- modlist
A list of individual model output lists returned by multimarkClosed
or markClosed
. The models must have the same number of chains and MCMC iterations.
- modprior
Vector of length length(modlist)
containing prior model probabilities. Default is modprior = rep(1/length(modlist), length(modlist))
.
- monparms
Parameters to monitor. Only parameters common to all models can be monitored (e.g., "pbeta[(Intercept)]
", "N
"), but derived capture ("p
") and recapture ("c
") probabilities can also be monitored. Default is monparms = "N"
.
- miter
The number of RJMCMC iterations per chain. If NULL
, then the number of MCMC iterations for each individual model chain is used.
- mburnin
Number of burn-in iterations (0 <= mburnin < miter
).
- mthin
Thinning interval for monitored parameters.
- M1
Integer vector indicating the initial model for each chain, where M1_j=i
initializes the RJMCMC algorithm for chain j in the model corresponding to modlist[[i]]
for i=1,..., length(modlist)
. If NULL
, the algorithm for all chains is initialized in the most general model. Default is M1=NULL
.
- pbetapropsd
Scaler specifying the standard deviation of the Normal(0, pbetapropsd) proposal distribution for "pbeta
" parameters. Default is pbetapropsd=1
. See Barker & Link (2013) for more details.
- zppropsd
Scaler specifying the standard deviation of the Normal(0, zppropsd) proposal distribution for "zp
" parameters. Only applies if at least one (but not all) model(s) include individual hetergeneity in detection probability. If NULL
, zppropsd = sqrt(sigma2_zp) is used. Default is zppropsd=NULL
. See Barker & Link (2013) for more details.
- sigppropshape
Scaler specifying the shape parameter of the invGamma(shape = sigppropshape, scale = sigppropscale) proposal distribution for sigma_zp
. Only applies if at least one (but not all) model(s) include individual hetergeneity in detection probability. Default is sigppropshape=6
. See Barker & Link (2013) for more details.
- sigppropscale
Scaler specifying the scale parameter of the invGamma(shape = sigppropshape, scale = sigppropscale) proposal distribution for sigma_zp
. Only applies if at least one (but not all) model(s) include individual hetergeneity in detection probability. Default is sigppropscale=4
. See Barker & Link (2013) for more details.
- printlog
Logical indicating whether to print the progress of chains and any errors to a log file in the working directory. Ignored when nchains=1
. Updates are printed to log file as 1% increments of iter
of each chain are completed. With >1 chains, setting printlog=TRUE
is probably most useful for Windows users because progress and errors are automatically printed to the R console for "Unix-like" machines (i.e., Mac and Linux) when printlog=FALSE
. Default is printlog=FALSE
.