Displaying 20 results from an estimated 200 matches similar to: "no solution yet, please help: extract p-value from mixed model in kinship package"
2011 Apr 14
0
extract p-value from mixed model in kinship package
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,
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 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
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,
2012 Nov 09
0
Kinship2 and GenABEL
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],
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
2011 Jul 27
1
SNP Tables
Hello,
I have indicators for the present of absent of a snps in columns and the
categorey (case control column). I would like to extract ONLY the tables and
the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when
one of the allelle is missing. The data look like the matrix snpmat below:
so the first snp should give me the following table: (aa=0, Aa=1 and AA=2)
aa
2010 May 16
2
sample
Hi,
I am sampling two random columns from females and two random columns
from males to produce tetraploid offspring. For every female I am
sampling a random male.
In the end I want to write out a a matrix with all the offspring, but
that does not work. I get always only the offspring from the last
females. There must be a mistake in my script:
moms<-read.delim("females.txt",
2007 Jun 11
0
lmekin() function in kinship package
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
2012 Sep 06
1
How to extract p value from the lmekin object obtained by fitting mixed model with function lmekin() in package coxme?
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)
2015 Mar 02
5
Import data set from another package?
I've moved nlme from Depends to Imports in my coxme package. However, a few of the
examples for lmekin use one of the data sets from nlme. This is on purpose, to show how
the results are the same and how they differ.
If I use data(nlme::ergoStool) the data is not found, data(nlme:::ergoStool) does no
better.
If I add importFrom(nlme, "ergoStool") the error message is that
2020 Jan 13
5
as-cran issue
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
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
2020 Jan 13
2
as-cran issue
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.
2020 Jan 13
2
as-cran issue ==> set _R_CHECK_LENGTH_1_* settings!
>>>>> 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,
2010 Apr 06
0
Strange error
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
2012 May 14
1
Vignette problem
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.
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
2012 Sep 14
1
Correlation between random effects in the package coxme
Hello,
Why the correlation between the random effects is negative?
library(coxme)
rats1 <- coxme(Surv(time, status) ~ (1|litter), rats)
random.effects(rats1)[[1]] #one value for each of the 50 litters
print(rats1)
rats2 <- lmekin(time ~ (1|litter), rats)
fixed.effects(rats2)
random.effects(rats2)[[1]] #one value for each of the 50 litters
print(rats2)
2011 Oct 06
1
multiple defines of diag
The current coxme code has functions that depend on bdsmatrix and others
that depend on Matrix, both those pacakges define S4 methods for diag.
When loaded, the message appears:
replacing previous import ?diag? when loading ?Matrix?
Questions:
1. Do I need to worry about this? If so, what can I do about it?
I suppose I could add an importFrom directive, but it will be a pain
unless there