[Rsiena-commits] r280 - in pkg/RSienaTest: . R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 19 23:53:48 CET 2014
Author: tomsnijders
Date: 2014-11-19 23:53:48 +0100 (Wed, 19 Nov 2014)
New Revision: 280
Modified:
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/inst/doc/RSiena.bib
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/inst/doc/RSiena_Manual.tex
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/sienaBayes.Rd
pkg/RSienaTest/man/sienaCompositionChange.Rd
pkg/RSienaTest/man/sienaGOF.Rd
Log:
Previous version 1.1-279 failed to compile for unknown reasons.
Modified: pkg/RSienaTest/ChangeLog
===================================================================
--- pkg/RSienaTest/ChangeLog 2014-11-13 22:29:47 UTC (rev 279)
+++ pkg/RSienaTest/ChangeLog 2014-11-19 22:53:48 UTC (rev 280)
@@ -1,3 +1,9 @@
+2014-11-19 R-Forge Revision 280
+Changes in RSiena and RSienaTest:
+ * Small changes in help pages for sienaGOF and for sienaCompositionChange.
+Changes in RSienaTest:
+ * New parameters nSampVarying and nSampConst in sienaBayes().
+
2014-11-13 R-Forge Revision 279
Changes in RSiena and RSienaTest:
* Effect AltsAvAlt renamed to avXAlt (with error message).
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2014-11-13 22:29:47 UTC (rev 279)
+++ pkg/RSienaTest/DESCRIPTION 2014-11-19 22:53:48 UTC (rev 280)
@@ -1,8 +1,8 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-279
-Date: 2014-11-13
+Version: 1.1-280
+Date: 2014-11-19
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders
Depends: R (>= 2.15.0)
Imports: Matrix
Modified: pkg/RSienaTest/R/sienaBayes.r
===================================================================
--- pkg/RSienaTest/R/sienaBayes.r 2014-11-13 22:29:47 UTC (rev 279)
+++ pkg/RSienaTest/R/sienaBayes.r 2014-11-19 22:53:48 UTC (rev 280)
@@ -23,7 +23,7 @@
reductionFactor=1,
gamma=0.5, delta=1e-4,
nwarm=50, nmain=250, nrunMHBatches=20,
- nImproveMH=100,
+ nSampVarying=1, nSampConst=1, nImproveMH=100,
lengthPhase1=round(nmain/5), lengthPhase3=round(nmain/5),
storeAll = FALSE, prevAns=NULL,
prevBayes = NULL, silentstart=TRUE,
@@ -153,7 +153,8 @@
repeat
{
iter <- iter + 1
- cyc <- MCMCcycle(nrunMH=totruns, change=FALSE, bgain=-1)
+ cyc <- MCMCcycle(nrunMH=totruns, nSampVar=1,
+ nSampCons=1, change=FALSE, bgain=-1)
actual <- cyc$BayesAcceptances
## actual is a vector of the expected number of acceptances by group
## and for the non-varying parameters, in the MH change of
@@ -230,7 +231,7 @@
##@MCMCcycle internal sienaBayes; some loops of
## (MH steps and sample parameters)
- MCMCcycle <- function(nrunMH, change=TRUE, bgain)
+ MCMCcycle <- function(nrunMH, nSampVar, nSampCons, change=TRUE, bgain)
{
# is for the storage in the object produced
# and for its by-effects on the MCMC state:
@@ -271,10 +272,16 @@
# After the nrunMH the loglik by group is used as logpOld,
# see below.
# sample the group-level parameters:
- mcmcc.accept <- sampleVaryingParameters(change, bgain)
+ for (i2 in 1:nSampVar)
+ {
+ mcmcc.accept <- sampleVaryingParameters(change, bgain)
+ }
if (any(z$set2) & (!frequentist))
{
- sampleConstantParameters(change, i%%2)
+ for (i2 in 1:nSampCons)
+ {
+ sampleConstantParameters(change, i%%2)
+ }
}
else
{
@@ -793,6 +800,8 @@
z$nrunMHBatches <- 2
nrunMHBatches <- 2
}
+ z$nSampVarying <- nSampVarying
+ z$nSampConst <- nSampConst
class(z) <- "sienaBayesFit"
# Determine multiplicative constants for proposal distribution
@@ -831,7 +840,8 @@
bgain <- initfgain*exp(-gamma)
for (ii in 1:nwarm)
{
- cyc <- MCMCcycle(nrunMH=nrunMHBatches, bgain=bgain)
+ cyc <- MCMCcycle(nrunMH=nrunMHBatches, nSampVar=nSampVarying,
+ nSampCons=nSampConst, bgain=bgain)
z$iimain <- ii
storeData(cyc)
cat('Warming step',ii,'(',nwarm,')\n')
@@ -961,7 +971,8 @@
bgain <- initfgain*exp(-gamma)
for (ii in (nwarm+1):endPhase1)
{
- cyc <- MCMCcycle(nrunMH=nrunMHBatches, bgain=bgain)
+ cyc <- MCMCcycle(nrunMH=nrunMHBatches, nSampVar=nSampVarying,
+ nSampCons=nSampConst, bgain=bgain)
z$iimain <- ii
storeData(cyc)
cat('main', ii, '(', nwarm+nmain, ')')
@@ -1008,7 +1019,8 @@
for (ii in (endPhase1+1):endPhase2)
{
bgain <- initfgain*exp(-gamma*log(ii-endPhase1))
- cyc <- MCMCcycle(nrunMH=nrunMHBatches, bgain=bgain)
+ cyc <- MCMCcycle(nrunMH=nrunMHBatches, nSampVar=nSampVarying,
+ nSampCons=nSampConst, bgain=bgain)
z$iimain <- ii
storeData(cyc)
