🪦Allow both mortalities simultaneously

DESCRIPTION

@@ -29,7 +29,7 @@ BugReports: https://github.com/Allgeier-Lab/arrR/issues
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 VignetteBuilder: knitr
 Depends: R (>= 3.1)
 Imports:

R/RcppExports.R

@@ -329,13 +329,13 @@ rcpp_modify_degree <- function(x, y) {
 #'
 #' @param fishpop,fishpop_track Matrix with fishpop and starting fishpop values.
 #' @param seafloor Matrix with seafloor values.
-#' @param pop_ldie, pop_n_body,pop_reserves_max Numeric with parameters.
+#' @param pop_linf,pop_ldie,pop_n_body,pop_reserves_max Numeric with parameters.
 #' @param extent Vector with extent (xmin,xmax,ymin,ymax).
 #' @param dimensions Vector with dimensions (nrow, ncol).
 #'
 #' @details
 #' Function to simulate background mortality of fish individuals.
-#' Fish automatically dies when \code{pop_mean_size} is greater than \code{pop_ldie}.
+#' Fish automatically dies when current size is greater than \code{pop_ldie}.
 #' If a individual dies, a new individual is created.
 #'
 #' @return void
@@ -344,8 +344,8 @@ rcpp_modify_degree <- function(x, y) {
 #' @rdname rcpp_mortality
 #'
 #' @keywords internal
-rcpp_mortality <- function(fishpop, fishpop_track, seafloor, pop_ldie, pop_n_body, pop_reserves_max, extent, dimensions) {
-    invisible(.Call(`_arrR_rcpp_mortality`, fishpop, fishpop_track, seafloor, pop_ldie, pop_n_body, pop_reserves_max, extent, dimensions))
+rcpp_mortality <- function(fishpop, fishpop_track, seafloor, pop_linf, pop_ldie, pop_n_body, pop_reserves_max, extent, dimensions) {
+    invisible(.Call(`_arrR_rcpp_mortality`, fishpop, fishpop_track, seafloor, pop_linf, pop_ldie, pop_n_body, pop_reserves_max, extent, dimensions))
 }
 
 #' rcpp_move_behav

R/run_simulation.R

@@ -120,7 +120,8 @@ run_simulation <- function(seafloor, fishpop, nutrients_input = 0.0,
 
   }
 
-  if (any(fishpop$length > parameters$pop_ldie)) {
+  # only check if pop_ldie is not equal to zero (default)
+  if (parameters$pop_ldie > 0.0 & (any(fishpop$length > parameters$pop_ldie))) {
 
     warning("Some individuals are larger than pop_ldie.", call. = FALSE)
 

inst/include/arrR_RcppExports.h

@@ -147,17 +147,17 @@ namespace arrR {
             throw Rcpp::exception(Rcpp::as<std::string>(rcpp_result_gen).c_str());
     }
 
