#' Unpack P
#'
#' Unpacks the object containing the processed MSOM results
#'
#' @param p_rn The p object subset to a region
#'
#' @details
#' Make sure to only supply p after it's been subset (e.g., \code{p[[1]]}). The structure of p is such that the first level is the regions, the second is the years, then the third contains the varius elements associated with the processed output of a single model run.
#'
#' @export
unpack_p <- function(p_rn){
rd <- p_rn$rd
processed <- p_rn$processed
bt <- p_rn$bt
colonization <- p_rn$colonization
param_iters <- p_rn$param_iters
ab <- p_rn$ab
naive_rich <- p_rn$naive_rich
reg <- processed[,una(reg)]
lang <- "JAGS"
if(lang == "Stan"){
pars_trace <- c("Omega","alpha_mu[1]", "alpha_mu[2]", "alpha_mu[3]", "alpha_mu[4]", "alpha_mu[5]", "beta_mu[1]")
}else{
pars_trace <- c("Omega","alpha_mu[1]", "alpha_mu[2]", "alpha_mu[3]", "alpha_mu[4]", "alpha_mu[5]", "beta_mu")
}
naive_rich <- naive_rich[,naive_rich, keyby='year']
reg_rich <- processed[,reg_rich, keyby='year']
bt_ann <- bt[,list(bt_ann=mean(bt, na.rm=TRUE)), keyby='year']
n_pars <- length(pars_trace)
n_yrs <- param_iters[,lu(year)]
n_spp <- rd[,lu(spp)]
spp_col <- colonization[[1]][col==1, una(spp)]
spp_ext <- colonization[[1]][ext==1, una(spp)]
spp_col_only <- spp_col[!spp_col %in% spp_ext]
spp_ext_only <- spp_ext[!spp_ext %in% spp_col]
spp_col_and_ext <- spp_col[spp_col%in%spp_ext]
spp_neither <- rd[!spp%in%spp_col & !spp%in%spp_ext, una(spp)]
output_list <- mget(
c(
'rd',
'processed',
'bt',
'colonization',
'param_iters',
'ab',
'naive_rich',
'reg',
'lang',
'pars_trace',
'reg_rich',
'bt_ann',
'n_pars',
'n_yrs',
'n_spp',
'spp_col',
'spp_ext',
'spp_col_only',
'spp_ext_only',
'spp_col_and_ext',
'spp_neither'
)
)
return(output_list)
}
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