Displaying 20 results from an estimated 2000 matches similar to: "Help with Subtracting an effect from a Mixed Model"
2005 Oct 26
1
syntax for interactions in lme
Hello,
I am trying to make the switch from SAS, and I have a fairly elemental
problem with syntax using the nlme package for analyzing mixed models.
There was a previous question on this topic posted to this list, so I
apologize for redundancy, but I didn't understand the advice given to
that inquiry. The model I want to run has the following factors:
Host (fixed)
Sire (random)
Dam
2011 Apr 16
3
lme4 problem: model defining and effect estimation ------ question from new bird to R community from SAS community
Hi R community,
I am new bird to R and moved recently from SAS. I am no means expert on
either but very curious learner. So your help crucial for me to learn R.
I have already got positive expression.
I was trying to fit a mixed model in animal experiment but stuck at simple
point. The following similar example is from SAS mixed model pp 212.
# data
genetic_evaluation <-
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
2007 Aug 29
2
Recoding multiple columns consistently
Hi,
I have a dataframe that contains pedigree information;
that is individual, sire and dam identities as separate
columns. It also has date of birth.
These identifiers are not numeric, or not sequential.
Obviously, an identifier can appear in one or two columns,
depending on whether it was a parent or not. These should
be consistent.
Not all identifiers appear in the individual column - it
is
2005 Jul 01
2
loop over large dataset
Hi All,
I'd like to ask for a few clarifications. I am doing some calculations
over some biggish datasets. One has ~ 23000 rows, and 6 columns, the
other has ~620000 rows and 6 columns.
I am using these datasets to perform a simulation of of haplotype
coalescence over a pedigree (the datestes themselves are pedigree
information). I created a new dataset (same number of rows as the
pedigree
2008 Feb 25
0
Extracting variance components from a Manova
I am trying to run a simple nested manova with two levels of nesting,
Sires, and Dams within Sires. The goal is to extract the among sires
covariance matrix and secondarily, the among Dams within Sires
covariance matrix. Both sires and dams are random effects. At present
there are four dependent variables, but that may change. This is part of
a larger bootstrapping project, so efficiency and
2009 Oct 22
1
help sub setting data frame
Hi,
I'm running into a problem subsetting a data frame that I have never
encountered before:
> dim(chkPd)
[1] 3213 6
> df = head(chkPd)
> df
PN WB Sire Dam MG SEX
601 1001 715349 61710 61702 67 F
969 1001_1 511092 616253 615037 168 F
986 1002_1 511082 616253 623905 168 F
667 1003 715617 61817 61441 67 F
2004 Dec 06
2
Re : LOOPS
Dear lists,
I want to construct a loop in R, but don't know how to do it. I can do it
in SAS, but I prefer in R (which I am hoping I will off SAS for good
soon). Could anyone help me to convert the SAS codes to equivalent R codes.
Basically, the following codes were written to establish the sire gametes
or phases for daughter design for one markers two alleles.
Here are the SAS code:
do
2005 Jul 21
3
vectorising ifelse()
Hi All,
is there any chance of vectorising the two ifelse() statements in the
following code:
for(i in gp){
new[i,1] = ifelse(srow[i]>0, new[srow[i],zippo[i]], sample(1:100, 1,
prob =Y1, rep = T))
new[i,2] = ifelse(drow[i]>0, new[drow[i]>0,zappo[i]], sample(1:100,
1, prob =Y1, rep = T))
}
Where I am forced to check if the value of drow and srow are >0 for each
line... in
2006 Oct 21
0
[Fwd: [AGDG-LIST:405] R Computing Contest]
-------- Original Message --------
Subject: [AGDG-LIST:405] R Computing Contest
Date: Sat, 21 Oct 2006 12:08:13 -0400
From: Larry Schaeffer <lrs at uoguelph.ca>
Reply-To: lrs at uoguelph.ca
To: Animal Geneticist's Discussion <agdg-list at colostate.edu>
For those that are interested only:
R Computer Programming Challenge
Given: y = Factor A + Factor B + b1(Covariate1) +
2007 Aug 30
0
R-help Digest, Vol 54, Issue 30
Ron Crump wrote:
> Hi,
>
> I have a dataframe that contains pedigree information;
> that is individual, sire and dam identities as separate
> columns. It also has date of birth.
