similar to: MCMCglmm heteroscedasticity dependent on predictor

Dear all, I would like to add mixed effects in a multinomial model and I am trying to use MCMCglmm for that. The main problem I face: my data set consits of a trapping data set, where the observation at eah trap (1 or 0 for each species) have been aggregated per traplines. Therefore we have a proportion of presence/absence for each species per trapline. ex: ID_line mesh habitat Apsy Mygl

Thanks for your answers Stephen and Ben, I hope I am posting on the correct list now. I managed so far to run the multinomial model with random effect with the following command: MCMCglmm(fixed=cbind(Apsy,Mygl,Crle,Crru,Miag,empty) ~ habitat:trait,random=~idh(trait):mesh,family="multinomial12", data=dataA,rcov=~trait:units) (where multiple responses are different species, Habitat

Hi, Thanks in advance for any help on this question. I'm running multinomial models using the MCMCglmm package. The models have 5 outcome variables (each with count data), and an additional two random effects built into the models. The issue is that when I use the following code, the summary only gives me results for four of the outcome variables. Here is the code for my model: m3.random

Hello, I'm having some trouble figuring out the correct model specification for my data. The system consists of multiple populations of an organism, which have been genetically sampled for several years. The problem is this: A minority of individuals are found in more than one sample, either they have survived into the next sampling at the same location, or have migrated to another another

> On Mar 22, 2018, at 1:31 PM, Michelle Kline <michelle.ann.kline at gmail.com> wrote: > > Hi, > > Thanks in advance for any help on this question. I'm running multinomial > models using the MCMCglmm package. The models have 5 outcome variables > (each with count data), and an additional two random effects built into the > models. The issue is that when I use

I have a question for users of MCMCglmm that have experience implementing the zero-inflated poisson model. I find that the documentation, and previous questions, do not offer a lot of clear guidance on specifying and interpreting the zipoisson model. In particular, I see a lot of zero-inflated poisson examples that use the at.level(trait, x):variableName syntax. Specifically, the MCMCglmm

Dear MCMCglmm users, I am currently struggling with the specification of a proper prior and model formula for a multi-response MCMCglmm with two of the three response variables being Gaussian and the third being za-poisson. The model includes several fixed effects and three nested random effects. In general, I would prefer to fit a model with a fixed effect of trait and suppressed intercept for

Hi David, Thanks for your comment. I haven't posted the data because they are unpublished and include human subjects so there are issues with sharing on a list serv, but I thought perhaps someone had encountered a similar problem and would already know the answer. I will reconsider whether my University's ethics approval would allow me to post the data and update the question if I think

Hi all, I'm hoping I might be able to get some help with some issues specifying priors for MCMCglmm. I'm trying to fit a gaussian glmm using MCMCglmm to a data set with two (correlated) response variables. The response variables are both logit-transformed proportions (there are a few reasons why I've chosen these with gaussian error over binomal glmm, which I won't go into).

Hi, Running: Ruby 1.8.7 p72, RSpec 1.1.12 and rcov 0.8.1.2.0, I get the following error message with $ rake spec:rcov -- /usr/local/ruby1.8.7//lib/ruby/1.8/rexml/formatters/pretty.rb:131:in `[]'': no implicit conversion from nil to integer (TypeError) from /usr/local/ruby1.8.7//lib/ruby/1.8/rexml/formatters/pretty.rb:131:in `wrap'' from

I am trying to get a customized rcov rake task working. What I have so far looks like this: desc "Rcov code coverage reports" require ''rcov/rcovtask'' require ''spec/rake/spectask'' require ''cucumber/rake/task'' task :rcov => "rcov:all" namespace :rcov do Rcov::RcovTask.new(:all) do task :rcov =>

Running rails 1.2.3, rcov (0.8.0.2), rspec trunk (2865) - When running rake spec:rcov, I''m getting the following: Finished in 245.717813 seconds 856 examples, 0 failures, 48 pending /usr/local/lib/ruby/1.8/rexml/text.rb:292:in `normalize'': private method `gsub'' called for 0:Fixnum (NoMethodError) from /usr/local/lib/ruby/1.8/rexml/element.rb:1084:in

I saw the RCov page at http://rspec.rubyforge.org/tools/rcov.html and decided to add it to my project. My rakefile looks like this: require "rake" require "spec/rake/spectask" desc "Run all specs with RCov" Spec::Rake::SpecTask.new("spec:rcov") do |t| t.spec_files = FileList["spec/**/*_spec.rb"] t.rcov = true end When I run rake spec:rcov,

I am now trying to get rcov to work for me, without much success. I stole the rake task code from the cucumber site: desc "Run all features" task :features => "features:all" task :features => ''db:test:prepare'' require ''cucumber/rake/task'' #I have to add this -mischa namespace :features do Cucumber::Rake::Task.new(:all) do |t|

On 3/14/06, David Holroyd <ruby-talk@badgers-in-foil.co.uk> wrote: > On Wed, Mar 15, 2006 at 02:23:04AM +0900, Mauricio Fernandez wrote: > > On Tue, Mar 14, 2006 at 09:27:14AM +0900, David Holroyd wrote: > > > On Wed, Mar 01, 2006 at 01:31:11AM +0900, Mauricio Fernandez wrote: > > > > Source code, additional information, screenshots... available at > >

Hi, Q1 - Know why rake doesn''t recognize "rake examples_with_rcov" per http://rspec.info/documentation/tools/rcov.html ? Q2 - Also when I run "rake spec:rcov" it seems to give me the same as if I just run "autotest" or "rake spec". I was expecting a heap of pointers to code I haven''t tested?

Hi all, I appreciate that this is not an RSpec question, but I wondered if anyone out there can offer some pointers. We''re using the latest versions of RSpec and RCov, and ruby --version says this (on the Ubuntu build server): ruby 1.8.6 (2008-07-17 patchlevel 279) [x86_64-linux] We''re getting intermittent (yes, intermittent!) segfaults from the build when running

Hello everyone: I am currently assigned to test a big project which uses JRuby to build a web application. The reason of using JRuby is the web application is communicating with Java Service. I am writing test cases using Rspec and looking for a code coverage tool. Rcov is no doubt a nice code coverage tool. However, it is said that Rcov is not compatible with JRuby so far. Sigh....I can not

Hi, I am trying to install the code coverage for Ruby(rcov).. but it is giving the following error message in commmand prompt. Used Ruby Version Ruby - 1.8.5 Rails - 1.2.2 C:\ruby\rcov-0.8.0.2>ruby setup.rb ---> bin <--- bin ---> lib ---> lib/rcov <--- lib/rcov <--- lib ---> ext ---> ext/rcovrt c:/ruby/bin/ruby.exe C:/ruby/rcov-0.8.0.2/ext/rcovrt/extconf.rb creating

I am working on a Rails 3 application. Recently bundler got an update for rspec, which upgraded it to 22, (previously we were using beta 20). After the update we are unable to run the old using ''rake spec:rcov'', while running with ''rake spec'' is running fine. When you do rake spec it does not give any output and finishes the task. something like below : $ rake