From f842bb784d7a1714a5d6da60dfc0b24d4b95253e Mon Sep 17 00:00:00 2001
From: "Joseph Caracappa (NOAA)"
 <57966543+jcaracappa1@users.noreply.github.com>
Date: Fri, 20 Sep 2024 10:57:28 -0400
Subject: [PATCH] added catch by fleet diagnostics - magnitude of catch -
 center of gravity of catch

---
 DESCRIPTION                |   3 +-
 NAMESPACE                  |   1 +
 R/diag_fleet_catch.R       | 122 +++++++++++++++++++++++++++++++++++++
 man/atlantisdiagnostics.Rd |  21 +++++++
 man/diag_fleet_catch.Rd    |  59 ++++++++++++++++++
 man/diag_reasonability.Rd  |   1 +
 man/diag_stability.Rd      |   1 +
 7 files changed, 207 insertions(+), 1 deletion(-)
 create mode 100644 R/diag_fleet_catch.R
 create mode 100644 man/diag_fleet_catch.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 02007e3..def7b4d 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/NAMESPACE b/NAMESPACE
index 0bbfdf6..84dfaa9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(diag_cohortBiomass)
 export(diag_combine)
+export(diag_fleet_catch)
 export(diag_maxsize)
 export(diag_persistence)
 export(diag_reasonability)
diff --git a/R/diag_fleet_catch.R b/R/diag_fleet_catch.R
new file mode 100644
index 0000000..67e1a3d
--- /dev/null
+++ b/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.file A character string. Path to location of functional groups file.
+#'@param fishery.file A character string. Path to the fishery definitions file.
+#'@param bgm.file 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.file,
+                             fishery.file,
+                             catch.file,
+                             bgm.file,
+                             catch.ref,
+                             speciesCodes = NULL,
+                             nYrs = 20,
+                             min.dist = 100,
+                             relChangeThreshold = 0.01){
+
+  boxes = atlantistools::convert_bgm(bgm.file)%>%
+    dplyr::distinct(polygon,inside_lat,inside_long)
+
+  catch.fleet =atlantisprocessing::process_catch_fleet(fishery.prm = fishery.file,
+                                          catch = catch.file,
+                                          groups.file = fgs.file)
+
+  if(!is.null(speciesCodes)){
+    fgs = read.csv(fgs.file,as.is =T)
+
+    spp.match  = fgs$LongName[which(fgs$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)
+}
diff --git a/man/atlantisdiagnostics.Rd b/man/atlantisdiagnostics.Rd
index 8b75837..2fe0a2d 100644
--- a/man/atlantisdiagnostics.Rd
+++ b/man/atlantisdiagnostics.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/atlantisdiagnostics.r
 \docType{package}
 \name{atlantisdiagnostics}
+\alias{atlantisdiagnostics-package}
 \alias{atlantisdiagnostics}
 \title{atlantisdiagnostics: Tools for calibrating Atlantis ecosystem models}
 \description{
@@ -23,3 +24,23 @@ Tools to aid in diagnosing issues in a parameterized Atlantis Ecosystem model
 To learn more about using \code{atlantisdiagnostics}, start with the vignette: \code{browseVignettes(package="atlantisdiagnostics")} or click the index below
 }
 
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/NOAA-EDAB/atlantisdiagnostics}
+  \item Report bugs at \url{https://github.com/NOAA-EDAB/atlantisdiagnostics/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Andy Beet \email{andrew.beet@noaa.gov} (\href{https://orcid.org/0000-0001-8270-7090}{ORCID})
+
+Authors:
+\itemize{
+  \item Sarah Gaichas \email{Sarah.Gaichas@noaa.gov}
+  \item Joeseph Caracappa \email{joseph.caracappa@noaa.gov}
+  \item Robert Gamble \email{Robert.Gamble@noaa.gov}
+  \item Scott Large \email{Scott.Large.gov}
+}
+
+}
diff --git a/man/diag_fleet_catch.Rd b/man/diag_fleet_catch.Rd
new file mode 100644
index 0000000..e3e02e3
--- /dev/null
+++ b/man/diag_fleet_catch.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diag_fleet_catch.R
+\name{diag_fleet_catch}
+\alias{diag_fleet_catch}
+\title{Test fleet catch}
+\usage{
+diag_fleet_catch(
+  fgs.file,
+  fishery.file,
+  catch.file,
+  bgm.file,
+  catch.ref,
+  speciesCodes = NULL,
+  nYrs = 20,
+  min.dist = 100,
+  relChangeThreshold = 0.01
+)
+}
+\arguments{
+\item{fgs.file}{A character string. Path to location of functional groups file.}
+
+\item{fishery.file}{A character string. Path to the fishery definitions file.}
+
+\item{bgm.file}{A character string. Path to the bgm file.}
+
+\item{catch.ref}{A data.frame containing reference catch by fleet data (species|fleet|polygon|ref.value)}
+
+\item{speciesCodes}{Character vector. A vector of Atlantis species codes in which to test for stability.}
+
+\item{nYrs}{Numeric scalar. Number of years from the end of the time series that stability must occur.}
+
+\item{min.dist}{Numeric Scalar. Maximum distance between model and reference center of gravity}
+
+\item{relChangeThreshold}{Numeric Scalar. Maximum magnitude of relative change of slope (Default = 0.01)}
+}
+\value{
+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?}
+}
+\description{
+\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.
+}
+\seealso{
+Other diags: 
+\code{\link{diag_reasonability}()},
+\code{\link{diag_stability}()}
+}
+\concept{diags}
diff --git a/man/diag_reasonability.Rd b/man/diag_reasonability.Rd
index 24bfdb1..a88dcd9 100644
--- a/man/diag_reasonability.Rd
+++ b/man/diag_reasonability.Rd
@@ -96,6 +96,7 @@ diag_reasonability(fgs, biomind, initialYr = 1964, speciesCodes =c("MAK","WHK"),
 }
 \seealso{
 Other diags: 
+\code{\link{diag_fleet_catch}()},
 \code{\link{diag_stability}()}
 }
 \concept{diags}
diff --git a/man/diag_stability.Rd b/man/diag_stability.Rd
index 1fba26d..c21439c 100644
--- a/man/diag_stability.Rd
+++ b/man/diag_stability.Rd
@@ -74,6 +74,7 @@ diag_stability(fgs,biomind, speciesCodes=c("HER","WHK"), nYrs = 10, relChangeThr
 }
 \seealso{
 Other diags: 
+\code{\link{diag_fleet_catch}()},
 \code{\link{diag_reasonability}()}
 }
 \concept{diags}