Merge branch 'master' into control3

statnet · Dec 24, 2024 · 762f582 · 762f582
2 parents 86288f9 + d0c5e5c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: ergm
-Version: 4.8.0-7026
+Version: 4.8.0-7505
 Date: 2024-12-22
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
 Authors@R: c(

diff --git a/R/InitErgmConstraint.R b/R/InitErgmConstraint.R
@@ -415,7 +415,7 @@ InitErgmConstraint.observed <- function(nw, arglist, ...){
 }
 
 warn_netsize <- function(.n, ...){
-  mismatch <- vapply(list(...), function(x) is.network(x) && network.size(x) != .n, logical(1))
+  mismatch <- map_lgl(list(...), function(x) (is.network(x) && network.size(x) != .n) || (is(x, "rlebdm") && nrow(x) != .n))
   if(any(mismatch))
     ergm_Init_warning("Network size of argument(s) ", paste.and(sQuote(...names()[mismatch])), " differs from that of the response network.")
 }
@@ -477,7 +477,7 @@ InitErgmConstraint.fixedas<-function(nw, arglist,...){
 #'
 #' @usage
 #' # fixallbut(free.dyads)
-#' @param free.dyads edgelist or network. Networks will be converted to the corresponding edgelist.
+#' @param free.dyads a two-column edge list, a [`network`], or an [`rlebdm`]. Networks will be converted to the corresponding edgelist.
 #'
 #' @template ergmConstraint-general
 #'
@@ -487,23 +487,24 @@ InitErgmConstraint.fixedas<-function(nw, arglist,...){
 InitErgmConstraint.fixallbut<-function(nw, arglist,...){
   a <- check.ErgmTerm(nw, arglist,
                       varnames = c("free.dyads"),
-                      vartypes = c("network,matrix"),
+                      vartypes = c("network,matrix,rlebdm"),
                       defaultvalues = list(NULL),
                       required = c(TRUE))
   free.dyads <- a$free.dyads
 
   warn_netsize(network.size(nw), free.dyads = free.dyads)
 
   list(
-    free_dyads = function(){
-      if(is.network(free.dyads)) free.dyads <- as.edgelist(free.dyads)
-      else free.dyads <- as.edgelist(free.dyads,
-                                     n=nw%n%"n",
-                                     directed=nw%n%"directed",
-                                     bipartite=nw%n%"bipartite",
-                                     loops=nw%n%"loops")
-      as.rlebdm(free.dyads)
-    },
+    free_dyads =
+      if(is(free.dyads, "rlebdm")) free.dyads
+      else function()
+        as.rlebdm(if(is.network(free.dyads)) as.edgelist(free.dyads)
+                  else as.edgelist(free.dyads,
+                                   n=nw%n%"n",
+                                   directed=nw%n%"directed",
+                                   bipartite=nw%n%"bipartite",
+                                   loops=nw%n%"loops")
+                  ),
     dependence = FALSE)
 }
 

diff --git a/R/InitErgmTerm.operator.R b/R/InitErgmTerm.operator.R
@@ -715,8 +715,6 @@ InitErgmTerm.Sum <- function(nw, arglist,...){
   nparam <- nparams[1]
 
   inputs <- unlist(wl%>%map(t))
-  inputs <- c(nf, length(inputs), inputs)
-
 
   if(is.function(a$label)){
     cns <- lapply(ms, param_names, canonical=TRUE)
@@ -770,7 +768,7 @@ InitErgmTerm.Sum <- function(nw, arglist,...){
     }
   }else offset <- FALSE
 
