Merge pull request #113 from stocnet/develop

RSiena version 1.4.23

Author: TomSnijders

DESCRIPTION

@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.4.22
-Date: 2025-02-08
+Version: 1.4.23
+Date: 2025-05-03
 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 +1,33 @@
+# RSiena 1.4.23
+
+2025-05-03
+
+## Changes in RSiena:
+### Bug corrections
+  * Repaired (hopefully) memory leak in `getTargetActorStatistics` and 
+    `getTargetsChangeContributions` in `siena07setup.cpp`. 
+  * Repaired (hopefully) memory leak in `move` in `MLSimulation.cpp`. 
+  * Repaired memory leak  in `DoubleCovariateCatFunction`. 
+### Effects
+  * New effects `fromAny`, `sameInXCycle4`. 
+  * Effect shortName `cycle4ND` replaced by `cycle4`.
+  * Better treatment of missing covariate values in effect `sameXCycle4`. 
+  * Internal effect parameter values 3 and 4 for `sameXInPop`,`diffXInPop`,
+    `sameXInPopIntn`,  `sameXInActIntn`, `homXOutAct2`. 
+  * New C++ class `CatCovariateDependentNetworkEffect` (for `homXOutAct2`). 
+  * Added `(#)` to the `effectName` of `from`, `sameXInPop`, `diffXInPop`, 
+	`sameXVInPop`, `sameXVInPop2`.
+### New functionality
+  * In `print.sienaEffects(..., includeShortNames=TRUE)`, the `effectNumber`
+    is also printed.
+### Coding
+  * Class `Covariate` has new variable `covariateN`, which then is transferred
+    as `covarN` to `CovariateDependentNetworkEffect` and 
+    `DoubleCovariateFunction`. 
+### Changes in documentation:
+  * Definition of effects `outRateLog`, `inRateLog`, and `recipRateLog`
+    corrected in the manual.
+
 # RSiena 1.4.22
 
 2025-02-08

R/effects.r

@@ -1411,7 +1411,7 @@ getEffects <- function(x, nintn = 10, behNintn=4, getDocumentation=FALSE, onePer
 				covObjEffects[covObjEffects$shortName %in%
 				c("altX", "altSqX",  "altLThresholdX", "altRThresholdX",
 					"homXOutAct", "homXOutAct2", "altXOutAct",
-					"inActX", "outActX"), ]
+					"inActX", "outActX", "sameInXCycle4"), ]
 			if (!tr & (!moreThan2))
 			{
 				covObjEffects <-

R/effectsMethods.r

@@ -50,8 +50,9 @@ print.sienaEffects <- function(x, fileName=NULL, includeOnly=TRUE,
         timeDummies <- !x$timeDummy[x$include] == ","
 		if (includeShortNames)
 		{
-			specs <- as.data.frame(x[, c("name", "effectName", "shortName", "include", "fix",
-                "test", "initialValue", "parm")])		
+			specs <- as.data.frame(x[, c("effectNumber", "name", "effectName", 
+				"shortName", "include", "fix",
+                "test", "initialValue", "parm")])	
 		}
 		else
 		{
@@ -77,7 +78,8 @@ print.sienaEffects <- function(x, fileName=NULL, includeOnly=TRUE,
         }
         if (nDependents == 1)
         {
-            specs <- specs[, -1]  # drop name of dependent variable
+			whichname <- which(names(specs)=="name")
+            specs <- specs[, -whichname]  # drop name of dependent variable
         }
         if (any(endowments))
         {

R/sienaRI.r

@@ -45,6 +45,8 @@ sienaRI <- function(data, ans=NULL, theta=NULL, algorithm=NULL, effects=NULL,
 		contributions <- getChangeContributions(algorithm = ans$x, data = data,
 			effects = ans$effects)
 		# contributions[[1]] is periods by effects by actors by actors
+#cat("a\n")
+#browser()
 		RI <- expectedRelativeImportance(conts = contributions,
 			effects = ans$effects, theta =ans$theta, thedata=data,
 			getChangeStatistics=getChangeStats)
@@ -157,6 +159,9 @@ getChangeContributions <- function(algorithm, data, effects)
 	for(i in 1:length(myeffectsOrder)){
 		myeffects[[i]]<-tmpeffects[[myeffectsOrder[i]]]
 	}
+#cat("e\n") #Hier gaat hij fout. 
+# Voor returnStaticChangeContributions=TRUE gaat het wel goed.
+#browser()
 	ans <- .Call(C_getTargets, PACKAGE=pkgname, pData, pModel, myeffects,
 		parallelrun=TRUE, returnActorStatistics=FALSE,
 		returnStaticChangeContributions=TRUE)
@@ -282,6 +287,9 @@ message('\nNote that for symmetric networks, effect sizes are for modelType 2 (f
 					cdec <- array(cdec, dim=c(1,dim(cdec)))
 				}
 ##
+
+#cat("b\n")
+#browser()
 				rownames(cdec) <- effectNa[currentDepEffs]
 				if (getChangeStatistics)
 				{

R/sienaeffects.r

@@ -42,6 +42,10 @@ includeEffects <- function(myeff, ..., include=TRUE, name=myeff$name[1],
 	{
 		stop("Effect AltsAvAlt now is called avXAlt. Use the new name please.")
 	}
+	if ("cycle4ND" %in% effectNames)
+	{
+		stop("Effect cycle4ND now is called cycle4. Use the new name please.")
+	}
 	use <- myeff$shortName %in% effectNames &
 	myeff$type==type &
 	myeff$name==name &
@@ -265,7 +269,6 @@ includeInteraction <- function(myeff, ...,
 			intn[effect3] <- TRUE
 		}
 		myeff2 <- myeff[intn,]	
-		myeff2$effectName <- paste(which(intn), myeff2$effectName)
 		print.sienaEffects(myeff2, includeOnly=FALSE, includeRandoms=random,
 								includeShortNames=TRUE)
 	}