Merge branch 'master' into 4.7

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ergm
-Version: 4.7.2
-Date: 2024-10-12
+Version: 4.7.3
+Date: 2024-11-05
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
 Authors@R: c(
              person(c("Mark", "S."), "Handcock", role=c("aut"), email="[email protected]"),

R/ergm.geodistn.R

@@ -105,13 +105,12 @@ ergm.geodistn <- function(edgelist, n=max(edgelist), directed=FALSE) {
 # convention, we want nodelist[1]=0 and in general, nodelist[i]=2*r(i)-2,
 # where r(i) is the first row in edgelist containing from node i.  (If
 # there are no edges from node i, just set nodelist[i]=0.)
-  nodelist<-match(1:n,edgelist[,1],nomatch=1)-1
+  nodelist<-match(1:n,edgelist[,1],nomatch=1L)-1L
 
 # Now everything is ready.  Call the C code.
-  ans<-.C("full_geodesic_distribution", as.integer(t(edgelist)),
-    as.integer(n), as.integer(nodelist), as.integer(dim(edgelist)[1]),
-    colors=integer(n), distances=integer(n), queue=integer(n),
-    distribution=integer(n), PACKAGE='ergm') $ distribution
+  ans<-.Call("full_geodesic_distribution", as.integer(t(edgelist)),
+             as.integer(n), as.integer(nodelist), as.integer(dim(edgelist)[1]),
+             PACKAGE='ergm')
   names(ans)<-c(1:(n-1),"Inf") # length n really means no path exists
   ans
 }

inst/CITATION

@@ -21,8 +21,8 @@ bibentry("Manual", author = structure(list(list(given = c("Mark",
         comment = NULL)), class = "person"), title = paste("ergm", 
     ": ", gsub("\n", " ", "Fit, Simulate and Diagnose Exponential-Family Models for Networks", 
         fixed = TRUE), sep = ""), organization = paste0("The Statnet Project (\\url{", 
-    "https://statnet.org", "})"), year = substr("2024-10-12", 
-    1, 4), note = paste("R package version ", "4.7.2", sep = ""), 
+    "https://statnet.org", "})"), year = substr("2024-11-05", 
+    1, 4), note = paste("R package version ", "4.7.3", sep = ""), 
     url = paste0("https://CRAN.R-project.org/package=", "ergm"))
 # ---- END AUTOGENERATED STATNET CITATION ----
 

inst/NEWS.Rd

@@ -66,53 +66,7 @@
 
 
 
-\section{Changes in version 4.7.2}{
-
-  \subsection{NEW FEATURES}{
-    \itemize{
-      \item{
-        \code{\link{ergm.godfather}()} now takes a \code{basis=} argument like \code{\link{ergm}()}, \code{\link{simulate.ergm}()}, and others. Its term options can be passed directly as well.
-      }
-    }
-  }
-
-
-  \subsection{BUG FIXES}{
-    \itemize{
-      \item{
-        Invalid \code{levels2} specification for \code{\link[=mm-ergmTerm]{mm()}} no longer causes memory errors.
-      }
-    }
-  }
-
-
-  \subsection{OTHER USER-VISIBLE CHANGES}{
-    \itemize{
-      \item{
-        \code{\link{ergm_model}()} constructor is now generic, with methods for \code{\link{formula}}, \code{\link[statnet.common]{term_list}}, and \code{\link{ergm_model}}.
-      }
-
-      \item{
-        \code{\link{is.dyad.independent}()} can now return dyadic-independence information for each term.
-      }
-
-      \item{
-        \code{\link{control.ergm.godfather}()} has been deprecated, since it is no longer used to pass term options.
-      }
-
-      \item{
-        R documentation macros \code{\\ergmTerm}, \code{\\ergmConstraint}, \code{\\ergmReference}, \code{\\ergmHint}, and \code{\\ergmProposal}.
-      }
-
-      \item{
-        Some improvements to the Terms API (see Vignette), particularly in handling of dyadic dependence and auxiliaries.
-      }
-    }
-  }
-}
-
-
-\section{Changes in version 4.7.1}{
+\section{Changes in version 4.7.3}{
 
