Merge pull request #72 from snlab-nl/develop

Version 1.3-22

DESCRIPTION

@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.3.20
-Date: 2023-04-22
+Version: 1.3.22
+Date: 2023-05-11
 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", "Ripley", role = "aut"),
               person("Krists", "Boitmanis", role = c( "aut","ctb")),

NEWS.md

@@ -1,3 +1,27 @@
+# RSiena 1.3.22
+
+## 
+
+2023-05-11
+
+## Changes in RSiena: 
+### Coding:
+  * Corrected and cleaned up virtual definitions in `AlterFunction` and its
+    descendants, in particular `CovariateNetworkAlterFunction`.
+  * Added `const` to virtual specification of `value` in `AlterFunction.h`
+    and all of its descendants.
+  * Replaced ambiguous call to `std::abs` in `AbsDiffFunction.cpp`. 
+### New functionality:
+  * For one-mode networks, new model options `DOUBLESTEP25`, `DOUBLESTEP50`,
+    `DOUBLESTEP75`, `DOUBLESTEP100`. 
+### Corrections:
+  * The first item in "Coding" implies correction of several distance-2 network 
+	 effects such as `altDist2`, `totDist2` and `altInDist2`.
+  * In `sienaAlgorithmCreate`, changed default `prML=2` back to `prML=1`; 
+    stop if Maximum Likelihood estimation is attempted for a data set
+    containing more than one dependent variable 
+    with `prML=2` (implemented in `initializeFRAN.r`). 
+
 # RSiena 1.3.20
 
 ## 

R/initializeFRAN.r

@@ -282,6 +282,17 @@ initializeFRAN <- function(z, x, data, effects, prevAns=NULL, initC,
 
 		## split and rejoin both versions before continuing
 		depvarnames <- names(data[[1]]$depvars)
+
+		if (x$maxlike & (length(depvarnames) > 1))
+		{
+			if(x$pridg + x$prcdg + x$prper + x$pripr + x$prdpr + x$prirms +
+				x$prdrms < 1)
+			{
+				cat("Maximum likelihood estimation with more than one dependent variable\n")
+				cat("is impossible with prML=2. Try prML=1.\n")
+				stop("Impossible algorithm-data combination.")
+			}
+		}
 
 		effects1 <- split(requestedEffects, requestedEffects$name)
 		effects1order <- match(c(depvarnames, "sde"), names(effects1))

R/printDataReport.r

@@ -48,7 +48,7 @@ DataReport <- function(z, x, f)
 			{
 				Report(sprintf("Network %d %s :", i, oneModeNames[i]), outf)
 			}
-			Report(sprintf(" %s\n",ModelTypeStrings(z$modelType[i])), outf)
+			Report(sprintf(" %s \n",ModelTypeStrings(z$modelType[i])), outf)
 		}
 		if (any(z$modelType != x$modelType))
 		{

R/sienaModelCreate.r

@@ -17,7 +17,7 @@ sienaModelCreate <- function(fn,
 	maxlike=FALSE, gmm=FALSE, diagonalize=0.2*!maxlike,
 	condvarno=0, condname='',
 	firstg=0.2, reduceg=0.5, cond=NA, findiff=FALSE,  seed=NULL,
-	prML=2,
+	prML=1,
 #	pridg=0.05, prcdg=0.05, prper=0.2, pripr=0.3, prdpr=0.3,
 #	prirms=0.05, prdrms=0.05,
 	maximumPermutationLength=40,
@@ -31,7 +31,7 @@ sienaModelCreate <- function(fn,
 	if (maxlike && (!is.null(MaxDegree)))
 	{
 		warning("maxlike and MaxDegree are incompatible")
-	}	
+	}
 	if (is.null(projname) | checking)
 	{
 		model$projname <- tempfile("Siena")
@@ -122,10 +122,13 @@ sienaModelCreate <- function(fn,
 
 	if (!is.null(modelType))
 	{
-		if (any(!(modelType %in% 1:6)))
+		if (any(!(modelType %in% 1:10)))
+		{
+			stop('modelType can only have integer values from 1 to 10\n')
+		}
+		if ((maxlike) & (any(modelType %in% 7:10)))
 		{
-			warning('modelType can only have values from 1 to 6; other values changed to 1\n')
-			model$modelType[!(modelType %in% 1:6)] <- 1
+			stop('Double step model type incompatible with maximum likelihood estimation')
 		}
 		if (any(is.null(names(modelType))))
 		{
@@ -171,7 +174,7 @@ sienaModelCreate <- function(fn,
 			model$prdrms <- 0.05   # delete random missing
 			# prob(move) = 0
 		}
-		else  # prML == 2 new default
+		else  # prML == 2 
 		{
 			model$pridg <-  0.05   # insert diagonal
 			model$prcdg <-  0.05   # cancel diagonal
@@ -232,14 +235,18 @@ sienaAlgorithmCreate <- sienaModelCreate
 
