[Rsiena-commits] r176 - in pkg/RSienaTest: . R doc inst/doc inst/scripts man src/model/variables tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Oct 14 15:28:30 CEST 2011
Author: ripleyrm
Date: 2011-10-14 15:28:28 +0200 (Fri, 14 Oct 2011)
New Revision: 176
Added:
pkg/RSienaTest/R/document.r
pkg/RSienaTest/doc/auto.tex
pkg/RSienaTest/inst/scripts/RSienaSNADescriptives.R
pkg/RSienaTest/tests/scriptfile.Rout.win
Modified:
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/siena07.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/RSienaDeveloper.tex
pkg/RSienaTest/doc/RSiena_Manual.tex
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/inst/scripts/Rscript01DataFormat.R
pkg/RSienaTest/inst/scripts/Rscript02SienaVariableFormat.R
pkg/RSienaTest/inst/scripts/Rscript03SienaRunModel.R
pkg/RSienaTest/inst/scripts/Rscript04SienaBehaviour.R
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/src/model/variables/DependentVariable.cpp
pkg/RSienaTest/tests/scriptfile.Rout.save
pkg/RSienaTest/tests/scripts.R
pkg/RSienaTest/tests/scripts.Rout.save
Log:
More on scripts testing system. Automated function table system. Fix to Diffusion effects.
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2011-10-06 17:21:47 UTC (rev 175)
+++ pkg/RSienaTest/DESCRIPTION 2011-10-14 13:28:28 UTC (rev 176)
@@ -1,13 +1,13 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.0.12.175
-Date: 2011-10-06
+Version: 1.0.12.176
+Date: 2011-10-14
Author: Various
Depends: R (>= 2.10.0)
Imports: Matrix
Suggests: tcltk, snow, rlecuyer, network, codetools, lattice, MASS,
- sna, igraph, xtable
+ sna, igraph, xtable, tools
SystemRequirements: GNU make, tcl/tk 8.5, Tktable
Maintainer: Ruth Ripley <ruth at stats.ox.ac.uk>
Description: Fits models to longitudinal networks
Added: pkg/RSienaTest/R/document.r
===================================================================
--- pkg/RSienaTest/R/document.r (rev 0)
+++ pkg/RSienaTest/R/document.r 2011-10-14 13:28:28 UTC (rev 176)
@@ -0,0 +1,171 @@
+#/******************************************************************************
+# * SIENA: Simulation Investigation for Empirical Network Analysis
+# *
+# * Web: http://www.stats.ox.ac.uk/~snidjers/siena
+# *
+# * File: RSienaAutoHelpTable.r
+# *
+# * Description: This module contains the code for the automatic extraction of
+# * documentation from the .Rd files
+# *****************************************************************************/
+##@RSienaAutoHelpTable Documentation Create latex source for a function table
+RSienaAutoHelpTable <- function(RSienaDir="../RSiena/man")
+{
+ ## Documentation of the Rd processing functions is in parseRd.pdf
+ ## a CRAN document.
+
+ ## All functions to be included need to be here in order, with
+ ## stage of processing relevant, and T or F in the arguments column
+ ## to indicate whether the arguments are to be included in the final
+ ## column of the table - TTT means all three arguments...