-  c(list(name="Sum", coef.names = coef.names, inputs=inputs, submodels=ms, emptynwstats=gs,
+  c(list(name="Sum", coef.names = coef.names, inputs=inputs, iinputs=nf, submodels=ms, emptynwstats=gs,
          dependence=dependence, offset=offset,
          ext.encode = if(ms %>% map("terms") %>% unlist(FALSE) %>% map("ext.encode") %>% compact %>% length)
                         function(el, nw0)

diff --git a/R/ergm.R b/R/ergm.R
@@ -491,7 +491,7 @@ ergm <- function(formula, response=NULL,
   model.obs <- NULL
   if(identical(proposal$auxiliaries, proposal.obs$auxiliaries)){
     ## Reuse auxiliaries from the unconstrained proposal if identical.
-    proposal.obs$slots.extra.aux <- model$slots.extra.aux$proposal
+    proposal.obs$aux.slots <- model$slots.extra.aux$proposal
   }else if(!is.null(proposal.obs$auxiliaries)){
     if (verbose) message("Constrained proposal requires different auxiliaries: reinitializing model...")
     model.obs <- ergm_model(formula, nw, extra.aux = NVL3(proposal.obs$auxiliaries,list(proposal=.)), term.options=control$term.options)

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -11,6 +11,15 @@
 \title{NEWS file for the \code{\link[=ergm-package]{ergm}} package}
 \encoding{UTF-8}
 
+
+%% Note: This needs to be kept in sync with man/macros/ergmTerm.Rd
+\newcommand{\ergmTerm}{\code{\link[#1:#2-ergmTerm]{#2#3}}}
+\newcommand{\ergmConstraint}{\code{\link[#1:#2-ergmConstraint]{#2#3}}}
+\newcommand{\ergmReference}{\code{\link[#1:#2-ergmReference]{#2#3}}}
+\newcommand{\ergmHint}{\code{\link[#1:#2-ergmHint]{#2#3}}}
+\newcommand{\ergmProposal}{\code{\link[#1:#2-ergmProposal]{#2#3}}}
+
+
 % When a release is forked, copy the sections to a new release and
 % delete unused sections.
 
@@ -65,6 +74,83 @@
 %% }
 
 
+\section{Changes in version 4.8.0}{
+
+  \subsection{NEW FEATURES}{
+    \itemize{
+      \item{
+        A new bipartite term operator \ergmTerm{ergm}{Project}{()}, with aliases \ergmTerm{ergm}{Proj1}{()} and \ergmTerm{ergm}{Proj2}{()}, evaluating the statistics on an undirected valued network of counts constructed by projecting the bipartite network onto one of its modes.
+      }
+      \item{
+        A new family of terms, \ergmTerm{ergm}{nodecovrange}{()}, \ergmTerm{ergm}{nodeocovrange}{()}, \ergmTerm{ergm}{nodeicovrange}{()}, \ergmTerm{ergm}{b1covrange}{()}, and \ergmTerm{ergm}{b2covrange}{()}, to evaluate the sum over the nodes of the range of the specified quantitative attribute value among the node's neighbors. (Thanks to Marion Hoffman for the idea!)
+      }
+      \item{
+        A new family of terms, \ergmTerm{ergm}{nodefactordistinct}{()}, \ergmTerm{ergm}{nodeofactordistinct}{()}, \ergmTerm{ergm}{nodeifactordistinct}{()}, \ergmTerm{ergm}{b1factordistinct}{()}, and \ergmTerm{ergm}{b2factordistinct}{()}, to evaluate the sum over the nodes of the number of distinct values of a categorical factor among the node's neighbors. (Thanks to Marion Hoffman for the idea!)
+      }
+      \item{
+        The \ergmConstraint{ergm}{fixallbut}{()} now supports an \code{\link{rlebdm}} (in addition to an edge list matrix and a \code{\link[network]{network}}) for its argument.
+      }
+    }
+  }
+
+
+  \subsection{BUG FIXES}{
+    \itemize{
+      \item{
+        Fix in stochastic approximation code for compatibility with most recent \CRANpkg{coda}.
+      }
+      \item{
+        In \code{\link[ergm]{ergm()}}, a bug in initialization of MH proposals for constrained sampling requesting auxiliaries has been fixed.
+      }
+    }
+  }
+
+
+  \subsection{OTHER USER-VISIBLE CHANGES}{
+    \itemize{
+      \item{
+        Precision of geometrically weighted statistics (degrees and shared partners) has been improved, particularly for large decay parameters.
+      }
+      \item{
+        Dynamic term documentation is now more robust to extension developer error.
+      }
+      \item{
+        A new \code{\link[=as.rle.rlebdm]{as.rle()}} method for \code{\link{rlebdm}} objects to cast it back to an \code{\link{rle}}.
+      }
+    }
+  }
+
+  \subsection{C-LEVEL FACILITIES}{
+    \itemize{
+      \item{
+        Degree-conditioned proposals are now exported in \file{inst/include/}.
+      }
+      \item{
+        The M-H proposal API now makes lengths of input vectors available to the proposals, paralleling the change statistics API.
+      }
+    }
+  }
+
+  %% \subsection{UTILITIES}{
+  %%   \itemize{
+  %%     \item Likewise, "UTILITIES" is probably unnecessary.
+  %%   }
+  %% }
+
+  %% \subsection{INSTALLATION}{
+  %%   \itemize{
+  %%     \item ... as is "INSTALLATION".
+  %%   }
+  %% }
+
+  %% \subsection{PACKAGE INSTALLATION}{
+  %%   \itemize{
+  %%     \item ditto.
+  %%   }
+  %% }
+
+}
+
 
