[Rsiena-commits] r251 - in pkg: RSiena RSiena/R RSiena/data RSiena/inst/doc RSiena/man RSiena/src RSiena/src/model RSiena/src/model/effects RSiena/src/model/effects/generic RSiena/src/model/tables RSiena/src/model/variables RSiena/src/network RSiena/src/network/iterators RSiena/src/network/layers RSiena/src/utils RSienaTest RSienaTest/R RSienaTest/data RSienaTest/inst/doc RSienaTest/man RSienaTest/src/model/effects RSienaTest/src/model/effects/generic RSienaTest/src/model/tables
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 14 00:03:26 CET 2014
Author: tomsnijders
Date: 2014-02-14 00:03:20 +0100 (Fri, 14 Feb 2014)
New Revision: 251
Added:
pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.cpp
pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.h
pkg/RSiena/src/model/effects/generic/HomCovariateMixedTwopathFunction.cpp
pkg/RSiena/src/model/effects/generic/HomCovariateMixedTwopathFunction.h
pkg/RSiena/src/model/effects/generic/MixedInStarFunction.cpp
pkg/RSiena/src/model/effects/generic/MixedInStarFunction.h
pkg/RSiena/src/model/effects/generic/SumFunction.cpp
pkg/RSiena/src/model/effects/generic/SumFunction.h
pkg/RSiena/src/network/INetworkChangeListener.h
pkg/RSiena/src/network/iterators/
pkg/RSiena/src/network/iterators/CombinedTieIterator.cpp
pkg/RSiena/src/network/iterators/CombinedTieIterator.h
pkg/RSiena/src/network/iterators/ITieIterator.h
pkg/RSiena/src/network/iterators/IntersectionTieIterator.cpp
pkg/RSiena/src/network/iterators/IntersectionTieIterator.h
pkg/RSiena/src/network/iterators/SymDiffTieIterator.cpp
pkg/RSiena/src/network/iterators/SymDiffTieIterator.h
pkg/RSiena/src/network/iterators/UnionTieIterator.cpp
pkg/RSiena/src/network/iterators/UnionTieIterator.h
pkg/RSiena/src/network/layers/
pkg/RSiena/src/network/layers/DistanceTwoLayer.cpp
pkg/RSiena/src/network/layers/DistanceTwoLayer.h
pkg/RSiena/src/network/layers/NetworkLayer.h
pkg/RSienaTest/src/model/effects/HomCovariateTransitiveTripletseffect.cpp
pkg/RSienaTest/src/model/effects/HomCovariateTransitiveTripletseffect.h
pkg/RSienaTest/src/model/effects/generic/HomCovariateMixedTwopathFunction.cpp
pkg/RSienaTest/src/model/effects/generic/HomCovariateMixedTwopathFunction.h
pkg/RSienaTest/src/model/effects/generic/MixedInStarFunction.cpp
pkg/RSienaTest/src/model/effects/generic/MixedInStarFunction.h
pkg/RSienaTest/src/model/effects/generic/SumFunction.cpp
pkg/RSienaTest/src/model/effects/generic/SumFunction.h
Modified:
pkg/RSiena/DESCRIPTION
pkg/RSiena/R/effects.r
pkg/RSiena/R/effectsMethods.r
pkg/RSiena/R/sienaGOF.r
pkg/RSiena/R/sienaeffects.r
pkg/RSiena/R/sienaprint.r
pkg/RSiena/changeLog
pkg/RSiena/data/allEffects.csv
pkg/RSiena/inst/doc/RSiena.bib
pkg/RSiena/inst/doc/RSiena_Manual.pdf
pkg/RSiena/inst/doc/RSiena_Manual.tex
pkg/RSiena/inst/doc/effects.pdf
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/man/Wald.Rd
pkg/RSiena/man/getEffects.Rd
pkg/RSiena/man/includeInteraction.Rd
pkg/RSiena/man/print.sienaEffects.Rd
pkg/RSiena/man/setEffect.Rd
pkg/RSiena/man/siena07.Rd
pkg/RSiena/man/siena08.Rd
pkg/RSiena/man/sienaFit.Rd
pkg/RSiena/man/sienaGOF-auxiliary.Rd
pkg/RSiena/man/sienaGOF.Rd
pkg/RSiena/src/model/StatisticCalculator.cpp
pkg/RSiena/src/model/effects/AllEffects.h
pkg/RSiena/src/model/effects/EffectFactory.cpp
pkg/RSiena/src/model/effects/FourCyclesEffect.cpp
pkg/RSiena/src/model/effects/FourCyclesEffect.h
pkg/RSiena/src/model/effects/StructuralRateEffect.cpp
pkg/RSiena/src/model/effects/StructuralRateEffect.h
pkg/RSiena/src/model/effects/generic/GwespFunction.cpp
pkg/RSiena/src/model/effects/generic/GwespFunction.h
pkg/RSiena/src/model/tables/TwoNetworkCache.cpp
pkg/RSiena/src/model/tables/TwoNetworkCache.h
pkg/RSiena/src/model/variables/DependentVariable.cpp
pkg/RSiena/src/model/variables/DependentVariable.h
pkg/RSiena/src/network/CommonNeighborIterator.cpp
