From noreply at r-forge.r-project.org  Tue Jul 13 16:53:29 2021
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 13 Jul 2021 16:53:29 +0200 (CEST)
Subject: [Rsiena-commits] r354 - in pkg/RSienaTest: . R man
Message-ID: <20210713145329.6828A180836@r-forge.r-project.org>

Author: tomsnijders
Date: 2021-07-13 16:53:29 +0200 (Tue, 13 Jul 2021)
New Revision: 354

Modified:
   pkg/RSienaTest/ChangeLog
   pkg/RSienaTest/DESCRIPTION
   pkg/RSienaTest/R/sienaBayes.r
   pkg/RSienaTest/man/RSiena-package.Rd
   pkg/RSienaTest/man/extract.sienaBayes.Rd
Log:
RSienaTest new version

Modified: pkg/RSienaTest/ChangeLog
===================================================================
--- pkg/RSienaTest/ChangeLog	2021-04-14 15:46:25 UTC (rev 353)
+++ pkg/RSienaTest/ChangeLog	2021-07-13 14:53:29 UTC (rev 354)
@@ -1,3 +1,8 @@
+2021-07-13 R-Forge Revision 354, package version 1.2-30.
+Changes in RSienaTest:
+   * sienaBayes: adaptation of nwarm and nmain 
+     at the end of initializeBayes dropped.
+
 2021-04-14 R-Forge Revision 353, package version 1.2-29.
 Changes in RSienaTest:
    * sienaBayes: break out of prewarming if in 2 consecutive steps

Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION	2021-04-14 15:46:25 UTC (rev 353)
+++ pkg/RSienaTest/DESCRIPTION	2021-07-13 14:53:29 UTC (rev 354)
@@ -2,8 +2,8 @@
 Package: RSienaTest
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.2-29
-Date: 2021-04-14
+Version: 1.2-30
+Date: 2021-07-13
 Authors at R: c(person("Tom", "Snijders", role = c("cre", "aut"), email = "tom.snijders at nuffield.ox.ac.uk", comment = c(ORCID = "0000-0003-3157-4157")),
               person("Christian", "Steglich", role = c("aut","ctb"), comment = c(ORCID = "0000-0002-9097-0873")),
               person("Johan", "Koskinen", role = c("aut","ctb"), comment = c(ORCID = "0000-0002-6860-325X")),

Modified: pkg/RSienaTest/R/sienaBayes.r
===================================================================
--- pkg/RSienaTest/R/sienaBayes.r	2021-04-14 15:46:25 UTC (rev 353)
+++ pkg/RSienaTest/R/sienaBayes.r	2021-07-13 14:53:29 UTC (rev 354)
@@ -160,9 +160,9 @@
 		}
 		else
 		{
-			desired <- c(rep(trunc(target[1]*totruns), z$nGroup), 
+			desired <- c(rep(trunc(target[1]*totruns), z$nGroup),
 						rep(trunc(target[2]*totruns), 2))
-		}		
+		}
 		iter <- 0
 		nearGoal <- rep(FALSE, z$nGroup+2)
 		farFromGoal <- rep(TRUE, z$nGroup+2)
@@ -782,7 +782,7 @@
 		}
 
