devtools build with citation

inst/CITATION

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+citHeader("To cite phylofactor in publications, please use:")
+
+citEntry(entry = "article",
+
+         title = "Phylogenetic factorization of compositional data yields lineage-level associations in microbiome data",
+
+         author = personList(person("Washburne", "Alex D."),
+                             person("Silverman", "Justin D."),
+                             person("Leff", "Jonathan W."),
+                             person("Bennett", "Dominic J."),
+                             person("Darcy", "John L."),
+                             person("Mukherjee", "Sayan"),
+                             person("Fierer", "Noah"),
+                             person("David", "Lawrence A.")),
+
+         journal = "PeerJ",
+
+         year = "2017",
+
+         volume = "5:e2969",
+
+         url = "https://doi.org/10.7717/peerj.2969",
+
+         textVersion  = paste("Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, Fierer N, and David LA (2017)",
+
+                              "Phylogenetic factorization of compositional data yields lineage-level associations in microbiome data",
+
+                              "PeerJ. 5:e2969",
+
+                              "https://doi.org/10.7717/peerj.2969"),
+
+         )

src-i386/phylofactor_init.c

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+#include <R.h>
+#include <Rinternals.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* FIXME: 
+   Check these declarations against the C/Fortran source code.
+*/
+
+/* .Call calls */
+extern SEXP bifurcations(SEXP, SEXP, SEXP);
+
+static const R_CallMethodDef CallEntries[] = {
+    {"bifurcations", (DL_FUNC) &bifurcations, 3},
+    {NULL, NULL, 0}
+};
+
+void R_init_phylofactor(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}

src-x64/bifurcations.c

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+#include <R.h>
+#include <Rinternals.h>
+
+// find the connecting edge from a node
+int getEdg(int nd, int * edge1, int * edge2,
+           int nedges)
+{
+  int i;
+  int edg=-1;
+  for (i=0;i<nedges;i++) {
+    if (nd==edge2[i]) {
+      edg=i;
+      break;
+    }
+  }
+  return edg;
+}
+
+// find the connecting edge from an edge
+int cnnctngEdg(int edge, int * edge1, int * edge2,
+               int nedges)
+{
+  int nxt;
+  int nd=edge1[edge];
+  nxt = getEdg(nd, edge1, edge2, nedges);
+  return nxt;
+}
+
+// return array of edge bipartitions
+SEXP bifurcations(SEXP e1, SEXP e2,
+                  SEXP nts)
+{
+  int i;
+  int edg;
+  SEXP res;
+  int* edge1 = INTEGER(e1);
+  int* edge2 = INTEGER(e2);
+  int nedges = length(e1);
+  int ntips = asInteger(nts);
+  PROTECT(res=allocMatrix(INTSXP, nedges, ntips));
+  int n = length(res);
+  for(i=0;i<n; i++) {
+    INTEGER(res)[i] = 0;
+  }
+  for(i=0;i<ntips; i++) {
+    edg=getEdg(i+1, edge1, edge2, nedges);
+    INTEGER(res)[edg + i * nedges]=1;
+    edg=cnnctngEdg(edg, edge1, edge2, nedges);
+    while(edg!=-1) {
+      INTEGER(res)[edg + i * nedges]=1;
+      edg=cnnctngEdg(edg, edge1, edge2, nedges);
+    }
+  }
+  UNPROTECT(1);
+  return res;
+}

src-x64/phylofactor_init.c

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+#include <R.h>
+#include <Rinternals.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* FIXME: 
+   Check these declarations against the C/Fortran source code.
+*/
+
+/* .Call calls */
+extern SEXP bifurcations(SEXP, SEXP, SEXP);
+
+static const R_CallMethodDef CallEntries[] = {
+    {"bifurcations", (DL_FUNC) &bifurcations, 3},
+    {NULL, NULL, 0}
+};
+
+void R_init_phylofactor(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}