[Rsiena-commits] r46 - in pkg/RSienaTest: . R doc inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 19 17:36:27 CET 2010
Author: ripleyrm
Date: 2010-01-19 17:36:27 +0100 (Tue, 19 Jan 2010)
New Revision: 46
Added:
pkg/RSienaTest/R/effectsDocumentation.r
pkg/RSienaTest/inst/doc/effects.pdf
pkg/RSienaTest/man/effectsDocumentation.Rd
Modified:
pkg/RSienaTest/R/sienaeffects.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/s_man400.tex
pkg/RSienaTest/inst/doc/s_man400.pdf
pkg/RSienaTest/man/includeEffects.Rd
pkg/RSienaTest/man/includeInteraction.Rd
pkg/RSienaTest/man/setEffect.Rd
Log:
New function, effectsDocumentation, and set some eol-styles to native.
Added: pkg/RSienaTest/R/effectsDocumentation.r
===================================================================
--- pkg/RSienaTest/R/effectsDocumentation.r (rev 0)
+++ pkg/RSienaTest/R/effectsDocumentation.r 2010-01-19 16:36:27 UTC (rev 46)
@@ -0,0 +1,138 @@
+#/******************************************************************************
+# * SIENA: Simulation Investigation for Empirical Network Analysis
+# *
+# * Web: http://www.stats.ox.ac.uk/~snidjers/siena
+# *
+# * File: effectsDocumentation.r
+# *
+# * Description: This module contains a function for documenting the shortNames
+# * and other fields of an effects object.
+# *****************************************************************************/
+
+##@effectsDocumentation Documentation
+effectsDocumentation <- function(type="html", display=type=="html",
+ filename="effects")
+{
+ x <- allEffects[, c(1:2,4:7, 15, 23)]
+ storage.mode(x$parm) <- "integer"
+ names(x)[4] <- "endow?"
+ names(x)[5] <- "inter1"
+ names(x)[6] <- "inter2"
+ names(x)[8] <- "ego?"
+ x$row <- as.integer(row.names(x))
+ x <- x[, c(9, 1:8)]
+
+ myorder <- c("nonSymmetricRate",
+ "covarNonSymmetricRate",
+
+ "symmetricRate",
+ "covarSymmetricRate",
+
+ "bipartiteRate",
+ "covarBipartiteRate",
+
+ "behaviorRate",
+ "behaviorOneModeRate",
+ "behaviorBipartiteRate",
+ "covarBehaviorRate",
+
+ "nonSymmetricObjective",
+ "dyadObjective",
+ "covarNonSymmetricObjective",
+ "unspecifiedNetInteraction",
+ "nonSymmetricNonSymmetricObjective",
+ "nonSymmetricSymmetricObjective",
+ "nonSymmetricBipartiteObjective",
+ "covarNetNetObjective",
+
+ "symmetricObjective",
+ "dyadObjective",
+ "covarSymmetricObjective",
+ "unspecifiedNetInteraction",
+
+ "bipartiteObjective",
+ "dyadObjective",
+ "covarBipartiteObjective",
+ "unspecifiedNetInteraction",
+ "bipartiteNonSymmetricObjective",
+ "bipartiteSymmetricObjective",
+ "bipartiteBipartiteObjective",
+ "covarNetNetObjective",
+
+ "behaviorObjective",
+ "behaviorOneModeObjective",
+ "behaviorBipartiteObjective",
+ "covarBehaviorObjective",
+ "behaviorOneModeObjective2",
+ "behaviorBipartiteObjective2",
+ "unspecifiedBehaviorInteraction")
+
+ mytab <- table(allEffects[,1])
+
+ addtorowPos <- cumsum(c(0, mytab[myorder]))[1:37]
+ addtorowText <- names(mytab[myorder])
+ if (type=="latex")
+ {
+ addtorowText <- paste(" \\hline \\multicolumn{4}{l}{",
+ addtorowText, "}\\\\ \\hline")
+ addtorowText[1] <- paste(" \\endhead ", addtorowText[1], collapse="")
+ }
+ else
+ {
+ x[is.na(x)] <- "FALSE" ## endow? field
+ x[x==""] <- "<br>"
+ addtorowText <- paste(' <TR> <TD colspan="8" >',
+ addtorowText, "</TD> </TR>")
+ }
+ add.to.row <- NULL
+ add.to.row$pos <- lapply(addtorowPos, function(x)x)