+ RSienaRequiredFunctions <- data.frame(functionName=c("installGui",
+ "siena01Gui",
+ "sienaNodeSet",
+ "sienaNet",
+ "coCovar",
+ "varCovar",
+ "coDyadCovar",
+ "varDyadCovar",
+ "sienaCompositionChange",
+ "sienaDataCreate",
+ "sienaDataCreateFromSession",
+ "sienaGroupCreate",
+ "effectsDocumentation",
+ "getEffects",
+ "print.sienaEffects",
+ "includeEffects",
+ "includeInteraction",
+ "setEffect",
+ "print01Report",
+ "sienaModelCreate",
+ "siena07",
+ "sienaFit",
+ "sienaTimeTest"),
+ stage=c("1", "3--5", rep("3", 10),
+ rep("4", 6), "5", "5", "5", "6", "6"),
+ arguments=c("", "F", "TTT",
+ rep("F", 20)), stringsAsFactors=FALSE)
+
+ numberPages <- nrow(RSienaRequiredFunctions)
+ usage <- vector("list", numberPages)
+ desc <- vector("list", numberPages)
+ exam <- vector("list", numberPages)
+ arguments <- vector("list", numberPages)
+
+ library(tools)
+
+ for (i in 1:nrow(RSienaRequiredFunctions))
+ {
+ ## find the path to the help file
+ infile <- file.path(RSienaDir, paste(RSienaRequiredFunctions[i, 1],
+ ".Rd", sep=""))
+ ## parse it
+ Rd <- tools::parse_Rd(infile)
+ ## extract the tags from the Rd object
+ tags <- tools:::RdTags(Rd)
+ usage[[i]] <- Rd[[which(tags=="\\usage")]]
+ desc[[i]] <- Rd[[which(tags=="\\description")]]
+ exam[[i]] <- Rd[[which(tags=="\\examples")]]
+ if (length(which(tags=="\\arguments")))
+ {
+ arguments[[i]] <- Rd[[which(tags=="\\arguments")]]
+ }
+ }
+
+ ## do some reformatting: use debug() to see what happens
+ usage1 <- sapply(usage, function(x)paste(unlist(x), collapse=""))
+ desc1 <- sapply(desc, function(x)paste(unlist(x), collapse=""))
+ exam1 <- sapply(exam, function(x)paste(unlist(x), collapse=""))
+ args1 <- lapply(arguments, function(x)
+ {
+ if (!is.null(x))
+ {
+ tmp <- tools:::RdTags(x)
+ tmp2 <- x[which(tmp=="\\item")]
+ lapply(tmp2, function(x)list(x[[1]],
+ gsub("\\n", "",
+ x[[2]])))
+ }
+ })
+
+ ## optional reformatting: some examples which could be used
+
+ ##usage2 <- sub("getDocumentation=FALSE", "", usage1)
+ ##usage2 <- sub(", )", ")", usage2)
+ ##usage2 <- gsub("\\n", " ", usage2)
+ ##desc2 <- gsub("\\n", " ", desc1)
+ ##exam2 <- gsub("\\n", " ", exam1)
+ ##usage2 <- gsub("#", " ", usage2)
+ ##exam2 <- gsub("#", "\\#", exam2, fixed=TRUE)
+ ##usage2 <- gsub("$", "\\$", usage2, fixed=TRUE)
+
+ ##exam2 <- gsub("<", "\\textless", exam1)
+
+ ##usage2 <- sub("^ *", "", usage2)
+ ##exam2 <- sub("^ *", "", exam2)
+
+ ##@sortout Internal RSienaAutoHelpTable
+ ##more formatting
+ sortout <- function(x, code=TRUE)
+ {
+ ## remove trailing \n
+ x <- gsub("\n$", "", x)
+ ## remove starting \n
+ x <- gsub("^\n", "", x)
+ ## retain the others if after a )
+ x <- gsub(")\n", ")\\\\ ", x)
+ ## remove the others
+ x <- gsub("\n", " ", x)
+ ## escape hash
+ x <- gsub("#", "\\#", x, fixed=TRUE)
+ ## escape dollar
+ x <- gsub("$", "\\$", x, fixed=TRUE)
+ ##remove spaces
+ x <- gsub("^ *", "", x)
+ ##remove spaces
+ x <- gsub(" +", " ", x)
+ if (code)
+ {
+ x <- paste("\\texttt{", x, "}", sep="")
+ }
+ x
+ }
+ ## create the table: check doc.tex for the output
+ mytab <-
+ sapply(1:numberPages, function(i, rs, usage, exam, desc, arg)
+ {
+ x <- rs[i, ]
+ includeArguments <- strsplit(x$arguments, "")[[1]]
+ includeArguments <- as.logical(includeArguments)
+ arg <- args1[[i]]
+ arg <- arg[includeArguments]
+ ## sort out usage
+ usage2 <- sortout(usage1[i])
+ usage2 <- sub("getDocumentation=FALSE", "", usage2)
+ if (nchar(x$functionName) > 20)
+ {
+ #browser()
+ usage2 <- paste("\\\\ &&", usage2)
+ }
+ exam2 <- sortout(exam1[[i]])
+ desc2 <- sortout(desc1[[i]], code=FALSE)
+ arg <- sapply(arg, function(x)
+ {
+ paste('\\texttt{"', unlist(x[[1]]), '"}=',
+ paste(unlist(x[[2]]), sep=" ", collapse=""),
+ sep="", collapse="")
+ })
+ tmp <- paste(x$stage, "&", x$functionName, "&",
+ usage2, "&",
+ exam2, "&", desc2, paste(arg, sep=" ",
+ collapse=""),
+ "\\\\ \\hline",
+ sep="", collapse="")
+ print(tmp)
+ tmp
+ }, rs=RSienaRequiredFunctions, usage=usage, desc=desc,
+ exam=exam, arg=args1)
+ write.table(mytab, "docn.tex", row.names=FALSE, col.names=FALSE,
+ quote=FALSE)
+ ## now run LaTeX on auto.tex in the doc directory.
