[Rsiena-commits] r342 - in pkg/RSienaTest: . R data doc man src src/model/effects
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Oct 24 14:49:21 CEST 2019
Author: tomsnijders
Date: 2019-10-24 14:49:20 +0200 (Thu, 24 Oct 2019)
New Revision: 342
Added:
pkg/RSienaTest/src/model/effects/AverageGroupEgoEffect.cpp
pkg/RSienaTest/src/model/effects/AverageGroupEgoEffect.h
Modified:
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/effects.r
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/R/sienaGOF.r
pkg/RSienaTest/R/sienaprint.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/setEffect.Rd
pkg/RSienaTest/man/sienaDependent.Rd
pkg/RSienaTest/src/model/effects/AllEffects.h
pkg/RSienaTest/src/model/effects/CovariateDependentNetworkEffect.cpp
pkg/RSienaTest/src/model/effects/EffectFactory.cpp
pkg/RSienaTest/src/sources.list
Log:
This R-Forge upload again only RSienaTest.
Modified: pkg/RSienaTest/ChangeLog
===================================================================
--- pkg/RSienaTest/ChangeLog 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/ChangeLog 2019-10-24 12:49:20 UTC (rev 342)
@@ -1,3 +1,13 @@
+2019-10-24 R-Forge Revision 342, package version 1.2-19.
+In this R-forge revision, only RSienaTest is updated.
+Changes in RSiena and RSienaTest:
+ * New effect avGroupEgoX.
+ * CovariateDependentNetworkEffect: + lSimulatedOffset taken out of
+ definition missings for ChangingCovariate (seems wrong).
+Changes in RSienaTest:
+ * In sienaBayes: more precise check that
+ prevAns has same specification as effects.
+
2019-10-16 R-Forge Revision 341, package version 1.2-18.
In this R-forge revision, only RSienaTest is updated.
Changes in RSiena and RSienaTest:
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/DESCRIPTION 2019-10-24 12:49:20 UTC (rev 342)
@@ -2,9 +2,10 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.2-18
-Date: 2019-10-16
-Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger
+Version: 1.2-19
+Date: 2019-10-24
+Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger,
+ Nynke Niezink
Depends: R (>= 2.15.0)
Imports: Matrix, tcltk, lattice, parallel, MASS, RUnit, methods
Suggests: xtable, network, tools, codetools
Modified: pkg/RSienaTest/R/effects.r
===================================================================
--- pkg/RSienaTest/R/effects.r 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/R/effects.r 2019-10-24 12:49:20 UTC (rev 342)
@@ -184,7 +184,7 @@
tmp <- covarOneModeEff(names(xx$cCovars)[j],
attr(xx$cCovars[[j]], 'poszvar'),
attr(xx$cCovars[[j]], 'moreThan2'),
- symmetric, name=varname)
+ symmetric, constant=TRUE, name=varname)
objEffects <- rbind(objEffects, tmp$objEff)
rateEffects <- rbind(rateEffects, tmp$rateEff)
}
@@ -197,7 +197,7 @@
tmp <- covarOneModeEff(names(xx$depvars)[j],
poszvar=TRUE,
attr(xx$depvars[[j]], 'moreThan2'),
- symmetric, name=varname)
+ symmetric, constant=FALSE, name=varname)
objEffects <- rbind(objEffects, tmp$objEff)
rateEffects <- rbind(rateEffects, tmp$rateEff)
}
@@ -209,7 +209,7 @@
tmp <- covarOneModeEff(names(xx$vCovars)[j],
attr(xx$vCovars[[j]], 'poszvar'),
attr(xx$vCovars[[j]], 'moreThan2'),
- symmetric, name=varname)
+ symmetric, constant=FALSE, name=varname)
objEffects <- rbind(objEffects,tmp$objEff)
rateEffects<- rbind(rateEffects,tmp$rateEff)
}
@@ -767,7 +767,7 @@
##@continuousNet internal getEffects
continuousNet <- function(depvars, varnames)
{
- nodeSet <- attr(depvars[[1]],'nodeSet') ## NN: nodeset should be the same for
+ nodeSet <- attr(depvars[[1]],'nodeSet') ## NN: nodeset should be the same for
## all continuous depvars
rateEffects <- createEffects("continuousRate", name="sde",
@@ -785,26 +785,26 @@
rateEffects[-c(1, 2), ])
}
- objEffects <- fbicEffects <- wEffects <- NULL # general effects, feedback
+ objEffects <- fbicEffects <- wEffects <- NULL # general effects, feedback
# and intercept, wiener
for (j in seq(along=varnames)) # for all continuous variables
