Merge pull request #37 from NOAA-EDAB/fleet_catch

added catch by fleet diagnostics

DESCRIPTION

@@ -47,5 +47,6 @@ Imports:
     tibble
 Remotes:
     Atlantis-Ecosystem-Model/atlantistools
+    NOAA-EDAB/atlantisprocessing
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(diag_cohortBiomass)
 export(diag_combine)
+export(diag_fleet_catch)
 export(diag_maxsize)
 export(diag_persistence)
 export(diag_reasonability)

R/diag_fleet_catch.R

@@ -0,0 +1,122 @@
+#'Test fleet catch
+#'
+#'\code{diag_fleet_catch} determines whether the simulated fleets catcht the right magnitude and spatial distribution of catch
+#'over the last n years of a run.
+#'
+#'
+#'@param fgs A character string. Path to location of functional groups file.
+#'@param fishery.prm A character string. Path to the fishery definitions file.
+#'@param bgm A character string. Path to the bgm file.
+#'@param catch.ref A data.frame containing reference catch by fleet data (species|fleet|polygon|ref.value)
+#'@param speciesCodes Character vector. A vector of Atlantis species codes in which to test for stability.
+#'@param nYrs Numeric scalar. Number of years from the end of the time series that stability must occur.
+#'@param relChangeThreshold Numeric Scalar. Maximum magnitude of relative change of slope (Default = 0.01)
+#'@param min.dist Numeric Scalar. Maximum distance between model and reference center of gravity
+#'
+#'@return Returns a data frame of all species and how they measure up against the catch by fleet criteria
+#'\item{species}{The common name of the species/functional group}
+#'\item{fleet}{The fleet name from the fisheries file}
+#'\item{catch.model}{Double. The mean catch in mT over the last nYrs of the model }
+#'\item{catch.ref}{Double. The reference catch (mT)}
+#'\item{cog.x.model}{Double. The mean x-coordinate center of gravity from the model}
+#'\item{cog.x.ref}{Double. The mean x-coordinate center of gravity from the reference}
+#'\item{cog.y.model}{Double. The mean y-coordinate center of gravity from the model}
+#'\item{cog.y.ref}{Double. The mean y-coordinate center of gravity from the reference}
+#'\item{dist}{Double. The mean distance between the center of gravity between the model and reference}
+#'\item{catch.magnitude}{Logical. Is the relative difference between model and refernece catch within +/- relChangeThreshold?}
+#'\item{catch.dist}{Logical. Is the distance between center of gravity betwene model and reference less than min.dist?}
+#'
+#'@family diags
+#'
+#'@export
+#'
+#'@importFrom magrittr %>%
+
+diag_fleet_catch <- function(fgs,
+                             fishery.prm,
+                             catch.file,
+                             bgm,
+                             catch.ref,
+                             speciesCodes = NULL,
+                             nYrs = 20,
+                             min.dist = 100,
+                             relChangeThreshold = 0.01){
+
+  boxes = atlantistools::convert_bgm(bgm)%>%
+    dplyr::distinct(polygon,inside_lat,inside_long)
+
+  catch.fleet =atlantisprocessing::process_catch_fleet(fishery.prm = fishery.prm,
+                                          catch = catch.file,
+                                          groups.file = fgs)
+
+  if(!is.null(speciesCodes)){
+    fgs.df = read.csv(fgs,as.is =T)
+
+    spp.match  = fgs.df$LongName[which(fgs.df$Code %in% speciesCodes)]
+
+    catch.fleet = catch.fleet %>%
+      dplyr::filter(species %in% spp.match)
+
+    catch.ref = catch.ref %>%
+      dplyr::filter(species %in% spp.match)
+  }
+  max.yr = max(catch.fleet$time)
+
+  #mnagnitude
+  catch.mag.model =catch.fleet %>%
+    dplyr::filter(time >= (max.yr - nYrs)) %>%
+    dplyr::group_by(species,fleet,time)%>%
+    dplyr::summarise(catch.model = sum(atoutput,na.rm=T))%>%
+    dplyr::group_by(species,fleet)%>%
+    dplyr::summarise(catch.model = mean(catch.model,na.rm=T))
+
+  catch.mag.ref = catch.ref %>%
+    dplyr::group_by(species,fleet)%>%
+    dplyr::summarise(catch.ref = mean(ref.value,na.rm=T))
+
+
+  catch.mag.all = catch.mag.model %>%
+    dplyr::left_join(catch.mag.ref)%>%
+    dplyr::mutate(catch.rel = catch.ref/catch.model,
+                  catch.magnitude = ifelse(catch.rel > (1 - relChangeThreshold) & catch.rel < (1+relChangeThreshold),T,F)
+    )
+
+  #distance
+  catch.cog.model =catch.fleet %>%
+    dplyr::filter(time >= (max.yr - nYrs))%>%
+    dplyr::left_join(boxes)%>%
+    dplyr::mutate(catch.wgt.x = inside_long * atoutput,
+                  catch.wgt.y = inside_lat * atoutput)%>%
+    dplyr::group_by(species,fleet,time)%>%
+    dplyr::summarise(cog.x = sum(catch.wgt.x,na.rm=T),
+                     cog.y = sum(catch.wgt.y,na.rm=T),
+                     catch.tot = sum(atoutput,na.rm=T))%>%
+    dplyr::mutate(cog.x = cog.x/catch.tot,
+           cog.y = cog.y/catch.tot)%>%
+    dplyr::group_by(species,fleet)%>%
+    dplyr::summarise(cog.x.model = mean(cog.x, na.rm=T),
+                     cog.y.model = mean(cog.y, na.rm=T))
+
+  catch.cog.ref =catch.ref %>%
+    dplyr::left_join(boxes)%>%
+    dplyr::mutate(catch.wgt.x = inside_long * ref.value,
+                  catch.wgt.y = inside_lat * ref.value)%>%
+    dplyr::group_by(species,fleet)%>%
+    dplyr::summarise(cog.x = sum(catch.wgt.x,na.rm=T),
+                     cog.y = sum(catch.wgt.y,na.rm=T),
+                     catch.tot = sum(ref.value,na.rm=T))%>%
+    dplyr::mutate(cog.x.ref = cog.x/catch.tot,
+           cog.y.ref = cog.y/catch.tot)
+
+  catch.cog.all = catch.cog.model %>%
+    dplyr::left_join(catch.cog.ref)%>%
+    dplyr::mutate(dist = sqrt((cog.x.ref - cog.x.model)^2 + (cog.y.ref-cog.y.model)^2),
+                  catch.dist = ifelse(dist <= min.dist,T,F))
+
+  #combine for output
+  catch.diag.all = catch.mag.all %>%
+    dplyr::left_join(catch.cog.all)%>%
+    dplyr::select(species,fleet,catch.model,catch.ref, cog.x.model,cog.x.model,cog.x.ref,cog.y.model,cog.y.ref,dist,catch.magnitude,catch.dist)
+
+  return(catch.diag.all)
+}