+}
Property changes on: pkg/RSienaTest/R/document.r
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: pkg/RSienaTest/R/siena07.r
===================================================================
--- pkg/RSienaTest/R/siena07.r 2011-10-06 17:21:47 UTC (rev 175)
+++ pkg/RSienaTest/R/siena07.r 2011-10-14 13:28:28 UTC (rev 176)
@@ -109,9 +109,13 @@
if (!capabilities("X11"))
{
batchUse <- TRUE
- cat("No X11 device available, must use batch")
+ cat("No X11 device available, forcing use of batch mode")
}
}
+ if(nzchar(Sys.getenv("RSIENA_TESTING")))
+ {
+ silent <- TRUE
+ }
}
is.batch(batchUse)
Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog 2011-10-06 17:21:47 UTC (rev 175)
+++ pkg/RSienaTest/changeLog 2011-10-14 13:28:28 UTC (rev 176)
@@ -1,3 +1,20 @@
+2011-10-14 r-forge revision 176 RSienaTest only
+
+ * inst/scripts/RScriptDataFormat.R,
+ inst/scripts/RScriptSienaVariable.R,
+ inst/scripts/RScriptSienaRunModel.R,
+ inst/scripts/RScriptSienaBehaviour.R,
+ inst/scripts/RSienaSNADescriptives.R: removed sna and network code to
+ separate file which is excluded from testing by containing 'SNA' in the
+ name
+ * R/siena07.r, tests/scripts.R, tests/scriptfile.Rout.save,
+ tests/scripts.Rout.save, tests/scriptfile.Rout.win:
+ amended to work better multi-platform, although linux not yet tested.
+ * R/document.r, doc/auto.tex, RSienaDeveloper.tex: new function to
+ automate construction of the function table in the manual.
+ * src/model/variables/DependentVariable.cpp: fix bug in diffusion
+ effects.
+
2011-10-06 R-forge revision 175 RSienaTest only
* doc/RScriptDataFormat.R, doc/RScriptSienaVariable.R,
@@ -12,7 +29,7 @@
terminate return the object unchanged if called non-interactively.
* R/sienaprint.r, NAMESPACE, man/xtable.Rd: added dummy xtable command
to call real one.
- * tests/scripts.R, tests/scripts.Rout,save, tests/scriptfile.Rout.save:
+ * tests/scripts.R, tests/scripts.Rout,save, tests/scriptfile.Rout.save:
added file to test
scripts, controlled by an environment variable.
* doc/RSiena_Manual.tex: altered path to scripts and file names.
Modified: pkg/RSienaTest/doc/RSienaDeveloper.tex
===================================================================
--- pkg/RSienaTest/doc/RSienaDeveloper.tex 2011-10-06 17:21:47 UTC (rev 175)
+++ pkg/RSienaTest/doc/RSienaDeveloper.tex 2011-10-14 13:28:28 UTC (rev 176)
@@ -122,6 +122,21 @@
autofit the columns and save as .xls.
\item NB You need RTools (see later) installed to do this on Windows.