{
for (k in seq(along=varnames))
{
- fbicEffects <- rbind(fbicEffects, createEffects("continuousFeedback",
+ fbicEffects <- rbind(fbicEffects, createEffects("continuousFeedback",
xName = varnames[j], yName = varnames[k],
name=varnames[j], groupName=groupName, group=group,
netType=netType))
- if (j <= k)
- wEffects <- rbind(wEffects, createEffects("continuousWiener",
+ if (j <= k)
+ wEffects <- rbind(wEffects, createEffects("continuousWiener",
xName = varnames[k], yName = varnames[j],
name=varnames[k], groupName=groupName, group=group,
netType=netType))
}
- fbicEffects <- rbind(fbicEffects, createEffects("continuousIntercept",
- xName = varnames[j], name = varnames[j],
+ fbicEffects <- rbind(fbicEffects, createEffects("continuousIntercept",
+ xName = varnames[j], name = varnames[j],
groupName=groupName, group=group, netType=netType))
-
+
for (k in seq(along=depvars))
{
if (types[k] == "oneMode" &&
@@ -811,7 +811,7 @@
attr(xx$depvars[[k]], "nodeSet") == nodeSet)
{
depvarname <- names(xx$depvars)[k]
-
+
tmpObjEffects <-
createEffects("continuousOneModeObjective",
varnames[j], depvarname, name=varnames[j],
@@ -860,15 +860,15 @@
}
}
interaction <- createEffects("unspecifiedContinuousInteraction",
- varnames[j], name=varnames[j],
- groupName=groupName, group=group,
+ varnames[j], name=varnames[j],
+ groupName=groupName, group=group,
netType=netType)
- objEffects <- rbind(objEffects, interaction[rep(1, behNintn),])
+ objEffects <- rbind(objEffects, interaction[rep(1, behNintn),])
}
-
+
fbicEffects$include <- TRUE
-
+
if (onePeriodSde)
{
wEffects$include <- TRUE
@@ -879,21 +879,21 @@
{
wEffects$fix[1] <- TRUE
rateEffects$include[1:observations] <- TRUE
- rateEffects$basicRate[1:observations] <- TRUE
+ rateEffects$basicRate[1:observations] <- TRUE
}
-
+
if (nContinuous > 1)
wEffects$include <- TRUE
-
- starts <- getContinuousStartingVals(depvars, onePeriodSde)
+
+ starts <- getContinuousStartingVals(depvars, onePeriodSde)
wEffects$initialValue <- starts$startWiener
rateEffects$initialValue[1:noPeriods] <- starts$startScale
fbicEffects$initialValue <- starts$startFbic
-
- list(effects = rbind(rateEffects, wEffects, fbicEffects, objEffects),
+
+ list(effects = rbind(rateEffects, wEffects, fbicEffects, objEffects),
starts = starts)
}
-
+
##@bipartiteNet internal getEffects
bipartiteNet <- function(depvar, varname)
{
@@ -1138,7 +1138,7 @@
}
##@covarOneModeEff internal getEffects
- covarOneModeEff<- function(covarname, poszvar, moreThan2, symmetric,
+ covarOneModeEff<- function(covarname, poszvar, moreThan2, symmetric, constant,
name)
{
if (symmetric)
@@ -1164,6 +1164,12 @@
netType=netType)
}
+ if (constant)
+ {
+ covObjEffects <-
+ covObjEffects[!(covObjEffects$shortName %in% c("avGroupEgoX")),]
+ }
+
# these lines tentatively dropped version 1.2-5
# if (!tr & (!poszvar)) # not (positive variance of z, or any z missing)
# {
@@ -1208,7 +1214,7 @@
"degAbsDiffX", "degPosDiffX", "degNegDiffX",
"altInDist2", "totInDist2",
"simEgoInDist2", "sameXInPop", "diffXInPop",
- "sameXCycle4", "inPopX", "inActX"), ]
+ "sameXCycle4", "inPopX", "inActX", "avGroupEgoX"), ]
covRateEffects <- createEffects("covarBipartiteRate", covarname,
name=varname,
groupName=groupName, group=group,
@@ -1385,7 +1391,7 @@
}
objEffects
}
-
+
##@covContEff internal getEffects
covContEff <- function(varname, covarname, nodeSet, same=FALSE,
## same indicates that varname and covarname are
@@ -1403,7 +1409,7 @@
}
list(objEff=covObjEffects)
}
-
+
###################################
## start of function getEffects
##################################
@@ -1453,12 +1459,12 @@
effects <- vector('list',n+1) # n+1 th place for all sde parameters
#nodeSetNames <- sapply(xx$nodeSets, function(x)attr(x, 'nodeSetName'))
names(effects) <- names(xx$depvars) # n+1 th place has no name
-
+
if (onePeriodSde && xx$observations > 2)
