[Rsiena-commits] r338 - in pkg/RSienaTest: . R data doc man src/model/effects src/model/ml tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 15 17:54:21 CET 2019
Author: tomsnijders
Date: 2019-01-15 17:54:20 +0100 (Tue, 15 Jan 2019)
New Revision: 338
Modified:
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/NAMESPACE
pkg/RSienaTest/R/bayesTest.r
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/R/sienatable.r
pkg/RSienaTest/data/allEffects.csv
pkg/RSienaTest/doc/RSiena.bib
pkg/RSienaTest/doc/RSiena_Manual.pdf
pkg/RSienaTest/doc/RSiena_Manual.tex
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/print.sienaBayesFit.Rd
pkg/RSienaTest/man/sienaAlgorithmCreate.Rd
pkg/RSienaTest/man/sienaBayes.Rd
pkg/RSienaTest/man/sienaFit.Rd
pkg/RSienaTest/src/model/effects/EffectFactory.cpp
pkg/RSienaTest/src/model/effects/SameCovariateActivityEffect.cpp
pkg/RSienaTest/src/model/effects/SameCovariateActivityEffect.h
pkg/RSienaTest/src/model/ml/MLSimulation.cpp
pkg/RSienaTest/tests/parallel.Rout.save
Log:
Only RSienaTest, for AdSUM
Modified: pkg/RSienaTest/ChangeLog
===================================================================
--- pkg/RSienaTest/ChangeLog 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/ChangeLog 2019-01-15 16:54:20 UTC (rev 338)
@@ -1,3 +1,17 @@
+2019-01-02 R-Forge Revision 338, packages version 1.2-15.
+Changes in RSiena and RSienaTest:
+ * New effects sameXReciAct and diffXReciAct.
+ * Increased length of MLSimulation::preburnin.
+ * Changes in sienaFitThetaTable, averageTheta.last, sdTheta.last in sienaprint.r
+ to enable change in extract.posteriorMeans (see below).
+ * siena.table adapted for sienaBayes results.
+Changes in RSienaTest:
+ * New functions shortBayesResults and plotPostMeansMDS.
+ * extract.posteriorMeans works also for an object saved as PartialBayesResult
+ (which has NA results for as yet unfinished runs)
+ (this was achieved by changes in sienaprint.r, see above).
+ * Examples added to help page for print.sienaBayesFit (in dontrun...).
+
2018-12-05 R-Forge Revision 337, packages version 1.2-14.
Changes in RSiena and RSienaTest:
* Check for length of parameter mult for ML estimation (initializeFRAN),
@@ -12,7 +26,9 @@
prior mean is used for initial parameter values;
prewarming phase introduced before improveMH;
in case prevBayes is used, also parameter nImproveMH in the function
- call of sienaBayes supersedes this parameter in the prevBayes object.
+ call of sienaBayes supersedes this parameter in the prevBayes object;
+ checks for dimensions of prior mean and covariance matrix
+ put earlier in the initialization phase.
2018-10-29 R-Forge Revision 336, packages version 1.2-13.
Changes in RSiena and RSienaTest:
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/DESCRIPTION 2019-01-15 16:54:20 UTC (rev 338)
@@ -2,8 +2,8 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.2-14
-Date: 2018-12-05
+Version: 1.2-15
+Date: 2019-01-02
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger
Depends: R (>= 2.15.0)
Imports: Matrix, tcltk, lattice, parallel, MASS, RUnit, methods
Modified: pkg/RSienaTest/NAMESPACE
===================================================================
--- pkg/RSienaTest/NAMESPACE 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/NAMESPACE 2019-01-15 16:54:20 UTC (rev 338)
@@ -18,7 +18,8 @@
export(
sienaBayes, glueBayes, simpleBayesTest, multipleBayesTest,
- extract.sienaBayes, extract.posteriorMeans, algorithms, profileLikelihoods,
+ extract.sienaBayes, extract.posteriorMeans, plotPostMeansMDS,
+ shortBayesResults, algorithms, profileLikelihoods,
sienaRIDynamics
)
Modified: pkg/RSienaTest/R/bayesTest.r
===================================================================
--- pkg/RSienaTest/R/bayesTest.r 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/R/bayesTest.r 2019-01-15 16:54:20 UTC (rev 338)
@@ -228,8 +228,9 @@
x
}
-plot.multipleBayesTest <- function(x, xlim=NULL, ylim=NULL,
- main=NULL, ...){
+
+##@plot.multipleBayesTest methods
+plot.multipleBayesTest <- function(x, xlim=NULL, ylim=NULL, main=NULL, ...){
if (!inherits(x, 'multipleBayesTest'))
{
stop("not a legitimate multipleBayesTest object")
@@ -430,7 +431,7 @@
stop('z must be a sienaBayesFit object')
}
- ntot <- dim(z$ThinPosteriorMu)[1]
+ ntot <- max(which(!is.na(z$ThinPosteriorMu[,1])))
nit <- ntot - nfirst + 1
nind <- sum(z$varyingParametersInGroup)
res <- matrix(NA, z$nGroup, 2*nind)
@@ -456,4 +457,45 @@
dimnames(res) <- list(1:dim(res)[1], fName)
}
res
+}
+
+
+##@plotPostMeansMDS MDS plot of posterior means for sienaBayesFit object
+plotPostMeansMDS <- function(x, pmonly=0, nfirst=NULL, ...){
+# This function makes an MDS plot of the posterior means in z;
+# for the method: see MASS (book) p. 308.