pkg/RSiena/src/network/CommonNeighborIterator.h
pkg/RSiena/src/network/IncidentTieIterator.cpp
pkg/RSiena/src/network/IncidentTieIterator.h
pkg/RSiena/src/network/Network.cpp
pkg/RSiena/src/network/Network.h
pkg/RSiena/src/network/OneModeNetwork.cpp
pkg/RSiena/src/network/OneModeNetwork.h
pkg/RSiena/src/siena07internals.cpp
pkg/RSiena/src/utils/Utils.cpp
pkg/RSiena/src/utils/Utils.h
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/effects.r
pkg/RSienaTest/R/effectsMethods.r
pkg/RSienaTest/R/print01Report.r
pkg/RSienaTest/R/siena07.r
pkg/RSienaTest/R/siena08.r
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/R/sienaGOF.r
pkg/RSienaTest/R/sienaeffects.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/data/allEffects.csv
pkg/RSienaTest/inst/doc/RSiena.bib
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/inst/doc/RSiena_Manual.tex
pkg/RSienaTest/inst/doc/effects.pdf
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/getEffects.Rd
pkg/RSienaTest/man/print.sienaEffects.Rd
pkg/RSienaTest/man/setEffect.Rd
pkg/RSienaTest/man/siena07.Rd
pkg/RSienaTest/man/siena08.Rd
pkg/RSienaTest/man/sienaBayes.Rd
pkg/RSienaTest/man/sienaFit.Rd
pkg/RSienaTest/man/sienaGOF-auxiliary.Rd
pkg/RSienaTest/man/sienaGOF.Rd
pkg/RSienaTest/src/model/effects/AllEffects.h
pkg/RSienaTest/src/model/effects/EffectFactory.cpp
pkg/RSienaTest/src/model/effects/FourCyclesEffect.cpp
pkg/RSienaTest/src/model/effects/FourCyclesEffect.h
pkg/RSienaTest/src/model/effects/generic/GwespFunction.cpp
pkg/RSienaTest/src/model/effects/generic/GwespFunction.h
pkg/RSienaTest/src/model/tables/TwoNetworkCache.cpp
pkg/RSienaTest/src/model/tables/TwoNetworkCache.h
Log:
Version 251, extensive updates, see changelog.
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/DESCRIPTION 2014-02-13 23:03:20 UTC (rev 251)
@@ -1,8 +1,8 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-250
-Date: 2013-12-04
+Version: 1.1-251
+Date: 2014-02-13
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders
Depends: R (>= 2.15.0)
Imports: Matrix
Modified: pkg/RSiena/R/effects.r
===================================================================
--- pkg/RSiena/R/effects.r 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/R/effects.r 2014-02-13 23:03:20 UTC (rev 251)
@@ -88,16 +88,6 @@
tmp
}
-##@addSettingseffects internal getEffects add effects for settings model
-addSettingsEffects <- function(effects)
-{
-depvar <- attr(effects, "depvar")
- ## This processes the settings (constant dyadic covariate) structure.
- ## Only for one-mode network.
- nbrSettings <- length(attr(depvar,"settings"))
- ## This leads to a warning in R CMD Check.
- ## Not important since this is just a stub, to be developed later.
-}
##@networkRateEffects internal getEffects create a set of rate effects
networkRateEffects <- function(depvar, varname, symmetric, bipartite)
{
@@ -333,6 +323,11 @@
rateEffects[1:noPeriods, "initialValue"] <- starts$startRate
rateEffects$basicRate[1:observations] <- TRUE
+ objEffects[objEffects$shortName == "density" &
+ objEffects$type == "eval",'randomEffects'] <- TRUE # added dec2013
+ objEffects[objEffects$shortName == "linear" &
+ objEffects$type == "eval",'randomEffects'] <- TRUE # added dec2013
+
objEffects$untrimmedValue <- rep(0, nrow(objEffects))
if (attr(depvar,'symmetric'))
{
Modified: pkg/RSiena/R/effectsMethods.r
===================================================================
--- pkg/RSiena/R/effectsMethods.r 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/R/effectsMethods.r 2014-02-13 23:03:20 UTC (rev 251)
@@ -11,7 +11,7 @@
## ****************************************************************************/
##@print.sienaEffects Methods
print.sienaEffects <- function(x, fileName=NULL, includeOnly=TRUE,
- expandDummies=FALSE, ...)
+ expandDummies=FALSE, includeRandoms = FALSE, ...)
