[Rsiena-commits] r354 - in pkg/RSienaTest: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jul 13 16:53:29 CEST 2021
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/}
}
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