 \section{Changes in version 4.7.5}{
 
@@ -105,7 +191,7 @@
         \code{\link[=blockdiag-ergmConstraint]{blockdiag}} constraint initialization now detects when blocks are non-contiguous and stops with an error. (Previously, it would behave in undefined ways.)
       }
       \item{
-        \code{\link[=Sum-ergmTerm]{Sum}} operator now handles \code{\link{I}()} label specifications correctly; this also fixes an error in the \code{\link[=Prod-ergmTerm]{Prod}} term.
+        \ergmTerm{ergm}{Sum}{} operator now handles \code{\link{I}()} label specifications correctly; this also fixes an error in the \ergmTerm{ergm}{Prod}{} term.
       }
       \item{
         Detection of dyadic dependence now ignores dyadic dependence of hints (since they do not affect the sample space) and auxiliaries (since they do not, in and of themselves, add dyad-dependent statistics).
@@ -123,7 +209,7 @@
         In proposal help, listing of proposal table entries works again.
       }
       \item{
-        \code{\link[=nodemix-ergmTerm]{nodemix}()} now uses correct parameter names.
+        \ergmTerm{ergm}{nodemix}{()} now uses correct parameter names.
       }
       \item{
         Godambe information for the MPLE now works if the model has an offset. (Thanks, Cornelius Fritz for reporting and Michał Bojanowski for fixing.)
@@ -132,7 +218,7 @@
         When constructing the starting networks for missing data MCMC, imputation of dyads is skipped if the constraints are dyad-dependent, since inserting edges may break the constraint.
       }
       \item{
-        \code{\link[=edgecov-ergmTerm]{edgecov}()} and \code{\link[=dyadcov-ergmTerm]{dyadcov}()} now handle \code{\link[network]{network}}-format input correctly.
+        \ergmTerm{ergm}{edgecov}{()} and \ergmTerm{ergm}{dyadcov}{()} now handle \code{\link[network]{network}}-format input correctly.
       }
       \item{
         Missing data MLE code can now handle the scenarios in which the statistics in the constrained sample are constant and/or the statistics in the unconstrained sample are highly correlated.
@@ -144,10 +230,10 @@
         Likelihood calculation is now robust to dropped parameters and parameters fixed at infinity.
       }
       \item{
-        \code{\link[Label-ergmTerm]{Label}()} operator now documents its behavior when the model is curved more clearly.
+        \ergmTerm{ergm}{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.
+        Invalid \code{levels2} specification for \ergmTerm{ergm}{mm}{()} no longer causes memory errors.
       }
       \item{
         Valued proposal updater function was not being passed the current edge state.
@@ -167,7 +253,7 @@
         \code{\link{LARGEST}}, \code{\link{SMALLEST}}, and \code{\link{COLLAPSE_SMALLEST}} now break ties lexicographically with a warning.
       }
       \item{
-        \code{\link[=absdiffcat-ergmTerm]{absdiffcat}} is now more memory-efficient during initialization.
+        \ergmTerm{ergm}{absdiffcat}{} is now more memory-efficient during initialization.
       }
       \item{
         MCMLE estimation code for missing data MLE with high missingness fraction is more robust.
@@ -191,7 +277,7 @@
         \code{\link{ergm_Init_stop}()}, \code{\link{ergm_Init_warning}()}, and \code{\link{ergm_Init_message}()} that behave more like their \pkg{base} counterparts have been added to the API. \code{\link{ergm_Init_abort}()}, \code{\link{ergm_Init_warn}()}, and \code{\link{ergm_Init_info}()} will eventually change to use their \CRANpkg{rlang} semantics.
       }
       \item{
-        \code{\link[=edgecov-ergmTerm]{edgecov}()} and \code{\link[=dyadcov-ergmTerm]{dyadcov}()} now check that their covariate matrix has the correct dimension.
+        \ergmTerm{ergm}{edgecov}{()} and \ergmTerm{ergm}{dyadcov}{()} now check that their covariate matrix has the correct dimension.
       }
       \item{
         Constraints \code{\link[fixedas-ergmConstraint]{fixedas}()} and \code{\link[fixedas-ergmConstraint]{fixallbut}()} now warn when given a network whose size does not match the LHS network's.
@@ -493,7 +579,7 @@
         New functions \code{\link{search.ergmHints}()} and \code{\link{search.ergmReferences}()} can now be used to search available \code{\link{ergmHints}} and \code{\link{ergmReferences}}, respectively.
       }
       \item{
-        A new \code{\link[=For-ergmTerm]{For}()} term operator to construct a list of terms with some varying parameter.
+        A new \ergmTerm{ergm}{For}{()} term operator to construct a list of terms with some varying parameter.
       }
       \item{
         Term API vignette is now more complete, and includes all API elements, not just the post-4.0 ones.
@@ -594,7 +680,7 @@
   \subsection{NEW FEATURES}{
     \itemize{
       \item{
-        In terms \code{\link[=edgecov-ergmTerm]{edgecov}()} and \code{\link[=dyadcov-ergmTerm]{dyadcov}()}, the argument can now be a network.
+        In terms \ergmTerm{ergm}{edgecov}{()} and \ergmTerm{ergm}{dyadcov}{()}, the argument can now be a network.
       }
     }
   }
@@ -704,7 +790,7 @@
       }
 