 	##@averageTheta internal sienaBayes; algorithm to average past theta values
-	averageTheta <- function()
+	averageTheta <- function(z)
 	{
 		thetaMean <- rep(NA, z$pp)
 		for (group in 1:z$nGroup)
@@ -791,7 +791,7 @@
 				z$ThinParameters[, group, !z$generalParametersInGroup,
 						drop=FALSE], na.rm=TRUE)
 		}
-		if ((priorRatesFromData <0) | incidentalBasicRates)
+		if ((z$priorRatesFromData <0) | z$incidentalBasicRates)
 		{
 		# then (z$set1)&(!z$basicRate) == (z$set1); just for clarity we write:
 		thetaMean[(z$set1)&(!z$basicRate)] <- colMeans(
@@ -826,7 +826,7 @@
 		}
 		else
 		{
-			z$theta <<- averageTheta()
+			z$theta <<- averageTheta(z)
 		}
 		save(z,file="PartialBayesResult.RData")
 		z$theta <<- saveTheta
@@ -1259,7 +1259,7 @@
 			scf <- (2.38^2)/z$TruNumPars
 # theoretically optimal value according to Roberts & Rosenthal, 2001
 # Also see page 99 (in chapter by Rosenthal) of the Chapman & Hall
-# Handbook of Markov Chain Monte Carlo, 2011. 
+# Handbook of Markov Chain Monte Carlo, 2011.
 # Until RSienaTest version 1.2-25, the scale factors were initialized
 # at 2.38/sqrt(z$TruNumPars); but this should be (2.38^2)/z$TruNumPars,
 # because they are applied to the variance.
@@ -1453,7 +1453,7 @@
 	}
 	else
 	{
-		z$theta <- averageTheta()
+		z$theta <- averageTheta(z)
 	}
 	z$frequentist <- frequentist
 	z$FRAN <- NULL
@@ -1975,7 +1975,7 @@
 	startupPrec <- prec[objective, objective]
 	priorPrec <- matrix(0, sum(objective), sum(objective))
 	diag(priorPrec) <- 0.01 # a prior variance of 100 if nothing else is said
-# In the following line, up to version 1.2-25, the ginv was missing!!!	
+# In the following line, up to version 1.2-25, the ginv was missing!!!
 	priorPrec[randomInObjective, randomInObjective] <-
 				ginv(z$priorSigma[objectiveInRandom, objectiveInRandom])
 	for (i in seq(along=z$set2prior))
@@ -2215,7 +2215,7 @@
 		z$TruNumPars <- sum(!z$basicRate )
 	}
 	scf <- (2.38^2)/z$TruNumPars
-# theoretically optimal value according to Roberts & Rosenthal, 2001; 
+# theoretically optimal value according to Roberts & Rosenthal, 2001;
 # also see earlier occurrence of 2.38.
 	z$scaleFactors <- rep(scf, z$nGroup)
 	if (z$p2 > 0)
@@ -2369,28 +2369,29 @@
 		lengthPhase1 <- round(nmain/5)
 		lengthPhase3 <- round(nmain/5)
 	}
-	if ((nwarm + lengthPhase1 + 5 + lengthPhase3) > nmain)
-	{
-		nwarm <- max(5,
-			round(nwarm*nmain/(nwarm + 2*lengthPhase1+lengthPhase3)))
-		oldLengthPhase1 <- lengthPhase1
-		lengthPhase1 <- max(5,
-			round(lengthPhase1*nmain/(nwarm + 2*lengthPhase1+lengthPhase3)))
-		lengthPhase3 <- max(5,
-			round(lengthPhase3*nmain/(nwarm + 2*oldLengthPhase1+lengthPhase3)))
-		nmain <<- nwarm + 2*lengthPhase1 + lengthPhase3
-		cat("Iteration numbers adapted:\n")
-		cat("nwarm = ", nwarm, "; nmain = ", nmain)
-		if (frequentist)
-		{
-			cat(", lengthPhase1 = ", lengthPhase1,
-				"; lengthPhase3 = ", lengthPhase3, ".\n")
-		}
-		else
-		{
-			cat(".\n")
-		}
-	}
+# adaptation of nwarn and nmain skipped version
+#	if ((nwarm + lengthPhase1 + 5 + lengthPhase3) > nmain)
+#	{
+#		nwarm <- max(5,
+#			round(nwarm*nmain/(nwarm + 2*lengthPhase1+lengthPhase3)))
+#		oldLengthPhase1 <- lengthPhase1
+#		lengthPhase1 <- max(5,
+#			round(lengthPhase1*nmain/(nwarm + 2*lengthPhase1+lengthPhase3)))
+#		lengthPhase3 <- max(5,
+#			round(lengthPhase3*nmain/(nwarm + 2*oldLengthPhase1+lengthPhase3)))
+#		nmain <<- nwarm + 2*lengthPhase1 + lengthPhase3
+#		cat("Iteration numbers adapted:\n")
+#		cat("nwarm = ", nwarm, "; nmain = ", nmain)
+#		if (frequentist)
+#		{
+#			cat(", lengthPhase1 = ", lengthPhase1,
+#				"; lengthPhase3 = ", lengthPhase3, ".\n")
+#		}
+#		else
+#		{
+#			cat(".\n")
+#		}
+#	}
 	z$nwarm <- nwarm
 	z$nprewarm <- nprewarm
 	z$nmain <- nmain

