Feature(#38): Fixes the integration with R for TAC. Adds functionality for effort

.github/workflows/build_run_SETAS1.yml

@@ -19,7 +19,7 @@ jobs:
     steps:
 
       - name: checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Ensures all branches and tags are fetched
 
@@ -39,13 +39,13 @@ jobs:
           r-version: '4.2.0'
 
 
-      - name: Compile and Run Atlantis in Ubuntu 18.04 using Docker
+      - name: Compile and Run Atlantis in Ubuntu 20.04 using Docker
         run: |
-          docker run --rm -v $(pwd):/workspace -w /workspace ubuntu:18.04 bash -c "
+          docker run --rm -v $(pwd):/workspace -w /workspace ubuntu:20.04 bash -c "
           TZ=America/New_York &&
           ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone &&
           apt-get update && 
-          apt-get install  -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev subversion valgrind dos2unix gawk nano r-base git &&
+          apt-get install  -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev subversion valgrind dos2unix gawk nano r-base r-base-dev git &&
           cd atlantis && aclocal && autoheader && autoconf && automake -a && ./configure --enable-rassesslink && make && make install &&
           echo 'Now run the model!' &&
           cd ../example &&

atlantis/PreRules.am

@@ -100,30 +100,28 @@ endif
 #	AM_CFLAGS += -D SS3_LINK_ENABLED -I$(top_srcdir)/atSS3Link/include
 #endif
 
-if RASSESS_LINK_ENABLED
-	AM_CFLAGS += -D RASSESS_LINK_ENABLED
-
-# NOTE: nested if statments
 # For the R links
 # A working R installation is required.
 # R must have been built with the '--enable-R-shlib' option enabled to provide the R shared library
 # Ensure the R_HOME environment variable is set appropriately
 #
 # R_HOME = $(shell R RHOME)
-# on Ubuntu Linux
 if OS_LINUX
-	R_HOME = /usr/lib/R
-	R_BASE = /usr/lib/R
-endif
-# on OS X
-if OS_MACOS
-	R_BASE = /Library/Frameworks/R.framework/Resources
-	R_HOME = /Library/Frameworks/R.framework/Resources
+  R_BASE = /usr/lib/R
+  R_HOME = /usr/lib/R
+else
+ #if OS_MACOS
+  R_BASE = /Library/Frameworks/R.framework/Resources
+  R_HOME = /Library/Frameworks/R.framework/Resources
 endif
 
-	AM_CFLAGS += -I$(R_BASE)/include -I/usr/share/R/include
+if RASSESS_LINK_ENABLED
+  AM_CFLAGS += -D RASSESS_LINK_ENABLED
+  AM_CFLAGS += -I$(R_BASE)/include -I/usr/share/R/include
+  AM_LDFLAGS = -L$(R_BASE)/lib
 	LIBS += -L$(R_BASE)/lib -lR
 endif
 
 #fetching repo version from git
 AM_CFLAGS += -DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
+

atlantis/atecology/atprocess.c

@@ -1941,6 +1941,7 @@ void Calculate_Catch(MSEBoxModel *bm, BoxLayerValues *boxLayerInfo, FILE *llogfp
 				if (FunctGroupArray[guild].isVertebrate == TRUE) {
 					FunctGroupArray[guild].SizeNumCaught[cohort][nf][bm->current_box] += bm->FishingResults[nf][CatchAtAge_result_id];
 					FunctGroupArray[guild].SizeNumDiscard[cohort][nf][bm->current_box] += bm->FishingResults[nf][DiscardsAtAge_result_id];
+					FunctGroupArray[guild].SizeCaught[cohort][nf][bm->current_box] += bm->FishingResults[nf][Catch_result_id];
 				}
 			} else {
 				bm->RecCatch[bm->current_box][guild][nf] += bm->FishingResults[nf][Catch_result_id];