   \subsection{NEW FEATURES}{
     \itemize{
@@ -136,6 +90,9 @@
           \item Excessive runtime check now works in terms of free dyad counts rather than network sizes.
         }
       }
+      \item{
+        \code{\link{ergm.godfather}()} now takes a \code{basis=} argument like \code{\link{ergm}()}, \code{\link{simulate.ergm}()}, and others. Its term options can be passed directly as well.
+      }
     }
   }
 
@@ -189,6 +146,15 @@
       \item{
         \code{\link[Label-ergmTerm]{Label}()} operator now documents its behavior when the model is curved more clearly.
       }
+      \item{
+        Invalid \code{levels2} specification for \code{\link[=mm-ergmTerm]{mm()}} no longer causes memory errors.
+      }
+      \item{
+        Valued proposal updater function was not being passed the current edge state.
+      }
+      \item{
+        Undefined behavior warnings flagged by CRAN's \code{clang-asan} have been fixed.
+      }
     }
   }
 
@@ -239,6 +205,27 @@
       \item{
        \code{\link{param_names}()} API now allows assignment, and its method for \code{\link{ergm_model}} objects is more explicit about whether canonical or curved parameters are being modified and when.
       }
+      \item{
+        \code{\link{ergm_model}()} constructor is now generic, with methods for \code{\link{formula}}, \code{\link[statnet.common]{term_list}}, and \code{\link{ergm_model}}.
+      }
+      \item{
+        \code{\link{is.dyad.independent}()} can now return dyadic-independence information for each term.
+      }
+      \item{
+        \code{\link{control.ergm.godfather}()} has been deprecated, since it is no longer used to pass term options.
+      }
+      \item{
+        R documentation macros \code{\\ergmTerm}, \code{\\ergmConstraint}, \code{\\ergmReference}, \code{\\ergmHint}, and \code{\\ergmProposal}.
+      }
+      \item{
+        Some improvements to the Terms API (see Vignette), particularly in handling of dyadic dependence and auxiliaries.
+      }
+      \item{
+        Documentation improvements to extended state and network callback APIs.
+      }
+      \item{
+        The main ERGM vignette is now in HTML.
+      }
     }
   }
 
@@ -274,6 +261,12 @@
       \item{
         \code{RLEBDM1D} C API now exports \code{FirstRLEBDM1D()} and \code{LastRLEBDM1D()} macros, providing dyad indices of the first and the last dyad in the RLEBDM, respectively.
       }
+      \item{
+        \code{ChangeStats()} function has been split into \code{ChangeStatsDo()} and \code{ChangeStatsUndo()}, the latter only called on rejection, which speeds up MCMC and SAN when the proposal has multiple toggles.
+      }
+      \item{
+        \code{setListElement()} now protects the value being stored in the list before assigning it (then unprotects it), preventing potential accidental garbage collection.
+      }
     }
   }
 }

inst/include/ergm_MHproposal.h

@@ -57,9 +57,9 @@ typedef struct MHProposalstruct {
   SEXP R;
   void (*i_func)(struct MHProposalstruct*, Network*);
   void (*p_func)(struct MHProposalstruct*, Network*);
-  void (*u_func)(Vertex tail, Vertex head, struct MHProposalstruct*, Network*, Rboolean);
+  void (*u_func)(Vertex, Vertex, struct MHProposalstruct*, Network*, Rboolean);
   void (*f_func)(struct MHProposalstruct*, Network*);
-  void (*x_func)(unsigned int type, void *data, struct MHProposalstruct*, Network*);
+  void (*x_func)(unsigned int, void *, struct MHProposalstruct*, Network*);
   Edge ntoggles;
   Vertex *toggletail;
   Vertex *togglehead;

inst/include/ergm_Rutil.h

@@ -30,13 +30,16 @@ static inline SEXP getListElement(SEXP list, const char *str){
 }
 
 static inline SEXP setListElement(SEXP list, const char *str, SEXP value){
+  value = PROTECT(value);
   SEXP names = getAttrib(list, R_NamesSymbol);
 
   for (unsigned int i = 0; i < length(list); i++)
     if(strcmp(CHAR(STRING_ELT(names, i)), str) == 0) {
       SET_VECTOR_ELT(list, i, value);
+      UNPROTECT(1);
       return value;
     }
+  UNPROTECT(1);
   error("List does not have element '%s' to set.", str);
   return R_NilValue;
 }