Modified: pkg/RSienaTest/man/RSiena-package.Rd
===================================================================
--- pkg/RSienaTest/man/RSiena-package.Rd	2021-04-14 15:46:25 UTC (rev 353)
+++ pkg/RSienaTest/man/RSiena-package.Rd	2021-07-13 14:53:29 UTC (rev 354)
@@ -14,10 +14,11 @@
 and multivariate networks are allowed.
 The models are stochastic actor-oriented models.
 
-Package \code{"RSienaTest"} is the development version, and
-is distributed through R-Forge, see
+Package \code{"RSienaTest"} has the extra functionality of function 
+\code{\link{sienaBayes}}, and is distributed through R-Forge, see
 \url{http://r-forge.r-project.org/R/?group_id=461}.
 Package \code{"RSiena"} is the official release.
+The 
 }
 \details{
   The main flow of operations of this package is as follows.
@@ -49,8 +50,8 @@
   \tabular{ll}{
     Package: \tab RSienaTest\cr
     Type: \tab Package\cr
-    Version: \tab 1.2-29\cr
-    Date: \tab 2021-04-14\cr
+    Version: \tab 1.2-30\cr
+    Date: \tab 2021-07-13\cr
     Depends: \tab R (>= 2.15.0)\cr
     Imports: \tab Matrix, lattice, parallel, MASS, methods\cr
     Suggests: \tab xtable, network, tools, codetools, utils, tcltk\cr

Modified: pkg/RSienaTest/man/extract.sienaBayes.Rd
===================================================================
--- pkg/RSienaTest/man/extract.sienaBayes.Rd	2021-04-14 15:46:25 UTC (rev 353)
+++ pkg/RSienaTest/man/extract.sienaBayes.Rd	2021-07-13 14:53:29 UTC (rev 354)
@@ -44,7 +44,7 @@
   \item{excludeRates}{Logical: whether to exclude the rate parameters.}
   \item{verbose}{Logical: gives some console output to show ongoing activity
        (may be reassuring for large number of groups).}
-}
+} 
 \details{
  \code{extract.sienaBayes} produces a 3-dimensional array, iterations by chains
  by parameters, suitable for use, e.g., in function \code{monitor()}
@@ -55,7 +55,7 @@
  \code{nSampRate}.\cr
  The number of iterations should be the same for all chains.\cr
  It is not checked that the specifications of the chains are identical.
- For the parameter names, the names in the first chain are used.
+ For the parameter names, the shortNames in the first chain are used.
 
  \code{extract.posteriorMeans} produces the posterior means of the
  groupwise varying parameters. The resulting matrix has the groups
@@ -68,7 +68,10 @@
   For \code{extract.posteriorMeans} a matrix with the groups in the rows
   and all effects in the columns, with for each effect two columns:
   first the posterior mean (effect name preceded by "p.m.") and then the
-  posterior standard deviation (effect name preceded by "psd.").
+  posterior standard deviation (effect name preceded by "psd.").\cr
+  If some names are duplicated (e.g., because of the presence of
+  evaluation and creation effects), these can be changed by the user
+  after creation of the array.
   }
 \references{See the manual and \url{http://www.stats.ox.ac.uk/~snijders/siena/}
 }