+ add.to.row$command <- as.vector(sapply(addtorowText, function(x)x))
+
+ order2 <- match(myorder, x[, 2])
+ order3 <- as.vector(mytab[myorder])
+
+ order4 <- unlist(apply(cbind(order2, order3), 1,
+ function(x)x[1]:(x[1] + x[2] -1)))
+ y <- x[order4, -2]
+ row.names(y) <- 1:nrow(y)
+
+ if (type =="latex")
+ {
+ 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,
+ tabular.environment="longtable", hline.after=c(-1),
+ floating=FALSE, include.rownames=FALSE)
+
+ cat(file=filename2, "\\documentclass[12pt,a4paper]{article}\n",
+ "\\usepackage[pdftex,dvipsnames]{color}\n",
+ "\\usepackage[landscape]{geometry}\n",
+ "\\usepackage{longtable}\n",
+ "\\pagestyle{empty}\n",
+ "\\textheight=7.25in\n",
+ "\\topmargin=-1in\n",
+ "\\evensidemargin=-0in\n",
+ "\\oddsidemargin=-0in\n",
+ "\\marginparwidth=-0in\n",
+ "\\begin{document}\n",
+ "\\include{", includepart, "}\n",
+ "\\end{document}\n", sep=""
+ )
+ }
+ else
+ {
+ filename <- paste(filename,".html", sep="", collapse="")
+ print(xtable(y), add.to.row=add.to.row,
+ file=filename,
+ type="html", hline.after=c(-1),
+ sanitize.text.function=function(x){x},
+ floating=FALSE, include.rownames=FALSE,
+ html.table.attributes="border=1 cellpadding=3 cellspacing=0")
+ if (display)
+ {
+ browseURL(paste("file://", getwd(), "/", filename,
+ collapse="", sep=""))
+ }
+ }
+}
Property changes on: pkg/RSienaTest/R/effectsDocumentation.r
___________________________________________________________________
Name: svn:eol-style
+ native
Property changes on: pkg/RSienaTest/R/sienaeffects.r
___________________________________________________________________
Name: svn:eol-style
+ native
Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog 2010-01-19 16:26:19 UTC (rev 45)
+++ pkg/RSienaTest/changeLog 2010-01-19 16:36:27 UTC (rev 46)
@@ -1,3 +1,12 @@
+2010-01-19 R-forge revision 46
+
+ * R/effectsDocumentation.r, man/effectsDocumentation.Rd,
+ inst/doc/effects.pdf: effects documentation system.
+
+2010-01-15 R-forge revision 42
+
+ * inst/doc/s_man400.pdf: new manual
+
2010-01-15 R-forge revision 41
* doc/*, .Rbuildignore, src/sienaProfile.cpp: added developer
@@ -5,14 +14,14 @@
* data/allEffects.csv: new effect, altered effect1-3 to integers
to remove bug in fix(myeff)
* inst/*.out, *.Rdata: removed stray files from examples directory
- * R/sienaeffects.r, NAMESPACE, man/includeEffects.Rd,
- man/includeInteraction.Rd, man/setEffect.Rd: utility functions to
+ * R/sienaeffects.r, NAMESPACE, man/includeEffects.Rd,
+ man/includeInteraction.Rd, man/setEffect.Rd: utility functions to
update effects object
* R/siena01.r, R/simstatsc.r, R/printDataReport.r, R/print07Report.r,
R/Sienatest.r: no longer necessary to include underlying effects
for interactions.
- * R/effects.r, man/getEffects.Rd: user parameter for number of
- unspecified behavior interactions
+ * R/effects.r, man/getEffects.Rd: user parameter for number of
+ unspecified behavior interactions
* R/print07report.r, R/sienaprint.r: remove extra sqrt roots in
standard error of rates for conditional estimation (see revision
31)
@@ -23,27 +32,27 @@
src/model/effects/PopularityAlterEffect.cpp: New effect
* src/model/variables/BehaviorVariable.h,
src/model/effects/BehaviorVariable.cpp: new method
- * tests/parallel.R, tests/parallel.R.save: reduce tests to
+ * tests/parallel.R, tests/parallel.R.save: reduce tests to
save time in Check.