- stop('onePeriodSde only possible in case of 2 observations')
+ stop('onePeriodSde only possible in case of 2 observations')
if (onePeriodSde && groupx)
- stop('onePeriodSde not possible in combination with multi-group')
+ stop('onePeriodSde not possible in combination with multi-group')
for (i in 1:(n-nContinuous))
{
@@ -1518,12 +1524,12 @@
group <- 1
noPeriods <- xx$observations - 1
netType <- "continuous"
- contIndices <- (n-nContinuous+1):n ## indicates continuous depvars
+ contIndices <- (n-nContinuous+1):n ## indicates continuous depvars
varnames <- names(xx$depvars)[contIndices]
- depvars <- xx$depvars[contIndices]
+ depvars <- xx$depvars[contIndices]
tmp <- continuousNet(depvars,varnames)
effects[[n+1]] <- tmp$effects
- attr(effects[[n+1]], 'starts') <- tmp$starts
+ attr(effects[[n+1]], 'starts') <- tmp$starts
for (i in contIndices)
{
# all the continuous variable specific effects are currently
@@ -1713,7 +1719,7 @@
depvars <- xx$depvars[contIndices]
starts <- getContinuousStartingVals(depvars, onePeriodSde = FALSE)
## At this point, onePeriodSde is always FALSE, as the combination
- ## of multi-group and onePeriodSde = TRUE is not feasible
+ ## of multi-group and onePeriodSde = TRUE is not feasible
for (i in 1:nContinuous) ## check whether all continous vars match
{
eff <- match(varnames[i], names(effects))
@@ -1731,7 +1737,7 @@
groupNames[group], group,
1:noPeriods)
}
-
+
period <- period + xx$observations ##periods used so far
}
}
@@ -1830,26 +1836,26 @@
nActors <- nrow(depvar) # no. of actors
nPeriods <- ncol(depvar) - 1 # no. of periods
nCont <- length(depvars) # no. of continuous variables
-
+
if(nCont > 1)
stop("getContinuousStartingVals not defined for more than one continuous variable")
# determine SDE parameters by regressing each observation on the
# preceding observation, using the Bergstrom formula
- # note: wiener process parameter G is set to 1 for identifiability
- LL <- function(theta)
+ # note: wiener process parameter G is set to 1 for identifiability
+ LL <- function(theta)
{
a <- theta[1]
b0 <- theta[2]
tau <- theta[3:(2+nPeriods)]
minlogliks <- rep(0, nPeriods)
-
+
for(i in 1:nPeriods)
{ # actors present at time i and i+1
act <- which(!is.na(depvar[,i] + depvar[,i+1]))
- R <- depvar[act,i+1] - exp(a * tau[i]) * depvar[act,i] -
+ R <- depvar[act,i+1] - exp(a * tau[i]) * depvar[act,i] -
(exp(a*tau[i]) - 1) * b0 / a
- R <- suppressWarnings(dnorm(R, 0, sqrt((exp(2 * a * tau[i]) - 1) / (2*a)),
+ R <- suppressWarnings(dnorm(R, 0, sqrt((exp(2 * a * tau[i]) - 1) / (2*a)),
log = TRUE))
minlogliks[i] <- -sum(R)
}
@@ -1863,13 +1869,13 @@
g <- theta[3]
# actors present at time 1 and 2
act <- which(!is.na(depvar[,1] + depvar[,2]))
- R <- depvar[act,2] - exp(a) * depvar[act,1] -
+ R <- depvar[act,2] - exp(a) * depvar[act,1] -
(exp(a) - 1) * b0 / a
- R <- suppressWarnings(dnorm(R, 0, sqrt((exp(2 * a) - 1) * g^2 / (2*a)),
+ R <- suppressWarnings(dnorm(R, 0, sqrt((exp(2 * a) - 1) * g^2 / (2*a)),
log = TRUE))
-sum(R)
}
-
+
if (onePeriodSde)
fit <- optim(theta <- c(-0.5, 3, 1), LLonePeriodSde, hessian = TRUE)
else
@@ -1885,10 +1891,10 @@
cat("SDE par stand errors:", sqrt(diag(solve(fit$hessian))), '\n')
if (onePeriodSde) # return: tau, g, a, b0
- list(startScale = 1, startWiener = fit$par[3], startFbic = fit$par[1:2])
+ list(startScale = 1, startWiener = fit$par[3], startFbic = fit$par[1:2])
else
- list(startScale = fit$par[3:(2+nPeriods)], startWiener = 1,
- startFbic = fit$par[1:2])
+ list(startScale = fit$par[3:(2+nPeriods)], startWiener = 1,
+ startFbic = fit$par[1:2])
}
##@getNetworkStartingVals DataCreate
getNetworkStartingVals <- function(depvar)
Modified: pkg/RSienaTest/R/sienaBayes.r
===================================================================
--- pkg/RSienaTest/R/sienaBayes.r 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/R/sienaBayes.r 2019-10-24 12:49:20 UTC (rev 342)
@@ -1664,12 +1664,35 @@