atlantis/atlantisUtil/atUtilGroupIO.c

@@ -840,7 +840,8 @@ int Util_Read_Functional_Group_XML(MSEBoxModel *bm, char *fileName, FILE *llogfp
             FunctGroupArray[i].X_RS = Util_Alloc_Init_1D_Double(FunctGroupArray[i].numCohortsXnumGenes, 0.0);
             FunctGroupArray[i].RAssessSpringSurvey = Util_Alloc_Init_2D_Double(bm->nbox, FunctGroupArray[i].numCohortsXnumGenes, 0.0);
             FunctGroupArray[i].RAssessAutumnSurvey = Util_Alloc_Init_2D_Double(bm->nbox, FunctGroupArray[i].numCohortsXnumGenes, 0.0);
-
+            FunctGroupArray[i].RAssessSpringSurveySize = Util_Alloc_Init_2D_Double(bm->nbox, FunctGroupArray[i].numCohortsXnumGenes, 0.0);
+            FunctGroupArray[i].RAssessAutumnSurveySize = Util_Alloc_Init_2D_Double(bm->nbox, FunctGroupArray[i].numCohortsXnumGenes, 0.0);
             FunctGroupArray[i].min_wgt = Util_Alloc_Init_1D_Double(FunctGroupArray[i].numCohortsXnumGenes, 0.0);
             FunctGroupArray[i].max_wgt = Util_Alloc_Init_1D_Double(FunctGroupArray[i].numCohortsXnumGenes, 0.0);
             FunctGroupArray[i].rolling_wgt = Util_Alloc_Init_2D_Double(bm->K_rolling_cap_num + 1, FunctGroupArray[i].numCohortsXnumGenes, 0.0);
@@ -1289,6 +1290,8 @@ void Free_Functional_Group_Memory(MSEBoxModel *bm) {
 			free4d(FunctGroupArray[i].boxPopRatio);
             free2d(FunctGroupArray[i].RAssessSpringSurvey);
             free2d(FunctGroupArray[i].RAssessAutumnSurvey);
+            free2d(FunctGroupArray[i].RAssessSpringSurveySize);
+            free2d(FunctGroupArray[i].RAssessAutumnSurveySize);
             free1d(FunctGroupArray[i].min_wgt);
             free1d(FunctGroupArray[i].max_wgt);
             free2d(FunctGroupArray[i].rolling_wgt);

atlantis/atlantisUtil/include/atFunctGroup.h

@@ -285,6 +285,9 @@ typedef struct {
     double ***SizeCaught; /**< Sampled catch - size in catch */
     double **RAssessSpringSurvey; /**< Spring survey abundance - for RAssess */
     double **RAssessAutumnSurvey; /**< Autumn survey abundance - for RAssess */
+    double **RAssessSpringSurveySize; /**< Spring survey size - for RAssess */
+    double **RAssessAutumnSurveySize; /**< Autumn survey size - for RAssess */
+
 
     /* Used in tracking informaiton for calcualting system cap in fisheries */
     double *min_wgt;

atlantis/atlantismain/Makefile.am

@@ -5,7 +5,8 @@ atlantisMergeddir=$(includedir)/atlantismain
 atlantisMerged_SOURCES = atlantismain.c atlantisboxmodel.h
 
 atlantisMerged_LDADD = -latlantisutil -latassess -latphysics -latecology -lateconomic -latmanage -latharvest \
-    -latimplementation -latphysics -latConvertAtlantis -latlantisutil  -lsjwlib -latSS3Link
+    -latimplementation -latphysics -latConvertAtlantis -latlantisutil  -lsjwlib -latSS3Link \
+    $(LIBS)
 
 SVNWCPATH = -D'ATLANTIS_WCPATH="$(shell svn info  ../| grep URL | sed  's/URL: //g')"'
 SVNWCDATE = -D'ATLANTIS_WCDATE="$(shell svn info  ../| grep "Last Changed Date:" | sed  's/Last Changed Date: //g')"'
@@ -61,6 +62,10 @@ atlantisMerged_INCLUDES += -I$(top_srcdir)/atCLAMLink/include
 atlantisMerged_DEPENDENCIES +=  $(top_srcdir)/atCLAMLink/libatCLAMLink.a
 endif
 
+if RASSESS_LINK_ENABLED
+LIBDIRS += -L$(R_BASE)/lib
+atlantisMerged_LDADD += -lR
+endif
 
 #if SS3_LINK_ENABLED
 #LIBDIRS += -L$(top_srcdir)/atSS3Link