[Rsiena-commits] r204 - in pkg: RSiena RSiena/R RSiena/inst/doc RSiena/man RSiena/po RSiena/src/model RSiena/src/model/effects RSiena/src/model/ml RSiena/src/model/variables RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/inst/doc RSienaTest/man RSienaTest/po RSienaTest/src/model RSienaTest/src/model/effects RSienaTest/src/model/ml RSienaTest/src/model/variables
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 29 20:09:13 CET 2012
Author: ripleyrm
Date: 2012-02-29 20:09:12 +0100 (Wed, 29 Feb 2012)
New Revision: 204
Modified:
pkg/RSiena/DESCRIPTION
pkg/RSiena/R/bayes.r
pkg/RSiena/R/initializeFRAN.r
pkg/RSiena/R/phase3.r
pkg/RSiena/R/robmon.r
pkg/RSiena/R/siena08.r
pkg/RSiena/R/sienaDataCreate.r
pkg/RSiena/R/sienaprint.r
pkg/RSiena/R/simstatsc.r
pkg/RSiena/changeLog
pkg/RSiena/inst/doc/RSiena_Manual.pdf
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/po/R-RSiena.pot
pkg/RSiena/src/model/EpochSimulation.cpp
pkg/RSiena/src/model/effects/SimilarityEffect.cpp
pkg/RSiena/src/model/ml/Chain.cpp
pkg/RSiena/src/model/variables/NetworkVariable.cpp
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/bayes.r
pkg/RSienaTest/R/initializeFRAN.r
pkg/RSienaTest/R/phase3.r
pkg/RSienaTest/R/robmon.r
pkg/RSienaTest/R/siena08.r
pkg/RSienaTest/R/sienaDataCreate.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/R/simstatsc.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/RSiena_Manual.tex
pkg/RSienaTest/doc/missingsEtc.tex
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/po/R-RSienaTest.pot
pkg/RSienaTest/src/model/EpochSimulation.cpp
pkg/RSienaTest/src/model/effects/SimilarityEffect.cpp
pkg/RSienaTest/src/model/ml/Chain.cpp
pkg/RSienaTest/src/model/variables/NetworkVariable.cpp
Log:
Various bug fixes
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/DESCRIPTION 2012-02-29 19:09:12 UTC (rev 204)
@@ -1,8 +1,8 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.203
-Date: 2012-02-19
+Version: 1.0.12.204
+Date: 2012-02-29
Author: Various
Depends: R (>= 2.10.0)
Imports: Matrix
Modified: pkg/RSiena/R/bayes.r
===================================================================
--- pkg/RSiena/R/bayes.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/bayes.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -87,7 +87,7 @@
update <- number < 3
z$scaleFactors[update] <<- z$scaleFactors[update] * ans[update]
cat(actual, ans, z$scaleFactors, '\n')
- if (all(success) | iter == maxiter)
+ if (all(success) || iter == maxiter)
{
break
}
@@ -186,9 +186,9 @@
z$thetaMat <<- thetaNew
logpNew <- getProbabilitiesFromC(z)[[1]]
proposalProbability <- priorNew - priorOld + logpNew - logpOld
-##cat(proposalProbability, priorNew, priorOld, logpNew, logpOld, '\n')
-
- z$accept <<- log(runif(length(proposalProbability))) < proposalProbability
+ ##cat(proposalProbability, priorNew, priorOld, logpNew, logpOld, '\n')
+ z$accept <<- log(runif(length(proposalProbability))) <
+ proposalProbability
thetaOld[, z$basicRate] <- exp(thetaOld[, z$basicRate])
if (!change)
{
@@ -422,7 +422,7 @@
}
z$FRAN <- getFromNamespace(model$FRANname, pkgname)
z <- initializeFRAN(z, model, data=data, effects=effects,
- prevAns=prevAns, initC=FALSE)
+ prevAns=prevAns, initC=FALSE, onlyLoglik=TRUE)
z$basicRate <- z$effects$basicRate
z$nGroup <- z$f$nGroup
is.batch(TRUE)
Modified: pkg/RSiena/R/initializeFRAN.r
===================================================================