(dim(prevAns$requestedEffects)[1] == sum(effects$include)) &
!prevAns$x$cconditional)
{
- nsub <- 0
- if (prevAns$n3 >= 500)
+ e1 <- prevAns$requestedEffects[prevAns$requestedEffects$include,]
+ e2 <- effects[effects$include,]
+ if (all(e1$name == e2$name) & all(e1$shortName == e2$shortName) &
+ all(e1$type == e2$type) & all(e1$effect1 == e2$effect1) &
+ all(e1$effect2 == e2$effect2) &
+ all(e1$effect3 == e2$effect3) &
+ all(e1$interaction1 == e2$interaction1) &
+ all(e1$interaction2 == e2$interaction2) &
+ all(e1$parm == e2$parm))
{
- startupSkip <- TRUE
+ nsub <- 0
+ if (prevAns$n3 >= 500)
+ {
+ startupSkip <- TRUE
+ }
+ else
+ {
+ message('prevAns is given with low value of n3.\n')
+ }
}
+ else
+ {
+ message('prevAns does not have same specification.\n')
+ }
}
+ else
+ {
+ message('prevAns does not have same number of effects.\n')
+ }
}
startupModel <- sienaAlgorithmCreate(n3=500, nsub=nsub, cond=FALSE,
firstg=initgainGlobal, lessMem=TRUE,
Modified: pkg/RSienaTest/R/sienaGOF.r
===================================================================
--- pkg/RSienaTest/R/sienaGOF.r 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/R/sienaGOF.r 2019-10-24 12:49:20 UTC (rev 342)
@@ -235,7 +235,6 @@
attr(ret, "key") <- plotKey
ret
}
-
res <- lapply(1:length(simStats),
function (i) {
applyTest(obsStats[[i]], simStats[[i]]) })
Modified: pkg/RSienaTest/R/sienaprint.r
===================================================================
--- pkg/RSienaTest/R/sienaprint.r 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/R/sienaprint.r 2019-10-24 12:49:20 UTC (rev 342)
@@ -397,12 +397,11 @@
rep('\n',x$qq), sep='')
}
cat(as.matrix(mymess1),'\n', sep='')
- cat("\nSimulated statistics are in ...$sf")
-# paste(objectName,'$sf',sep=""))
+ cat("\nSimulated statistics are in ", objectName,'$sf',sep="")
if (x$returnDeps)
{
- cat("\nand simulated dependent variables in ...$sims.\n")
-# paste(objectName,'$sims',sep=""), ".\n")
+ cat("\nand simulated dependent variables in ",
+ objectName,'$sims.\n',sep="")
}
else
{
Modified: pkg/RSienaTest/data/allEffects.csv
===================================================================
--- pkg/RSienaTest/data/allEffects.csv 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/data/allEffects.csv 2019-10-24 12:49:20 UTC (rev 342)
@@ -228,6 +228,7 @@
covarSymmetricObjective,xxxxxx in-alter dist 2,xxxxxx in-alter dist 2,altInDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarSymmetricObjective,xxxxxx tot in-alter dist 2,xxxxxx tot in-alter dist 2,totInDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarSymmetricObjective,xxxxxx ego-in-alter dist 2 similarity,xxxxxx ego-in-alter dist 2 similarity,simEgoInDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic,FALSE
+covarSymmetricObjective,xxxxxx group-av. ego,Sum of degr. x aver. xxxxxx,avGroupEgoX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
covarBipartiteObjective,xxxxxx alter,Sum of indegrees x xxxxxx,altX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarBipartiteObjective,xxxxxx alter,Sum of indegrees x xxxxxx,altX,TRUE,xxxxxx,,gmm,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,gmm,NA,NA,0,0,0,0,dyadic,FALSE
covarBipartiteObjective,xxxxxx squared alter,Sum of indegrees x squared xxxxxx,altSqX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
@@ -252,6 +253,7 @@
covarBipartiteObjective,4-cycles (#) same xxxxxx,sum 4-cycles^1/# same xxxxxx,sameXCycle4,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
covarBipartiteObjective,outd. act. to hom. xxxxxx,sum sqr. outd. to hom. values on xxxxxx,homXOutAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
covarBipartiteObjective,outd. act. weight alt. xxxxxx,sum sqr. outd. weight alt. xxxxxx,altXOutAct,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
+covarBipartiteObjective,xxxxxx group-av. ego,Sum of outdegr. x aver. xxxxxx,avGroupEgoX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
