Merge pull request #92 from stocnet/develop

Version 1.4.8

DESCRIPTION

@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.4.7
-Date: 2024-02-20
+Version: 1.4.8
+Date: 2024-02-29
 Authors@R: c(person("Tom A.B.", "Snijders", role = c("cre", "aut"), email = "tom.snijders@nuffield.ox.ac.uk", 
                 comment = c(ORCID = "0000-0003-3157-4157")),
               person("Ruth M.", "Ripley", role = "aut"),

NEWS.md

@@ -1,3 +1,15 @@
+# RSiena 1.4.8
+
+2024-02-29
+
+
+## Changes in RSiena:
+
+### Bug corrections:
+  * Correction of memory leak in `siena07setup.ccp` for ML estimation.
+### New functionality:
+  * New parameter `silent` in `sienaAlgorithmCreate`. 
+
 # RSiena 1.4.7
 
 2024-02-20
@@ -64,6 +76,10 @@
 
 ## Changes in RSiena:
 
+### Package
+
+  * Migrated package repository to "stocnet" organisation.
+
 ### Bug corrections:
   * Put `#include <Rinternals.h>` as the last of the include commands
     in various `.cpp` files (Tomas Kalibera). 

R/sienaModelCreate.r

@@ -24,7 +24,7 @@ sienaModelCreate <- function(fn,
 	minimumPermutationLength=2, initialPermutationLength=20,
 	modelType=NULL, behModelType=NULL, mult=5, simOnly=FALSE, localML=FALSE,
 	truncation=5, doubleAveraging=0, standardizeVar=(diagonalize<1),
-	lessMem=FALSE)
+	lessMem=FALSE, silent=FALSE)
 {
 	model <- NULL
 	checking <- any(grepl("_R_CHECK", names(Sys.getenv())))

docs/manual/RSiena_Manual.tex

@@ -195,7 +195,7 @@
 by Mark Huisman, Michael Schweinberger, and Christian Steglich.
 
 This manual is frequently updated, mostly only in a minor way.
-This version was renewed for \RS version 1.4.7.
+This version was renewed for \RS version 1.4.8.
 \end{abstract}
 
 
@@ -1146,7 +1146,7 @@ \subsection{Getting help with problems}
   of \rs. Details of the latest version available can
   be found at the `Downloads' page.
   The version is
-  identified by a version number (e.g.\ 1.4.7).
+  identified by a version number (e.g.\ 1.4.8).
   You can find the number of your current installed version by
   opening \R, and typing\\
   \verb|packageVersion("RSiena")|   \\
@@ -16344,12 +16344,12 @@ \section{For programmers: Building, installing and checking the package}
 them to the repository.
 \item [Check] Checking is a process designed to ensure that packages are likely
   to work correctly when installed. Type\\
-\verb|R CMD check RSiena_1.4.7.tar.gz|\\
+\verb|R CMD check RSiena_1.4.8.tar.gz|\\
 (where the version number is adjusted to match the tar ball name.)
 \item[zip file] To make a zip file that can be used in Windows for
 `installing from a local zip file', and therefore is easy for distribution
 to others, type\\
-\verb|R CMD INSTALL --build RSiena_1.4.7.tar.gz| \\
+\verb|R CMD INSTALL --build RSiena_1.4.8.tar.gz| \\
 (where again the version number is adjusted to match the tar ball name.)
 \end{description}
 
@@ -17408,7 +17408,23 @@ \section{Appendix: Changes compared to earlier versions}
 
 
 
-\item 2024-02-19 GitHub, package version 1.4.7
+\item 2024-02-29 GitHub, package version 1.4.8.
+
+
+Changes in RSiena:
+\begin{itemize}
+\item Bug corrections:
+   \begin{itemize}
+   \item Correction of memory leak in \texttt{siena07setup.ccp} for ML estimation.
+    \end{itemize}
+\item New functionality:
+   \begin{itemize}
+   \item New parameter \texttt{silent} in \sfn{sienaAlgorithmCreate}.
+    \end{itemize}
+\end{itemize}
+
+
+\item 2024-02-20 GitHub and CRAN (2024-02-22), package version 1.4.7
 
 Changes in RSiena:
 \begin{itemize}

man/RSiena-package.Rd

@@ -47,8 +47,8 @@ Bug reports can be submitted at
   \tabular{ll}{
     Package: \tab RSiena\cr
     Type: \tab Package\cr
-    Version: \tab 1.4.7\cr
-    Date: \tab 2024-02-20\cr
+    Version: \tab 1.4.8\cr
+    Date: \tab 2024-02-29\cr
     Depends: \tab R (>= 3.5.0)\cr
     Imports: \tab Matrix, lattice, parallel, MASS, methods, xtable\cr
     Suggests: \tab network, tools, codetools, tcltk\cr

man/sienaAlgorithmCreate.Rd

@@ -26,7 +26,7 @@ sienaAlgorithmCreate(fn, projname = "Siena", MaxDegree = NULL, Offset = NULL,
      minimumPermutationLength=2, initialPermutationLength=20,
      modelType=NULL, behModelType=NULL, mult=5, simOnly=FALSE, localML=FALSE,
      truncation=5, doubleAveraging=0, standardizeVar=(diagonalize<1),
-     lessMem=FALSE)
+     lessMem=FALSE, silent=FALSE)
 
 sienaModelCreate(fn, projname = "Siena", MaxDegree = NULL, Offset = NULL,
      useStdInits = FALSE, n3 = 1000, nsub = 4, n2start = NULL,
@@ -38,7 +38,7 @@ sienaModelCreate(fn, projname = "Siena", MaxDegree = NULL, Offset = NULL,
      minimumPermutationLength=2, initialPermutationLength=20,
      modelType=NULL, behModelType=NULL, mult=5, simOnly=FALSE, localML=FALSE,
      truncation=5, doubleAveraging=0, standardizeVar=(diagonalize<1),
-     lessMem=FALSE)
+     lessMem=FALSE, silent=FALSE)
 }
 \arguments{
   \item{fn}{Function to do one simulation in the Robbins-Monro
@@ -182,6 +182,7 @@ sienaModelCreate(fn, projname = "Siena", MaxDegree = NULL, Offset = NULL,
     if \code{lessMem=TRUE}, it will be impossible to run
     \code{\link{sienaTimeTest}} or \code{\link{sienaGOF}} on
     the object produced by \code{\link{siena07}}.}
+  \item{silent}{Logical: whether to give a note about the output file.}
 }
 \details{Model specification is done via this object for
   \code{\link{siena07}}.

src/siena07setup.cpp

@@ -1058,9 +1058,9 @@ SEXP mlMakeChains(SEXP DATAPTR, SEXP MODELPTR,
 				pMLSimulation->rVariables();
 			int numberVariables = rVariables.size();
 
-			SEXP accepts1 = PROTECT(Rf_allocMatrix(INTSXP, numberVariables, 9));
-			SEXP rejects1 = PROTECT(Rf_allocMatrix(INTSXP, numberVariables, 9));
-			SEXP aborts1 = PROTECT(Rf_allocVector(INTSXP, 9));
+			SEXP accepts1 = PROTECT(Rf_allocMatrix(INTSXP, numberVariables, NBRTYPES));
+			SEXP rejects1 = PROTECT(Rf_allocMatrix(INTSXP, numberVariables, NBRTYPES));
+			SEXP aborts1 = PROTECT(Rf_allocVector(INTSXP, NBRTYPES));
 			int * iaccepts = INTEGER(accepts1);
 			int * irejects = INTEGER(rejects1);
 			int * iaborts = INTEGER(aborts1);