{
if (!inherits(x, "sienaEffects"))
stop("not a legitimate Siena effects object")
@@ -44,6 +44,7 @@
nDependents <- length(unique(x$name))
userSpecifieds <- x$shortName[x$include] %in% c("unspInt", "behUnspInt")
endowments <- !x$type[x$include] %in% c("rate", "eval")
+ # includes creations
timeDummies <- !x$timeDummy[x$include] == ","
specs <- x[, c("name", "effectName", "include", "fix", "test",
"initialValue", "parm")]
@@ -71,6 +72,10 @@
specs <- cbind(specs, effect3=x[x$include, "effect3"])
}
}
+ if (includeRandoms)
+ {
+ specs <- cbind(specs, randomEffects=x[x$include, "randomEffects"])
+ }
specs[, "initialValue"] <- format(round(specs$initialValue,digits=5),
width=10)
if (nrow(specs) > 0)
Modified: pkg/RSiena/R/sienaGOF.r
===================================================================
--- pkg/RSiena/R/sienaGOF.r 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/R/sienaGOF.r 2014-02-13 23:03:20 UTC (rev 251)
@@ -22,6 +22,11 @@
require(MASS)
## require(Matrix)
## Check input
+ if (sienaFitObject$maxlike)
+ {
+ stop(
+ "sienaGOF can only operate on results from Method of Moments estimation.")
+ }
if (! sienaFitObject$returnDeps)
{
stop("You must instruct siena07 to return the simulated networks")
@@ -219,6 +224,7 @@
InvCovSimStats=a,
Rank=arank)
class(ret) <- "sienaGofTest"
+ attr(ret,"sienaFitName") <- deparse(substitute(sienaFitObject))
attr(ret,"auxiliaryStatisticName") <-
attr(obsStats,"auxiliaryStatisticName")
attr(ret, "key") <- plotKey
@@ -663,14 +669,15 @@
trellis.par.set("plot.symbol", plot.symbol)
panelFunction <- function(..., x=x, y=y, box.ratio){
- ind.lower = max( round(itns * perc/2), 1)
- ind.upper = round(itns * (1-perc/2))
- yperc.lower = sapply(1:ncol(sims), function(i)
+ ind.lower <- max( round(itns * perc/2), 1)
+ ind.upper <- round(itns * (1-perc/2))
+ yperc.lower <- sapply(1:ncol(sims), function(i)
sort(sims[,i])[ind.lower] )
- yperc.upper = sapply(1:ncol(sims), function(i)
+ yperc.upper <- sapply(1:ncol(sims), function(i)
sort(sims[,i])[ind.upper] )
if (violin) {
- panel.violin(x, y, box.ratio=box.ratio, col = "transparent", ...)
+ panel.violin(x, y, box.ratio=box.ratio, col = "transparent",
+ bw="nrd", ...)
}
panel.bwplot(x, y, box.ratio=.1, fill = "gray", ...)
panel.xyplot(xAxis, yperc.lower, lty=3, col = "gray", lwd=3, type="l",
@@ -799,8 +806,8 @@
# values in X to structural values in S
# X must have values 0, 1.
# NA values in X will be 0 in the result.
-changeToStructural <- function(X, S)
- {if (any(S >= 10, na.rm=TRUE))
+changeToStructural <- function(X, S) {
+ if (any(S >= 10, na.rm=TRUE))
{
S[is.na(S)] <- 0
S0 <- Matrix(S==10)
@@ -817,8 +824,7 @@
# for tie variables that have no structural values in SBefore.
# X must have values 0, 1.
# NA values in X or SBefore or SAfter will be 0 in the result.
-changeToNewStructural <- function(X, SBefore, SAfter)
- {
+changeToNewStructural <- function(X, SBefore, SAfter) {
SB <- Matrix(SBefore>=10)
SA <- Matrix(SAfter>=10)
if (any(SA>SB, na.rm=TRUE))
@@ -946,12 +952,10 @@
dimsOfDepVar<- attr(obsData[[groupName]]$depvars[[varName]], "netdims")
isbipartite <- (attr(obsData[[groupName]]$depvars[[varName]], "type")
=="bipartite")
-# sparseData may be dropped - if that's OK
-# sparseData <- (attr(obsData[[groupName]]$depvars[[varName]], "sparse"))
# For bipartite networks in package <network>,
# the number of nodes is equal to
# the number of actors (rows) plus the number of events (columns)
- # with all actors preceeding all events.
+ # with all actors preceding all events.
