add Mdeath fxn

calculates death (000s mt) from M

WHAM/Mdeaths.R

@@ -0,0 +1,30 @@
+#' @title Calculate the amount of fish dying given M 
+#' 
+#' @description Calculates the amount (metric tons) of fish dying given the assumed or estimated M; uses Jan-1 biomass, so an approximation
+#' 
+#' @param mod An rds from a WHAM fit
+#' 
+#' @return A dataframe with two columns. Year and Deaths
+#'
+#' @example
+#' mod.dir="m168"
+#' write.dir <- paste("C:/Herring/2022 Assessment/Assessments/WHAM",mod.dir,sep="/")
+#' setwd(write.dir)
+#' mod <- readRDS(paste0(mod.dir,".rds"))
+#' m168deaths=Mdeaths(mod=mod)
+#' plot(m168deaths$Year,m168deaths$Deaths,type='o',ylab="Dead Fish (000's mt)",xlab="")
+
+Mdeaths=function(mod=NULL){
+  MAA=mod$rep$MAA
+  ZAA=mod$rep$ZAA
+  NAA=mod$rep$NAA
+  WAA.pt=mod$input$data$waa_pointer_jan1
+  WAA=mod$input$data$waa[WAA.pt,,]
+
+
+  cons.aa<-((MAA/ZAA)*(1-exp(-ZAA))*NAA*WAA)/1000
+  cons.annual=data.frame(Year=mod$input$years,Deaths=rowSums(cons.aa))
+  return(cons.annual)
+}
+
+