Atlnts 289 mortality

DESCRIPTION

@@ -14,6 +14,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Imports: 
     angstroms,
+    atlantistools,
     abind,
     bgmfiles,
     data.table,
@@ -48,4 +49,4 @@ Imports:
     visNetwork,
     zoo
 Remotes:
-    alketh/atlantistools
+    andybeet/atlantistools

R/get_atl_paramfiles.R

@@ -22,6 +22,8 @@ get_atl_paramfiles = function(param.dir,atl.dir,include_catch){
   dietcheck = paste0(atl.dir,run.prefix,'DietCheck.txt')
   yoy = paste0(atl.dir,run.prefix,'YOY.txt')
   ssb = paste0(atl.dir,run.prefix,'SSB.txt')
+  mort <- paste0(atl.dir,run.prefix,'Mort.txt')
+  specificmort <- paste0(atl.dir,run.prefix,'SpecificMort.txt')
 
   #If catch is turned on all generate paths for CATCH and TOTCATCH
   if(include_catch){
@@ -79,7 +81,9 @@ get_atl_paramfiles = function(param.dir,atl.dir,include_catch){
                     yoy =yoy,
                     ssb = ssb,
                     catch = ifelse(include_catch,catch,NA),
-                    catchtot = ifelse(include_catch,catchtot,NA)
+                    catchtot = ifelse(include_catch,catchtot,NA),
+                    mort = mort,
+                    specificmort = specificmort
                     )
 
   return(param.list)

R/make_atlantis_diagnostic_figures.R

@@ -33,6 +33,7 @@
 #'@plot.spatial.biomass logical. Plots showing the spatial (box/level) structure of groups' biomass
 #'@plot.LTL logical. Plots comparing LTL groups (domain-wide) to data
 #'@plot.catch logical. Plots annual catch(mt) age based catch (numbers) and age based %ages
+#'@plot.mortality logical. Plots Mortality (F, M1, M2) from two output sources (Mort, SpecificMort)
 
 #'
 #'@return A series of figures and tables based on output grouping flags
@@ -136,7 +137,8 @@ make_atlantis_diagnostic_figures = function(
   plot.consumption,
   plot.spatial.biomass,
   plot.LTL,
-  plot.catch
+  plot.catch,
+  plot.mortality
 ){
 
   `%>%` = dplyr::`%>%`
@@ -182,6 +184,7 @@ make_atlantis_diagnostic_figures = function(
     rm(biomass.spatial.stanza)
   }
 
+  # Catch Timeseries ------------------------------------------------------
 
   if(plot.catch|plot.all) {
 
@@ -217,6 +220,92 @@ make_atlantis_diagnostic_figures = function(
     rm(totcatch,catchmt)
   }
 