# Therefore the bipartiteOffset will come in handy:
bipartiteOffset <- ifelse (isbipartite, 1 + dimsOfDepVar[1], 1)
@@ -977,10 +981,17 @@
# the 1 in the 3d column of cbind below is redundant
# because of the default ignore.eval=TRUE in network.edgelist.
# But it is good to be explicit.
+ if (sum(matrixNetwork) <= 0) # else network.edgelist() below will not work
+ {
+ returnValue <- emptyNetwork
+ }
+ else
+ {
returnValue <- network.edgelist(
cbind(sparseMatrixNetwork at i + 1,
sparseMatrixNetwork at j + bipartiteOffset, 1),
emptyNetwork)
+ }
returnValue
}
Modified: pkg/RSiena/R/sienaeffects.r
===================================================================
--- pkg/RSiena/R/sienaeffects.r 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/R/sienaeffects.r 2014-02-13 23:03:20 UTC (rev 251)
@@ -218,7 +218,8 @@
##@setEffect DataCreate
setEffect <- function(myeff, shortName, parameter=0,
- fix=FALSE, test=FALSE, initialValue=0,
+ fix=FALSE, test=FALSE, random=FALSE,
+ initialValue=0,
timeDummy=",",
include=TRUE, name=myeff$name[1],
type="eval", interaction1="", interaction2="",
@@ -236,7 +237,7 @@
myeff$interaction2 == interaction2 &
(is.na(myeff$period) | myeff$period == period) &
myeff$group == group
- if (shortName == "unspInt")
+ if (shortName %in% c("unspInt", "behUnspInt"))
{
use <- use & (myeff$include) & (myeff$effect1 == effect1) &
(myeff$effect2 == effect2) & (myeff$effect3 == effect3)
@@ -249,7 +250,7 @@
cat(paste("interaction2 = <",interaction2,">, ", sep=""))
cat(paste("type = <",type,">, ", sep=""))
cat(paste("period = <",period,">, ", sep=""))
- if (shortName == "unspInt")
+ if (shortName %in% c("unspInt", "behUnspInt"))
{
cat(paste("effects1-2-3 = <",effect1, effect2, effect3,">,", sep=" "))
}
@@ -267,10 +268,10 @@
myeff[use, "test"] <- test
myeff[use, "initialValue"] <- initialValue
myeff[use, "timeDummy"] <- timeDummy
+ myeff[use, "randomEffects"] <- random
# print.data.frame(myeff[use, c("name", "shortName", "type", "interaction1",
# "interaction2", "include", "parm", "fix", "test",
# "initialValue", "timeDummy", "period", "group")])
- print.sienaEffects(myeff[use,])
-
+ print.sienaEffects(myeff[use,], includeRandoms = random)
myeff
}
Modified: pkg/RSiena/R/sienaprint.r
===================================================================
--- pkg/RSiena/R/sienaprint.r 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/R/sienaprint.r 2014-02-13 23:03:20 UTC (rev 251)
@@ -73,10 +73,13 @@
mymat <- matrix("", 7, 2)
mymat[1,] <- c("Dependent variable", attr(xj, "name"))
mymat[2,] <- c("Type", attr(xj, "type"))
+ if (attr(xj,"type") == "oneMode")
+ {
if (attr(xj,"symmetric"))
{
mymat[2,2] <- c(mymat[2,2],", symmetric")
}
+ }
mymat[3,] <- c("Observations", attr(xj, "netdims")[3])
if (attr(xj, "type") == "bipartite")
{
@@ -276,12 +279,12 @@
cat('\nEstimated means and standard deviations, standard errors of the mean \n')
dmsf <- diag(x$msf)
mean.stats <- colMeans(x$sf) + x$targets
-# cov.dev may be droppec - just for now (07-10-13) I keep it in
+# cov.dev may be dropped - just for now (07-10-13) I keep it in
# cov.dev <- x$msf
sem <- sqrt(dmsf/dim(x$sf)[1])
if (x$x$dolby)
{
- scores <- apply(x$ssc, c(1,3), sum) # z$nit by z$pp matrix
+ scores <- apply(x$ssc, c(1,3), sum) # x$nit by x$pp matrix
mean.scores <- colMeans(scores)
mean.stats <- mean.stats - (x$regrCoef * mean.scores)
sem <- sem*sqrt(1 - (x$regrCor)^2)
@@ -515,10 +518,17 @@
invisible(x)
}
##@sienaFitThetaTable Miscellaneous
-sienaFitThetaTable <- function(x, tstat=FALSE)
+sienaFitThetaTable <- function(x, fromBayes=FALSE, tstat=FALSE)
{
- effects <- x$requestedEffects
+ theEffects <- x$requestedEffects
+ if (fromBayes)
+ {
+ pp <- x$TruNumPars
+ }
+ else
+{
pp <- x$pp
+ }
if (x$cconditional)
{
nrates <- length(x$rate)
@@ -527,6 +537,7 @@
{
nrates <- 0
}
+ xp <- pp
pp <- pp + nrates
## mydf stores the data before formatting
mydf <- data.frame(dummy=rep(" ", pp),
@@ -607,7 +618,7 @@
if (nBehavs > 0)
{
- behEffects <- effects[effects$netType == 'behavior',]
+ behEffects <- theEffects[theEffects$netType == 'behavior',]
behNames <- unique(behEffects$name)
}
if (nBehavs > 1)
@@ -617,27 +628,27 @@
behNames)],
'> ', behEffects$effectName,
sep='')
- effects$effectName[effects$netType=='behavior'] <-
