[Rsiena-commits] r146 - in pkg: RSiena RSiena/R RSiena/inst/doc RSiena/man RSiena/src RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/inst/doc RSienaTest/man RSienaTest/src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 16 16:37:24 CEST 2011
Author: ripleyrm
Date: 2011-05-16 16:37:22 +0200 (Mon, 16 May 2011)
New Revision: 146
Modified:
pkg/RSiena/DESCRIPTION
pkg/RSiena/R/siena08.r
pkg/RSiena/R/sienaDataCreate.r
pkg/RSiena/R/sienaDataCreateFromSession.r
pkg/RSiena/changeLog
pkg/RSiena/inst/doc/s_man400.pdf
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/src/Makevars.win
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/siena08.r
pkg/RSienaTest/R/sienaDataCreate.r
pkg/RSienaTest/R/sienaDataCreateFromSession.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/RSIENAspec.tex
pkg/RSienaTest/doc/RSiena.bib
pkg/RSienaTest/doc/RSienaDeveloper.tex
pkg/RSienaTest/doc/s_man400.tex
pkg/RSienaTest/doc/simstats0c.tex
pkg/RSienaTest/inst/doc/s_man400.pdf
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/src/Makevars.win
Log:
Fix to Makefile.win to reduce length of link command. Pajek non-directed file input. Other minor changes.
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2011-04-20 12:49:03 UTC (rev 145)
+++ pkg/RSiena/DESCRIPTION 2011-05-16 14:37:22 UTC (rev 146)
@@ -1,8 +1,8 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.145
-Date: 2011-04-20
+Version: 1.0.12.146
+Date: 2011-05-16
Author: Various
Depends: R (>= 2.9.0), xtable
Imports: Matrix
Modified: pkg/RSiena/R/siena08.r
===================================================================
--- pkg/RSiena/R/siena08.r 2011-04-20 12:49:03 UTC (rev 145)
+++ pkg/RSiena/R/siena08.r 2011-05-16 14:37:22 UTC (rev 146)
@@ -92,19 +92,22 @@
{
if (sum((x1$se < bound)) >= 3)
{
- suppressWarnings(check.correl <- cor.test(x1$theta, x1$se, method="spearman"))
- ## warnings will be given in case of ties, not important here
+ suppressWarnings(check.correl <- cor.test(x1$theta, x1$se,
+ method="spearman"))
+ ## warnings will be given in case of ties, not important here
}
else
{
- check.correl <- data.frame(estimate=NA, p.value=NA, method="no correlation test")
+ check.correl <- data.frame(estimate=NA, p.value=NA,
+ method="no correlation test")
}
regfit <- iwlsm(theta ~ 1, psi=psi.iwlsm, data=x1,
ses=x1$se^2)
regfit$terms <- NA
regfit$model <- NULL
regfit$psi <- NULL
- ## symbols ttilde, Qstat, Tsq as in Snijders & Baerveldt (2003), (18), (17), (15)
+ ## symbols ttilde, Qstat, Tsq as in Snijders & Baerveldt (2003),
+ ##(18), (17), (15)
Tsq <- sum((x1$theta / x1$se)^2)
regsummary <- summary(regfit)
tratio <- regsummary$coef[1, 3]
@@ -115,13 +118,13 @@
cjminus <- -2 * sum(pnorm(x1$theta / x1$se, log=TRUE))
cjplusp <- 1 - pchisq(cjplus, 2 * nrow(x1))
cjminusp <- 1 - pchisq(cjminus, 2 * nrow(x1))
- ## ML estimates and confidence intervals
+ ## 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)
ret1 <- list(cor.est=check.correl$estimate,
cor.pval=check.correl$p.value,
- cor.meth=check.correl$method,
+ cor.meth=check.correl$method,
regfit=regfit, regsummary=regsummary,
Tsq=Tsq, pTsq=1 - pchisq(Tsq, nrow(x1) - 1),
tratio=tratio,