 ##@ModelTypeStrings DataCreate
 ModelTypeStrings <- function(i){
-	ifelse(((i %in% 1:6) && (!is.null(i))),
+	ifelse(((i >= 1) && (i <= 8) && (!is.null(i))),
 		switch(i,
 			"Standard actor-oriented model",
 			"Forcing model",
 			"Initiative model",
 			"Pairwise forcing model",
 			"Pairwise mutual model",
-			"Pairwise joint model"), "")
+			"Pairwise joint model",
+			"Double Step Model 0.25",
+			"Double Step Model 0.50",
+			"Double Step Model 0.75",
+			"Double Step Model 1.00"), "")
 }
 
 ##@BehaviorModelTypeStrings DataCreate

R/sienaprint.r

@@ -728,7 +728,7 @@ print.sienaAlgorithm <- function(x, ...)
 		}
 		for (i in 1:length(x$modelType))
 		{
-			cat(sprintf(" %s: %d %s\n", names(x$modelType)[i], (x$modelType)[i],
+			cat(sprintf(" %s: %d %s \n", names(x$modelType)[i], (x$modelType)[i],
 					ModelTypeStrings(x$modelType[i])))
 		}
 	}
@@ -968,7 +968,7 @@ sienaFitThetaTable <- function(x, fromBayes=FALSE, tstat=FALSE, groupOnly=0, nfi
 	  pp <- pp + nrates
 	}
 	else
-	{ 
+	{
 	  pp <- sum(x$requestedEffects$include==TRUE)
 	  xp <- pp - sum(x$requestedEffects$type=="gmm")
 	  pp <- xp + nrates
@@ -1092,10 +1092,10 @@ sienaFitThetaTable <- function(x, fromBayes=FALSE, tstat=FALSE, groupOnly=0, nfi
 	    ses <- sqrt(diag(x$covtheta))
 	    ses[x$fixed] <- NA
 	  }
-	  else 
+	  else
 	  {
 	    ses <- sqrt(diag(x$covtheta))
-	    ses[x$fixed[-which(x$requestedEffects$type=="gmm")]] <- NA  
+	    ses[x$fixed[-which(x$requestedEffects$type=="gmm")]] <- NA
 	  }
 	}
 	if (fromBayes)

README.md

@@ -13,8 +13,7 @@ Networks here are understood as entire (complete) networks, not as personal (ego
 it is assumed that a set of nodes (social actors) is given, and all ties (links) between these nodes are known - 
 except perhaps for a moderate amount of missing data.
 The name SIENA stands for Simulation Investigation for Empirical Network Analysis.
-The R package is called RSiena; there also is the development package RSienaTest,
-available from R-Forge.
+The R package is called RSiena.
 
 ## Installation
 
@@ -105,7 +104,7 @@ The development version of RSiena can be similarly installed as:
 
 To cite the RSiena package in publications use:
 
-> Ruth M. Ripley, Tom A. B. Snijders, Zsofia Boda, Andras Voros, and Paulina Preciado(2023). Manual
+> Ruth M. Ripley, Tom A. B. Snijders, Zsofia Boda, Andras Voros, and Paulina Preciado (2023). Manual
 > for Siena version 4.0. R package version 1.3.19.
 > https://www.cran.r-project.org/web/packages/RSiena/.
 
@@ -117,7 +116,7 @@ A BibTeX entry for LaTeX users is
   author = {Ruth M. Ripley and Tom A. B. Snijders and Zsofia B'{o}da and Andr'{a}s V"{o}r"{o}s and Paulina Preciado},
   year = {2023},
   institution = {Oxford: University of Oxford, Department of Statistics; Nuffield College},
-  note = {R package version 1.3.19. https://www.cran.r-project.org/web/packages/RSiena/},
+  note = {R package version 1.3.22. https://www.cran.r-project.org/web/packages/RSiena/},
 }
 ```