[Rsiena-commits] r157 - in pkg: RSiena RSiena/R RSiena/inst/doc RSiena/man RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/inst/doc RSienaTest/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jun 19 01:40:22 CEST 2011
Author: ripleyrm
Date: 2011-06-19 01:40:21 +0200 (Sun, 19 Jun 2011)
New Revision: 157
Modified:
pkg/RSiena/DESCRIPTION
pkg/RSiena/NAMESPACE
pkg/RSiena/R/RSienaRDocumentation.r
pkg/RSiena/R/bayes.r
pkg/RSiena/R/effectsDocumentation.r
pkg/RSiena/R/maxlikec.r
pkg/RSiena/R/phase1.r
pkg/RSiena/R/phase2.r
pkg/RSiena/R/siena08.r
pkg/RSiena/R/sienaprint.r
pkg/RSiena/changeLog
pkg/RSiena/inst/doc/RSiena_Manual.pdf
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/man/sienaFit.Rd
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/NAMESPACE
pkg/RSienaTest/R/RSienaRDocumentation.r
pkg/RSienaTest/R/bayes.r
pkg/RSienaTest/R/effectsDocumentation.r
pkg/RSienaTest/R/maxlikec.r
pkg/RSienaTest/R/phase1.r
pkg/RSienaTest/R/phase2.r
pkg/RSienaTest/R/siena08.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/RSiena_Manual.tex
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/sienaFit.Rd
Log:
xtable, sd bug, warnings
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/DESCRIPTION 2011-06-18 23:40:21 UTC (rev 157)
@@ -1,12 +1,12 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.156
-Date: 2011-06-13
+Version: 1.0.12.157
+Date: 2011-06-18
Author: Various
-Depends: R (>= 2.10.0), xtable
+Depends: R (>= 2.10.0)
Imports: Matrix
-Suggests: tcltk, snow, rlecuyer, network, codetools, lattice, MASS
+Suggests: tcltk, snow, rlecuyer, network, codetools, lattice, MASS, xtable
SystemRequirements: GNU make, tcl/tk 8.5, Tktable
Maintainer: Ruth Ripley <ruth at stats.ox.ac.uk>
Description: Fits models to longitudinal networks
Modified: pkg/RSiena/NAMESPACE
===================================================================
--- pkg/RSiena/NAMESPACE 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/NAMESPACE 2011-06-18 23:40:21 UTC (rev 157)
@@ -2,13 +2,12 @@
export(coCovar, coDyadCovar, getEffects, model.create, print01Report,
siena01Gui, siena07, sienaCompositionChange,
sienaCompositionChangeFromFile, sienaDataCreate, sienaDataCreateFromSession,
-sienaGroupCreate, sienaModelCreate, sienaNet, sienaNodeSet, #simstats0c,
+sienaGroupCreate, sienaModelCreate, sienaNet, sienaNodeSet, xtable.sienaFit,
varCovar, varDyadCovar, setEffect, includeEffects, includeInteraction,
- effectsDocumentation, sienaDataConstraint, #maxlikefn,
+ effectsDocumentation, sienaDataConstraint, print.xtable.sienaFit,
installGui, siena08, iwlsm, sienaTimeTest, includeTimeDummy)
import(Matrix)
-import(xtable)
S3method(print, siena)
S3method(print, sienaGroup)
@@ -16,8 +15,6 @@
S3method(print, summary.sienaFit)
S3method(print, sienaModel)
S3method(summary, sienaFit)
-S3method(xtable, sienaFit)
-S3method(print, xtable.sienaFit)
S3method(print, sienaMeta)
S3method(print, summary.sienaMeta)
S3method(summary, sienaMeta)
Modified: pkg/RSiena/R/RSienaRDocumentation.r
===================================================================
--- pkg/RSiena/R/RSienaRDocumentation.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/RSienaRDocumentation.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -39,7 +39,7 @@
##@getRSienaDocumentation Documentation
getRSienaRDocumentation <- function(Rdir)
{
- # library(xtable)
+ library(xtable)
library(codetools)
thisdir <- getwd()
Modified: pkg/RSiena/R/bayes.r
===================================================================
--- pkg/RSiena/R/bayes.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/bayes.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -16,7 +16,6 @@
createStores <- function(z)
{
npar <- length(z$theta)
- basicRate <- z$basicRate
numberRows <- nmain * nrunMHBatches
z$posteriorTot <- matrix(0, nrow=z$nGroup, ncol=npar)
z$posteriorMII <- array(0, dim=c(z$nGroup, npar, npar))
@@ -31,7 +30,6 @@
{
start <- z$sub + 1
nrun <- nrow(z$parameters)
- basicRate <- z$basicRate
npar <- length(z$theta)
end <- start + nrun - 1
z$acceptances[, start:end] <- z$accepts
Modified: pkg/RSiena/R/effectsDocumentation.r
===================================================================
--- pkg/RSiena/R/effectsDocumentation.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/effectsDocumentation.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -103,7 +103,7 @@
filename2 <- paste(filename,".tex", sep="", collapse="")
includefile <- paste(filename,".include.tex", sep="", collapse="")
includepart <- paste(filename,".include", sep="", collapse="")
- print(xtable(y), add.to.row=add.to.row, file=includefile,
+ print(xtable::xtable(y), add.to.row=add.to.row, file=includefile,
tabular.environment="longtable", hline.after=c(-1),
floating=FALSE, include.rownames=FALSE)
@@ -125,7 +125,7 @@
else
{
filename <- paste(filename,".html", sep="", collapse="")
- print(xtable(y), add.to.row=add.to.row,
+ print(xtable::xtable(y), add.to.row=add.to.row,