--- pkg/RSiena/R/initializeFRAN.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/initializeFRAN.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -137,6 +137,15 @@
requestedEffects$functionName <- effects[effects$requested,
"functionName"]
+ if (attr(data, "compositionChange"))
+ {
+ if (x$maxlike)
+ {
+ stop("Not possible to use maximum likelihood estimation ",
+ "with composition change")
+ }
+ }
+
## if not specified whether conditional or nor, set to conditional
## iff there is only one dependent variable (therefore number 1)
## and not maxlike
@@ -446,10 +455,9 @@
z$maxlikeTargets <- rowSums(ans)
z$maxlikeTargets2 <- ans
z$mult <- x$mult
- z$nrunMH <-
- z$mult * colSums(z$maxlikeTargets2[z$requestedEffects$basicRate,
- , drop=FALSE ])
- z$nrunMH < pmax(z$nrunMH, 2)
+ z$nrunMH <- floor(z$mult *
+ colSums(z$maxlikeTargets2[z$requestedEffects$basicRate,
+ , drop=FALSE ]))
## make the number pretty
z$nrunMH <- ifelse (z$nrunMH > 100,
round(z$nrunMH / 100) * 100, z$nrunMH)
@@ -489,7 +497,6 @@
simpleRates <- FALSE
}
z$simpleRates <- simpleRates
-
ans <- .Call("setupModelOptions", PACKAGE=pkgname,
pData, pModel, MAXDEGREE, CONDVAR, CONDTARGET,
profileData, z$parallelTesting, x$modelType, z$simpleRates)
@@ -522,20 +529,15 @@
{
z$prmib <- rep(0, length(nbrMissBeh))
}
- ## cat (z$prmin, z$prmib, "\n")
z$probs <- c(x$pridg, x$prcdg, x$prper, x$pripr, x$prdpr, x$prirms,
x$prdrms)
- ##cat(z$probs,"\n")
ans <- .Call("mlMakeChains", PACKAGE=pkgname, pData, pModel,
z$probs, z$prmin, z$prmib,
x$minimumPermutationLength,
x$maximumPermutationLength,
x$initialPermutationLength)
-
f$minimalChain <- ans[[1]]
f$chain <- ans[[2]]
- ## print(nrow(ans[[1]][[1]]))
- ## print(nrow(ans[[2]][[1]]))
}
else ## set up the initial chains in the sub processes
{
Modified: pkg/RSiena/R/phase3.r
===================================================================
--- pkg/RSiena/R/phase3.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/phase3.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -194,12 +194,12 @@
Report('Autocorrelations during phase 3 : \n', outf)
Report(paste(format(1:z$pp, width=3), '. ',
format(z$sfl, width=8, digits=4),
- '\n', collapse=""), outf)
+ '\n', collapse="", sep=""), outf)
Report ('\n', outf)
Report('Autocorrelations during phase 3 : \n', cf)
Report(paste(format(1:z$pp, width=3), '. ',
format(z$sfl, width=8, digits=4),
- '\n', collapse=""), cf)
+ '\n', collapse="", sep=""), cf)
Report ('\n', cf)
}
for (j in 1:z$pp)
Modified: pkg/RSiena/R/robmon.r
===================================================================
--- pkg/RSiena/R/robmon.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/robmon.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -69,6 +69,7 @@
{
stop("Not enough observations to use the nodes")
}
+ unlink("cluster.out")
if (clusterType == "FORK")
{
cl <- makeCluster(nbrNodes, type = clusterType,
Modified: pkg/RSiena/R/siena08.r
===================================================================
--- pkg/RSiena/R/siena08.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/siena08.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -651,7 +651,7 @@
"\nScore tests:\nFisher combination\n",
paste(rep("-", 65), collapse=""), "\n"), sep="", outf)
- by(x$thetadf, x$thetadf$effects, function(x, y)
+ invisible(by(x$thetadf, x$thetadf$effects, function(x, y)
{
i <- match(x$effects[1], effects)
y <- y[[effects[i]]]
@@ -676,7 +676,7 @@
" (d.f. = ", 2 * y$ns, "), ",
reportp(y$scoreminusp, 3), "\n"), sep="", outf)