+# if pmonly=0 posterior means and standard deviations,
+# if pmonly=1 only the posterior means,
+# if pmonly=2 only the posterior standard deviations.
+ if (!inherits(x, "sienaBayesFit"))
+ {
+ stop('x must be a sienaBayesFit object')
+ }
+ if (is.null(nfirst))
+ {
+ nfirst <- x$nwarm+1
+ }
+# requireNamespace(MASS)
+ is.even <- function(k){k %% 2 == 0}
+ is.odd <- function(k){k %% 2 != 0}
+ cat('extracting posterior means ...\n')
+ pm <- extract.posteriorMeans(x, nfirst=nfirst)
+ if (pmonly <= 0)
+ {
+ vars <- (1:dim(pm)[2])
+ }
+ else if (pmonly == 1)
+ {
+ vars <- is.odd(1:dim(pm)[2])
+ }
+ else
+ {
+ vars <- is.even(1:dim(pm)[2])
+ }
+ cat('calculating MDS solution ...\n')
+ corpm <- cor(t(pm[,vars]))
+ mds <- isoMDS(1-corpm)
+ eqscplot(mds$points, type='n', ...)
+ text(mds$points, labels=as.character(1:dim(mds$points)[1]), ...)
+ invisible(mds$points)
}
\ No newline at end of file
Modified: pkg/RSienaTest/R/sienaBayes.r
===================================================================
--- pkg/RSienaTest/R/sienaBayes.r 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/R/sienaBayes.r 2019-01-15 16:54:20 UTC (rev 338)
@@ -2860,11 +2860,10 @@
}
##@protectedInverse inverse of p.s.d matrix
-protectedInverse <- function(x)
+protectedInverse <- function(x){
+ if (inherits(try(xinv <- chol2inv(chol(x)),
+ silent=TRUE), "try-error"))
{
- if (inherits(try(xinv <- chol2inv(chol(x)),
- silent=TRUE), "try-error"))
- {
# Now make this x positive definite, if it is not.
# See above for a more extensive treatment of the same.
# Adapted from function make.positive.definite in package corpcor
@@ -2872,24 +2871,21 @@
# but changed to make the matrix positive definite (psd)
# instead of nonnegative definite.
# The idea is to left-truncate all eigenvalues to delta0.
- # The construction with tol, not used now,
- # is to ensure positive definiteness given numerical inaccuracy.
- es <- eigen(x)
- esv <- es$values
- delta0 <- 1e-6
- cat("protectedInverse: Eigenvalues Sigma = ", sort(esv), "\n")
- if (min(esv) < delta0)
- {
- delta <- delta0
- tau <- pmax(delta, esv)
- # cat("Smallest eigenvalue of Sigma now is ",
- # min(esv),"; make posdef.\n")
- xinv <- es$vectors %*%
- diag(1/tau, dim(x)[1]) %*% t(es$vectors)
- }
+ es <- eigen(x)
+ esv <- es$values
+ delta0 <- 1e-6
+ cat("protectedInverse: Eigenvalues Sigma = ", sort(esv), "\n")
+ if (min(esv) < delta0)
+ {
+ delta <- delta0
+ tau <- pmax(delta, esv)
+ # cat("Smallest eigenvalue of Sigma now is ",
+ # min(esv),"; make posdef.\n")
+ xinv <- es$vectors %*% diag(1/tau, dim(x)[1]) %*% t(es$vectors)
}
- xinv
}
+ xinv
+}
##@trafo link function rates
Modified: pkg/RSienaTest/R/sienaprint.r
===================================================================
--- pkg/RSienaTest/R/sienaprint.r 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/R/sienaprint.r 2019-01-15 16:54:20 UTC (rev 338)
@@ -700,11 +700,10 @@
}
##@averageTheta.last Miscellaneous
-
averageTheta.last <- function(z, groupOnly=0, nfirst=z$nwarm+1)
{
ntot <- sum(!is.na(z$ThinPosteriorMu[,1]))
- ntott <- dim(z$ThinParameters)[1]
+ ntott <- sum(!is.na(z$ThinParameters[,1,1]))
if (nfirst > ntot)
{
@@ -719,11 +718,12 @@
for (group in 1:z$nGroup)
{
thetaMean[z$ratePositions[[group]]] <- colMeans(
- z$ThinParameters[nfirst:ntott, group,
+ z$ThinParameters[nfirst:ntott, group,
!z$generalParametersInGroup, drop=FALSE], na.rm=TRUE)
postVarMean[z$ratePositions[[group]]] <- apply(
- z$ThinParameters[nfirst:ntott,
- group, !z$generalParametersInGroup, drop=FALSE], 3, var, na.rm=TRUE)
+ z$ThinParameters[nfirst:ntott,
+ group, !z$generalParametersInGroup, drop=FALSE], 3,
+ var, na.rm=TRUE)
}
if (is.null(z$priorRatesFromData))
@@ -734,32 +734,33 @@
if (groupOnly != 0)
{
thetaMean[(z$set1)&(!z$basicRate)] <- colMeans(
- z$ThinParameters[(nfirst):ntott, groupOnly,
- z$varyingGeneralParametersInGroup, drop=FALSE], na.rm=TRUE)