>
> These identifiers are not numeric, or not sequential.
>
> Obviously, an identifier can appear in one or two columns,
> depending on whether it was a parent or not. These should
> be
2009 Apr 19
0
Tow to perform diallel analysis in R?
I want to use a diallel analysis in R, for some of my own data. I've been
through the primary literature and textbooks, and remain stumped as to how
to implment this in R.
I can illustrate the problem using a published example dataset: [Cockerham
and Weir (1977) Quadratic Analyses of Reciprocal Crosses. Biometrics, Vol.
33, No. 1 pp. 187-203]
In this study, 8 different individuals were
2013 Mar 11
4
Pedigreemm
Hola a todos, me gustaría realizar una consulta asociada a la generación
de valores genéticos del pedigreemm en R. Primero generé el archivo de
pedigree incluyendo los parentales para posteriormente estimar la varianza
aditiva y los valores genéticos para cada individuo, relacionando los
individuos por medio de la matriz de parentesco.
Me da todo perfecto, el complemento pedigreemm trabaja muy
2011 Mar 10
1
snp-chip table
Dear R helpers
I have a table and i need to make new table
table1:
sire snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10
snp11 snp12 snp13 snp14 snp15 8877 -1 -1 -1 -1 0 0 -1 -1 -1 0 1 1 1 -1 -1
7765 1 1 1 0 0 0 -1 1 1 1 0 0 0 1 0 8766 1 1 -1 0 -1 -1 0 -1 0 -1 -1 -1 0 1
0 6756 0 1 0 -1 1 -1 -1 0 0 0 0 -1 0 1 1 5644 -1 0 1 -1 0 0 0 0 -1 -1 0 0 0
0 1
I have table2
sire
2009 Apr 17
1
Missing getopt_long in Solaris 8 Sparc
Hi Jean-Marc,
Am 17.04.2009 um 13:35 schrieb Jean-Marc Valin:
> It should be using getopt1.c when getopt isn't available.c. Can you
> check why it doesn't? In any case, that's only required for the Ogg
> tools, not for the library.
config.log says
ac_cv_func_getopt_long=no
ac_cv_header_getopt_h=no
ac_cv_lib_gnugetopt_getopt_long=no
LIBOBJS='
2002 Aug 28
0
Extracting variance component estimates from lme
I assume I'm missing something obvious here...
The short form of my main question is: how do I extract variance
components from an lme object?
The longer form (plus optional supplementary question!): I'm looking at
some quantitative genetics, and want to estimate two variance components
so that I can then calculate a statistic called Qst from them. So I
have this:
reg1 <- lme(y ~
2001 Jul 10
1
Object finalization
I see some code in R to attach finalizers to external pointer references
(Register[C]Finalizer). Anyone have an example of how to code the
finalizer? R_RegisterCFinalizer accepts a C function, but I can't see
how to get it to operate on the pointer, since the pointer is not passed
to the function when its called. RegisterFinalizer takes an R closure,
but how is it called from R (tried
2008 May 06
2
list manipulation
Hello,
I have a set of one-liners (many thanks to previous responses from this
list) that I use to look at newly imported data sets with functions like
dim(), names(), str(), etc. within lapply(). Generally, these commands
work for me but, I am apparently still missing some aspect of list
manipulation. I don't understand why I get a set of NULL list elements
at the end of each output as
2006 Feb 15
3
RailsTidy: validates your HTML
Hello everybody,
I needed something to validates my HTML templates so I wrote a plugin
and here is its first version:
RailsTidy is a plugin for Ruby On Rails. It allows you to
* validate your rhtml templates,
* validate the html output of your functional tests,
* clean the html generated by rails.
For doing all this, it uses
* Tidy[1], the popular HTML validator and
2003 Apr 18
1
MCMCpack gelman.plot and gelman.diag
Hi,
A question. When I run gelman.diag and gelman.plot
with mcmc lists obtained from MCMCregress, the results are following.
> post.R <- MCMCregress(Size~Age+Status, data = data, burnin = 5000, mcmc = 100000,
+ thin = 10, verbose = FALSE, beta.start = NA, sigma2.start = NA,
+ b0 = 0, B0 = 0, nu = 0.001, delta = 0.001)
> post1.R <- MCMCregress(Size~Age+Status, data