[Rsiena-commits] r161 - in pkg: RSiena RSiena/R RSiena/inst/doc RSiena/man RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/inst/doc RSienaTest/inst/examples RSienaTest/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Jul 2 17:20:33 CEST 2011 

Author: ripleyrm
Date: 2011-07-02 17:20:33 +0200 (Sat, 02 Jul 2011)
New Revision: 161

Modified:
   pkg/RSiena/DESCRIPTION
   pkg/RSiena/R/RSienaRDocumentation.r
   pkg/RSiena/R/bayes.r
   pkg/RSiena/R/effects.r
   pkg/RSiena/R/maxlikec.r
   pkg/RSiena/R/sienaDataCreate.r
   pkg/RSiena/changeLog
   pkg/RSiena/inst/doc/RSiena_Manual.pdf
   pkg/RSiena/man/RSiena-package.Rd
   pkg/RSiena/man/siena07.Rd
   pkg/RSiena/man/siena08.Rd
   pkg/RSiena/man/simstats0c.Rd
   pkg/RSienaTest/DESCRIPTION
   pkg/RSienaTest/R/RSienaRDocumentation.r
   pkg/RSienaTest/R/bayes.r
   pkg/RSienaTest/R/effects.r
   pkg/RSienaTest/R/maxlikec.r
   pkg/RSienaTest/R/sienaDataCreate.r
   pkg/RSienaTest/changeLog
   pkg/RSienaTest/doc/RSiena_Manual.tex
   pkg/RSienaTest/doc/RscriptSienaRunModel.R
   pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
   pkg/RSienaTest/inst/examples/algorithms.r
   pkg/RSienaTest/man/RSiena-package.Rd
   pkg/RSienaTest/man/siena07.Rd
   pkg/RSienaTest/man/siena08.Rd
   pkg/RSienaTest/man/simstats0c.Rd
Log:
Fix for Bayes routine, other minor bug fixes. 

Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/DESCRIPTION	2011-07-02 15:20:33 UTC (rev 161)
@@ -1,8 +1,8 @@
 Package: RSiena
 Type: Package
 Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.160
-Date: 2011-06-24
+Version: 1.0.12.161
+Date: 2011-07-02
 Author: Various
 Depends: R (>= 2.10.0)
 Imports: Matrix

Modified: pkg/RSiena/R/RSienaRDocumentation.r
===================================================================
--- pkg/RSiena/R/RSienaRDocumentation.r	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/R/RSienaRDocumentation.r	2011-07-02 15:20:33 UTC (rev 161)
@@ -16,6 +16,7 @@
     mylist <- ls(parent.frame())
     ##  print(mylist)
     library(codetools)
+	## fnlist has a row number at the front: column 3 contains the function names
     mylist <- mylist[mylist %in% fnlist[, 3]]
     mytt <- lapply(mylist, function(x)
        {
@@ -44,16 +45,26 @@
 
     thisdir <- getwd()
     ## temporarily move directory
+	on.exit(setwd(thisdir))
     setwd(Rdir)
 
     ## extract comment lines
-    shell('grep "##@" *.r *.R > comments.lis')
+    if (.Platform$OS.type == "windows")
+    {
+        shell('grep "##@" *.r *.R > comments.lis')
+    }
+    else
+    {
+        system('grep "##@" *.r *.R > comments.lis')
+    }
     ## read them in
     comms <- readLines('comments.lis')
     ## remove the file
     file.remove("comments.lis")
     ## remove the shell line
     comms <- comms[!grepl("comments.lis", comms)]
+	## get rid of tabs
+	comms <- gsub("\t", "", comms)
     ## split off
     mystr <- paste("##", "@", sep="")
     comms1 <- strsplit(comms, mystr)
@@ -70,7 +81,7 @@
                      }
                      else
                      {
-                         c(x[1], tmp[1], tmp[2], paste(tmp[-c(1,2)],
+                         c(x[1], tmp[1], tmp[2], paste(tmp[-c(1, 2)],
                                                        collapse=" "))
                      }
                  }
@@ -96,26 +107,55 @@
 