+ z$ThinParameters[nfirst:ntott, groupOnly,
+ z$varyingGeneralParametersInGroup, drop=FALSE], na.rm=TRUE)
}
else
{
if ((z$priorRatesFromData <0) | z$incidentalBasicRates)
{
- thetaMean[(z$set1)&(!z$basicRate)] <- colMeans(
- z$ThinPosteriorMu[(nfirst):dim(z$ThinPosteriorMu)[1],
- , drop=FALSE], na.rm=TRUE)
- postVarMean[z$varyingObjectiveParameters] <- sapply(1:(dim(z$ThinPosteriorSigma)[2]),
- function(i){mean(z$ThinPosteriorSigma[nfirst:dim(z$ThinPosteriorSigma)[1],i,i], na.rm=TRUE)})
+ thetaMean[(z$set1)&(!z$basicRate)] <- colMeans(
+ z$ThinPosteriorMu[nfirst:ntot, , drop=FALSE], na.rm=TRUE)
+ postVarMean[z$varyingObjectiveParameters] <-
+ sapply(1:(dim(z$ThinPosteriorSigma)[2]),
+ function(i){mean(z$ThinPosteriorSigma[nfirst:ntot,i,i], na.rm=TRUE)})
}
+
else
{
- thetaMean[(z$set1)&(!z$basicRate)] <- colMeans(
- z$ThinPosteriorMu[(nfirst):dim(z$ThinPosteriorMu)[1],
- z$objectiveInVarying, drop=FALSE], na.rm=TRUE)
- postVarMean[z$varyingObjectiveParameters] <- sapply(1:(dim(z$ThinPosteriorSigma)[2]),
- function(i){mean(z$ThinPosteriorSigma[nfirst:dim(z$ThinPosteriorSigma)[1],i,i], na.rm=TRUE)}
+ thetaMean[(z$set1)&(!z$basicRate)] <- colMeans(
+ z$ThinPosteriorMu[nfirst:ntot,
+ z$objectiveInVarying, drop=FALSE], na.rm=TRUE)
+ postVarMean[z$varyingObjectiveParameters] <-
+ sapply(1:(dim(z$ThinPosteriorSigma)[2]),
+ function(i){mean(z$ThinPosteriorSigma[nfirst:ntot,i,i], na.rm=TRUE)}
)[z$objectiveInVarying]
+ }
}
- }
- thetaMean[z$set2] <-
- colMeans(z$ThinPosteriorEta[nfirst:dim(z$ThinPosteriorEta)[1],, drop=FALSE],
- na.rm=TRUE)
+ thetaMean[z$set2] <-
+ colMeans(z$ThinPosteriorEta[nfirst:ntot,, drop=FALSE], na.rm=TRUE)
thetaMean[z$fix & (!z$basicRate)] <- z$thetaMat[1,z$fix & (!z$basicRate)]
list(thetaMean, postVarMean)
}
@@ -768,7 +769,7 @@
sdTheta.last <- function(z, groupOnly=0, nfirst=z$nwarm+1)
{
ntot <- sum(!is.na(z$ThinPosteriorMu[,1]))
- ntott <- dim(z$ThinParameters)[1]
+ ntott <- sum(!is.na(z$ThinParameters[,1,1]))
if (nfirst >= ntot-1)
{
stop('Sample did not come beyond warming')
@@ -1261,7 +1262,15 @@
}
else
{
- cat("Note: this summary does not contain a convergence check.\n\n")
+ cat("Note: this summary does not contain a convergence check.\n")
+ if (is.null(nfirst))
+ {
+ cat("Note: the print function for sienaBayesFit objects")
+ cat(" can also use a parameter nfirst,\n")
+ cat(" indicating the first run")
+ cat(" from which convergence is assumed.\n")
+ }
+ cat("\n")
if (length(x$f$groupNames) > 1)
{
cat("Groups:\n")
@@ -1563,3 +1572,32 @@
invisible(x)
}
+##@shortBayesResult abbreviated sienaBayesFit results
+shortBayesResults <- function(x, nfirst=NULL){
+ if (!inherits(x, "sienaBayesFit"))
+ {
+ stop('x must be a sienaBayesFit object')
+ }
+ if (is.null(nfirst))
+ {
+ nfirst <- x$nwarm+1
+ }
+ df1 <- sienaFitThetaTable(x, fromBayes=TRUE, nfirst=nfirst)[[1]][,
+ c("text", "value", "se", "cFrom", "cTo", "postSd", "cSdFrom", "cSdTo" )]
+ df1$postSd[is.na(df1$cSdFrom)] <- NA
+ df1$postSd <- as.numeric(df1$postSd)
+ df1$cSdFrom <- as.numeric(df1$cSdFrom)
+ df1$cSdTo <- as.numeric(df1$cSdTo)
+ df2 <- as.data.frame(x$requestedEffects[,c("name","shortName", "interaction1", "interaction2",
+ "type", "randomEffects", "fix", "parm", "period", "effect1", "effect2", "effect3", "group")])
+ df2$period <- as.numeric(df2$period)
+ replace1 <- function(x){ifelse(x=="text", "effectName", x)}
+ replace2 <- function(x){ifelse(x=="value", "postMeanGlobal", x)}
+ replace3 <- function(x){ifelse(x=="se", "postSdGlobal", x)}
+ replace4 <- function(x){ifelse(x=="postSd", "postSdBetween", x)}
+ dfs <- cbind(df2, df1)
+ dfr <- dfs
+ names(dfr) <- replace1(replace2(replace3(replace4(names(dfs)))))
+ dfr
+}
+
Modified: pkg/RSienaTest/R/sienatable.r
===================================================================
--- pkg/RSienaTest/R/sienatable.r 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/R/sienatable.r 2019-01-15 16:54:20 UTC (rev 338)