+ theEffects$effectName[theEffects$netType=='behavior'] <-
behEffects$effectName
}
- mydf[nrates + (1:x$pp), 'row'] <- 1:x$pp
- mydf[nrates + (1:x$pp), 'type' ] <- ifelse(effects$type == "creation",
- "creat", effects$type)
- mydf[nrates + (1:x$pp), 'text' ] <- effects$effectName
- mydf[nrates + (1:x$pp), 'value' ] <- theta
+ mydf[nrates + (1:xp), 'row'] <- 1:xp
+ mydf[nrates + (1:xp), 'type' ] <- ifelse(theEffects$type == "creation",
+ "creat", theEffects$type)
+ mydf[nrates + (1:xp), 'text' ] <- theEffects$effectName
+ mydf[nrates + (1:xp), 'value' ] <- theta
if (exists("ses"))
{
- mydf[nrates + (1:x$pp), 'se' ] <- ses
+ mydf[nrates + (1:xp), 'se' ] <- ses
}
if (!is.null(x$tstat))
{
mydf[1:nrates, "tstat"] <- NA
- mydf[nrates + (1:x$pp), 'tstat' ] <- x$tstat
+ mydf[nrates + (1:xp), 'tstat' ] <- x$tstat
}
if (nBehavs > 0 && nNetworks > 0)
{
- nNetworkEff <- nrow(effects) - nrow(behEffects)
+ nNetworkEff <- nrow(theEffects) - nrow(behEffects)
addtorow$command[addsub] <-
'Behavior Dynamics'
addtorow$pos[[addsub]] <- nrates + 2 + nNetworkEff
@@ -758,19 +769,24 @@
x$requestedEffects[x$requestedEffects$groupName==name1,]
x$pp <- length(x$theta)
x$fixed <- x$fixed[x$effects$groupName==name1]
- tmp <- sienaFitThetaTable(x)
+ tmp <- sienaFitThetaTable(x, fromBayes=TRUE)
mydf <- tmp$mydf
mymat <- as.matrix(mydf[,names(mydf)!="tstat"])
+ mynames <- colnames(mymat)
+ mymat <- cbind(mymat, rep.int(NA, dim(mymat)[1]))
+ colnames(mymat) <- c(mynames, 'random')
mymat[, 'value'] <- format(round(mydf$value, digits=4))
mymat[, 'se'] <- format(round(mydf$se, digits=4))
+ mymat[, 'random'] <-
+ ifelse(x$requestedEffects$randomEffects, " + ", " - ")
mymat[, 'type'] <- format(mymat[, 'type'])
mymat[, 'text'] <- format(mymat[, 'text'])
mymat[mydf$row < 1, 'row'] <-
format(mydf[mydf$row < 1, 'row'])
mymat[mydf[,'row'] >= 1, 'row'] <-
paste(format(mydf[mydf$row >= 1, 'row']), '.', sep='')
- mymat <- rbind(c(rep("", 4), "Post. ", "", "Post. ", ""),
- c(rep("", 4), "mean ", "", "s.d. ", ""),
+ mymat <- rbind(c(rep("", 4), "Post. ", "", "Post. ", "", "varying"),
+ c(rep("", 4), "mean ", "", "s.d. ", "", ""),
mymat)
mymat <- apply(mymat, 2, format)
tmp1 <- apply(mymat, 1, function(x) paste(x, collapse=" "))
@@ -822,17 +838,34 @@
else
{
cat("for global mean parameters\n\n")
- nmain <- dim(x$ThinPosteriorMu)[1]
+ ntot <- dim(x$ThinPosteriorMu)[1]
if (x$frequentist)
{
- first <- nmain - x$lengthPhase3 + 1
+ first <- x$nwarm + x$nmain - x$lengthPhase3 + 1
}
else
{
- first <- 1
+ first <- x$nwarm + 1
}
- x$theta <- colMeans(x$ThinPosteriorMu[first:nmain,])
- x$covtheta <- cov(x$ThinPosteriorMu)
+
+ if (ntot < x$nwarm + x$nmain)
+ {
+ cat("This object resulted from an intermediate save, after",
+ ntot, "MCMC runs.\n")
+ }
+ if (ntot > first+2)
+ {
+ cat("Posterior means and standard deviations are averages over",
+ ntot - first + 1, "MCMC runs (counted after thinning).\n\n")
+# x$theta <- c(colMeans(x$ThinPosteriorMu[first:ntot,]),
+# colMeans(x$ThinPosteriorEta[first:ntot,, drop=FALSE]))
+# x$covtheta <- cov(cbind(x$ThinPosteriorMu[first:ntot,],
+# x$ThinPosteriorEta[first:ntot,]))
+ }
+ else
+ {
+ stop("This object did not come beyond the warming phase.\n")
+ }
}
tmps <- makeTemp(x)
tmp <- tmps[[1]]
@@ -857,16 +890,29 @@
if (length(x$f$groupNames) > 1)
{
cat("\n")
+ if (x$frequentist)
+ {
+ mean.Sigma <- x$Sigma
+ cat("Estimated covariance matrix (varying parameters)\n")
+ }
+ else
+ {
mean.Sigma <-
- apply(x$ThinPosteriorSigma[first:nmain,,], c(2,3), mean)
- sd.Sigma <- apply(x$ThinPosteriorSigma[first:nmain,,], c(2,3), sd)
- cat("Posterior mean of global covariance matrix\n")
+ apply(x$ThinPosteriorSigma[first:ntot,,], c(2,3), mean)
+ sd.Sigma <-
+ apply(x$ThinPosteriorSigma[first:ntot,,], c(2,3), sd)
+ cat("Posterior mean of global covariance matrix (varying parameters)\n")
+ }
printmat(mean.Sigma)
+ if (!x$frequentist)
+ {
cat("\nPosterior standard deviations of ")
cat("elements of global covariance matrix\n")
printmat(sd.Sigma)
}
- cat("\nTotal of", dim(x$ThinPosteriorMu)[1], "samples.\n\n")
+ }
+# cat("\nTotal of", ntot-nfirst+1, "samples.\n\n")
+ cat("\n")
}
invisible(x)
}
@@ -884,19 +930,23 @@
##@print.summary.sienaBayesFit Methods
print.summary.sienaBayesFit <- function(x, ...)