@@ -237,14 +240,16 @@
else
{
Report(c(": \n", y$cor.meth, " =", format(round(y$cor.est, 4),
- width=9),
+ width=9),
", two-sided ",reportp(y$cor.pval,3), "\n\n"), sep="",
outf)
}
- Report("Estimates and test based on IWLS modification of Snijders & Baerveldt (2003)\n",
- outf)
- Report("----------------------------------------------------------------------------\n",
- outf)
+ Report(c("Estimates and test based on IWLS modification of",
+ "Snijders & Baerveldt (2003)\n"),
+ outf)
+ Report(c("---------------------------------------------------",
+ "-------------------------\n"), sep="",
+ outf)
Report(c("Test that all parameters are 0 : \n"), outf)
Report(c("chi-squared =", format(round(y$Tsq, 4), width=9),
", d.f. = ", y$n1, ", ",
@@ -261,27 +266,30 @@
Report(c("Chi-squared = ", format(round(y$Qstat, 4), width=9),
" (d.f. = ", y$n1-1, "), ", reportp(y$pttilde, 3),
"\n\n"), sep="", outf)
- Report("Estimates and confidence intervals under normality assumptions\n",
- outf)
- Report("--------------------------------------------------------------\n", outf)
+ Report(c("Estimates and confidence intervals under normality",
+ "assumptions\n"),
+ outf)
+ Report(c("-------------------------------------------------------",
+ "-------\n"), outf)
Report(c("Estimated mean parameter",
- format(round(y$mu.ml, 4), width=9),
- " (s.e.",format(round(y$mu.ml.se, 4), width=9), "), two-sided ",
+ format(round(y$mu.ml, 4), width=9),
+ " (s.e.",format(round(y$mu.ml.se, 4), width=9),
+ "), two-sided ",
reportp(2 * pt(-abs(y$mu.ml/y$mu.ml.se),
y$n1 - 1), 3), "\n"), sep="", outf)
- Report(c(format(round(y$mu.confint[3], 2), width=4),
+ Report(c(format(round(y$mu.confint[3], 2), width=4),
"level confidence interval [",
format(round(y$mu.confint[1], 4), width=7),
- ",",
+ ",",
format(round(y$mu.confint[2], 4), width=7), "]\n"), outf)
Report(c("Estimated standard deviation",
- ifelse((y$sigma.ml > 0.0001)|(y$sigma.ml < 0.0000001),
- format(round(y$sigma.ml, 4), width=9), " < 0.0001"),
+ 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),
+ Report(c(format(round(y$sigma.confint[3], 2), width=4),
"level confidence interval [",
format(round(y$sigma.confint[1], 4), width=7),
- ",",
+ ",",
format(round(y$sigma.confint[2], 4), width=7), "]\n\n"), outf)
Report("Fisher's combination of one-sided tests\n", outf)
Report("----------------------------------------\n", outf)
@@ -362,8 +370,8 @@
plot.sienaMeta <- function(x, ..., layout = c(2,2))
{
library(lattice)
- tmp <- xyplot(theta ~ se|effects,
- data=x$thetadf[is.na(x$thetadf$scoretests),],
+ tmp <- xyplot(theta ~ se|effects,
+ data=x$thetadf[is.na(x$thetadf$scoretests),],
ylab="estimates",
xlab="standard errors", layout=layout,
panel=function(x, y)
@@ -371,7 +379,7 @@
panel.xyplot(x, y)
panel.abline(0, qnorm(0.025))
panel.abline(0, qnorm(0.975))
- },
+ },
prepanel=function(x,y)
{ list(xlim=c(min(0,min(x)),max(0,max(x))),
ylim=c(min(0,min(y)),max(0,max(y))))
Modified: pkg/RSiena/R/sienaDataCreate.r
===================================================================
--- pkg/RSiena/R/sienaDataCreate.r 2011-04-20 12:49:03 UTC (rev 145)
+++ pkg/RSiena/R/sienaDataCreate.r 2011-05-16 14:37:22 UTC (rev 146)