+  # Mortality Timeseries ------------------------------------------------------
+
+  if(plot.mortality|plot.all) {
+
+    # plot mortality from Mort.txt
+    mort = readRDS(paste0(out.dir,'mort.rds'))
+    itype <- 1
+    plotMort <- list()
+    # Annual Mortality time series M, F by species on same plot
+    temp.plot.1 = atlantistools::plot_line(mort,col="source")
+    temp.plot.1 = ggplot2::update_labels(temp.plot.1,labels = list(x='Time (years)', y = 'Mortality'))
+    temp.plot.1 = add.title(temp.plot.1,'Mortality (F & M2)')
+    plotMort[[itype]] <- temp.plot.1
+
+    # plot mortaliy from specificMort.txt
+    specificmort <- readRDS(paste0(out.dir,'specificmort.rds'))
+
+    # plot absolute mortality. 3 pages, one page for F,M1,M2
+    for (atype in rev(unique(specificmort$mort))) {
+      itype <- itype + 1
+      mort <- specificmort %>% 
+        dplyr::filter(mort == atype)
+      temp.plot = atlantistools::plot_line(mort, col = 'agecl')
+      temp.plot = ggplot2::update_labels(p = temp.plot, labels = c(list(x='Time (years)', y = 'Mortality'), list(colour = 'Ageclas')))
+      temp.plot = add.title(temp.plot,paste0('Mortality at Age (',atype,')'))
+
+      plotMort[[itype]] <- temp.plot
+
+    }
+
+    # plot relative mortality by age class
+    # select species with 10 age classes
+    for (iage in 1:max(specificmort$agecl)) {
+      mortality <- specificmort %>%
+        dplyr::filter(code %in% atlantistools::get_cohorts(param.ls$fgs,numCohorts = 10)) %>%
+        dplyr::filter(agecl == iage)
+
+      pct = atlantistools::agg_perc(mortality, groups = c('time','species'))
+      temp.plot = atlantistools::plot_bar(pct, fill = 'mort', wrap = 'species')
+      temp.plot = ggplot2::update_labels(temp.plot,labels = list(x='Time (years)', y = 'Rate (proportion)'))+
+        ggplot2::scale_y_continuous(labels = scales::label_number(accuracy = 0.01))
+      temp.plot = add.title(temp.plot, paste0("Relative Mortality Rates for species with 10 age classes (Age ",iage, ")"))
+
+      plotMort[[itype + iage]] <- temp.plot
+    }
+
+    # select species with 2 age classes
+    for (i2age in 1:2) {
+      mortality <- specificmort %>%
+        dplyr::filter(code %in% atlantistools::get_cohorts(param.ls$fgs,numCohorts = 2)) %>%
+        dplyr::filter(agecl == i2age)
+
+      pct = atlantistools::agg_perc(mortality, groups = c('time','species'))
+      temp.plot = atlantistools::plot_bar(pct, fill = 'mort', wrap = 'species')
+      temp.plot = ggplot2::update_labels(temp.plot,labels = list(x='Time (years)', y = 'Rate (proportion)'))+
+        ggplot2::scale_y_continuous(labels = scales::label_number(accuracy = 0.01))
+      temp.plot = add.title(temp.plot, paste0("Relative Mortality Rates for species with 2 age classes (Age ",i2age, ")"))
+
+      plotMort[[itype + iage + i2age]] <- temp.plot
+    }
+
+    # select species with 1 age classes (Biomass pool)
+    mortality <- specificmort %>%
+      dplyr::filter(code %in% atlantistools::get_cohorts(param.ls$fgs,numCohorts = 1)) %>%
+      dplyr::filter(agecl == 1)
+
+    pct = atlantistools::agg_perc(mortality, groups = c('time','species'))
+    temp.plot = atlantistools::plot_bar(pct, fill = 'mort', wrap = 'species')
+    temp.plot = ggplot2::update_labels(temp.plot,labels = list(x='Time (years)', y = 'Rate (proportion)'))+
+      ggplot2::scale_y_continuous(labels = scales::label_number(accuracy = 0.01))
+    temp.plot = add.title(temp.plot, paste0("Relative Mortality Rates for species with 1 age class (Age 1) "))
+
+    plotMort[[itype + iage + i2age + 1]] <- temp.plot
+
+
+
+    pdf(paste0(fig.dir,run.name,' Specific Mortality Timeseries.pdf'),width = 20, height = 20, onefile = T)
+    for (iplot in 1:(itype+iage+i2age+1)) {
+      gridExtra::grid.arrange(plotMort[[iplot]])
+    }
+    dev.off()
+
+
+    rm(mort,specificmort)
+  } 
+
   # Overall biomass ---------------------------------------------------------
 
 
@@ -368,7 +457,7 @@ make_atlantis_diagnostic_figures = function(
     temp.plot.2 = atlantistools::custom_grid(temp.plot.2,grid_x = 'polygon',grid_y = 'species')
     temp.plot.2 = add.title(temp.plot.2, 'Invert Biomass by Box')
 
-    pdf(file = paste0(out.dir,run.name,' Biomass Box Timeseries.pdf'),width = 48, height = 60, onefile =T)
+    pdf(file = paste0(fig.dir,run.name,' Biomass Box Timeseries.pdf'),width = 48, height = 60, onefile =T)
     gridExtra::grid.arrange(temp.plot.1)
     gridExtra::grid.arrange(temp.plot.2)
     dev.off()

R/process_atl_output.R

@@ -26,7 +26,7 @@ process_atl_output = function(param.dir,
 
   # memory.limit(size = 56000)
   source(here::here('R','load_nc_temp.R'))
-  
+
   #Utility function
   bind.save = function(x,name){
     x2 = dplyr::bind_rows(x)
@@ -581,4 +581,14 @@ process_atl_output = function(param.dir,
 
     rm(catch,totcatch,catchmt)
   }
+
+  # Do mortality -------------------------------------------------------------------
+   mortality <- atlantistools::load_mort(param.ls$mort,prm_run=param.ls$run.prm,fgs=param.ls$groups.file,convert_names = T) #%>%
+  #   dplyr::group_by(species,time) %>% 
+  #   dplyr::summarise(atoutput = atoutput[source == "F"]/atoutput[source == "M"],.groups="drop") %>% 
+  #   dplyr::mutate(atoutput = ifelse(is.infinite(atoutput),NA,atoutput))
+  saveRDS(mortality,paste0(out.dir,'mort.RDS'))
+
+  specificMortality <- atlantistools::load_spec_mort(param.ls$specificmort,prm_run=param.ls$run.prm,fgs=param.ls$groups.file,convert_names = T,removeZeros = F)
+  saveRDS(specificMortality,paste0(out.dir,'specificmort.RDS'))
 }