@@ -6,18 +6,44 @@
## * File: sienatable.r
## *
## * Description: This file contains the code to save a latex or html table of
-## * estimates for a sienaFit object
+## * estimates for a sienaFit or sienaBayesFit object
## * Written by Charlotte Greenan; small modifications by Tom Snijders.
## *
## ***************************************************************************/
##@siena.table siena07 Saves latex or html table of estimates
-## for a sienaFit object
+## for a sienaFit or sienaBayesFit object
siena.table <- function(x, type='tex',
file=paste(deparse(substitute(x)),'.',type,sep=""),
vertLine=TRUE, tstatPrint=FALSE,
- sig=FALSE, d=3)
+ sig=FALSE, d=3, nfirst=NULL)
{
+ fromBayes <- FALSE
+ xkind.string <- "sienaFit"
+ if (!inherits(x, "sienaFit"))
+ {
+ if (inherits(x, "sienaBayesFit"))
+ {
+ fromBayes <- TRUE
+ sig <- FALSE
+ tstatPrint <- FALSE
+ if (is.null(nfirst))
+ {
+ nfirst <- x$nwarm + 1
+ cat("Note: the print function for sienaBayesFit objects")
+ cat(" can also use a parameter nfirst,\n")
+ cat(" indicating the first run")
+ cat(" from which convergence is assumed.\n")
+ cat(" The default value used now is nfirst =",
+ x$nwarm + 1, ".\n")
+ }
+ xkind.string <- "sienaBayesFit"
+ }
+ else
+ {
+ stop('x must be a sienaFit or sienaBayesFit object')
+ }
+ }
tstat <- tstatPrint
effects <- x$requestedEffects
p <- x$pp
@@ -28,23 +54,34 @@
{
condrates <- length(x$rate)
}
-
- theta <- x$theta
- theta[diag(x$covtheta) < 0.0 | x$fixed] <- NA
- ses <- sqrt(diag(x$covtheta))
- ses[x$fixed] <- NA
- max.t1 <- max(abs(x$tstat[!x$fixed]))
- dd <- 2
- max.t <- round(max.t1, digits = dd)
- if (max.t < max.t1)
+
+ if (fromBayes)
{
- max.t <- max.t + 10^{-dd} #needs to be rounded up
+ xx <- shortBayesResults(x, nfirst=nfirst)
+ theta <- xx$postMeanGlobal
+ ses <- xx$postSdGlobal
+ se.string <- 'psd.'
}
- maxlincomb.t1 <- x$tconv.max
- maxlincomb.t <- round(maxlincomb.t1, digits = dd)
- if (maxlincomb.t < maxlincomb.t1)
+ else
{
- maxlincomb.t <- maxlincomb.t + 10^{-dd} #needs to be rounded up
+ theta <- x$theta
+ theta[diag(x$covtheta) < 0.0 | x$fixed] <- NA
+ ses <- sqrt(diag(x$covtheta))
+ ses[x$fixed] <- NA
+ max.t1 <- max(abs(x$tstat[!x$fixed]))
+ dd <- 2
+ max.t <- round(max.t1, digits = dd)
+ if (max.t < max.t1)
+ {
+ max.t <- max.t + 10^{-dd} #needs to be rounded up
+ }
+ maxlincomb.t1 <- x$tconv.max
+ maxlincomb.t <- round(maxlincomb.t1, digits = dd)
+ if (maxlincomb.t < maxlincomb.t1)
+ {
+ maxlincomb.t <- maxlincomb.t + 10^{-dd} #needs to be rounded up
+ }
+ se.string <- 's.e.'
}
if (length(x$condvarno) == 0)
{
@@ -302,19 +339,28 @@
startTable <- tableSection(c("<TABLE border=1 rules=none frame = hsides>",
paste("<TR><TD>Effect</TD><TD> par.</TD><TD></TD>
- <TD> (s.e.)</TD>",start.tstat,"</TR>")))
+ <TD> ",se.string,"</TD>",start.tstat,"</TR>")))
midTable <- tableSection(c("",""))
indentTable <- tableSection("")
ruleTable <- tableSection("<TR> <TD colspan='9'><HR/></TD> </TR>")
footnoteStart <- c("</TABLE>","<TABLE border=1 rules=none frame = below>")
- footnote <- c(paste(" <TR> <TD colspan=9 align=left>
+ if (fromBayes)
+ {
+ footnote <- "<TR> <TD colspan=9 align=left> par=posterior mean;
+ psd = posterior standard deviation.
