probitCJS Error: vcv matrix not avaiable in model

questions concerning analysis/theory using the R package 'marked'

probitCJS Error: vcv matrix not avaiable in model

Postby emilisak » Fri Mar 06, 2026 8:40 am

I have a dataset of 300+ individuals, each with a capture history of length 60. For Phi, I have variables: sex (binary factor), origin (binary factor), days between capture occasion and first recapture (continuous numerical), season (time-varying 4-level factor), and age (time-varying numeric). For p, I have sex, origin, days between capture occasion and first recapture, trap-dependency (as described in the marked vignette), days per season we tried to recapture individuals (continuous numerical), and season (time-varying 4-level factor).

If I run a full parametrized model with crm(...), it works fine. However, when I run a probitCJS model, I get the error that "vcv matrix not available in model". And if I run it with 500K iterations (reasonable iteration based on similar studies), I get error "cannot allocate vector of size ~50GB.
Regardless of MCMC specifications, any probitCJS model I try to run gives warnings that the functions 'nobars' and 'findbars' have moved to the formulas package.

I've tried to find explanations for these issues elsewhere without luck.
What do these errors entail and is there a fix to them?
Thank you for the help.
emilisak
 
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