From bdb2601d2b75a1699892e8989db7be52f269a37b Mon Sep 17 00:00:00 2001
From: Brad Duthie <brad.duthie@gmail.com>
Date: Sat, 1 Dec 2018 15:04:29 +0000
Subject: [PATCH] Fix paras vector in manager function for Issue #46 and #47

---
 src/manager.c | 29 +++++++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/src/manager.c b/src/manager.c
index 7e797fb4..670c0eb9 100644
--- a/src/manager.c
+++ b/src/manager.c
@@ -399,6 +399,7 @@ SEXP manager(SEXP RESOURCE, SEXP LANDSCAPE, SEXP PARAMETERS, SEXP AGENT,
     int jacobian_dim;        /* Dimensions of the (square) Jacobian matrix */
     int protected_n;         /* Number of protected R objects */
     int vec_pos;             /* Vector position for making arrays */
+    int len_PARAMETERS;      /* Length of the parameters vector */
     int *dim_RESOURCE;       /* Dimensions of the RESOURCE array incoming */
     int *dim_LANDSCAPE;      /* Dimensions of the LANDSCAPE array incoming */
     int *dim_AGENT;          /* Dimensions of the AGENT array incoming */
@@ -410,7 +411,9 @@ SEXP manager(SEXP RESOURCE, SEXP LANDSCAPE, SEXP PARAMETERS, SEXP AGENT,
     int **lookup;            /* Lookup table for resource & land interactions */
     double *R_ptr;           /* Pointer to RESOURCE (interface R and C) */
     double *land_ptr;        /* Pointer to LANDSCAPE (interface R and C) */
+    double *paras_ptr;       /* Pointer to PARAMETERS (interface R and C) */
     double *paras;           /* Pointer to PARAMETER (interface R and C) */
+    double *paras_ptr_new;   /* Pointer to new paras (interface R and C) */
     double *agent_ptr;       /* Pointer to AGENT (interface R and C) */
     double *cost_ptr;        /* Pointer to COST (interface R and C) */
     double *action_ptr;      /* Pointer to ACTION (interface R and C) */
@@ -472,8 +475,9 @@ SEXP manager(SEXP RESOURCE, SEXP LANDSCAPE, SEXP PARAMETERS, SEXP AGENT,
     
     PROTECT( PARAMETERS = AS_NUMERIC(PARAMETERS) );
     protected_n++;
-    paras = REAL(PARAMETERS);
+    paras_ptr = REAL(PARAMETERS);
     
+    len_PARAMETERS  = GET_LENGTH(PARAMETERS);
     dim_RESOURCE    = INTEGER( GET_DIM(RESOURCE)  );
     dim_LANDSCAPE   = INTEGER( GET_DIM(LANDSCAPE) );
     dim_AGENT       = INTEGER( GET_DIM(AGENT) );
@@ -625,6 +629,14 @@ SEXP manager(SEXP RESOURCE, SEXP LANDSCAPE, SEXP PARAMETERS, SEXP AGENT,
         }
     }
     
+    /* Code below copies the paras vector into C */
+    paras   = malloc(len_PARAMETERS * sizeof(double *));
+    vec_pos   = 0;
+    for(xloc = 0; xloc < len_PARAMETERS; xloc++){
+        paras[xloc] = paras_ptr[vec_pos];
+        vec_pos++;
+    } /* The parameters vector is now copied into C */
+    
     /* Do the biology here now */
     /* ====================================================================== */
 
@@ -725,6 +737,18 @@ SEXP manager(SEXP RESOURCE, SEXP LANDSCAPE, SEXP PARAMETERS, SEXP AGENT,
         }
     }
     
+    SEXP PARAMETERS_NEW;
+    PROTECT( PARAMETERS_NEW = allocVector(REALSXP, len_PARAMETERS) );
+    protected_n++;
+    
+    paras_ptr_new = REAL(PARAMETERS_NEW);
+    
+    vec_pos = 0;
+    for(xloc = 0; xloc < len_PARAMETERS; xloc++){
+        paras_ptr_new[vec_pos] = paras[xloc];
+        vec_pos++;
+    }  
+    
     SEXP EVERYTHING;
     EVERYTHING = PROTECT( allocVector(VECSXP, 6) );
     protected_n++;
@@ -733,10 +757,11 @@ SEXP manager(SEXP RESOURCE, SEXP LANDSCAPE, SEXP PARAMETERS, SEXP AGENT,
     SET_VECTOR_ELT(EVERYTHING, 2, NEW_LANDSCAPE);
     SET_VECTOR_ELT(EVERYTHING, 3, NEW_ACTIONS);
     SET_VECTOR_ELT(EVERYTHING, 4, NEW_COSTS);
-    SET_VECTOR_ELT(EVERYTHING, 5, PARAMETERS);
+    SET_VECTOR_ELT(EVERYTHING, 5, PARAMETERS_NEW);
     
     UNPROTECT(protected_n);
 
+    free(paras);
     /* Free all of the allocated memory used in the observation array */
     for(row = 0; row < obs_d0; row++){
         free(obs_array[row]);