-    inline void rcpp_mortality(Rcpp::NumericMatrix fishpop, Rcpp::NumericMatrix fishpop_track, Rcpp::NumericMatrix seafloor, double pop_ldie, double pop_n_body, double pop_reserves_max, Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions) {
-        typedef SEXP(*Ptr_rcpp_mortality)(SEXP,SEXP,SEXP,SEXP,SEXP,SEXP,SEXP,SEXP);
+    inline void rcpp_mortality(Rcpp::NumericMatrix fishpop, Rcpp::NumericMatrix fishpop_track, Rcpp::NumericMatrix seafloor, double pop_linf, double pop_ldie, double pop_n_body, double pop_reserves_max, Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions) {
+        typedef SEXP(*Ptr_rcpp_mortality)(SEXP,SEXP,SEXP,SEXP,SEXP,SEXP,SEXP,SEXP,SEXP);
         static Ptr_rcpp_mortality p_rcpp_mortality = NULL;
         if (p_rcpp_mortality == NULL) {
-            validateSignature("void(*rcpp_mortality)(Rcpp::NumericMatrix,Rcpp::NumericMatrix,Rcpp::NumericMatrix,double,double,double,Rcpp::NumericVector,Rcpp::IntegerVector)");
+            validateSignature("void(*rcpp_mortality)(Rcpp::NumericMatrix,Rcpp::NumericMatrix,Rcpp::NumericMatrix,double,double,double,double,Rcpp::NumericVector,Rcpp::IntegerVector)");
             p_rcpp_mortality = (Ptr_rcpp_mortality)R_GetCCallable("arrR", "_arrR_rcpp_mortality");
         }
         RObject rcpp_result_gen;
         {
             RNGScope RCPP_rngScope_gen;
-            rcpp_result_gen = p_rcpp_mortality(Shield<SEXP>(Rcpp::wrap(fishpop)), Shield<SEXP>(Rcpp::wrap(fishpop_track)), Shield<SEXP>(Rcpp::wrap(seafloor)), Shield<SEXP>(Rcpp::wrap(pop_ldie)), Shield<SEXP>(Rcpp::wrap(pop_n_body)), Shield<SEXP>(Rcpp::wrap(pop_reserves_max)), Shield<SEXP>(Rcpp::wrap(extent)), Shield<SEXP>(Rcpp::wrap(dimensions)));
+            rcpp_result_gen = p_rcpp_mortality(Shield<SEXP>(Rcpp::wrap(fishpop)), Shield<SEXP>(Rcpp::wrap(fishpop_track)), Shield<SEXP>(Rcpp::wrap(seafloor)), Shield<SEXP>(Rcpp::wrap(pop_linf)), Shield<SEXP>(Rcpp::wrap(pop_ldie)), Shield<SEXP>(Rcpp::wrap(pop_n_body)), Shield<SEXP>(Rcpp::wrap(pop_reserves_max)), Shield<SEXP>(Rcpp::wrap(extent)), Shield<SEXP>(Rcpp::wrap(dimensions)));
         }
         if (rcpp_result_gen.inherits("interrupted-error"))
             throw Rcpp::internal::InterruptedException();