inst/include/ergm_changestat.h

@@ -20,7 +20,7 @@ typedef struct ModelTermstruct {
   void (*f_func)(struct ModelTermstruct*, Network*);
   void (*s_func)(struct ModelTermstruct*, Network*);
   SEXP (*w_func)(struct ModelTermstruct*, Network*);  
-  void (*x_func)(unsigned int type, void *data, struct ModelTermstruct*, Network*);
+  void (*x_func)(unsigned int, void *, struct ModelTermstruct*, Network*);
   void (*z_func)(struct ModelTermstruct*, Network*, Rboolean);
   double *attrib; /* Ptr to vector of covariates (if necessary; generally unused) */
   int *iattrib; /* Ptr to vector of integer covariates (if necessary; generally unused) */

inst/include/ergm_dyadgen.h

@@ -47,8 +47,8 @@ DyadGen *DyadGenInitialize(DyadGenType type, void *dyads, void *track_nwp);
 DyadGen *DyadGenInitializeR(SEXP pR, void *any_nwp, Rboolean el);
 void DyadGenDestroy(DyadGen *gen);
 
-void DyadGenUpdate(Vertex tail, Vertex head, DyadGen *gen, Network *nwp, Rboolean edgestate);
-void WtDyadGenUpdate(Vertex tail, Vertex head, double weight, DyadGen *gen, WtNetwork *nwp, double edgestate);
+void DyadGenUpdate(Vertex tail, Vertex head, void *gen, Network *nwp, Rboolean edgestate);
+void WtDyadGenUpdate(Vertex tail, Vertex head, double weight, void *gen, WtNetwork *nwp, double edgestate);
 
 static inline void DyadGenRandDyad(Vertex *tail, Vertex *head, DyadGen *gen){
   switch(gen->type){

inst/include/ergm_khash.h

@@ -123,8 +123,8 @@ int main() {
 */
 
 
-#ifndef __AC_KHASH_H
-#define __AC_KHASH_H
+#ifndef _ERGM_KHASH_H_
+#define _ERGM_KHASH_H_
 
 /*!
   @header
@@ -771,4 +771,4 @@ typedef const char *kh_cstr_t;
     }								\
   }
 
-#endif /* __AC_KHASH_H */
+#endif /* _ERGM_KHASH_H_ */

inst/include/ergm_kvec.h

@@ -68,8 +68,8 @@ int main() {
 
 */
 
-#ifndef _AC_KVEC_H_
-#define _AC_KVEC_H_
+#ifndef _ERGM_KVEC_H_
+#define _ERGM_KVEC_H_
 
 #include <R.h>
 
@@ -78,7 +78,7 @@ int main() {
 #define kvec_t(type) struct { size_t n, m; type *a; }
 #define kv_init(v) ((v).n = (v).m = 0, (v).a = NULL) // Not necessary if the data structure is calloc()ed.
 #define kv_blank {.n = 0, .m = 0, .a = NULL}
-#define kv_destroy(v) R_Free((v).a)
+#define kv_destroy(v) {R_Free((v).a); (v).n = (v).m = 0;}
 #define kv_A(v, i) ((v).a[(i)])
 #define kv_pop(v) ((v).a[--(v).n])
 #define kv_size(v) ((v).n)

inst/include/ergm_model.h

@@ -103,6 +103,8 @@ int GetIndexForAttrValue(int value);
 
 /* *** don't forget tail-> head, so this function accepts toggletail first, not togglehead  */
 
+void ChangeStatsDo(unsigned int ntoggles, Vertex *tails, Vertex *heads, Network *nwp, Model *m);
+void ChangeStatsUndo(unsigned int ntoggles, Vertex *tails, Vertex *heads, Network *nwp, Model *m);
 void ChangeStats(unsigned int ntoggles, Vertex *tails, Vertex *heads, Network *nwp, Model *m);
 void ChangeStats1(Vertex tail, Vertex head, Network *nwp, Model *m, Rboolean edgestate);
 void ZStats(Network *nwp, Model *m, Rboolean skip_s);