}
- }, y=x)
+ }, y=x))
}
}
Modified: pkg/RSiena/R/sienaDataCreate.r
===================================================================
--- pkg/RSiena/R/sienaDataCreate.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/sienaDataCreate.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -409,12 +409,12 @@
vardims <- attr(dyvCovars[[i]], "vardims")
if (!validNodeSet(nattr[1], vardims[1]))
{
- stop('dyadic changing covariate incorrect nbr rows',
+ stop('dyadic changing covariate incorrect number of rows ',
names(dyvCovars)[i])
}
if (!validNodeSet(nattr[2], vardims[2]))
{
- stop('dyadic changing covariate incorrect nbr columns',
+ stop('dyadic changing covariate incorrect number of columns ',
names(dyvCovars)[i])
}
if (vardims[3] < (observations - 1))
Modified: pkg/RSiena/R/sienaprint.r
===================================================================
--- pkg/RSiena/R/sienaprint.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/sienaprint.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -296,7 +296,8 @@
{
if (is.na(x$cconditional) || !x$cconditional)
{
- cat(" Unconditional simulation\n")
+ cat(" Unconditional simulation if more than one dependent",
+ "variable\n")
}
else
{
Modified: pkg/RSiena/R/simstatsc.r
===================================================================
--- pkg/RSiena/R/simstatsc.r 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/R/simstatsc.r 2012-02-29 19:09:12 UTC (rev 204)
@@ -73,7 +73,7 @@
fromFiniteDiff, f$pModel, f$myeffects, z$theta,
randomseed2, returnDeps, z$FinDiff.method,
!is.null(z$cl) && useStreams, z$addChainToStore,
- returnChains, returnLoglik)
+ z$returnChains, returnLoglik)
if (!fromFiniteDiff)
{
if (z$FinDiff.method)
Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/changeLog 2012-02-29 19:09:12 UTC (rev 204)
@@ -1,3 +1,29 @@
+2012-02-29 R-forge revision 204
+
+ * src/model/effects/SimilarityEffect.cpp: fixed bugs in
+ endowment/creation statistics.
+ * src/model/ml/Chain.cpp: fixed bug causing failure in connect
+ with constraints
+ * src/model/EpochSimulation.cpp: allow for underflow of sigma2
+ when taking square root.
+ * src/model/variables/NetworkVariable.cpp: fix bug in creation and
+ endowment effect scores for pairwise symmetric network models.
+ * R/simstatsc.r: fix bug which stopped chains being returned
+ * R/sienaprint.r: amend model print
+ * R/sienaDataCreate.r: amend error message for incorrect dyadic
+ covariate.
+ * R/siena08.r: suppress printed NULLS at end of summary.
+ * R/robmon.r: remove cluster.out before using it again.
+ * R/phase3.r: change format of report of autocorrelations in phase
+ 3.
+ * R/initializeFRAN.r: forbid maximum likelihood estimation with
+ composition change, round calculation of number of MH steps.
+ * R/bayes.r: fix incorrect condition, allow to work with non
+ constant rates if a dfra is provided, minor reformatting.
+ * doc/missingEtc.tex: minor update.
+ * po/R-RSiena.pot, po/R-RSienaTest.pot: updated error message
+ files
+
2012-02-19 R-forge revision 203
* src/siena07setup.cpp: initialize permutation length correctly in
Modified: pkg/RSiena/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSiena/inst/doc/RSiena_Manual.pdf 2012-02-19 19:24:53 UTC (rev 203)
+++ pkg/RSiena/inst/doc/RSiena_Manual.pdf 2012-02-29 19:09:12 UTC (rev 204)
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[TRUNCATED]
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