* man/RSiena-package.Rd, man/siena07.Rd, man/simstats0c.Rd,
man/sienaFit.Rd: made examples faster.
-
+
2010-01-15 R-forge revision 40: RSiena only
-
+
2010-01-12 R-forge revisions 38 and 39: RSiena only
2010-01-12 R-forge revision 37
* inst/sienascript: reverted to LF eol-style
-
+
2010-01-12 R-forge revision 36
* all source files: eol-style: native
-
+
2010-01-11 R-forge revision 35
-
+
* inst: added manual and examples to RSienaTest
-
+
2010-01-02 R-forge revision 34
* R/sienaprint.r: corrected layout of sienaFitThetaTable for
Modified: pkg/RSienaTest/doc/s_man400.tex
===================================================================
--- pkg/RSienaTest/doc/s_man400.tex 2010-01-19 16:26:19 UTC (rev 45)
+++ pkg/RSienaTest/doc/s_man400.tex 2010-01-19 16:36:27 UTC (rev 46)
@@ -230,7 +230,7 @@
and van Duijn (1997), Snijders (2001), and
Snijders, Steglich, and Schweinberger (2007); also see
Steglich, Snijders, and Pearson (2010).
-A tutorial for these models is in Snijders, van de Bunt, and Steglich (2009).
+A tutorial for these models is in Snijders, van de Bunt, and Steglich (2010).
Some examples are
presented, e.g., in van de Bunt (1999); van de Bunt, van Duijn, and
Snijders (1999); and van Duijn, Zeggelink, Stokman, and Wasseur (2003);
@@ -930,44 +930,70 @@
# fix() may not be usable if you do not have tcl/tk available
-# Alternatively we can edit the dataframe directly using more data slicing
-# this command is another way to set "include" to TRUE or FALSE. TRUE or FALSE
-# will always be located at the 9th column, but not always at the 11th row as we
-# add or remove rate parameters depending on the model. In general the advantage
-# of this method is that we can save the last parameters and rerun the model
+# Alternatively we can edit the dataframe directly by using R functions.
+# Note that the columns of the dataframe of effects have names indicated
+# in the top of the dataframe:
+# name, effectName, type, include, fix, test, initialValue, parm,
+# effectnumber, effect1, effect2, effect3.
+# The commands below are used to set "include" to TRUE or FALSE,
+# as an alternative to using the data editor.
+# TRUE or FALSE will always be located at the 9th column,
+# transitive triplets will not always be at the 11th row as this depends
+# on the number of periods; further, the list of available effects
+# may change in future versions.
+# In general the advantage of this method is
+# that we can save the last parameters and rerun the model
# later without opening the editor. (Saving can now be done in the GUI).
-# NB These row numbers may not be the current ones.
+# Note: These row numbers may not be the current ones, as they depend on the
+# list of effects implemented, which is changeable.
