Displaying 20 results from an estimated 100 matches similar to: "Rd-file error: non-ASCII input and no declared encoding"
2008 Jan 21
1
Reading Genepop files
Dear list,
Does there exist R routines for reading output files from Genepop?
(GENEPOP is a population genetics software package by Raymond & Rousset;
http://genepop.curtin.edu.au/ )
I find several R packages that contain function for writing Genepop input
files, but
non that does the reverse.
Regards,
hans
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2008 Apr 19
1
resampling from distributions
Hello All,
Once again thanks for all of the help to date. I am climbing my R learning
curve. I've got a few more questions that I hope I can get some guidance on
though. I am not sure whether the etiquette is to break up multiple
questions or not but I'll keep them together here for now as it may help put
the questions in context despite the fact that the post may get a little
long.
2010 Jan 26
0
problem with read.genepop function
I'm trying to use the package ARES to produce allelic richness
estimates with extrapolation beyond the sample size. I've begun by
testing the program with the butterfly_borneo data provided with the
package, but I seem to be having a problem with the read.genepop
function. Below, I've included my R code along with the error I
receive after trying to read the genepop file. I'm
2012 Sep 10
1
Calculating Linkage Disequilibrium for Microsatellite Markers?
Dear R helpers,
I am trying to test for linkage disequilibrium (LD) in R between all pairs
of loci. Importantly, my loci are microsatellites and have up to 30
alleles per locus. Do you know of any R packages that can either (1)
calculate measures of LD directly or (2) test for the presence of LD within
a statistical framework? Every package I have run across seems to be only
able to handle
2018 Apr 03
2
names lost in functions from packages installed by R-devel r74500
Dear list members,
If I install with R-devel r74500 on Windows (sessionInfo below) the
attached 'bugdemo' package with the single function
foo <- function() {
? named <- c("bar"=TRUE)
? print(named)
? return(named)
}
then run
> bugdemo::foo()
[1] TRUE
[1] TRUE
The "bar" name is lost. It is not lost when I define foo in the R
session instead of using
2006 Mar 01
1
write.pop.file (genetics package)
Hello,
Can anybody tell me what the format of the input data file should be for
this R function?
Poor package documentation.
Thanks,
Matt
********************************************************
Matthew D. MacManes
PhD Student
UC- Berkeley
Department of Integrative Biology
Museum of Vertebrate Zoology
3101 VLSB #3140
Berkeley, CA 94720
(510)642-7782
EMAIL: macmanes@berkeley.edu
WEBSITE:
2018 Apr 03
1
names lost in functions from packages installed by R-devel r74500
>>>>> Martin Maechler <maechler at stat.math.ethz.ch>
>>>>> on Tue, 3 Apr 2018 17:03:02 +0200 writes:
>>>>> Francois Rousset <francois.rousset at umontpellier.fr>
>>>>> on Tue, 3 Apr 2018 16:38:42 +0200 writes:
>> Dear list members,
>> If I install with R-devel r74500 on Windows (sessionInfo
2009 Jan 13
3
problem whit Geneland
I do the these passages:
library(Geneland)
set.seed(1)
data <- simdata(nindiv=200,
coord.lim=c(0,1,0,1) ,
number.nuclei=5 ,
allele.numbers=rep(10,20),
IBD=FALSE,
npop=2,
give.tess.grid=FALSE)
geno <- data$genotypes
coord <- t(data$coord.indiv)
path.mcmc <-
2012 Nov 13
2
Discrete trait Ornstein–Uhlenbeck in R?
Is there a package that will allow me to fit Brownian motion and
Ornstein?Uhlenbeck models of evolution for discrete traits? I know that
geiger and ouch have commands for fitting these models for continuous
traits, but these aren't suitable for discrete trait evolution, correct?
--
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2007 Sep 21
1
Help create a loopto conduct multiple pairwise operations
#Hello,
#I have three data frames, X,Y and Z with two columns each and different
numbers of rows.