\end{enumerate}
+\item[Table of functions for the manual]
+\begin{enumerate}
+\item The file \sfn{document.r} in \sfn{RSienaTest} contains a function
+ \sfn{RSienaAutoHelpTable} which will generate \LaTeX source from the .Rd
+ files for a table of functions similar to that in the manual
+\item You need to run \sfn{RSienaAutoHelpTables} and then run \LaTeX on the file
+ \sfn{auto.tex} in the doc directory of the source (not installed) package.
+\item It is controlled by a data frame of functions hard coded in the file
+ \sfn{document.r}.
+\item The text is based on the \sfn{Description} field in the .Rd file. Moving
+ information from this field to the \sfn{Details} field should allow sufficient
+ flexibility to get the required table.
+\item There are a few sample text processing commands commented out in the
+ source file \sfn{document.r} which might prove useful.
+\end{enumerate}
\end{description}
\subsection{Other documentation}
There are other documentation files:
Modified: pkg/RSienaTest/doc/RSiena_Manual.tex
===================================================================
--- pkg/RSienaTest/doc/RSiena_Manual.tex 2011-10-06 17:21:47 UTC (rev 175)
+++ pkg/RSienaTest/doc/RSiena_Manual.tex 2011-10-14 13:28:28 UTC (rev 176)
@@ -9423,6 +9423,8 @@
repository.)
\begin{small}
\begin{itemize}
+\item 2011-10-14 R-forge revision 176 (RSienaTest only)
+bug fix in diffusion effects, altered scipts in manual a little
\item 2011-10-06 R-forge revision 175
\begin{itemize}
\item Fix bug with multiple symmetric networks.
Added: pkg/RSienaTest/doc/auto.tex
===================================================================
--- pkg/RSienaTest/doc/auto.tex (rev 0)
+++ pkg/RSienaTest/doc/auto.tex 2011-10-14 13:28:28 UTC (rev 176)
@@ -0,0 +1,46 @@
+\documentclass[a4paper, fleqn]{article}
+% for the print version, 11pt must be added in the documentclass options;
+% this must be deleted in the screen version.
+
+%Required files: pdfscreen.sty, pdfscreen.cfg, ilcampo_bg.jpg, ilcampo.jpg
+%\usepackage{times}
+%\usepackage[DIV=11]{typearea}
+\usepackage{natbib}
+\usepackage{rotating}
+\usepackage{longtable, lscape}
+\usepackage{threeparttablex}
+\usepackage{amsmath}
+\begin{document}
+\begin{landscape}
+%\begin{footnotesize}
+\begin{longtable}{c | p{3cm} | p{5.2cm} | p{4.2cm} | p{8.5cm} }
+\caption[List of Functions: Execution] {List of Functions in order of
+Execution}
+\label{tab:ListSienaExec} \\
+\hline
+
+\multicolumn{1}{c}{\textbf{Stage}} & \multicolumn{1}{c}{\textbf{Name}} &
+\multicolumn{1}{c}{\textbf{Syntax}} & \multicolumn{1}{c}{\textbf{Examples}} &
+\multicolumn{1}{c}{\textbf{Description}} \\
+\hline
+\endfirsthead
+
+\multicolumn{5}{c}%
+{{\bfseries \tablename\ \thetable{} -- continued from previous page}} \\
+\hline \multicolumn{1}{c}{\textbf{Stage}} & \multicolumn{1}{c}{\textbf{Name}} &
+\multicolumn{1}{c}{\textbf{Syntax}} & \multicolumn{1}{c}{\textbf{Examples}} &
+\multicolumn{1}{c}{\textbf{Description}} \\
+\hline
+\endhead
+
+\hline \multicolumn{5}{|r|}{{\tiny{Continued...}}} \\
+\hline
+\endfoot
+
+\hline \hline
+\endlastfoot
+\input{docn.tex}
+%\raggedright
+\end{longtable}
+\end{landscape}
+\end{document}
Property changes on: pkg/RSienaTest/doc/auto.tex
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
===================================================================
--- pkg/RSienaTest/inst/doc/RSiena_Manual.pdf 2011-10-06 17:21:47 UTC (rev 175)
+++ pkg/RSienaTest/inst/doc/RSiena_Manual.pdf 2011-10-14 13:28:28 UTC (rev 176)
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[TRUNCATED]
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