- #myeff[11,9]=TRUE #transitive triples
- #myeff[15,9]=TRUE #3 cycles
- #myeff[17,9]=TRUE #transitive ties
- #myeff[27,9]=TRUE #indegree popularity
- #myeff[31,9]=TRUE #outdegree popularity
- #myeff[34,9]=TRUE #indegree based activity
- #myeff[36,9]=TRUE #outdegree based activity
- #myeff[46,9]=TRUE #indegree-indegree assortivity
- #myeff[48,9]=TRUE #alcohol alter
- #myeff[50,9]=TRUE #alcohol alter (squared)
- #myeff[52,9]=TRUE #alcohol ego
- #myeff[54,9]=TRUE #alcohol similarity
- #myeff[62,9]=TRUE #alcohol alter by ego
+ #myeff[11,9] <- TRUE #transitive triples
+ #myeff[15,9] <- TRUE #3 cycles
+ #myeff[17,9] <- TRUE #transitive ties
+ #myeff[27,9] <- TRUE #indegree popularity
+ #myeff[31,9] <- TRUE #outdegree popularity
+ #myeff[34,9] <- TRUE #indegree based activity
+ #myeff[36,9] <- TRUE #outdegree based activity
+ #myeff[46,9] <- TRUE #indegree-indegree assortativity
+ #myeff[48,9] <- TRUE #alcohol alter
+ #myeff[50,9] <- TRUE #alcohol alter (squared)
+ #myeff[52,9] <- TRUE #alcohol ego
+ #myeff[54,9] <- TRUE #alcohol similarity
+ #myeff[62,9] <- TRUE #alcohol ego x alcohol alter
-# (Alternatively, and more robustly against future changes in the structure,
-# use
+# Alternatively, and more robustly against future changes in the structure,
+# use the following for the last effect:
#myeff[myeff$effectName=='alcohol ego x alcohol alter' &
#myeff$type=='eval', 'include']=TRUE)
+
+# and similarly for the earlier ones.
# To specify an interaction between say alcohol and reciprocity,
-# where 69 is the row number of an unspecified interaction effect:
+# where 69 is the row number of an unspecified interaction effect,
+# and 52 and 9 are now used as the numbers of the effects
+# that get the roles of effect1 and effect2,
+# meaning that they are to be interacted, the following can be used;
+# the name will be created by siena07.
#myeff[69, c('effect1', 'effect2')] <- c(52, 9)
#myeff[69, 'include'] <- TRUE
+
+
# new, more robust, methods to amend an effects object:
+
#myeff <- includeEffects(myeff, transTrip, cycle3, between)
#myeff <- includeInteraction(myeff, egoX, recip,
# interaction1="alcohol")
#myeff <- setParameter(myeff, outInv, 3)
+# There is a table of short names etc available as pdf via
+
+ #RShowDoc("effects", package="RSiena")
+
+# or as html by running the function
+
+ #effectsDocumentation()
+
# siena07 actually fits the specified model to the data
ans <- siena07(mymodel, data=mydata, effects=myeff, batch=FALSE, verbose=TRUE)
@@ -1217,7 +1243,8 @@
\label{S_multipleProcesses}
\begin{enumerate}
\item
-Multiple processes can be used to speed up the estimation in \sfn{siena07}.
+If multiple processors are available, then using
+multiple processes can speed up the estimation in \sfn{siena07}.
\item In Phases 1 and 3 the simulations are performed in parallel. In Phase 2,
multiple simulations are done with the same parameters, and the resulting
@@ -1292,7 +1319,7 @@
\noindent
Ripley, Ruth M., and Snijders, Tom A.B.
-2009.
+2010.
Manual for SIENA version 4.0 (provisional version, \today).
Oxford: University of Oxford, Department of Statistics; Nuffield College.
\textsf{http://www.stats.ox.ac.uk/siena/}
@@ -1309,12 +1336,12 @@
fit tests and Schweinberger and Snijders (2007) for the calculation of standard
errors of the Method of Moments estimators .
-A tutorial is Snijders, van de Bunt, and Steglich (2009).
+A tutorial is Snijders, van de Bunt, and Steglich (2010).
\subsection{Getting help with problems}
\label{sec:problems}
-If you have a problem running \RS, please read through the following hints to
+If you have a problem running \rs, please read through the following hints to
see if any of them help. If not, please send an email to
rsiena-help at lists.r-forge.r-project.org, or post in the help forum for \RS in
R-forge. You need to be a registered member of R-forge (and possibly of \rs)
@@ -1322,8 +1349,8 @@
please tell us which operating system , which version of \Rn, and which version
of \RS you are using.
-For queries about the modelling aspects of \SI, or interpretation, please
-continue to use the \SN mailing list.
+For queries about the modelling aspects of \si, or interpretation, please
+continue to use the \SN/ \RS mailing list.
\begin{description}
@@ -1953,7 +1980,7 @@
For the longitudinal case, three types of
effects are distinguished (see Snijders, 2001; Snijders,
-van de Bunt, and Steglich, 2009):
+van de Bunt, and Steglich, 2010):
\begin{itemize}
\item {\em rate function effects}\\
@@ -2802,15 +2829,31 @@
It is possible for the user to define additional interaction effects for the
network. % and the behavior.
