[#37] Satisfy checks

.gitignore

@@ -4,3 +4,4 @@ src-x86_64
 releases
 build
 .directory
+.DS_Store

DESCRIPTION

@@ -2,7 +2,7 @@ Package: cheddar
 Type: Package
 Title: Analysis and Visualisation of Ecological Communities
 Version: 0.1-632
-Date: 2017-04-21
+Date: 2018-06-06
 Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
 Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
 Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

NAMESPACE

@@ -23,3 +23,10 @@ S3method(print, CommunityCollection)
 S3method(subset, CommunityCollection)
 S3method(summary, Community)
 S3method(summary, CommunityCollection)
+S3method('$<-', Community)
+S3method('$<-', CommunityCollection)
+S3method('[', CommunityCollection)
+S3method('[<-', Community)
+S3method('[<-', CommunityCollection)
+S3method('[[<-', Community)
+S3method('[[<-', CommunityCollection)

man/cheddar.Rd

@@ -20,8 +20,8 @@ release history:
     \tabular{ll}{
     Package: \tab cheddar\cr
     Type: \tab Package\cr
-    Version: \tab 0.1-631\cr
-    Date: \tab 2017-04-21\cr
+    Version: \tab 0.1-632\cr
+    Date: \tab 2018-06-06\cr
     License: \tab BSD 2 clause\cr
     }
 }

src/anneal.cpp

@@ -8,6 +8,7 @@
 #include <functional>
 #include <vector>
 
+#include "cheddar.h"
 #include "cheddar_exception.h"
 
 //#define DEBUG_ANNEAL

src/cheddar.cpp

@@ -0,0 +1,72 @@
+#include <R.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+
+#include "cheddar.h"
+
+
+extern "C"
+{
+
+static const R_CMethodDef cMethods[] = {
+  {
+    "trophic_chains_size", (DL_FUNC) &trophic_chains_size, 8,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP
+    }
+  },
+  {
+    "print_chains", (DL_FUNC) &print_chains, 6,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP
+    }
+  },
+  {
+    "trophic_chains", (DL_FUNC) &trophic_chains, 9,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP
+    }
+  },
+  {
+    "trophic_chains_stats", (DL_FUNC) &trophic_chains_stats, 10,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP, INTSXP,
+      INTSXP
+    }
+  },
+  {
+    "shortest_paths", (DL_FUNC) &shortest_paths, 8,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, INTSXP, INTSXP, REALSXP, INTSXP, REALSXP, INTSXP
+    }
+  },
+  {
+    "sum_diet_gaps", (DL_FUNC) &sum_diet_gaps, 5,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, INTSXP, INTSXP, INTSXP
+    }
+  },
+  {
+    "minimise_sum_diet_gaps", (DL_FUNC) &minimise_sum_diet_gaps, 10,
+    (R_NativePrimitiveArgType [])
+    {
+      INTSXP, INTSXP, REALSXP, REALSXP, REALSXP, INTSXP, INTSXP, INTSXP, INTSXP,
+      INTSXP
+    }
+  },
+  {NULL, NULL, 0, NULL},
+};
+
+void R_init_myLib(DllInfo *info) 
+{
+  R_registerRoutines(info, cMethods, NULL, NULL, NULL);
+  R_useDynamicSymbols(info, FALSE);
+}
+
+} // extern C

src/cheddar.h

@@ -0,0 +1,65 @@
+extern "C"
+{
+
+void sum_diet_gaps(const int *network, const int *nodes,
+                   const int *row_order,
+                   int *sum_diet_gaps,
+                   int *status);
+
+void minimise_sum_diet_gaps(const int *network,
+                            const int *nodes,
+                            const double *T_start,
+                            const double *T_stop,
+                            const double *c,
+                            const int *swaps_per_T,
+                            const int *trace_anneal,
+                            int *best_cost,
+                            int *best,
+                            int *status);
+
+void trophic_chains_size(const int *adjacency,
+                     const int *adjacency_length,
+                     const int *is_basal,
+                     const int *node_count,
+                     const int *test_overflow,
+                     const int *max_queue,
+                     int *n_chains,
+                     int *longest,
+                     int *status);
+
+void print_chains(const int *adjacency,
+                  const int *adjacency_length,
+                  const int *is_basal,
+                  const int *node_count,
+                  const int *max_queue,
+                  int *status);
+
+void trophic_chains(const int *adjacency,
+                    const int *adjacency_length,
+                    const int *is_basal,
+                    const int *node_count,
+                    const int *ncols,
+                    const int *nrows,
+                    const int *max_queue,
+                    int *chains,
+                    int *status);
+
+void trophic_chains_stats(const int *adjacency,
+                          const int *adjacency_length,
+                          const int *is_basal,
+                          const int *node_count,
+                          const int *n_chains,
+                          const int *longest,
+                          const int *max_queue,
+                          int *node_pos_counts,
+                          int *chain_lengths,
+                          int *status);
+
+void shortest_paths(const int *consumers, const int *consumers_length,
+                    const int *resources, const int *resources_length,
+                    const double *weights,
+                    const int *node_count,
+                    double *lengths,
+                    int *status);
+
+}

src/shortest_paths.cpp

@@ -4,16 +4,22 @@
 #include <R.h>
 #include <Rmath.h>
 #include <vector>
+
+#include "cheddar.h"
+
 typedef std::vector<bool> BoolVector;
 typedef std::vector<int> IntVector;
 typedef std::vector<double> DoubleVector;
+
 /*#define DEBUG_DIJKSTRA*/
 #ifdef DEBUG_DIJKSTRA
 #define DEBUG(X) { X; }
 #else
 #define DEBUG(X)
 #endif
 #ifdef DEBUG_DIJKSTRA
+
+
 static void print_weights(const DoubleVector &weights, int n)
 {
   for(int row=0; row<n; ++row)
@@ -25,6 +31,7 @@ static void print_weights(const DoubleVector &weights, int n)
     Rprintf("\n");
   }
 }
+
 static void print_adjacency(const IntVector &adjacency, int n)
 {
   for(int i=0; i<n; ++i)
@@ -36,6 +43,7 @@ static void print_adjacency(const IntVector &adjacency, int n)
   }
 }
 #endif
+
 static DoubleVector dijkstra(const IntVector &consumers,
                              const IntVector &resources,
                              const DoubleVector &weights,
@@ -104,6 +112,7 @@ static DoubleVector dijkstra(const IntVector &consumers,
   }
   return (lengths);
 }
+
 extern "C"
 {
 void shortest_paths(const int *consumers, const int *consumers_length,
@@ -160,4 +169,5 @@ resources_length: the number of ints in resources
     REprintf("Unexpected error in shortest_paths\n");
   }
 }
-}   // extern C
+
+}   // extern C