+ </TD> </TR> <TR> </TR></TABLE>"
+ }
+ else
+ {
+ footnote <- c(paste(" <TR> <TD colspan=9 align=left>
all convergence t ratios < ",
max.t,".</TD> </TR> <TR> </TR>",
" <TR> <TD colspan=9 align=left>
Overall maximum convergence ratio ",
maxlincomb.t,".</TD> </TR> <TR> </TR>",
sep="",collapse=""),"</TABLE>")
+ }
if (sig)
{
footnote <- c(footnoteStart, "<TR> <TD colspan=4 align=left> † p < 0.1;
@@ -346,7 +392,7 @@
{
linesep=""
}
- startTable <- tableSection(c(paste("% Table based on sienaFit object",
+ startTable <- tableSection(c(paste("% Table based on", xkind.string, "object",
deparse(substitute(x)), ',', date()),
paste("\\begin{tabular}{l",
linesep,
@@ -356,14 +402,23 @@
"\\rule{0pt}{2ex}\\relax",
paste("Effect &\\multicolumn{2}{c}{par.}&\\multicolumn{2}{c",
linesep,
- "}{(s.e.)}",
+ "}{",se.string,"}",
start.tstat2,"\\\\[0.5ex]"),
"\\hline"))
midTable <- tableSection(c("\\hline",
"\\rule{0pt}{2ex}\\relax"))
indentTable <- tableSection("\\rule{0pt}{2ex}\\relax")
ruleTable <- tableSection("\\hline")
- footnote <- c(paste("\\multicolumn{5}{l}\n ",
+ if (fromBayes)
+ {
+ footnote <- c(paste("\\multicolumn{5}{l}\n ",
+ "{\\footnotesize{par = posterior mean; psd = posterior standard deviation.}}\\\\\n",
+ sep="",collapse=""),
+ "\\end{tabular}")
+ }
+ else
+ {
+ footnote <- c(paste("\\multicolumn{5}{l}\n ",
"{\\footnotesize{convergence $t$ ratios all $<$ ", max.t,
".}}\\\\\n",
"\\multicolumn{5}{l}",
@@ -371,13 +426,13 @@
maxlincomb.t,".}}",
sep="",collapse=""),
"\\end{tabular}")
-
- if (sig == TRUE)
- {
- footnote <- c("\\multicolumn{5}{l}{\\footnotesize{$^\\dagger$ $p$ $<$ 0.1;
- $^\\ast$ $p$ $<$ 0.05; $^{\\ast\\ast}$ $p$ $<$ 0.01;
- $^{\\ast\\ast\\ast}$ $p$ $<$ 0.001;}}\\\\" ,footnote)
- }
+ if (sig == TRUE)
+ {
+ footnote <- c("\\multicolumn{5}{l}{\\footnotesize{$^\\dagger$ $p$ $<$ 0.1;
+ $^\\ast$ $p$ $<$ 0.05; $^{\\ast\\ast}$ $p$ $<$ 0.01;
+ $^{\\ast\\ast\\ast}$ $p$ $<$ 0.001;}}\\\\" ,footnote)
+ }
+ }
}
endTable <- tableSection(footnote)
Modified: pkg/RSienaTest/data/allEffects.csv
===================================================================
--- pkg/RSienaTest/data/allEffects.csv 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/data/allEffects.csv 2019-01-15 16:54:20 UTC (rev 338)
@@ -289,6 +289,8 @@
covarNonSymmetricObjective,outd. act. to hom. xxxxxx,sum sqr. outd. to hom. values on xxxxxx,homXOutAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
covarNonSymmetricObjective,outd. act. weight alt. xxxxxx,sum sqr. outd. weight alt. xxxxxx,altXOutAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
covarNonSymmetricObjective,outd. act. to dif. xxxxxx,sum sqr. outd. to dif. values on xxxxxx,diffXOutAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
+covarNonSymmetricObjective,rec.deg. act. to same xxxxxx,sum sqr. outd. to same values on xxxxxx,sameXReciAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
+covarNonSymmetricObjective,rec.deg. act. to dif. xxxxxx,sum sqr. outd. to dif. values on xxxxxx,diffXReciAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
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,,FALSE
covarNonSymmetricObjective,transitive triplets diff. xxxxxx,Number of transitive triplets diff. on xxxxxx,diffXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
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,,FALSE
Modified: pkg/RSienaTest/doc/RSiena.bib
===================================================================
--- pkg/RSienaTest/doc/RSiena.bib 2018-12-05 21:44:35 UTC (rev 337)
+++ pkg/RSienaTest/doc/RSiena.bib 2019-01-15 16:54:20 UTC (rev 338)
@@ -79,11 +79,14 @@
year = {2010}
}
+
+
@book{Agresti2012,
author = {Alan Agresti},
publisher = {Wiley-Interscience},
title = {Categorical Data Analysis},
series = {Wiley Series in Probability and Statistics},
+ address = {New York},
edition = {3rd},
year = {2012}
}
@@ -418,13 +421,31 @@
@book{Blau55,
- Author = {Blau, Peter},
+ Author = {Blau, Peter M.},
Title = {The Dynamics of Bureaucracy},
Publisher = {University of Chicago Press},
Address = {Chicago},
Year = {1955} }
+ at book{Blau77,
+ Author = {Blau, Peter M.},
+ Title = {Inequality and heterogeneity: {A} primitive theory of social structure },
+ Publisher = {Free Press},
+ Address = {New York},
+ Year = {1977}
+}
+
+
+ at book{Byrn71,
+ Author = {Byrne, Donn Erwin},
+ Title = {The Attraction Paradigm},
+ Publisher = {Academic Press},
+ Address = {New York},
+ Year = {1971}
+}
+
+
@article{Block2015,
title = "Reciprocity, transitivity, and the mysterious three-cycle",
journal = "Social Networks ",
@@ -918,6 +939,16 @@
year={2011}
}
+ at article{CheadleSchwadel2012,
+title = "The 'friendship dynamics of religion,' or the 'religious dynamics of friendship'?
