Jan 2020 11:49:09 -0500 writes: > 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. Indeed,

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],

Someone just sent me a data set that causes the lmekin function, part of the kinship package, to fail. In chasing it down I get an error I have never seen before. fit <- lmekin(icam1 ~ factor(center) + age + factor(sex), random= ~1|iid, data=chaidata, varlist=kmat) Error in Y - fitted : non-numeric argument to binary operator Add the recover option, and the offending lines are

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,

Those of us stuck on Windows but who attempt to develop properly are wounded to the quick, sir! :) Avi On Mon, Jan 13, 2020 at 12:24 PM Martin Maechler <maechler at stat.math.ethz.ch> wrote: > >>>>> Ben Bolker > >>>>> on Mon, 13 Jan 2020 11:49:09 -0500 writes: > > > From R NEWS (changes in 3.6.0) > > Experimentally, setting

CRAN (and crantastic) updates this week New packages ------------ * bdoc (1.0) Michael Anderson http://crantastic.org/packages/bdoc This package contains a function that will classify DNA barcodes as well as a few test and reference data sets. * bdsmatrix (1.0) Terry Therneau http://crantastic.org/packages/bdsmatrix This is a special case of sparse matrices, used by coxme and

Full_Name: Jerome Asselin Version: 1.6.1 OS: RedHat Linux 7.2 Submission from: (NULL) (142.103.173.179) Hello, I get a segmentation fault when I run the following code. I wouldn't expect meaningful results because my response variable contains only missing values. However, I would expect something like a regular error (not a segmentation fault). library(survival) data <-