     ## now the internal ones
     ## find the list of files from comms3
+#	browser()
+	internals <- comms3[grepl("internal to", comms3[, 4]), ]
     ttmp <- unique(comms3[grepl("internal to", comms3[, 4]), 4])
-    ttmp <- sub("internal to ", "", ttmp)
-    ttmp2 <- comms3[match(ttmp, comms3[, 2]), 1]
-    ttmp2 <- sub(":", "", ttmp2)
-
+    ttmp1 <- sub("internal to ", "", ttmp)
+	ttmp3 <- lapply(ttmp1, function(x)
+				{
+					tmp <- x
+					while(!is.na(sub <- match(tmp[1], internals[, 2])))
+					{
+						tmp1 <- internals[sub, 4]
+						tmp1 <- sub("internal to ", "", tmp1)
+						tmp <- c(tmp1, tmp)
+					}
+					tmp
+				})
+    #ttmp2 <- comms3[match(ttmp1, comms3[, 2]), 1]
+    #ttmp2 <- sub(":", "", ttmp2)
     ## write out the fnlist in the Rdir
     write.csv(data.frame(comms3), "RSienafnlist.csv")
     ## get the list of internals
-    tt <- lapply(1:length(ttmp), function(x, y, z)
-             {
-                 yy <- y[x]
-                 yy <- getFromNamespace(yy, pkgname)
+	tt <- lapply(ttmp3, function(x)
+			 {
+				 yy <- getFromNamespace(x[1], pkgname)
                  targs <- formals(yy)
-                 n <- length(targs)
-                 myargs <- targs
-                 for (i in 1:n)
-                     myargs[[i]] <- 1
-                 myargs['getDocumentation'] <- TRUE
-                 do.call(yy, myargs)
-             }, y=ttmp, z=ttmp2)
+				 targs[1:length(targs)] <- 1
+				 if (length(x) > 1)
+				 {
+					 targs['getDocumentation'] <- x[-1]
+				 }
+				 else
+				 {
+					 targs['getDocumentation'] <- TRUE
+				 }
+                 do.call(yy, targs)
+			 })
+    #tt <- lapply(1:length(ttmp3), function(x, y)
+    #         {
+    #             yy <- y[x]
+    #             yy <- getFromNamespace(yy, pkgname)
+    #             targs <- formals(yy)
+    #             n <- length(targs)
+    #             myargs <- targs
+    #             for (i in 1:n)
+#				 {
+#                     myargs[[i]] <- 1#
+				 #}
+                 #myargs['getDocumentation'] <- TRUE
+                 #do.call(yy, myargs)
+             #}, y=ttmp)
     names(tt) <- ttmp
     ## remove the file
     file.remove("RSienafnlist.csv")
@@ -240,7 +280,7 @@
     tmp12 <- do.call(rbind, tmp11)
     names(tmp12)[2] <- "Function"
 
-    tmp12 <- tmp12[order(tmp12[, "type"], row.names(tmp12)), ]
+    tmp12 <- tmp12[order(tmp12[, "type"], as.numeric(row.names(tmp12))), ]
     tmp12 <- tmp12[, c(3, 2, 5, 6, 4, 1)]
     ff <- xtable(tmp12)
     ## go back to start directory

Modified: pkg/RSiena/R/bayes.r
===================================================================
--- pkg/RSiena/R/bayes.r	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/R/bayes.r	2011-07-02 15:20:33 UTC (rev 161)
@@ -8,11 +8,12 @@
 ## * Description: This file contains the code to run Bayesian simulation
 ## *
 ## ****************************************************************************/
-##@bayes algorithm  fit a Bayesian model
+##@bayes Bayesian fit a Bayesian model
 bayes <- function(data, effects, model, nwarm=100, nmain=100, nrunMHBatches=20,
                   nrunMH=100, save=TRUE, nbrNodes=1, seed=1, dfra=NULL,
-                  priorSigma=NULL, prevAns=NULL)
+                  priorSigma=NULL, prevAns=NULL, getDocumentation=FALSE)
 {
+    ##@createStores internal bayes Bayesian set up stores
     createStores <- function(z)
     {
         npar <- length(z$theta)
@@ -26,6 +27,7 @@
         z$MHproportions <- array(NA, dim=c(numberRows, z$nGroup, 7))
         z
     }
+    ##@storeData internal bayes Bayesian put data in stores
     storeData <- function()
     {
         start <- z$sub + 1
@@ -50,12 +52,14 @@
         z$sub <- z$sub + nrun
         z
     }
+	##@improveMH internal bayes Bayesian find scale factors
     improveMH <- function(z, x, tiny=1.0e-15, desired=40, maxiter=100,
-                          tolerance=15)
+                          tolerance=15, getDocumentation=FALSE)
     {
+		##@rescaleCGD internal improveMH Bayesian
         rescaleCGD <- function(iter)
         {
-            u <- ifelse (actual > desired,
+			u <- ifelse (actual > desired,
                          2 - ((iter - actual) / (iter - desired)),
                          1 / (2 - (actual / desired)))
             number <<- ifelse(abs(actual - desired) <= tolerance,
@@ -63,6 +67,11 @@
             success <<- number >= 2
             u
         }
+		if (getDocumentation)
+		{
+			tt <- getInternals()
+			return(tt)
+		}
         iter <- 0
         number <- rep(0, z$nGroup)
         success <- rep(FALSE, z$nGroup)
@@ -92,6 +101,25 @@
     ## ################################
     ## start of function proper
     ## ################################
+	if (getDocumentation != FALSE)
+	{
+		if (getDocumentation == TRUE)
+		{
+			tt <- getInternals()
+			return(tt)
+		}
+		else ## need to run getInternals on the argument value
+		{
+			targs <- formals(getDocumentation[1])
+			targs[1:length(targs)] <- 1
+			targs['getDocumentation'] <- TRUE
+			if (length(getDocumentation) > 1)
+			{
+				targs['getDocumentation'] <- getDocumentation[-1]
+			}
+			return(do.call(getDocumentation[1], targs))
+		}
+	}
 