covarNonSymmetricObjective,xxxxxx alter,Sum indegrees x xxxxxx,altX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,xxxxxx simmelian alter,Sum simm. indegrees x xxxxxx,simmelianAltX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,xxxxxx alter,Sum indegrees x xxxxxx,altX,TRUE,xxxxxx,,gmm,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,gmm,NA,NA,0,0,0,0,dyadic,FALSE
@@ -311,6 +313,7 @@
covarNonSymmetricObjective,xxxxxx in-alter dist 2,xxxxxx in-alter dist 2,altInDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,xxxxxx tot in-alter dist 2,xxxxxx tot in-alter dist 2,totInDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,xxxxxx ego-in-alter dist 2 similarity,xxxxxx ego-in-alter dist 2 similarity,simEgoInDist2,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,dyadic,FALSE
+covarNonSymmetricObjective,xxxxxx group-av. ego,Sum of outdegr. x aver. xxxxxx,avGroupEgoX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
covarBehaviorNetObjective,xxxxxx: av. sim. (zzzzzz) x ego's yyyyyy,xxxxxx av. sim. (zzzzzz) x ego's yyyyyy,avSimEgoX,TRUE,yyyyyy,zzzzzz,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
covarBehaviorNetObjective,xxxxxx: tot. sim. (zzzzzz) x ego's yyyyyy,xxxxxx tot. sim. (zzzzzz) x ego's yyyyyy,totSimEgoX,TRUE,yyyyyy,zzzzzz,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
covarBehaviorNetObjective,xxxxxx: av. alters (zzzzzz) x ego's yyyyyy,xxxxxx av. alters (zzzzzz) x ego's yyyyyy,avAltEgoX,TRUE,yyyyyy,zzzzzz,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 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/doc/RSiena.bib 2019-10-24 12:49:20 UTC (rev 342)
@@ -977,7 +977,7 @@
}
@article{CH56,
-author ={Cartwright, D., and F. Harary},
+author ={Dorwin Cartwright and Frank Harary},
year = 1956,
title = {Structural Balance: A Generalization of Heider’s Theory},
journal = {Psychological Review},
@@ -1341,6 +1341,8 @@
title={Transitivity correlation: {A} descriptive measure of network transitivity},
journal={Network Science},
author={Dekker, David and Krackhardt, David and Snijders, Tom A. B.},
+ volume = 7,
+ pages = {353--375},
year={2019}
}
@@ -1416,6 +1418,16 @@
Pages = {331--357},
Year = {1994} }
+ at article{DonnatHolmes2018,
+ author = "Donnat, Claire and Holmes, Susan",
+ journal = "The Annals of Applied Statistics",
+ issue = "2",
+ pages = "971--1012",
+ title = "Tracking network dynamics: {A} survey using graph distances",
+ volume = "12",
+ year = "2018"
+}
+
@article{Doreian1980,
title={Linear models with spatially distributed data: {S}patial disturbances or spatial effects?},
author={Doreian, Patrick},
@@ -2627,8 +2639,9 @@
@book{HBPM2012,
Author = {Marina Hennig and Ulrik Brandes and J\"{u}rgen Pfeffer and Ines Mergel},
- title = {Studying Social Networks: A Guide to Empirical Research},
+ title = {Studying Social Networks: {A} Guide to Empirical Research},
Publisher = {Campus-Verlag},
+ address = {Frankfurt/New York},
Year = "2012"
}
@@ -4284,6 +4297,17 @@
}
+
+ at article{LospinosoSnijders2019,
+ AUTHOR = {Joshua A. Lospinoso and {Tom A. B.} Snijders},
+ title = "Goodness of fit for Stochastic Actor-Oriented Models",
+ publisher = "Presentation at the XXXI Sunbelt Social Networks conference,
+ February 8-13, St. Pete's Beach, Florida",
+ journal = {Methodological Innovations},
+ year = "2019",
+ pages = {in press}
+}
+
@article{LottLott1965,
year={1965},
journal={Psychological Bulletin },
Modified: pkg/RSienaTest/doc/RSiena_Manual.pdf
===================================================================
(Binary files differ)
Modified: pkg/RSienaTest/doc/RSiena_Manual.tex
===================================================================
--- pkg/RSienaTest/doc/RSiena_Manual.tex 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/doc/RSiena_Manual.tex 2019-10-24 12:49:20 UTC (rev 342)
@@ -186,7 +186,7 @@
by Mark Huisman, Michael Schweinberger, and Christian Steglich.