{
+# Still to do: quantile(x$ThinPosteriorSigma, probs=c(0.025, 0.5, 0.975))
+# etcetera
if (!inherits(x, "summary.sienaBayesFit"))
{
stop("not a legitimate summary of a Siena Bayes model fit")
}
- nmain <- dim(x$ThinPosteriorMu)[1]
+ ntot <- dim(x$ThinPosteriorMu)[1]
+
if (x$frequentist)
{
cat("Frequentist estimation.\n")
- first <- nmain - x$lengthPhase3 + 1
+ first <- x$nwarm + x$nmain - x$lengthPhase3 + 1
}
else
{
- first <- 1
+ cat("Bayesian estimation.\n")
+ first <- x$nwarm + 1
cat("Prior distribution:\n")
cat("\nMu ")
for (i in seq(along=x$priorMu))
@@ -913,11 +963,46 @@
{
cat("\nKappa ",sprintf("%8.4f", x$priorKappa),"\n")
}
- cat("\nFor the basic rate parameters, ")
- cat("the prior is on the square root scale.\n\n")
+# cat("\nFor the basic rate parameters, ")
+# cat("the prior is on the square root scale.\n\n")
}
+ if (x$incidentalBasicRates)
+ {
+ cat("\nBasic rates parameters are treated as incidental parameters.\n\n")
+ }
+ cat("\nAlgorithm specifications were nwarm =",x$nwarm,", nmain =", x$nmain,
+ ", nrunMHBatches =", x$nrunMHBatches, ".\n")
+ if (ntot < x$nwarm + x$nmain)
+ {
+ cat("This object resulted from an intermediate save, after",
+ ntot, " MCMC runs.")
+ }
+ if (x$frequentist)
+ {
+ cat("Lengths of phases were:\n")
+ cat("Phase 1:", x$lengthPhase1, ", phase 2:",
+ x$nmain - x$lengthPhase3 - x$lengthPhase1,
+ ", phase 3:", x$lengthPhase1, ".\n")
+ cat("Posterior means and standard deviations are")
+ cat(" averages over phase 3.\n\n")
+ }
+ else
+ {
+ cat("Posterior means and standard deviations are averages over")
+ cat(" the last", ntot - first + 1, "runs.\n\n")
+ }
+ if (ntot > first+2)
+ {
+ cat("Proportion of acceptances in MCMC proposals after warming up:\n")
+ cat(sprintf("%4.2f",
+ colMeans(x$ThinBayesAcceptances[first:ntot,])/x$nrunMHBatches),
+ fill=TRUE,"\n")
+ cat("This should ideally be close to 0.25.\n")
+ }
print.sienaBayesFit(x)
+ if (ntot > first+2)
+ {
cat("Posterior means and standard deviations per group\n")
for (i in 1:length(x$f$groupNames))
{
@@ -925,8 +1010,8 @@
# Make temporary changes to make x look like a sienaFit object
# so that sienaFitThetaTable can be applied.
# This is done in function makeTemp.
- x$theta <- colMeans(x$ThinParameters[first:nmain,i,])
- x$covtheta <- cov(x$ThinParameters[first:nmain,i,])
+ x$theta <- colMeans(x$ThinParameters[first:ntot,i,])
+ x$covtheta <- cov(x$ThinParameters[first:ntot,i,])
tmps <- makeTemp(x)
tmp <- tmps[[1]]
tmp1 <- tmps[[2]]
@@ -946,6 +1031,7 @@
}
}
cat(tmp1[i], '\n')
+ }
}
}
invisible(x)
Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/changeLog 2014-02-13 23:03:20 UTC (rev 251)
@@ -1,3 +1,36 @@
+2014-02-13 R-Forge Revision 251
+Changes in RSiena and RSienaTest:
+ * Also cater for behavior user-specified interactions in includeInteraction
+ and setEffect (sienaeffects.r).