     z <- initializeBayes(data, effects, model, nbrNodes, seed, priorSigma,
                          prevAns=prevAns)
@@ -163,8 +191,10 @@
             ##thetadf <- data.frame(z$candidates)
             acceptsdf <- data.frame(z$MHproportions,
                                     z$acceptances)
-            ratesdf <- thetadf[, -1][, z$basicRate]
-            thetadf <- cbind(Group=thetadf[, 1], thetadf[, -1][, !z$basicRate])
+            ratesdf <- thetadf[, -1, drop=FALSE][, z$basicRate, drop=FALSE]
+            thetadf <- cbind(Group=thetadf[, 1, drop=FALSE],
+							 thetadf[, -1, drop=FALSE][,
+										   !z$basicRate, drop=FALSE])
             thetaNames<- paste(z$effects$name[!z$basicRate],
                                z$effects$shortName[!z$basicRate], sep=".")
             rateNames <- paste(z$effects$name[basicRate],
@@ -172,7 +202,7 @@
                                            z$effects$period[basicRate],
                                            z$effects$group[basicRate], sep=".")
             names(ratesdf) <- rateNames
-            ratesdf <- cbind(Group=thetadf[, 1], ratesdf)
+            ratesdf <- cbind(Group=thetadf[, 1, drop=FALSE], ratesdf)
             names(thetadf)[-1] <- make.names(thetaNames, unique=TRUE)
             names(acceptsdf) <- c("InsDiag", "CancDiag", "Permute", "InsPerm",
                                   "DelPerm", "InsMissing", "DelMissing",
@@ -226,7 +256,7 @@
     z$FRAN <- NULL
     z
 }
-
+##@MCMCcycle algorithms do some loops of (MH steps and sample parameters)
 MCMCcycle <- function(z, nrunMH, nrunMHBatches, change=TRUE)
 {
     z$accepts <- matrix(NA, nrow=z$nGroup, nrunMHBatches)
@@ -259,6 +289,7 @@
     z$nrunMH <- storeNrunMH
     z
 }
+##@sampleParameters algorithms propose new parameters and accept them or not
 sampleParameters <- function(z, change=TRUE)
 {
     ## get a multivariate normal with covariance matrix dfra multiplied by a
@@ -325,7 +356,7 @@
     z
 }
 
-
+##@initializeBayes algorithms do set up for Bayesian model
 initializeBayes <- function(data, effects, model, nbrNodes, seed, priorSigma,
                             prevAns)
 {
@@ -395,7 +426,7 @@
                                                 function(x) 1:x))))
     z
 }
-
+##@getDFRA algorithms do a few ML iterations and calculate a derivative matrix
 getDFRA <- function(z, n)
 {
     ## do n MLmodelsteps with the initial thetas and get
@@ -425,7 +456,7 @@
     ##z$covFactor <- z$eS$vectors %*% diag(sqrt(pmax(z$ev, 0)), z$pp)
     z
 }
-
+##@getLikelihood algorithms calculated likelihood for one chain
 getLikelihood <- function(chain, nactors, lambda, simpleRates)
 {
     loglik <- 0
@@ -437,11 +468,11 @@
     logChoiceProb <- sapply(chain, function(x)x[[9]])
     logOptionSetProb <- sapply(chain, function(x)x[[8]])
     loglik <- sum(logChoiceProb)  + sum(logOptionSetProb)
-                                        #print(sum(logOptionSetProb))
+	##print(sum(logOptionSetProb))
     if (simpleRates)
     {
         loglik <- loglik - sum(nactors * lambda) + sum(nc * log(lambda))# -
-           # sum(lfactorial(nc))
+		## sum(lfactorial(nc)) don't need factorial in bayes!
     }
     else
     {
@@ -453,7 +484,7 @@
     }
     loglik
 }
-
+##@getProbs algorithms calculates likelihood sum over nested list of chains
 getProbs <- function(z, chain)
 {
     sapply(1: length(chain), function(i)
@@ -471,7 +502,7 @@
        }
            )
 }
-
+##@flattenChains algorithms converts a nested list of chains to a single list
 flattenChains <- function(zz)
 {
         for (i in 1:length(zz)) ##group
@@ -485,7 +516,8 @@
     zz <- do.call(c, zz)
     zz
 }
-
+##@dmvnorm algorithms calculated multivariate normal density:
+##inefficient: should not call mahalanobis and eigen with same sigma repeatedly
 dmvnorm <- function(x, mean , sigma)
 {
     if (is.vector(x))

