[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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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rsiena -r 146


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