src/RcppExports.cpp

@@ -316,26 +316,27 @@ BEGIN_RCPP
 END_RCPP
 }
 // rcpp_mortality
-void rcpp_mortality(Rcpp::NumericMatrix fishpop, Rcpp::NumericMatrix fishpop_track, Rcpp::NumericMatrix seafloor, double pop_ldie, double pop_n_body, double pop_reserves_max, Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions);
-static SEXP _arrR_rcpp_mortality_try(SEXP fishpopSEXP, SEXP fishpop_trackSEXP, SEXP seafloorSEXP, SEXP pop_ldieSEXP, SEXP pop_n_bodySEXP, SEXP pop_reserves_maxSEXP, SEXP extentSEXP, SEXP dimensionsSEXP) {
+void rcpp_mortality(Rcpp::NumericMatrix fishpop, Rcpp::NumericMatrix fishpop_track, Rcpp::NumericMatrix seafloor, double pop_linf, double pop_ldie, double pop_n_body, double pop_reserves_max, Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions);
+static SEXP _arrR_rcpp_mortality_try(SEXP fishpopSEXP, SEXP fishpop_trackSEXP, SEXP seafloorSEXP, SEXP pop_linfSEXP, SEXP pop_ldieSEXP, SEXP pop_n_bodySEXP, SEXP pop_reserves_maxSEXP, SEXP extentSEXP, SEXP dimensionsSEXP) {
 BEGIN_RCPP
     Rcpp::traits::input_parameter< Rcpp::NumericMatrix >::type fishpop(fishpopSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericMatrix >::type fishpop_track(fishpop_trackSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericMatrix >::type seafloor(seafloorSEXP);
+    Rcpp::traits::input_parameter< double >::type pop_linf(pop_linfSEXP);
     Rcpp::traits::input_parameter< double >::type pop_ldie(pop_ldieSEXP);
     Rcpp::traits::input_parameter< double >::type pop_n_body(pop_n_bodySEXP);
     Rcpp::traits::input_parameter< double >::type pop_reserves_max(pop_reserves_maxSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type extent(extentSEXP);
     Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type dimensions(dimensionsSEXP);
-    rcpp_mortality(fishpop, fishpop_track, seafloor, pop_ldie, pop_n_body, pop_reserves_max, extent, dimensions);
+    rcpp_mortality(fishpop, fishpop_track, seafloor, pop_linf, pop_ldie, pop_n_body, pop_reserves_max, extent, dimensions);
     return R_NilValue;
 END_RCPP_RETURN_ERROR
 }
-RcppExport SEXP _arrR_rcpp_mortality(SEXP fishpopSEXP, SEXP fishpop_trackSEXP, SEXP seafloorSEXP, SEXP pop_ldieSEXP, SEXP pop_n_bodySEXP, SEXP pop_reserves_maxSEXP, SEXP extentSEXP, SEXP dimensionsSEXP) {
+RcppExport SEXP _arrR_rcpp_mortality(SEXP fishpopSEXP, SEXP fishpop_trackSEXP, SEXP seafloorSEXP, SEXP pop_linfSEXP, SEXP pop_ldieSEXP, SEXP pop_n_bodySEXP, SEXP pop_reserves_maxSEXP, SEXP extentSEXP, SEXP dimensionsSEXP) {
     SEXP rcpp_result_gen;
     {
         Rcpp::RNGScope rcpp_rngScope_gen;
-        rcpp_result_gen = PROTECT(_arrR_rcpp_mortality_try(fishpopSEXP, fishpop_trackSEXP, seafloorSEXP, pop_ldieSEXP, pop_n_bodySEXP, pop_reserves_maxSEXP, extentSEXP, dimensionsSEXP));
+        rcpp_result_gen = PROTECT(_arrR_rcpp_mortality_try(fishpopSEXP, fishpop_trackSEXP, seafloorSEXP, pop_linfSEXP, pop_ldieSEXP, pop_n_bodySEXP, pop_reserves_maxSEXP, extentSEXP, dimensionsSEXP));
     }
     Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
     if (rcpp_isInterrupt_gen) {
@@ -835,7 +836,7 @@ static int _arrR_RcppExport_validate(const char* sig) {
         signatures.insert("double(*rcpp_get_max_dist)(std::string,Rcpp::List,int)");
         signatures.insert("Rcpp::NumericMatrix(*rcpp_get_reef)(Rcpp::NumericMatrix)");
         signatures.insert("void(*rcpp_mineralization)(Rcpp::NumericMatrix,double,double)");
-        signatures.insert("void(*rcpp_mortality)(Rcpp::NumericMatrix,Rcpp::NumericMatrix,Rcpp::NumericMatrix,double,double,double,Rcpp::NumericVector,Rcpp::IntegerVector)");
+        signatures.insert("void(*rcpp_mortality)(Rcpp::NumericMatrix,Rcpp::NumericMatrix,Rcpp::NumericMatrix,double,double,double,double,Rcpp::NumericVector,Rcpp::IntegerVector)");
         signatures.insert("void(*rcpp_move_wrap)(Rcpp::NumericMatrix,Rcpp::NumericMatrix,std::string,double,double,double,double,double,double,Rcpp::NumericMatrix,Rcpp::NumericVector,Rcpp::IntegerVector)");
         signatures.insert("void(*rcpp_nutr_input)(Rcpp::NumericMatrix,double)");
         signatures.insert("void(*rcpp_nutr_output)(Rcpp::NumericMatrix,double,double)");
@@ -882,7 +883,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_arrR_rcpp_get_reef", (DL_FUNC) &_arrR_rcpp_get_reef, 1},
     {"_arrR_rcpp_mineralization", (DL_FUNC) &_arrR_rcpp_mineralization, 3},
     {"_arrR_rcpp_modify_degree", (DL_FUNC) &_arrR_rcpp_modify_degree, 2},
-    {"_arrR_rcpp_mortality", (DL_FUNC) &_arrR_rcpp_mortality, 8},
+    {"_arrR_rcpp_mortality", (DL_FUNC) &_arrR_rcpp_mortality, 9},
     {"_arrR_rcpp_move_behav", (DL_FUNC) &_arrR_rcpp_move_behav, 11},
     {"_arrR_rcpp_move_rand", (DL_FUNC) &_arrR_rcpp_move_rand, 8},
     {"_arrR_rcpp_move_wrap", (DL_FUNC) &_arrR_rcpp_move_wrap, 12},

src/rcpp_mortality.cpp

@@ -2,6 +2,7 @@
 
 #include "rcpp_mortality.h"
 #include "rcpp_shuffle.h"
+#include "rcpp_runif.h"
 #include "rcpp_reincarnate.h"
 
