similar to: Extracting variance component estimates from lme

I've got a colleague who's using a GLMM to analyse her data, and I've told her that she needs to include an offset. However, glmmPQL doesn't seem to allow one to be included. Is there anyway of doing this? Bob -- Bob O'Hara Rolf Nevanlinna Institute P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of Helsinki Finland Telephone: +358-9-191 23743 Mobile: +358 50 599

Moi! I was helping to teach a course on mixed models this week, and we came across a problem with coding more than one random effect in lme when they aren't nested. As an example, suppose we have an experiment where we sample moths from several populations, and place the moths on different trees, and measure a trait (in this case survival of offspring, but that's less important). We

Moi! I have a problem where I want to find the ML estimate of a discrete parameter. I just want a function like optim that finds the max/min value for a function. Does anyone know of such a function for R? Thanks. Bob -- Bob O'Hara Rolf Nevanlinna Institute P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of Helsinki Finland Telephone: +358-9-191 23743 Mobile: +358 50 599 0540 Fax:

I want to draw a figure with several panels of unequal size, so i thought I would try using screen(). However, I can't figure out how to define the sizes as a matrix. I've tried this: split.screen(matrix(c(0,0.5,0,0.5, 0.5,1,0.5,1), byrow=F, ncol=4)) and a couple of variants on it, but get the same error: Error in par(.split.screens[[cur.screen]]) : invalid value specified

Hello from a presently sunny Helsinki! I've bee trying to repeat an analysis I did about 18 months ago (the reviewers of the paper want something adding to it). I'm using R1.5.0, but I couldn't see anything in the list of changes between this and 1.5.1 to suggest it would act any differently. The data is observational, on the changes in the population status of carabid beetles, and

Moi! I'm trying to add a rather long label to a y-axis, and it's so long that it won't fit into one line. However, things get strange when I try and split it over 2 lines. The problem seems to be the plus/minus symbol, which means I have to use expression(). I'm using R1.6.1 on Windoze 2000. As an example: thing1 <- expression(paste("log odds of survival probability (

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

I can only assume I'm betraying my ignorance here, but this is not what I would expect. I'm getting the following from a stepwise selection (with both step and stepAIC): > step(lm(sqrt(Grids)~ SE + Edge + NH), scope=~ (Edge + SE + NH)^2) Start: AIC= 593.56 sqrt(Grids) ~ SE + Edge + NH Df Sum of Sq RSS AIC <none> 2147.0 593.6 + Edge:NH 1

Hi folks, I have assumed that ratios of variance components (Fst and Qst in population genetics) could be estimated using the output of mcmcsamp (the series on mcmc sample estimates of variance components). What I have started to do is to use the matrix output that included the log(variances), exponentiate, calculate the relevant ratio, and apply either quantile or or HPDinterval to get

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 <-

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

Hi Everyone, I posted a similar question about a week ago, but haven't gotten any replies -- I'm afraid that's because my previous question was too vague. Let me try again with a more specific question, and I hope someone can help. NOTE, I know I should be using the newer lme4 package, I just haven't had a chance to update my version of R yet, so the question below relates

Dear list, For educational purposes I have been working with the script below. I have a observation: line 31 #CScal[i] = (amo^2) # IT IS WRONG, I KNOW, BUT IT MAKE R TO CRASHES! I'm thinking this is a possible bug in the R! And I have a couple of doubts: 1) line 51 #curve(dchisq(x, n-1), add = T, col = 'red' I think that it is correct, but the function no

On Saturday, November 2, 2019 10:40:45 PM EET Stephan Bosch <stephan at rename-it.nl> wrote: > I think we already know about this issue (tracked as DOP-942). It > apparently happens because qmail masks the SIGCHLD signal while Dovecot > doesn't unmask it before waiting for children. You're right. Isn't this a simple fix - a call to sigprocmask ? This should not be a

The background: I'm trying to fit a Poisson-lognormal distrbutuion to some data. This is a way of modelling species abundances: N ~ Pois(lam) log(lam) ~ N(mu, sigma2) The number of individuals are Poisson distributed with an abundance drawn from a log-normal distrbution. To fit this to data, I need to integrate out lam. In principle, I can do it this way: PLN1 <- function(lam, Count,

Dear all, I didn't find any graphical solution in the package "mva" to plot the canonical scores from a CCA (canonical correlation analysis). Does anybody knows how to plot or has anybody already programmed : - the map of the canonical scores, - the graph of the canonical weights, - the correlation circle i.e. the canonical loadings ? Thank you for help ...

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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

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

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