file=filename,
type="html", hline.after=c(-1),
sanitize.text.function=function(x){x},
Modified: pkg/RSiena/R/maxlikec.r
===================================================================
--- pkg/RSiena/R/maxlikec.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/maxlikec.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -11,7 +11,7 @@
# *****************************************************************************/
##@maxlikec siena07 ML Simulation Module
maxlikec <- function(z, x, INIT=FALSE, TERM=FALSE, initC=FALSE, data=NULL,
- effects=NULL, profileData=FALSE, prevAns=NULL,
+ effects=NULL, profileData=FALSE, prevAns=NULL,
returnDeps=FALSE, returnChains=FALSE, byGroup=FALSE,
returnDataFrame=FALSE)
{
Modified: pkg/RSiena/R/phase1.r
===================================================================
--- pkg/RSiena/R/phase1.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/phase1.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -261,8 +261,10 @@
{
# Report(c('Phase', z$Phase, 'Iteration ', z$nit, '\n'))
if (is.batch())
+ {
Report(c('Phase ', z$Phase, ' Iteration ', z$nit, ' Progress: ',
round(progress), '%\n'), sep='')
+ }
else
{
DisplayTheta(z)
Modified: pkg/RSiena/R/phase2.r
===================================================================
--- pkg/RSiena/R/phase2.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/phase2.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -42,7 +42,7 @@
tkconfigure(z$tkvars$subphaselabel,state='normal')
}
z$Deriv <- FALSE
- z$sd <- sqrt(apply(z$sf, 2, function(x) sum(x^2) / z$n1 - mean(x)^2))
+ z$sd <- sqrt(apply(z$sf, 2, function(x) sum(x^2) / nrow(z$sf) - mean(x)^2))
z$sd[z$fixed] <- 0
## browser()
Report(paste('\nPhase 2 has', x$nsub, 'subphases.\n'), cf)
Modified: pkg/RSiena/R/siena08.r
===================================================================
--- pkg/RSiena/R/siena08.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/siena08.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -119,9 +119,9 @@
cjplusp <- 1 - pchisq(cjplus, 2 * nrow(x1))
cjminusp <- 1 - pchisq(cjminus, 2 * nrow(x1))
## ML estimates and confidence intervals
- maxxlik <- maxlik(x1$theta,x1$se)
- cmu <- confint.mu(x1$theta,x1$se,alpha)
- csig <- confint.sig(x1$theta,x1$se,alpha)
+ maxxlik <- maxlik(x1$theta, x1$se)
+ cmu <- confint.mu(x1$theta, x1$se, alpha)
+ csig <- confint.sig(x1$theta, x1$se, alpha)
ret1 <- list(cor.est=check.correl$estimate,
cor.pval=check.correl$p.value,
cor.meth=check.correl$method,
@@ -133,7 +133,7 @@
pttilde=1 - pchisq(Qstat, nrow(x1) - 1),
cjplus=cjplus, cjminus=cjminus,
cjplusp=cjplusp, cjminusp=cjminusp, n1=nrow(x1),
- mu.ml=maxxlik$mu, sigma.ml=maxxlik$sig,
+ mu.ml=maxxlik$mu, sigma.ml=maxxlik$sigma,
mu.ml.se=maxxlik$se.mu,
mu.confint=cmu, sigma.confint=csig)
}
@@ -283,7 +283,7 @@
",",
format(round(y$mu.confint[2], 4), width=7), "]\n"), outf)
Report(c("Estimated standard deviation",
- ifelse((y$sigma.ml > 0.0001)|(y$sigma.ml < 0.0000001),
+ ifelse((y$sigma.ml > 0.0001) | (y$sigma.ml < 0.0000001),
format(round(y$sigma.ml, 4), width=9), " < 0.0001"),
"\n"), outf)
Report(c(format(round(y$sigma.confint[3], 2), width=4),
Modified: pkg/RSiena/R/sienaprint.r
===================================================================
--- pkg/RSiena/R/sienaprint.r 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/R/sienaprint.r 2011-06-18 23:40:21 UTC (rev 157)
@@ -458,7 +458,7 @@
format(mydf[mydf$row < 1, 'row'])
mydf[mydf[,'row'] >= 1, 'row'] <- paste(format(mydf[mydf$row >= 1,
'row']), '.', sep='')
- tmp <- list(xtable(mydf, caption=caption, label=label, align=align,
+ tmp <- list(xtable::xtable(mydf, caption=caption, label=label, align=align,
digits=digits, display=display), add.to.row=addtorow,
include.colnames=FALSE, include.rownames=FALSE, ...)
class(tmp) <- c("xtable.sienaFit", "xtable")
Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/changeLog 2011-06-18 23:40:21 UTC (rev 157)
@@ -1,3 +1,15 @@
+2011-06-18 R-forge revision 157
+
+ * R/phase2.r: corrected definition of standard deviation used to control
+ maximum jump. Was incorrect if using prevAns as it had the deviations
+ from phase 3 rather than phase 1.
+ * R/phase1.r, R/maxlikec.r, R/siena08.r: reformatting, using complete
+ object names
+ * R/bayes.r: remove unused variables to avoid warnings
+ * man/sienaFit.Rd, R/effectsDocumentation.r, R/RSienaRDocumentation.r,
+ R/sienaprint.r, DESCRIPTION, NAMESPACE: alter interface to xtable to
+ allow loading package without it.
+
2011-06-13 R-forge revision 156
* R/bayes.r, R/maxlikec.r, R/initializeFRAN.r, R/phase1.r,
Modified: pkg/RSiena/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSiena/inst/doc/RSiena_Manual.pdf 2011-06-13 14:32:32 UTC (rev 156)
+++ pkg/RSiena/inst/doc/RSiena_Manual.pdf 2011-06-18 23:40:21 UTC (rev 157)
@@ -51,18 +51,17 @@
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 157
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