similar to: Tidiest way of modifying S4 classes?

hello, if i load the RSQLite package in addition to the RPostgreSQL package, i get various errors when trying to use RPostgreSQL functions. here is an example transcript showing one such error: ========================================================== R version 2.15.0 (2012-03-30) [...] > packageVersion('RPostgreSQL') [1] 0.3.2 > packageVersion('RSQLite') [1] 0.11.1

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

I'm currently packaging up some of the kinship matrix routines more formally, these are used in coxme when dealing with family correlation structures. One of my test programs exercises error conditions, i.e., it purposely feeds particular types of invalid pedigree data in to see if the right error message results. So there are comment-action pairs # the next line should generate a

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

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.

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

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

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:

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,

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,

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

Hi, I found the following on Windows 2000/NT R Version 1.9.1 (2004-06-21) (also Version 1.9.0): The S4 group "Math" doesn't work as documented; i.e., "log", "log10", "gamma" and "lgamma" are included in the documentation but don't work. See example code below. Moreover, what about 'genericForPrimitive' which is used in

I like the fact that the postscript function enables the possbiility of a more useful title than before. However, I'd prefer the default to be the file name. It's very simple for me to make my own postscript function that does just that simply by setting title = file. I always use onefile = TRUE, so it always works (so far). However, I'm a little reluctant to do that in case some

I like the fact that the postscript function enables the possbiility of a more useful title than before. However, I'd prefer the default to be the file name. It's very simple for me to make my own postscript function that does just that simply by setting title = file. I always use onefile = TRUE, so it always works (so far). However, I'm a little reluctant to do that in case some

after this setClass("A") setGeneric("bar", function(x, y) standardGeneric("bar")) setMethod(bar, signature(x="A", y="A"), function(x, y) {}) setMethod(bar, signature(x="A", y="ANY"), function(x, y) {}) the method for signature c("A", "A") contains package information > str(getMethod(bar,

Hi, I've noticed an issue with S4 methods and namespaces which only arises in particular, difficult to reproduce configurations. One example is the ggbio package in Bioconductor, which currently emits these warnings when its namespace is loaded: ---------------------- library(ggbio) Loading required package: ggplot2 Attaching package: ‘ggbio’ The following object(s) are masked from

Hi, Strange things happen. Here is a simple example: > setClass("A", contains="integer") > setMethod("as.matrix", "A", function(x, ...) t(callNextMethod())) Creating a generic function for ?as.matrix? from package ?base? in the global environment [1] "as.matrix" > a <- new("A", 1:3) > as.matrix(a)

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)) >

Hi, There seems to be a problem with setGroupGeneric() from package 'methods'. The symptoms are somewhat erratic, in the sense that small changes may lead to any of the following behaviours. 1.Package works without problems on Windows and installs on Linux but gives error when loaded with library(). 2.Package installs on both systems and gives error when loaded on any of them. 3.

I need to repeat a function many times, with differing parameters held constant across iterations. To accomplish this, I would like to create a list (or vector) of parameters, and then insert that list into the function. For example: q<-("l,a,b,s") genericfunction<-function(q){ } ###### The equivalent code would of course be genericfunction<-function(l,a,b,s){ } Any help