+ {A} social network analysis of adolescents who attend small schools",
+journal = "Social Science Research",
+volume = "41",
+pages = "1198--1212",
+year = "2012",
+author = "Jacob E. Cheadle and Philip Schwadel"
+}
+
@article{Cheadle_etal2013,
author ={Jacob E. Cheadle and Michael Stevens and Deadric T. Williams and
Bridget J. Goosby},
@@ -1045,7 +1076,18 @@
publisher= {Belknap Press of Harvard University Press},
year = 1990}
+ at Article{CookSchwadelCheadle2017,
+ author="Cook, J. Benjamin and Schwadel, Philip and Cheadle, Jacob E.",
+ title="The Origins of Religious Homophily in a Medium and Large School",
+ journal="Review of Religious Research",
+ year="2017",
+ volume="59",
+ number="1",
+ pages="65--80"}
+}
+
+
@book{Coombs1964,
author = {Clyde H. Coombs},
title = {A Theory of Data},
@@ -1117,6 +1159,15 @@
pages={843--852}
}
+ at article{Davis1967,
+ title={Clustering and structural balance in graphs},
+ author={Davis, James A},
+ journal={Human Relations},
+ volume={20},
+ pages={181--187},
+ year={1967}
+}
+
@INCOLLECTION{Davis79,
AUTHOR = "James A. Davis",
TITLE = {The Davis/Holland/Leinhardt studies: {An} overview},
@@ -1185,7 +1236,7 @@
@article{Delitsch1900,
author = {Johannes {Delitsch}},
- title = {\"{U}ber Sch\"{u}lerfreundschaften in einer {V}olksschulklasse},
+ title = {\"{U}ber {S}ch\"{u}lerfreundschaften in einer {V}olksschulklasse},
journal = {Zeitschrift f\"{u}r {K}inderforschung},
year = 1900,
volume = 5,
@@ -1445,8 +1496,15 @@
publisher={Houghton-Mifflin}
}
+ at article{Emerson1976,
+ author = {Richard M. Emerson},
+ year = {1976},
+ title = {Social exchange theory},
+ journal = {Annual Review of Sociology},
+ volume = {2},
+ pages = {335--362}
+}
-
@ARTICLE{EmirbayerGoodwin94,
AUTHOR = "M. {Emirbayer} and J. {Goodwin}",
TITLE = {Network Analysis, Culture, and the Problem of Agency},
@@ -1476,6 +1534,13 @@
PAGES = "1495--1533"
}
+ at book{Epstein2006,
+ title={Generative social science: {S}tudies in agent-based computational modeling},
+ author={Epstein, Joshua M},
+ year={2006},
+ location={Princeton},
+ publisher={Princeton University Press}
+}
% Erdos first name is Paul
@@ -1574,6 +1639,15 @@
ADDRESS = "Oxford, U.K."
}
+ at article{FelmleeSprecherBassin1990,
+ author = {Diane Felmlee and Susan Sprecher and Edward Bassin},
+ journal = {Social Psychology Quarterly},
+ pages = {13--30},
+ title = {The Dissolution of Intimate Relationships: {A} Hazard Model},
+ volume = {53},
+ year = {1990}
+}
+
@article{Field2003,
title={The problems in using fixed-effects models of meta-analysis on real-world data},
author={Field, Andy P},
@@ -1807,6 +1881,17 @@
year={2017}
}
+ at article{FujimotoEA2018,
+ author={Kayo Fujimoto and {Tom A.B.} Snijders and Thomas W. Valente},
+ title={Multivariate dynamics of one-mode and two-mode networks:
+ {E}xplaining similarity in sports participation among friends},
+ volume={6},
+ issue={3},
+ journal={Network Science},
+ year={2018},
+ pages={370–395}
+}
+
@ARTICLE{GalaskiewiczBurt1991,
AUTHOR = {Joseph {Galaskiewicz} and Ronald S. {Burt}},
TITLE = {Interorganization Contagion in Corporate Philanthropy},
@@ -2363,6 +2448,31 @@
Address = {Cambridge},
Year = {2005} }
+ at book{HedstromSwedberg1998,
+ title={Social mechanisms: An analytical approach to social theory},
+ editor={Hedstr{\"o}m, Peter and Swedberg, Richard},
+ year={1998},
+ address = {Cambridge},
+ publisher={Cambridge University Press}
+}
+
+ at book{HedstromSwedberg,
+ Author = {Peter Hedstr\"om},
+ Title = {Dissecting the Social: On the Principles of Analytical Sociology},
+ Publisher = {Cambridge University Press},
+ Address = {Cambridge},
+ Year = {2005} }
+
+
+ at article{Heider1948,
+ Author = {Fritz Heider},
+ Title = {Attitudes and cognitive organization},
+ Journal = {Journal of Psychology},
+ Volume = {21},
+ Pages = {107--112},
+ Year = {1948} }
+
+
@BOOK{Heider58,
AUTHOR = "Fritz {Heider}",
TITLE = {The Psychology of Interpersonal Relations},
