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Feature/i38 rlink #73

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cc08fd8
Removed nested ifstatements to make RASSESS_LINK_ENABLED work
erlasturl Apr 24, 2026
7880b52
Read_RAssess_output reads in TAC or Effort values
erlasturl Apr 27, 2026
12c4ebb
Fixing bugs and adding arrays for size. Removed swept area as that is…
erlasturl Apr 27, 2026
381e8d9
Adding biomass into SizeCaught which only contained zeros
erlasturl Apr 30, 2026
bdef848
GenData not used as not working. Fixing bugs when writing to RAssess …
erlasturl Apr 30, 2026
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23 changes: 11 additions & 12 deletions atlantis/PreRules.am
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Original file line number Diff line number Diff line change
Expand Up @@ -100,27 +100,26 @@ 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
R_BASE = /usr/lib/R
R_HOME = /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 = /Library/Frameworks/R.framework/Resources
R_HOME = /Library/Frameworks/R.framework/Resources
endif

AM_CFLAGS += -I$(R_BASE)/include -I/usr/share/R/include
LIBS += -L$(R_BASE)/lib -lR
endif
if RASSESS_LINK_ENABLED
AM_CFLAGS += -D RASSESS_LINK_ENABLED
AM_CFLAGS += -I$(R_BASE)/include -I/usr/share/R/include
LIBS += -L$(R_BASE)/lib -lR
endif
1 change: 1 addition & 0 deletions atlantis/atecology/atprocess.c
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Expand Up @@ -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];
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5 changes: 4 additions & 1 deletion atlantis/atlantisUtil/atUtilGroupIO.c
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Expand Up @@ -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);
Expand Down Expand Up @@ -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);
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3 changes: 3 additions & 0 deletions atlantis/atlantisUtil/include/atFunctGroup.h
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Expand Up @@ -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;
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