       \item{
-        Term \code{\link[=nodemix-ergmTerm]{nodemix}} can now be passed a \code{levels2} argument that is a \code{\link{factor}} or \code{\link{character}} and optionally a matrix, allowing multiple cells to be mapped to the same statistic. (Joyce Cheng)
+        Term \ergmTerm{ergm}{nodemix}{} can now be passed a \code{levels2} argument that is a \code{\link{factor}} or \code{\link{character}} and optionally a matrix, allowing multiple cells to be mapped to the same statistic. (Joyce Cheng)
       }
 
       \item{
@@ -733,7 +819,7 @@
       }
 
       \item{
-        \code{\link[=edgecov-ergmTerm]{edgecov}} and \code{\link[=dyadcov-ergmTerm]{dyadcov}} now detect and stop with an error when the specified network attribute is not found.
+        \ergmTerm{ergm}{edgecov}{} and \ergmTerm{ergm}{dyadcov}{} now detect and stop with an error when the specified network attribute is not found.
       }
 
       \item{
@@ -813,7 +899,7 @@
       }
 
       \item{
-        \code{\link{check.ErgmTerm}()} helper function can now also capture the expressions resulting in term arguments. This incidentally fixes a regression in statistic naming of \code{\link{edgecov-ergmTerm}} and \code{\link{dyadcov-ergmTerm}} effects.
+        \code{\link{check.ErgmTerm}()} helper function can now also capture the expressions resulting in term arguments. This incidentally fixes a regression in statistic naming of \ergmTerm{ergm}{edgecov}{()} and \ergmTerm{ergm}{dyadcov}{()} effects.
       }
 