@@ -2623,8 +2733,7 @@
year={2013}
}
- at article{
-Hubert85,
+ at article{Hubert85,
Author = {Hubert, Lawrence J.},
Title = {Combinatorial Data Analysis: Association and Partial Association},
Journal = {Psychometrika},
@@ -2635,8 +2744,7 @@
- at book{
-Hubert87,
+ at book{Hubert87,
Author = {Hubert, Lawrence J.},
Title = {Assignment Methods in Combinatorial Data Analysis},
Publisher = {Marcel Dekker, INC.},
@@ -2645,8 +2753,7 @@
Series = {Statistics: Textbooks and Monographs},
Year = {1987} }
- at article{
-HubertGolledge81,
+ at article{HubertGolledge81,
Author = {Hubert, Lawrence J. and Golledge, Reginald G.},
Title = {A Heuristic Method for the Comparison of Related Structures},
Journal = {Journal of Mathematical Psychology},
@@ -2769,6 +2876,15 @@
year={2000}
}
+ at article{HustonLevinger1978,
+author = {Huston, T L and Levinger, G},
+title = {Interpersonal Attraction and Relationships},
+journal = {Annual Review of Psychology},
+volume = {29},
+pages = {115--156},
+year = {1978}
+}
+
@article{IacobucciWasserman1990,
title={Social networks with two sets of actors},
author={Iacobucci, Dawn and Wasserman, Stanley},
@@ -2954,6 +3070,26 @@
pages = { 863--871}
}
+ at Article{KalterKroneberg2014,
+author="Kalter, Frank and Kroneberg, Clemens",
+title="Between Mechanism Talk And Mechanism Cult:
+ {N}ew Emphases in Explanatory Sociology And Empirical Research",
+journal="KZfSS K{\"o}lner Zeitschrift f{\"u}r Soziologie und Sozialpsychologie",
+year="2014",
+volume="66",
+pages="91--115"
+}
+
+ at incollection{Kalter2016,
+ author = {Kalter, Frank},
+ publisher = {Wiley},
+ title = {Social Network Analysis in the Study of Ethnic Inequalities},
+ booktitle = {Emerging Trends in the Social and Behavioral Sciences},
+ editor = {R. A. Scott and S. M. Kosslyn},
+ note = {doi:10.1002/9781118900772.etrds0397},
+ year = {2016}
+}
+
@TechReport{CILS4EU,
title={Children of Immigrants Longitudinal Survey in Four {E}uropean Countries
({CILS4EU}): {M}otivation, Aims, and Design},
@@ -2964,21 +3100,50 @@
year={2013}
}
- at InCollection{KalterKruse2015,
+
+ at TechReport{CILS4EU2016,
+ title={Children of Immigrants Longitudinal Survey in Four {E}uropean Countries.
+ {S}ociometric Fieldwork Report},
+ institution={Mannheim University},
+ address={Mannheim},
+ author={Hanno Kruse and K. Jacob},
+ note = {Wave 1 - 2010/2011, v1.2.0},
+ year={2016}
+}
+
+ at TechReport{CILS4EU2016B,
+ title={Children of Immigrants Longitudinal Survey in Four {E}uropean Countries.
+ {S}ociometric Fieldwork Report},
+ institution={Mannheim University},
+ address={Mannheim},
+ author={Hanno Kruse and M. Wei{\ss}man and K. Jacob},
+ note = {Wave 2 - 2011/2012, v2.3.0},
+ year={2016}
+}
+
+ at TechReport{CILS4EU2017,
+ title={Children of Immigrants Longitudinal Survey in Four {E}uropean Countries
+ ({CILS4EU}) -- Full Version},
+ author={Kalter, Frank and Heath, Anthony F and Hewstone, Miles and Jonsson, Janne O
+ and Kalmijn, Matthijs and Kogan, Irena and {van Tubergen}, Frank},
+ institution={GESIS: GESIS Data Archive},
+ address={Cologne},
+ note = {ZA5353 Data file Version 3.3.0, doi:10.4232/cils4eu.5353.3.3.0},
+ doi = {10.4232/cils4eu.5353.3.3.0},
+ year={2017}
+}
+
+ at InCollection{KalterKruse2014,
title={Ethnic diversity, homophily, and network cohesion in {European} classrooms},
author={Kalter, Frank and Kruse, Hanno},
booktitle={Social Cohesion and Immigration in Europe and North America:
{M}echanisms, Conditions, and Causality},
- editors={Ruud Koopmans, Bram Lancee, Merlin Schaeffer},
- pages={187-207},
+ editor={Ruud Koopmans, Bram Lancee, Merlin Schaeffer},
+ pages={187--207},
chapter={10},
year={2014},
publisher={Routledge}
}
-Kalter, F., Kruse, H., 2015. Ethnic diversity, homophily, and network cohesion inEuropean classrooms.
- In: Koopmans, R., Lancee, B., Schaeffer, M. (Eds.),
- SocialCohesion and Immigration in Europe and North America: Mechanisms,
- Condi-tions, and Causality. Routledge, London, pp. 187–207.