This manual is frequently updated, mostly only in a minor way.
-This version was renewed for \RS version 1.2-17.
+This version was renewed for \RS version 1.2-18.
\end{abstract}
@@ -350,7 +350,8 @@
standard errors of the Method of Moments estimators.
For assessing and
correcting time heterogeneity, and goodness of fit assement and associated model
-selection considerations, refer to \citet*{Lospinoso2011} and \citet{Lospinoso2012}.
+selection considerations, refer to \citet*{Lospinoso2011} and
+\citet{LospinosoSnijders2019}.
A basic reference for the Bayesian estimation is \citet{KoskinenSnijders07}
and for the maximum likelihood estimation \citet*{SnijdersEA10a}.
For Generalized Method of Moments estimators,
@@ -894,7 +895,7 @@
\end{itemize}
Installation from a downloaded file can be done as follows, assuming
- the root name of the file is \texttt{RSienaTest\_1.2-17}, and filling in the correct path name.
+ the root name of the file is \texttt{RSienaTest\_1.2-18}, and filling in the correct path name.
It will be convenient to first navigate to the directory
containing the \RS binary or source file so that this is the current directory.
Then the pathname consists only of the filename.
@@ -901,17 +902,17 @@
\begin{itemize}
\item In \R from binary:\\
for Windows:\\
- \texttt{install.packages("pathname to RSienaTest\_1.2-17.zip", repos = NULL, type="binary")}\\
+ \texttt{install.packages("pathname to RSienaTest\_1.2-18.zip", repos = NULL, type="binary")}\\
for Mac:\\
- \texttt{install.packages("pathname to RSienaTest\_1.2-17.tgz", repos = NULL, type="binary")}
+ \texttt{install.packages("pathname to RSienaTest\_1.2-18.tgz", repos = NULL, type="binary")}
\item In \R from source:\\
- \texttt{install.packages("RSienaTest\_1.2-17.tar.gz", repos = NULL, type="source")}
+ \texttt{install.packages("RSienaTest\_1.2-18.tar.gz", repos = NULL, type="source")}
\item In \text{command.com} or in batch mode (Windows) from binary:\\
- \texttt{R CMD INSTALL RSienaTest\_1.2-17.zip}
+ \texttt{R CMD INSTALL RSienaTest\_1.2-18.zip}
\item In the terminal (Mac) from binary:\\
- \texttt{R CMD INSTALL RSienaTest\_1.2-17.tgz}
+ \texttt{R CMD INSTALL RSienaTest\_1.2-18.tgz}
\item In \text{command.com} or in batch mode (Windows) or in the terminal (Mac) from source:\\
- \texttt{R CMD INSTALL RSienaTest\_1.2-17.tar.gz}
+ \texttt{R CMD INSTALL RSienaTest\_1.2-18.tar.gz}
\item In drop-down menu in \Rn:\\
for Windows: go to Packages $\rightarrow$ Install package(s) from local zip file\\
for Mac: go to Packages \& Data $\rightarrow$ Package Installer
@@ -1111,7 +1112,7 @@
of \rs. Details of the latest version available can
be found at \small{\url{http://r-forge.r-project.org/R/?group_id=461}}.
The version is
- identified by a version number (e.g.\ 1.2-17) and an R-Forge revision
+ identified by a version number (e.g.\ 1.2-18) and an R-Forge revision
number. You can find both numbers of your current installed version by
opening \R, and typing \\
\verb|packageDescription("RSiena")|. The version is
@@ -3840,7 +3841,8 @@
also of these other statistics.
