Displaying 20 results from an estimated 10000 matches similar to: "error checks"
2010 Apr 23
2
Deferred Default Marker
I've finally narrowed down a puzzling problem: here is the short test
case.
tmt34% R --vanilla
R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
> temp <- matrix(runif(50), ncol=2)
> t(temp) %*% temp
[,1] [,2]
[1,] 7.916016 6.049698
[2,] 6.049698 7.650694
> library(kinship)
Loading required package:
2006 Mar 30
1
Random Coefficients using coxme
Hello, I was hoping someone could answer a question for me that may
either be statistical or script related. I don't come from a statistics
background, so I am not positive if I am using the correct nomenclature
or even the correct procedure. Is it possible to model "random
coefficients" in a mixed effects cox-regression using coxme from the
Kinship package? For example, using
2011 Jul 15
1
Confusing inheritance problem
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
2008 Mar 05
1
coxme - fitting random treatment effect nested within centre
Dear all,
I am using "coxme" function in Kinship library to fit random treatment effect nested within centre. I got 3 treatments (0,1,2) and 3 centres. I used following commands, but got an error.
> ugroup=paste(rep(1:3,each=3),rep(0:2,3),sep='/')
> mat1=bdsmatrix(rep(c(1,1,1,1,1,1,1,1,1),3),blocksize=rep(3,3),dimnames=list(ugroup,ugroup))
>
2011 Apr 15
1
no solution yet, please help: extract p-value from mixed model in kinship package
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
2010 Mar 18
2
Pedigree / Identifying Immediate Family of Index Animal
I have a data frame containing the Id, Mother, Father and Sex from about
10,000 animals in our colony. I am interested in graphing simple family
trees for a given subject or small number of subjects. The basic idea is:
start with data frame from entire colony and list of index animals. I need
to identify all immediate relatives of these index animals and plot the
pedigree for them. We're
2005 Nov 14
1
Tidiest way of modifying S4 classes?
I wish to make modifications to the plot.pedigree function in the
kinship package. My attempts to contact the maintainer have been
unsuccessful, but my question is general, so specifics of the kinship
package might not be an issue.
My first attempt was to make a new function Plot.pedigree in the
.GlobalEnv which mostly achieved what I wanted to. However, I'm sure
that's not the tidiest
2008 Feb 06
2
kinship package: drawing pedigree error
Hi
Im using the kinship package to draw a pedigree. On my data set this works fine but when i add indivudals to the pedigree i keep getting an error i hope someone can help me!
This is the code im using:
Data<-read.table("Tree.txt", header=T, sep=",")
attach(Data)
ped<-pedigree(id, dadid, momid, sex, aff)
par(xpd=T)
plot.pedigree(ped)
This is my data looks like
2005 Apr 24
1
R CMD check doesn't stop with checking examples
Hello!
I am building a package, which includes also one Fortran subroutine,
which works fine if I compile it as a shared library and load it into
R via dyn.load(). However, when I launch R CMD check it doesn't stop
with checking examples. It's just doing and doing ... I pasted the
whole output from R CMD check. Does anyone have any suggestions?
I'm still using R 2.0.1.
2009 Aug 05
1
inheriting C symbols
The package coxme depends heavily on bdsmatrix, to the point of needing
access to some of its C calls. The kinship package (in progress) uses
the R level functions in bdsmatrix, but not the C calls. That is, I
don't want to always export the symbols.
For testing I can use an explicit dyn.load('somepath/bsdmatrix.so',
local=F). How do I incorporate such a dependency in the
2019 Jun 18
1
making a vignette optional
I had added a vignette to the coxme package and all worked well locally, but it failed at
CRAN.???? The issue is that the vignette involves using coxme for pedigree data, it
doesn't work without the kinship2 package, and I hadn't put in the necessary "if
(require(...." logic.
The question is, how do I make the entire vignette conditional? If the package isn't
available,
2012 Nov 24
1
Bootstrap lmekin model
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,
2005 Nov 06
1
kinship package example data
I've been looking at the kinship package which looks as though it
might be appropriate for my purposes. What I can't find is any
reference to the data that is used in the example code. A dataframe
called d10 with column names, upn, dadid, momid, sex and affect is
required. One can get an idea of what sort of values should be in
most columns from the description in the pedigree function,
2008 Dec 28
1
Random coefficients model with a covariate: coxme function
Dear R users:
I'm new to R and am trying to fit a mixed model
Cox regression model with coxme function.
I have one two-level factor (treat) and one
covariate (covar) and 32 different groups
(centers). I'd like to fit a random coefficients model, with treat and covar
as fixed factors and a random intercept, random
treat effect and random covar slope per center.
I haver a couple of
2015 Mar 02
1
clarification on import/depends for a method
User of the coxme library (mixed effects Cox models) are instructed to use ranef(),
fixed(), VarCorr(), etc to retrieve bits out of a fitted model; it purposely uses the same
methods as nlme and/or lmer.
The current behavior is to "depend" on nlme. If I defined the methods myself in coxme,
then someone who had both nlme and coxme loaded will suffer from "last loaded wins",
2011 Jun 01
0
Anyone have experience with kinship pedigree plot?
Hello,
I am using the Kinship package to draw a pedigree plot. I am trying
to control the spacing between individuals in the pedigree.
Currently, it is drawing a pedigree with too little space, so the text
is overlapping. I'd like to increase the distance between
individuals. According to the documentation, I would expect the
following to be relevant:
2008 Feb 21
2
Nested frailty model
Dear R-help,
I am trying to estimate a Cox model with nested effects, or better
h(t,v,w)=v*w*h0(t)*exp(B'x)
where h(t,v,w) is the individual hazard function
w and v are both frailty terms (gamma or normal distributed)
I have 12 clusters and for each one of them I would like to associate a
realization of v, while w is a random effect for the whole population.
At the population level
2010 Apr 08
2
erasing an area of a graph
I have a case where the easiest way to draw a particular symbol would be
to draw something a little bigger, and then use polygon(... , col=0) to
erase the extra stuff. Just how to do this best when par('bg') =
'transparent' is, however, eluding me. I've looked through the archives
and the book R Graphics without quite seeing the light.
Help or pointers to help would be
2011 Feb 04
1
GWAF package: lme.batch.imputed(): object 'kmat' not found
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
2011 Jul 26
0
kinship2
Dear useRs:
Announcing the release of kinship2, version 1.2.1, to CRAN.
kinship2 is a branch from the original kinship package with some key
updates for the pedigree and kinship functions, with some additional
functions that work with the pedigree object.
Highlights:
* pedigree and pedigreeList objects implemented with S3 methods print
and "[,"
* pedigree plotting routine