R/unpack_p.R

In rBatt/trawlDiversity: Long-term changes in species richness along the North American coastline

#' 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)
	
}