cat('main', ii, '(', nwarm+nmain, ')')
@@ -1074,7 +1086,8 @@
if (frequentist){cat('Phase 3\n')}
for (ii in (endPhase2+1):(nwarm+nmain))
{
- cyc <- MCMCcycle(nrunMH=nrunMHBatches, bgain=0.000001)
+ cyc <- MCMCcycle(nrunMH=nrunMHBatches, nSampVar=nSampVarying,
+ nSampCons=nSampConst, bgain=0.000001)
z$iimain <- ii
storeData(cyc)
cat('main', ii, '(', nwarm+nmain, ')')
@@ -1945,6 +1958,22 @@
{
dif <- TRUE
}
+ if (z1$nSampConst == z2$nSampConst)
+ {
+ z$nSampConst <- z1$nSampConst
+ }
+ else
+ {
+ dif <- TRUE
+ }
+ if (z1$nSampVarying == z2$nSampVarying)
+ {
+ z$nSampVarying <- z1$nSampVarying
+ }
+ else
+ {
+ dif <- TRUE
+ }
if (all(z1$effectName == z2$effectName))
{
z$effectName <- z1$effectName
Modified: pkg/RSienaTest/R/sienaprint.r
===================================================================
--- pkg/RSienaTest/R/sienaprint.r 2014-11-13 22:29:47 UTC (rev 279)
+++ pkg/RSienaTest/R/sienaprint.r 2014-11-19 22:53:48 UTC (rev 280)
@@ -1206,7 +1206,9 @@
cat("\nBasic rates parameters are treated as incidental parameters.\n\n")
}
cat("\nAlgorithm specifications were nwarm =",x$nwarm,", nmain =", x$nmain,
- ", nrunMHBatches =", x$nrunMHBatches, ", mult =", x$mult, ".\n")
+ ", nrunMHBatches =", x$nrunMHBatches,
+ ", nSampVarying =", x$nSampVarying, ", nSampConst =", x$nSampConst,
+ ", mult =", x$mult, ".\n")
if (!is.null(nfirst))
{
cat("For the results, nwarm is superseded by nfirst = ", nfirst, ".")
Modified: pkg/RSienaTest/inst/doc/RSiena.bib
===================================================================
--- pkg/RSienaTest/inst/doc/RSiena.bib 2014-11-13 22:29:47 UTC (rev 279)
+++ pkg/RSienaTest/inst/doc/RSiena.bib 2014-11-19 22:53:48 UTC (rev 280)
@@ -2979,6 +2979,16 @@
PAGES = "1861--1869"
}
+ at article{Milgram1967,
+ title={The small world problem},
+ author={Milgram, Stanley},
+ journal={Psychology Today},
+ volume={2},
+ number={1},
+ pages={60--67},
+ year={1967}
+}
+
% No first names in published paper
@article{MSIKCA02,
author = {R. Milo and S. Shen-Orr and S. Itzkovitz and N. Kashtan and
@@ -3730,7 +3740,7 @@
@article{RWP05,
author = {Robins, Garry L. and Woolcock, Jodie and Pattison, Philippa},
-title = {Small and Other Worlds: Global Network Structures from Local Processes},
+title = {Small and Other Worlds: {G}lobal Network Structures from Local Processes},
year = 2005,
journal = {American Journal of Sociology},
volume = 110,
@@ -4200,13 +4210,13 @@
year = 1999,
}
- at Article{SnijdersSteglich13,
+ at Article{SnijdersSteglich14,
author = {Tom A. B. Snijders and Christian E.G. Steglich},
title = {Representing Micro-Macro Linkages by
Actor-Based Dynamic Network Models},
journal = {Sociological Methods \& Research},
- year = 2013,
- volume = 37,
+ year = 2014,
+ volume = 38,
pages = {xxx-xxx}}
@@ -4462,7 +4472,7 @@
From Samples to Populations: From Polarization to Integration},
journal = {Multivariate Behavioral Research},
volume = {44},
- pages = {711 -- 740}
+ pages = {711--740}
}
@@ -4548,6 +4558,13 @@
address = {Cambridge},
year = 2003}
+ at article{TraversMilgram1969,
+ title={An experimental study of the small world problem},
+ author={Travers, Jeffrey and Milgram, Stanley},
+ journal={Sociometry},
+ pages={425--443},
+ year={1969}
+}
@InCollection{TubaroSNDE,
author = {Paola Tubaro and Lise Mounier and Emmanuel Lazega and
@@ -4865,6 +4882,15 @@
pages = {243--270}
}
+ at article{WattsStrogatz1998,
+ title={Collective dynamics of small-world' networks},
+ author={Watts, Duncan J and Strogatz, Steven H},
+ journal={Nature},
+ volume={393},
+ number={6684},
+ pages={440--442},
+ year={1998}
+}
@ARTICLE{Wejnert02,
@@ -4970,8 +4996,8 @@
}
@book{Zeggelink93diss,
title={Strangers into friends:
- The evolution of friendship networks using an individual oriented modeling approach},
- author={Zeggelink, Evelien},
+ {T}he evolution of friendship networks using an individual oriented modeling approach},
+ author={Zeggelink, Evelien P.H.},
year={1993},
publisher={Thesis publishers Amsterdam}
}
Modified: pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSienaTest/inst/doc/RSiena_Manual.pdf 2014-11-13 22:29:47 UTC (rev 279)
+++ pkg/RSienaTest/inst/doc/RSiena_Manual.pdf 2014-11-19 22:53:48 UTC (rev 280)
@@ -62,15 +62,13 @@
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[TRUNCATED]
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