R/define_matrix_fn.R

In CWetzel/XSSS: Extended Simple Stock Synthesis

##' Create the quant matrix
##' @param N
##' @param ofl.yrs
##' @param depl.yr
##' @param n.extra.se
##' @author Chantel Wetzel
##' @export 
define_matrix <- function(N, ofl.yrs, depl.yr, n.survey, n.extra.se){

	names <- c("M_f","M_m","h","depl","LnR0",
			   "SB0",paste0("SPB_",ofl.yrs[1]),paste0("Dep_TgtYr_",depl.yr),
               paste0("Dep_", ofl.yrs[1]), paste0("OFL_",ofl.yrs[2]), paste0("AdjCatch_",ofl.yrs[2]),
               "SBMSY/SB0","SSB_Unfished","SmryBio_Unfished","SSB_SPRtgt","Fstd_SPRtgt",
               "TotYield_SPRtgt","SSB_MSY","Fstd_MSY","NLL","LL_survey","Crash","MissDep",
               paste0("Survey_Q_",1:n.survey))

	if (n.extra.se > 0) { names <- c(names, paste0("extra_se_",1:n.extra.se)) }

 	out  <-as.matrix(matrix(NA, nrow=N, ncol=length(names)))
 	colnames(out) <- names
 	return(out)
}