       \item{

diff --git a/inst/include/ergm_MHproposal.h b/inst/include/ergm_MHproposal.h
@@ -65,8 +65,10 @@ typedef struct MHProposalstruct {
   Vertex *togglehead;
   double logratio;
   int status;
-  double *inputs; /* may be used if needed, ignored if not. */
-  int *iinputs; /* may be used if needed, ignored if not. */
+  int ninputs;
+  double *inputs;
+  int niinputs;
+  int *iinputs;
   void *storage;
   void **aux_storage;
   unsigned int n_aux;
@@ -79,8 +81,11 @@ MHProposal *MHProposalInitialize(SEXP pR, Network *nwp, void **aux_storage);
 void MHProposalDestroy(MHProposal *MHp, Network *nwp);
 
 /* Helper macros */
+#define MH_N_DINPUTS MHp->ninputs
 #define MH_DINPUTS MHp->inputs
+#define MH_N_INPUTS MH_N_DINPUTS
 #define MH_INPUTS MH_DINPUTS
+#define MH_N_IINPUTS MHp->niinputs
 #define MH_IINPUTS MHp->iinputs
 
 #define Mtail (MHp->toggletail)

diff --git a/inst/include/ergm_constants.h b/inst/include/ergm_constants.h
@@ -12,7 +12,7 @@
 
 // Macros indicating the version of the C API.
 #define ERGM_API_MAJOR 4
-#define ERGM_API_MINOR 7
+#define ERGM_API_MINOR 8
 
 typedef enum MCMCStatus_enum {
   MCMC_OK = 0,

diff --git a/inst/include/ergm_wtMHproposal.h b/inst/include/ergm_wtMHproposal.h
@@ -66,8 +66,10 @@ typedef struct WtMHProposalstruct {
   double *toggleweight;
   double logratio;
   int status;
-  double *inputs; /* may be used if needed, ignored if not. */
-  int *iinputs; /* may be used if needed, ignored if not. */
+  int ninputs;
+  double *inputs;
+  int niinputs;
+  int *iinputs;
   void *storage;
   void **aux_storage;
   unsigned int n_aux;
@@ -79,8 +81,11 @@ WtMHProposal *WtMHProposalInitialize(SEXP pR, WtNetwork *nwp, void **aux_storage
 void WtMHProposalDestroy(WtMHProposal *MH, WtNetwork *nwp);
 
 /* Helper macros */
+#define MH_N_DINPUTS MHp->ninputs
 #define MH_DINPUTS MHp->inputs
+#define MH_N_INPUTS MH_N_DINPUTS
 #define MH_INPUTS MH_DINPUTS
+#define MH_N_IINPUTS MHp->niinputs
 #define MH_IINPUTS MHp->iinputs
 
 #define Mtail (MHp->toggletail)

diff --git a/man/fixallbut-ergmConstraint-ea96b2e0.Rd b/man/fixallbut-ergmConstraint-ea96b2e0.Rd
diff --git a/src/MHproposal.c b/src/MHproposal.c
@@ -62,9 +62,11 @@ MHProposal *MHProposalInitialize(SEXP pR, Network *nwp, void **aux_storage){
   MHp->x_func=(void (*)(unsigned int, void *, MHProposal*, Network*)) R_FindSymbol(fn,sn,NULL);
 
   SEXP tmp = getListElement(pR, "inputs");
-  MHp->inputs=length(tmp) ? REAL(tmp) : NULL;
+  MHp->ninputs = length(tmp);
+  MHp->inputs = MHp->ninputs ? REAL(tmp) : NULL;
   tmp = getListElement(pR, "iinputs");
-  MHp->iinputs=length(tmp) ? INTEGER(tmp) : NULL;
+  MHp->niinputs = length(tmp);
+  MHp->iinputs = MHp->niinputs ? INTEGER(tmp) : NULL;
 
   /*Clean up by freeing sn and fn*/
   R_Free(fn);