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I am working on a dataset with 12 different sessions and multiple individual covariates (sex, age, disease status). The covariates don't necessarily have the same levels for all sessions (e.g. sometimes only healthy animals are captured) causing secr to return an error. I was hoping to fix this problem by assigning the correct levels to all covariates in R but for some reason I am not able to write to the covariates.

While

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covariates(capthist)[,"sex"]<-newsex

works fine for a single session capture history,

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covariates(capthist)[[1]][,"sex"]<-newsex

does not work. Any suggestions on how to solve this issue without importing each session as a single capture history and them merging them (which would require creating new input files for each session).

Thanks,

Mathias

As so often happens, just after hitting the Submit button I realized that this exact question was answered a few posts back and I found the mistake in my code.

Instead of

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covariates(capthist)[[1]][,"sex"]<-newsex

it obviously should be

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covariates(capthist[[1]])[,"sex"]<-newsex

and as Murray pointed out before the levels can easily be set with the following code:

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for (i in 1:length(capthist))
  levels(covariates(capthist[[i]])$sex) <- c('M','F')

All works now.

Mathias