+ * New effects: "cl.XWX", "homXTransTrip", "homWXClosure", and "sharedPop".
+ * Effect "cycle4" extended to non-directed one-mode networks
+ * (for directed one-mode networks it is "sharedPop").
+ * Effects "gwesp.." modified; extended to non-directed networks.
+ * Correction: Effect "to" is not a dyadic effect (allEffects.csv)
+ * sienaGOF: added the name of the siena fit object
+ as attribute "sienaFitName" to each of the sienaGofTest objects.
+ * Manual: added paragraph about how to import results from
+ xtable() and siena.table() into MS-Word.
+ * Correction in sparseNetworkExtraction() to avoid errors occurring
+ when the extracted network has no edges (sienaGOF.r).
+ * In the help page for sienaGOF-auxiliary, geodesic distances
+ changed to non-directed; which avoids a further error
+ when the extracted network has no edges.
+ * Correction of an error in print.siena for data sets including
+ other types than "oneMode".
+ * Changed bandwidth selector for violin plots in plot.sienaGOF to "nrd",
+ to avoid long violins in cases where all simulations have the same outcome.
+ * Added parameter "includeRandoms" to print.sienaEffects.
+ * sienaGOF checks that the sienaFitObject object was not made
+ by maximum likelihood estimation.
+Changes in RSiena:
+ * Ported effects outRateLog and outTrunc2 from RSienaTest.
+ * Ported changes (new folders and files) in \src\network\ from RSienaTest.
+Changes in RSienaTest:
+ * Major changes to sienaBayes and print.sienaBayes,
+ to permit estimation of multilevel stochastic actor-oriented model with
+ effects varying between groups for only a subset of the effects.
+
2013-12-04 R-Forge Revision 250
Changes in RSiena and RSienaTest:
* New option "centered" in coCovar and varCovar (sienautils.r,
@@ -3,5 +36,5 @@
sienaDataCreate.r, print01Report.r, sienaprint.r).
* setEffect, updateTheta, and prevAns in siena07() now also cater
- for unspecified interactions (sienaeffects.r, initializeFRAN.r).
+ for user-specified interactions (sienaeffects.r, initializeFRAN.r).
* Wald.RSiena and Multipar.RSiena added (Sienatest.r).
* Error occurrence with message about cvalue in EvaluateTestStatistic
Modified: pkg/RSiena/data/allEffects.csv
===================================================================
--- pkg/RSiena/data/allEffects.csv 2013-12-04 16:15:33 UTC (rev 250)
+++ pkg/RSiena/data/allEffects.csv 2014-02-13 23:03:20 UTC (rev 251)
@@ -67,14 +67,17 @@
nonSymmetricRate,indegree effect on rate xxxxxx,Amount of change x indegrees,inRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
nonSymmetricRate,reciprocity effect on rate xxxxxx,Amount of change x reciprocity,recipRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
nonSymmetricRate,effect 1/outdegree on rate xxxxxx,Amount of change x (1/outdegrees),outRateInv,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+nonSymmetricRate,effect ln(outdegree+1) on rate xxxxxx,Amount of change x ln(outdegrees+1),outRateLog,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,rate,NA,structural,0,0,0,0,
bipartiteRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0,
bipartiteRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0,
bipartiteRate,outdegree effect on rate xxxxxx,Amount of change x outdegrees,outRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
bipartiteRate,effect 1/outdegree on rate xxxxxx,Amount of change x (1/outdegrees),outRateInv,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+bipartiteRate,effect ln(outdegree+1) on rate xxxxxx,Amount of change x ln(outdegrees+1),outRateLog,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,rate,NA,structural,0,0,0,0,
symmetricRate,basic rate parameter xxxxxx,Amount of network change,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,1,NA,0,0,0,0,
symmetricRate,constant xxxxxx rate (period nnnnnn),Amount of network change in period nnnnnn,Rate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,nnnnnn,NA,0,0,0,0,
symmetricRate,degree effect on rate xxxxxx,Amount of change x outdegrees,outRate,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
symmetricRate,effect 1/degree on rate xxxxxx,Amount of change x (1/outdegrees),outRateInv,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,structural,0,0,0,0,
+symmetricRate,effect ln(degree+1) on rate xxxxxx,Amount of change x ln(outdegrees+1),outRateLog,NA,,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,rate,NA,structural,0,0,0,0,
dyadObjective,xxxxxx,Sum of ties x xxxxxx,X,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
dyadObjective,xxxxxx x reciprocity,Sum reciprocated ties x xxxxxx,XRecip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
dyadObjective,WW=>X closure of xxxxxx,WW=>X closure of xxxxxx,WWX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
@@ -94,6 +97,9 @@
covarSymmetricObjective,xxxxxx squared,Sum of degrees x squared xxxxxx,altSqX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarSymmetricObjective,xxxxxx similarity,xxxxxx similarity,simX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarSymmetricObjective,same xxxxxx,same xxxxxx,sameX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
+covarSymmetricObjective,transitive triads same xxxxxx,Number of transitive triads same on xxxxxx,sameXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+covarSymmetricObjective,transitive triplets homog. xxxxxx,Number of transitive triplets homogeneous on xxxxxx,homXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+covarSymmetricObjective,transitive triads jumping xxxxxx,Number of transitive triads jumping xxxxxx,jumpXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