 using namespace Rcpp;
@@ -15,13 +16,13 @@ using namespace Rcpp;
 //'
 //' @param fishpop,fishpop_track Matrix with fishpop and starting fishpop values.
 //' @param seafloor Matrix with seafloor values.
-//' @param pop_ldie, pop_n_body,pop_reserves_max Numeric with parameters.
+//' @param pop_linf,pop_ldie,pop_n_body,pop_reserves_max Numeric with parameters.
 //' @param extent Vector with extent (xmin,xmax,ymin,ymax).
 //' @param dimensions Vector with dimensions (nrow, ncol).
 //'
 //' @details
 //' Function to simulate background mortality of fish individuals.
-//' Fish automatically dies when \code{pop_mean_size} is greater than \code{pop_ldie}.
+//' Fish automatically dies when current size is greater than \code{pop_ldie}.
 //' If a individual dies, a new individual is created.
 //'
 //' @return void
@@ -32,21 +33,43 @@ using namespace Rcpp;
 //' @keywords internal
 // [[Rcpp::export]]
 void rcpp_mortality(Rcpp::NumericMatrix fishpop, Rcpp::NumericMatrix fishpop_track,
-                    Rcpp::NumericMatrix seafloor,
-                    double pop_ldie, double pop_n_body, double pop_reserves_max,
-                    Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions) {
+                    Rcpp::NumericMatrix seafloor, double pop_linf, double pop_ldie, double pop_n_body,
+                    double pop_reserves_max, Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions) {
 
   // create random order if fish id because detritus can run out
   Rcpp::NumericVector row_id = rcpp_shuffle(fishpop(_, 0), false);
 
   // loop through all fish ids
   for (int i = 0; i < row_id.length(); i++) {
 
+    // init flag for mortality
+    bool flag_die = false;
+
     // use Rcpp indexing counter of current loop iteration
     int row_id_temp = row_id[i] - 1;
 
-    // individual dies if current size is larger than pop_mean_size + X
-    if (fishpop(row_id_temp, 5) > pop_ldie) {
+    // use fixed mortality
+    if (pop_ldie > 0.0) {
+
+      // update mortality flag based on current size and ldie
+      flag_die = fishpop(row_id_temp, 5) > pop_ldie;
+
+    // use probability based mortality
+    } else {
+
+      // create death probability
+      double death_prob = std::exp(fishpop(row_id_temp, 5) - pop_linf);
+
+      // create random number to test death prob against
+      double random_prob = rcpp_runif(0.0, 1.0);
+
+      // update mortality flag based on probability
+      flag_die = random_prob < death_prob;
+
+    }
+
+    // individual dies if flag is TRUE
+    if (flag_die) {
 
       rcpp_reincarnate(fishpop, fishpop_track, row_id_temp,
                        seafloor, extent, dimensions, pop_n_body, pop_reserves_max,

src/rcpp_mortality.h

@@ -2,8 +2,7 @@
 //#define RCPP_MORTALITY
 
 void rcpp_mortality(Rcpp::NumericMatrix fishpop, Rcpp::NumericMatrix fishpop_track,
-                    Rcpp::NumericMatrix seafloor,
-                    double pop_ldie, double pop_n_body, double pop_reserves_max,
-                    Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions);
+                    Rcpp::NumericMatrix seafloor, double pop_linf, double pop_ldie, double pop_n_body,
+                    double pop_reserves_max, Rcpp::NumericVector extent, Rcpp::IntegerVector dimensions);
 
 //#endif // RCPP_MORTALITY

src/rcpp_simulate.cpp

@@ -257,7 +257,7 @@ void rcpp_simulate(Rcpp::NumericMatrix seafloor, Rcpp::NumericMatrix fishpop, Rc
                           extent, dimensions, min_per_i);
 
       // simulate mortality
-      rcpp_mortality(fishpop, fishpop_track[0], seafloor,
+      rcpp_mortality(fishpop, fishpop_track[0], seafloor, parameters["pop_linf"],
                      parameters["pop_ldie"], parameters["pop_n_body"],
                      parameters["pop_reserves_max"], extent, dimensions);