The \sfn{sienaGOF} function, proposed and elaborated by
-\citet{Lospinoso2012}, operates basically by comparing
+\citet{Lospinoso2012} and presented further
+in \citet{LospinosoSnijders2019}, operates basically by comparing
the observed values, at the ends of the periods, with the
simulated values for the ends of the periods.
The differences are assessed by combining the auxiliary statistics
@@ -8405,7 +8407,10 @@
the number of actors to whom $i$
is not directly tied, and tied through twopaths via at least two intermediaries,\\
$s^{\rm net}_{i\vit}(x) = \#\{j \mid x_{ij} = 0,\, \sum_h (x_{ih}\, x_{hj}) \geq 2 \}$;\\
- endowment effect only likelihood-based;
+ evidently, this is even more difficult to interpret than \texttt{(nbrDist2)};
+ both effects should be used if there are very specific
+ and convincing reasons to include them in the model;\\
+ endowment effect only likelihood-based;\\
\item {\em number of dense triads} \texttt{(denseTriads)},
@@ -9650,6 +9655,18 @@
\end{minipage}
\setcounter{savenumi}{\value{enumi}}
+
+ \item {\em group average} \texttt{(avGroupEgoX)}, defined by ego's value multiplied by the
+ average of the covariate for this period, \\
+ $s^{\rm beh}_{i\vit}(x, z) = \sum_j x_{ij} \, \overline {v} $;\\
+ here $\overline {v}$ is the mean of the values $v_{ih}$ for all actors $h$
+ in the actor set: for changing covariate, the mean of the wave at the
+ start of the period; for behavioral dependent variables,
+ the current mean.
+ This effect is not meaningful for constant covariates.
+ It is useful especially for multigroup data sets, where the average value
+ varies between groups.
+ Note that always, the average $\overline {v} $ is centered by the global mean.
\end{enumerate}
\noindent
@@ -12089,10 +12106,11 @@
in the group, and $c_p$ is a centering constant depending on the internal effect parameter $p$.
Denote the overall mean used for centering the observed $Z$ values by
$m_Z$ (see the footnote on p.~\pageref{meandef}).
- If $p \leq 0$, centering is no different than for the $z_i$ values generally,
- so $c_p = 0$; if $p \geq 1$, centering is by $c_p = p - m_Z$.
+ If $p \leq 0.5$, centering is no different than for the $z_i$ values generally,
+ so $c_p = 0$; if $p > 0.5$, centering is by $c_p = p - m_Z$.
For the original non-centered values of $Z$, this means that the mean
- is centered around the value $p$.\\
+ is centered around the value $p$, the effect parameter itself.
+ Note that this can be any real value, not necessarily integer.\\
This effect is useful especially for multigroup data sets, where the average value
varies between groups. For multigroup data sets, centering by the groupwise
mean may be less desirable, and it will be better to center by a value $p$
@@ -15182,6 +15200,37 @@
\begin{small}
\begin{itemize} % Also update version number in abstract
+
+\item 2019-10-17 R-Forge Revision 341, RSienaTest version 1.2-18.
+
+Changes in RSienaTest:
+\begin{itemize}
+ \item Continuous dependent behavior variables implemented (Nynke Niezink).
+ This implies new effect types \texttt{continuousFeedback},
+ \texttt{ continuousIntercept}, \\
+ \texttt{continuousOneModeObjective},
+ \texttt{ continuousRate}, \texttt{ continuousWiener}, \\
+ \texttt{ unspecifiedContinuousInteraction}.
+ \item \texttt{imputationValues} allowed in \sfn{sienaDependent} (Nynke Niezink).
+ \item New effect \texttt{outMore}.
+ \item component \texttt{startingDate} added to \sfn{sienaFit} object;
+ this date is reported in \sfn{siena.table(..., type='tex', ...)}.
+ \item Object names are given in \sfn{sienaFit.print} if \texttt{simOnly}.
+ \item Speeded up calculation of \sfn{IndegreeDistribution} and \sfn{OutdegreeDistribution}
+ for \sfn{sienaGOF} if there are no missings or structurals.
+ \item \texttt{regrCoef} and \texttt{regrCor} added to the \sfn{sienaFit} object
+ also when not \texttt{dolby}.
+ \item Immediate stop if \texttt{useCluster} and \texttt{returnChains}
+ both are used (in this case, no chains would be returned anyway).
+ \item \sfn{sienaDataCreate}: more informative message in case of constraints.
+ \item Small improvements in many help pages.