# creation of data frame X
X.alleles <- c(1,5,6,7,8)
X.Freq <- c(0.35, 0.15, 0.05 , 0.10, 0.35)
Loc1 <- cbind( X.alleles,X.Freq)
X <- data.frame(Loc1)
#creation of data frame Y
Y.alleles <- c(1,4,6,8)
Y.Freq <- c(0.35, 0.35, 0.10, 0.20 )
2018 Apr 03
0
names lost in functions from packages installed by R-devel r74500
>>>>> Francois Rousset <francois.rousset at umontpellier.fr>
>>>>> on Tue, 3 Apr 2018 16:38:42 +0200 writes:
> Dear list members,
> If I install with R-devel r74500 on Windows (sessionInfo below) the
> attached 'bugdemo' package with the single function
> foo <- function() {
> ? named <-
2007 Aug 30
2
How to multiply all dataframe rows by another dataframe's columns
Hello,
I have two data frames, X and Y, with two columns each and different numbers
of rows.
# creation of data frame X
Loc1.alleles <- c(1,5,6,7,8)
Loc1.Freq <- c(0.35, 0.15, 0.05, 0.10, 0.35)
Loc1 <- cbind( Loc1.alleles,Loc1.Freq)
X <- data.frame(Loc1)
#creation of data frame Y
Loc2.alleles <- c(1,4,6,8)
Loc2.Freq <- c(0.35, 0.35,
2008 Aug 10
1
Scripting - query
I have a vector:
alleles.present<-c("D3", "D16", ... )
The alleles present changes given the case I'm dealing with - i.e. either
all of the alleles I use for my calculations are present, or some of them.
Depending on what alleles are present, I need to make matrices and do
calculations on those alleles present and completely disregard any formula
or other use of the
2007 Mar 16
1
ideas to speed up code: converting a matrix of integers to a matrix of normally distributed values
Hi all,
[this is a bit hard to describe, so if my initial description is
confusing, please try running my code below]
#WHAT I'M TRYING TO DO
I'd appreciate any help in trying to speed up some code. I've written
a script that converts a matrix of integers (usually between 1-10,000
- these represent allele names) into two new matrices of normally
distributed values (representing
2008 Mar 20
3
create matrix
Hi all,
I have a dataset consisting of 5 columns and over 5000 rows. Each row
gives information about an individual animal, including longevity, i.e.
at what age an animal died.
For the model I use I need to create n rows for each animal, n being its
longevity, and a new column 'survival' with a binary 0/1 outcome. When
an animal died e.g. at age 5, there have to be 5 rows of identical
2003 Sep 04
1
Allelic Differentiation, sampling, unique(), duplicated()
Hi people,
I have made some progress trying to work out how to solve this problem
but I have got a bit stuck - sorry if this turns out to be a simple
exercise . .
Allelic Differentiation (AD) in genetics measures the number of
different alleles between (say) two populations eg:
Organisms in Pop 1 have alleles: a, b, c, d, e
Organisms in Pop 2 have alleles: b, b, c, d, e
Different
2005 Jul 07
3
What method I should to use for these data?
Dear R user:
I am studying the allele data of two populations.
the following is the data:
a1 a2 a3 a4 a5 a6 a7 a8 a9
a10 a11 a12 a13 a14 a15 a16 a17
pop1 0.0217 0.0000 0.0109 0.0435 0.0435 0.0000 0.0109 0.0543
0.1739 0.0761 0.1413 0.1522 0.1087 0.0870 0.0435 0.0217 0.0109
pop2 0.0213 0.0213 0.0000 0.0000 0.0000 0.0426 0.1702 0.2128
0.1596 0.1809 0.0957 0.0745 0.0106
2007 Aug 21
1
Output from while and for loop
Hello,
I am new and am having a hard time getting the proper syntax for output
from loops. I am working on a simulation to generate a null expectation of
bee behavior. Pieces of it work. The part that I am having specific
difficulty is in output of a vector from within the while loop that I am
using. Basically the simulation works as such: I have a starting point
and a neighbor matrix and a
2010 Dec 07
1
randomForest: How to append ID column along with predictions
Hi all,
When running a prediction using RF on another data, I get two columns
returned: row number(?) and predicted class. Is there a way of
appending the unique row value from an ID column in the dataframe to
the predictions instead of the row number? I'm assuming that the
returned results follow the data frame in that the first result
returned equals the first entry in the dataframe.
i.e.,
2024 Nov 15
1
R coding to extract allele frequencies from NCBI for ALL alleles of one SNP?
Dear All,
The following code extracts from NCBI very nice output for ONE allele of a SNP (often the allele with the second largest frequency - usually termed the minor allele). It gives an average minor allele frequency from all NCBI sources (which is what I want, except I'd like the addition of data for all the other alleles of one SNP) plus a table of minor allele frequencies from each