Modified: pkg/RSiena/R/effects.r
===================================================================
--- pkg/RSiena/R/effects.r	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/R/effects.r	2011-07-02 15:20:33 UTC (rev 161)
@@ -8,7 +8,7 @@
 # * Description: This module contains the code for the creation of the
 # * effects object to go with a Siena data object or group object.
 # *****************************************************************************/
-##@substituteNames  replace xxxxxx, yyyyyy, zzzzzz
+##@substituteNames DataCreate replace xxxxxx, yyyyyy, zzzzzz
 substituteNames <- function(nameVectors, xName=NULL, yName=NULL, zName=NULL)
 {
     effects <- nameVectors[, c("effectName", "functionName",
@@ -32,7 +32,7 @@
                     "interaction1", "interaction2")] <- effects
     nameVectors
 }
-##@createEffects  Extract required rows and change text
+##@createEffects DataCreate Extract required rows and change text
 createEffects <- function(effectGroup, xName=NULL, yName=NULL, zName = NULL,
 						  name, groupName, group, netType)
 {
@@ -70,7 +70,7 @@
     effects <- data.frame(name=effectsname, effects, stringsAsFactors=FALSE)
     effects
 }
-##@getEffects DataCreate
+##@getEffects DataCreate create effects object
 getEffects<- function(x, nintn = 10, behNintn=4, getDocumentation=FALSE)
 {
     ##@duplicateDataFrameRow internal getEffects Put period numbers in
@@ -122,7 +122,7 @@
         }
         rateEffects
     }
-    ##@oneModeNet internal getEffects
+    ##@oneModeNet internal getEffects process a one mode net
     oneModeNet <- function(depvar, varname)
     {
         symmetric <- attr(depvar, "symmetric")

Modified: pkg/RSiena/R/maxlikec.r
===================================================================
--- pkg/RSiena/R/maxlikec.r	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/R/maxlikec.r	2011-07-02 15:20:33 UTC (rev 161)
@@ -68,7 +68,13 @@
                      z$returnChains)
         ans[[6]] <- list(ans[[6]])
         ans[[7]] <- list(ans[[7]])
-    }
+        if (byGroup)
+        {
+			ans[[8]] <- list(ans[[8]])
+			ans[[9]] <- list(ans[[9]])
+			ans[[10]] <- list(ans[[10]])
+        }
+   }
     else
     {
         if (z$int2 == 1)

Modified: pkg/RSiena/R/sienaDataCreate.r
===================================================================
--- pkg/RSiena/R/sienaDataCreate.r	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/R/sienaDataCreate.r	2011-07-02 15:20:33 UTC (rev 161)
@@ -8,7 +8,7 @@
 # * Description: This module contains the code to create
 # * Siena data object and group data objects.
 # *****************************************************************************/
-##@addeAttributes DataCreate method for attaching attributes to objects
+##@addAttributes DataCreate method for attaching attributes to objects
 addAttributes <- function(x, name, ...) UseMethod("addAttributes")
 
 ##@addAttributes.coCovar DataCreate

Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/changeLog	2011-07-02 15:20:33 UTC (rev 161)
@@ -1,3 +1,15 @@
+2011-07-02 R-forge revision 161
+
+	* man.siena08.Rd: add note about names of effects need to match
+	* man/siena07.Rd, man/simstats0c.Rd: minor edits.
+	* R/effects.r, R/sienaDataCreate.r: minor edits of comments
+	* R/bayes.r, R/maxlikec.r, inst/examples/algorithms.r: Bayesian routine
+	was failing for single data objects.
+	* R/RSienaRDocumentation.r: fix for internal functions of internal
+	functions. Clumsy at present.
+	* man/RscriptSienaRunModel.R: minor correction to text, many trailing
+	spaces removed.
+
 2011-06-24 R-forge revision 160
 
 	* src/model/effects/BehaviorInteractionEffect.cpp,

Modified: pkg/RSiena/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSiena/inst/doc/RSiena_Manual.pdf	2011-06-24 12:39:15 UTC (rev 160)
+++ pkg/RSiena/inst/doc/RSiena_Manual.pdf	2011-07-02 15:20:33 UTC (rev 161)
@@ -51,17 +51,14 @@
 endstream
 endobj
 414 0 obj <<
-/Length 1163      
+/Length 1161      
 /Filter /FlateDecode
 >>
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rsiena -r 161

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