+ \item Corrected error in names of array returned by \sfn{extract.posteriorMeans}.
+ \item New parameter \texttt{excludeRates} in \sfn{extract.posteriorMeans},
+ \sfn{plotPostMeansMDS}.
+ \item Use parameter \texttt{pmonly} also in \sfn{plotPostMeansMDS}.
+\end{itemize}
+
+
\item 2019-05-20 R-Forge Revision 340, package version 1.2-17.
Changes in RSiena and RSienaTest:
@@ -15433,7 +15482,7 @@
Changes in RSienaTest:
\begin{itemize}
\item new function \sfn{extract.posteriorMeans} for \sfn{sienaBayes} results.
- \item Restrict check of maximum
+ \item Restrict check in \sfn{sienaBayes} of maximum
estimated parameter value after initialization to non-fixed effects.
\item Correct construction of groupwise effects object in \sfn{sienaBayes}
so that this
@@ -15444,7 +15493,8 @@
In \sfn{print.sienaBayesFit}, include fixed parameters and
give credibility intervals for rate parameters; include variance parameters;
allow shorter \texttt{ThinParameters};
- print objects returned through \texttt{partialBayesResult.RData}
+ print objects returned through \\
+ \texttt{partialBayesResult.RData}
(by adding \texttt{na.rm=TRUE} to quantile).
\item \sfn{multipleBayesTest} corrected (there was an error for testing
2 or more linear combinations simultaneously)
Modified: pkg/RSienaTest/man/RSiena-package.Rd
===================================================================
--- pkg/RSienaTest/man/RSiena-package.Rd 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/man/RSiena-package.Rd 2019-10-24 12:49:20 UTC (rev 342)
@@ -49,8 +49,8 @@
\tabular{ll}{
Package: \tab RSienaTest\cr
Type: \tab Package\cr
- Version: \tab 1.2-18\cr
- Date: \tab 2019-10-16\cr
+ Version: \tab 1.2-19\cr
+ Date: \tab 2019-10-24\cr
Depends: \tab R (>= 3.0.0)\cr
Imports: \tab Matrix\cr
Suggests: \tab tcltk, network, codetools, lattice, MASS, parallel,
@@ -63,9 +63,10 @@
}
}
\author{
- Ruth Ripley, Krists Boitmanis, Tom Snijders, Felix Schoenenberger.
+ Ruth Ripley, Krists Boitmanis, Tom Snijders, Felix Schoenenberger,
+ Nynke Niezink.
Contributions by Josh Lospinoso, Charlotte Greenan, Christian Steglich,
- Johan Koskinen, Mark Ortmann, Nynke Niezink, Natalie Indlekofer,
+ Johan Koskinen, Mark Ortmann, Natalie Indlekofer,
Christoph Stadtfeld, Per Block, Marion Hoffman, and Robert Hellpap.
Maintainer: Tom A.B. Snijders <tom.snijders at nuffield.ox.ac.uk>
Modified: pkg/RSienaTest/man/setEffect.Rd
===================================================================
--- pkg/RSienaTest/man/setEffect.Rd 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/man/setEffect.Rd 2019-10-24 12:49:20 UTC (rev 342)
@@ -94,10 +94,9 @@
The call of \link{setEffect} will set, for this effect,
the column elements of the resulting effects object for \code{parameter},
\code{fix}, \code{test}, \code{randomEffects}, \code{initialValue},
- \code{timeDummy}, and \code{include} to the values requested.}
-
+ \code{timeDummy}, and \code{include} to the values requested.\cr
The \code{shortName} must not be set between quotes,
- unless you use \code{character=TRUE}.
+ unless you use \code{character=TRUE}.}
\value{
An object of class \code{\link{sienaEffects}} or
\code{\link{sienaGroupEffects}}. This will be an updated version of the
Modified: pkg/RSienaTest/man/sienaDependent.Rd
===================================================================
--- pkg/RSienaTest/man/sienaDependent.Rd 2019-10-16 20:25:33 UTC (rev 341)
+++ pkg/RSienaTest/man/sienaDependent.Rd 2019-10-24 12:49:20 UTC (rev 342)
@@ -18,9 +18,14 @@
nodeSet="Actors", sparse=is.list(netarray), allowOnly=TRUE, imputationValues=NULL)
}
\arguments{
- \item{netarray}{matrix (type="behavior" or "continuous" only)
- or (for the other types) array of values or list of sparse matrices
- of type "dgTMatrix".}
+ \item{netarray}{type="behavior" or "continuous": matrix
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 342
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