@@ -708,10 +708,12 @@
if (sparse)
{
mymat <- myarray[[j]]
+ diag(mymat) <- NA
}
else
{
mymat <- myarray[, , j]
+ diag(mymat) <- NA
}
if (suppressMessages(!isSymmetric(mymat)))
{
@@ -1005,16 +1007,19 @@
rvals <- range(vals,na.rm=TRUE)
}
rvals1 <- rvals[2] - rvals[1]
- tmp <- apply(vals, 2, function(v){
- sapply(1: length(v), function(x, y, r){
- z <- y
- z[x] <- NA
- #browser()
- tmp1 <- 1 - abs(y[x] - z) / r
- list(sum(tmp1, na.rm=TRUE), sum(!is.na(tmp1)))
- },
- y=v, r=rvals1)})
-
+ tmp <- apply(vals, 2, function(v)
+ {
+ sapply(1: length(v), function(x, y, r)
+ {
+ z <- y
+ z[x] <- NA
+ ##browser()
+ tmp1 <- 1 - abs(y[x] - z) / r
+ list(sum(tmp1, na.rm=TRUE), sum(!is.na(tmp1)))
+ },
+ y=v, r=rvals1)
+ }
+ )
tmp <- unlist(tmp)
raw <- tmp[seq(1, length(tmp), by=2)]
cnts <- tmp[seq(2, length(tmp), by=2)]
Modified: pkg/RSiena/R/sienaDataCreateFromSession.r
===================================================================
--- pkg/RSiena/R/sienaDataCreateFromSession.r 2011-04-20 12:49:03 UTC (rev 145)
+++ pkg/RSiena/R/sienaDataCreateFromSession.r 2011-05-16 14:37:22 UTC (rev 146)
@@ -380,6 +380,12 @@
c(nonzero[[x]], 10, 11)), 3] <- 0
myedgelist[myedgelist[,3] %in%
nonzero[[x]], 3] <- 1
+ if (!is.directed(namefiles[[x]]))
+ {
+ perm <- c(2, 1, 3)
+ myedgelist <- rbind(myedgelist, myedgelist[, perm])
+ }
+
if (network.size(namefiles[[x]]) != nActors)
stop("number of actors inconsistent")
Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog 2011-04-20 12:49:03 UTC (rev 145)
+++ pkg/RSiena/changeLog 2011-05-16 14:37:22 UTC (rev 146)
@@ -1,3 +1,16 @@
+2011-05-16 R-forge revision 146
+
+ * src/Makevars.win: alter linking to reduce command line length
+ * doc/s_man400.tex: add tex code to reduce size of pdf, many
+ updates
+ * doc/RSiena.bib, doc/simstatsc.tex, doc/RSienaDeveloper.tex:
+ updated documentation for symmetric networks and other minor changes.
+ * R/siena08.r: formatting changes only
+ * R/sienaDataCreate.r: set diagonals to NA for sparse matrices
+ when calculating degree and setting attributes
+ * R/sienaDataCreateFromSession.r: if using read.pajek to read a
+ non-directed network duplicate the ties in the edgelist.
+
2011-04-20 R-forge revision 145
* src/model/effects/outTruncEffect.cpp: reformating
Modified: pkg/RSiena/inst/doc/s_man400.pdf
===================================================================
--- pkg/RSiena/inst/doc/s_man400.pdf 2011-04-20 12:49:03 UTC (rev 145)
+++ pkg/RSiena/inst/doc/s_man400.pdf 2011-05-16 14:37:22 UTC (rev 146)
@@ -1,628 +1,61 @@
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îÖ_Rì)TSl.xÑ}¯ó3¡uFæ¦DTU¦5§2d»þ½OºOCølàì½×|ùØÞ¡#ý¾G°ÿqÑòâîìo>ö
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+q Pä]§ÞÿMU.ða>êÅ_×?°jp@D<©æ_{w® x#=è-!(afj°XrHüsQ
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+¨í:/f% jYí(ñ/ÌIe5Þ 0g~ôPÔnE :&+ouËF¤úöo³f×SÓÀÁ4@Á¡æêâì××;»-9
+Bàß÷l0Ó+å {Kª=G d BýÓ¸ÕÖöWàWêª/ÕBöôÒ(ôÅÏûs~ØÈ<³ÈËïbÓª¶+"hEtQ*ËsccJTÈËÔÈLnËÒ(¢ºÚ¬
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+ü´Z@êßN$tSOHÙE6ª0öß×
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 146
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