@article{KatzProctor1959,
author = {Leo Katz and Charles H. Proctor},
@@ -3190,8 +3355,8 @@
}
@article{KnechtEA2010,
-AUTHOR = {Andrea Knecht and Tom A. B. Snijders and Chris Baerveldt and
- {Christian E. G.} Steglich and Werner Raub},
+AUTHOR = {Andrea Knecht and Tom A. B. Snijders and Chris Baerveldt and
+ Christian E. G. Steglich and Werner Raub},
YEAR = {2010},
TITLE = {Friendship and Delinquency: Selection and Influence Processes in Early Adolescence},
journal ={Social Development},
@@ -3200,7 +3365,7 @@
}
@article{KnechtBurkEA2010,
-AUTHOR = {Andrea Knecht and William J. Burk and Jeroen Weesie and {Christian E. G.} Steglich},
+AUTHOR = {Andrea Knecht and William J. Burk and Jeroen Weesie and Christian E. G. Steglich},
YEAR = {2010},
TITLE = {Friendship and alcohol use in early adolescence: {A} multilevel social network approach},
journal ={Journal of Research on Adolescence},
@@ -3266,10 +3431,10 @@
ADDRESS = "New York"
}
- at report{KoskinenSnijders18,
+ at report{KoskinenSnijders19,
author = {Johan H. Koskinen and Tom A. B. Snijders},
title = {Multilevel Longitudinal Analysis of Social Networks},
- year = 2018,
+ year = 2019,
note = {In preparation}}
@@ -3789,6 +3954,18 @@
publisher = {Aldine de Gruyter},
address = {New York}}
+
+ at INCOLLECTION{Lindenberg1992,
+AUTHOR = "Siegwart M. {Lindenberg}",
+TITLE = {The Method of Decreasing Abstraction},
+BOOKTITLE = "Rational Choice Theory. {A}dvocacy and Critique",
+PAGES = "3--20",
+PUBLISHER = "Sage",
+YEAR = "1992",
+EDITOR = "James S. Coleman and Thomas J. Fararo",
+ADDRESS = "Newbury Park, CA"
+}
+
@INCOLLECTION{Lindenberg93,
AUTHOR = "Siegwart M. {Lindenberg}",
TITLE = {Framing, empirical evidence and applications},
@@ -4090,6 +4267,15 @@
Volume = {48},
Pages = {35--71}}
+ at article{Manzo2010,
+ title={Analytical sociology and its critics},
+ author={Manzo, Gianluca},
+ journal={European Journal of Sociology/Archives europ{\'e}ennes de sociologie},
+ volume={51},
+ pages={129--170},
+ year={2010}
+}
+
@ARTICLE{Mark98,
AUTHOR="Noah {Mark}",
TITLE = "Beyond individual differences: Social differentiation from first
@@ -4243,6 +4429,15 @@
year={2004}
}
+ at article{MeerTolsma2014,
+author = {Tom {van der Meer} and Jochem Tolsma},
+title = {Ethnic Diversity and Its Effects on Social Cohesion},
+journal = {Annual Review of Sociology},
+volume = {40},
+pages = {459--478},
+year = {2014}
+}
+
@article{MerckenEA09,
Author = {Liesbeth Mercken and Tom A. B. Snijders and Christian E. G. Steglich and Hein de Vries},
Title = {Dynamics of adolescent friendship networks and smoking behavior:
@@ -4402,6 +4597,15 @@
year={2003}
}
+ at article{Moody2001,
+ author = {James Moody},
+ journal = {American Journal of Sociology},
+ pages = {679--716},
+ title = {Race, School Integration, and Friendship Segregation in America},
+ volume = {107},
+ year = {2001}
+}
+
@article{Moran1950,
title={Notes on continuous stochastic phenomena},
author={Moran, Patrick A.P.},
@@ -4423,6 +4627,15 @@
year = {2008},
URL = {http://jasss.soc.surrey.ac.uk/11/1/5.html}}
+ at article{MouwEntwisle2006,
+ author = {Ted Mouw and Barbara Entwisle},
+ journal = {American Journal of Sociology},
+ pages = {394--441},
+ title = {Residential Segregation and Interracial Friendship in Schools},
+ volume = {112},
+ year = {2006}
+}
+
@article{MSF2007,
author = {John W. McDonald and Peter W.F. Smith and Jonathan J. Forster},
title = {Markov chain {M}onte {C}arlo exact inference for social networks},
@@ -4610,8 +4823,17 @@
pages="111--134"
}
+ at Manual{nlme,
+ title = {{nlme}: {L}inear and Nonlinear Mixed Effects Models},
+ author = {Jose Pinheiro and Douglas Bates and Saikat DebRoy
+ and Deepayan Sarkar and {R Core Team}},
+ year = {2018},
+ note = {R package version 3.1-137},
+ url = {https://CRAN.R-project.org/package=nlme}
+}
+
@PhdThesis{Nordlie58,
author = {P.G. Nordlie},
title = {A longitudinal study of interpersonal attraction in a natural group setting},
@@ -4755,8 +4977,15 @@
}
+ at book{Pajek2018,
+ title={Exploratory social network analysis with Pajek},
+ author={De Nooy, Wouter and Mrvar, Andrej and Batagelj, Vladimir},
+ year={2018},
+ edition={3rd},
+ publisher={Cambridge University Press},
+ location={Cambridge}
+}
-
[TRUNCATED]
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svnlook diff /svnroot/rsiena -r 338
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