covarSymmetricObjective,xxxxxx ego x xxxxxx alter,xxxxxx ego x xxxxxx alter,egoXaltX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarSymmetricObjective,xxxxxx of indirect ties,xxxxxx of indirect ties,IndTies,FALSE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarSymmetricObjective,xxxxxx alter at distance 2 (#),xxxxxx alter at distance 2 (#),altDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic
@@ -112,6 +118,7 @@
covarNonSymmetricObjective,same xxxxxx,Same values on xxxxxx,sameX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarNonSymmetricObjective,same xxxxxx x reciprocity,Same values x reciprocity on xxxxxx,sameXRecip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarNonSymmetricObjective,transitive triplets same xxxxxx,Number of transitive triplets same on xxxxxx,sameXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+covarNonSymmetricObjective,transitive triplets homog. xxxxxx,Number of transitive triplets homogeneous on xxxxxx,homXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
covarNonSymmetricObjective,transitive triplets jumping xxxxxx,Number of transitive triplets jumping xxxxxx,jumpXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
covarNonSymmetricObjective,xxxxxx ego x xxxxxx alter,Sum xxxxxx ego x xxxxxx alter,egoXaltX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
covarNonSymmetricObjective,xxxxxx ego x xxxxxx alter x recipr.,Sum xxxxxx ego x xxxxxx rec.alter,egoXaltXRecip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
@@ -129,7 +136,8 @@
bipartiteObjective,indegree - popularity (sqrt),Sum of indegrees x sqrt(indegree),inPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
bipartiteObjective,outdegree - activity,Sum of squared outdegrees,outAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
bipartiteObjective,outdegree - activity (sqrt),Sum of outdegrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-bipartiteObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,
+bipartiteObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
+bipartiteObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,
bipartiteObjective,1/(outdegree + #),Sum 1/(outdegrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
bipartiteObjective,1/(outdegree+#)(outdegree+1+#),Sum 1/(outdegrees + #)(outdegrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
bipartiteObjective,anti in-isolates,Number of indegrees at least 1,antiInIso,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego
@@ -154,6 +162,7 @@
nonSymmetricObjective,GWESP I <- K -> J (#),Number of edgewise shared partners by out two stars (#),gwespFB,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,GWESP I -> K <- J (#),Number of edgewise shared partners by in two stars (#),gwespBF,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,GWESP I <> K <> J (#),Number of edgewise shared partners both in AND out two stars (#),gwespRR,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,
+nonSymmetricObjective,shared popularity,(Number 2-2PU)^1/#),sharedPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,indegree - popularity,Sum of squared indegrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,indegree - popularity (sqrt),Sum of indegrees x sqrt(indegree),inPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,outdegree - popularity,Sum of crossproducts indegree x outdegree,outPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic
@@ -162,7 +171,8 @@
nonSymmetricObjective,indegree - activity (sqrt),Sum of outdegrees x sqrt(indegree),inActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego
nonSymmetricObjective,outdegree - activity,Sum of squared outdegrees,outAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,outdegree - activity (sqrt),Sum of outdegrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-nonSymmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,
+nonSymmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
+nonSymmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,1/(outdegree + #),Sum 1/(outdegrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,1/(outdegree+#)(outdegree+1+#),Sum 1/(outdegrees + #)(outdegrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
nonSymmetricObjective,in-isolate Outdegree,Sum outdegrees for in-isolates,inIsDegree,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego
@@ -183,10 +193,13 @@
symmetricObjective,balance,Amount of balance,balance,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
symmetricObjective,number of actor pairs at distance 2,Number of distances equal to 2,nbrDist2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
symmetricObjective,number pairs at doubly achieved distance 2,Number of doubly achieved distances 2,nbrDist2twice,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
+symmetricObjective,GWESP (#),Number of edgewise shared partners (#),gwesp,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,
+symmetricObjective,4-cycles,(Number 4-cycles)^1/#),cycle4ND,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
symmetricObjective,degree of alter,Sum of squared degrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
symmetricObjective,sqrt degree of alter,Sum of degrees x sqrt(degree),inPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
symmetricObjective,degree^(1.5),Sum of degrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,
-symmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,
+symmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
+symmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,
symmetricObjective,1/(degree + #),Sum 1/(degrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 251
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