-The basis is provided by the initial definition, by \si, of ``unspecified
-interaction effects''. Modifying two or three of the columns named ``effect1'',
-``effect2'', and ``effect3'' of these effects allows the definition of two-way
+The basis is provided by the initial definition, by \si, of `unspecified
+interaction effects'. Modifying two or three of the columns named `effect1',
+`effect2', and `effect3' of the effects dataframe
+allows the definition of two-way
or three-way interactions. The \emph{effectNumber} of the effects between which
-an interaction is required should be entered in the ``effect1'' and ``effect2'',
-and for three-way effects, the ``effect3'' columns. The interaction effect must
-also be ``included'', but the underlying effects need only be ``included'' if
+an interaction is required should be entered in the `effect1' and `effect2',
+and for three-way effects, the `effect3' columns. The interaction effect must
+also be `included', but the underlying effects need only be `included' if
they are also required individually.
+\sfn{includeInteraction} is an \R function provided to facilitate the definition
+of interaction effects. Such effects can be specified simply by short names and
+the names of any variables required to identify the underlying effects: it is
+not necessary to know the effectNumbers of the effects. (The effectNumbers would
+change if new effects are introduced to \rs.) Information about short names of
+effects can be found in the file `effects.pdf' in the doc directory of the
+library, accessible from within \R using the command
+
+\verb|RShowDoc("effects", package="RSiena")|
+
+Alternatively a new version of this list can be displayed in a browser by using
+the function:
+
+\verb|effectsDocumentation()|
+
\subsubsection{Interaction effects for network dynamics}
The following kinds of user-defined interactions are possible
@@ -2828,7 +2871,8 @@
dyadic effects, two dyadic effects and an ego effect, or two ego effects and
another effect.
-All effects used in interactions must be defined on the same network: that for
+All effects used in interactions must be defined on the same network
+(in the role of dependent variable): that for
which the ``unspecified
interaction effects'' is defined. And either all must be evaluation effects or
all must be endowment effects.
@@ -4021,12 +4065,28 @@
Most goodness-of-fit tests will have the following form: some model
is specified and one or more parameters are restricted to some
-constant, in most cases $0$.
-Parameters can be restricted by %opening the \textsf{{\em pname}.MO}
-%file, going to the parameters of interest and setting the values in
-%the fourth column equal to {\tt 1}.
+constant, in most cases $0$ -- these constant values
+define the null hypothesis being tested.
+This can be obtained in \RS by appropriate choices in the effects dataframe
+(called \sfn{myeff} in Section~ \ref{S_Rscript}).
+Parameters can be restricted by
putting 1 in the \sfn{fix} and \sfn{test} columns when editing the effects, and
-the constant value in the \sfn{initialValue} column. The goodness-of-fit test
+the tested value in the \sfn{initialValue} column.
+For example, when the effect for which the score test
+is desired has \sfn{effectNumber} equal to 46, the
+commands can be as follows.
+
+\begin{verbatim}
+myeff[46,9] <- TRUE
+myeff[46, 'fix'] <- TRUE
+myeff[46, 'test'] <- TRUE
+myeff[46, 'initialValue'] <- ((value to be used for test))
+\end{verbatim}
+
+
+
+
+The goodness-of-fit test
proceeds by simply estimating the restricted model (not the unrestricted model,
with unrestricted parameters) by the standard \SI estimation algorithm. No more
information needs to be communicated.% When the model is restricted, \SI by
@@ -5907,7 +5967,7 @@
for only those actors who decreased in behavior.
More precisely, it is
\begin{equation}
-\sum_{m=1}^{M-1} \sum_{i=1}^n I\{z_{ij}(t_{m+1}) < z_{ij}(t_m) \}\,
+\sum_{m=1}^{M-1} \sum_{i=1}^n I\{z_{i}(t_{m+1}) < z_{i}(t_m) \}\,
\big( s^{\rm beh}_{ik}(x(t_{m+1})) - s^{\rm beh}_{ik}(x(t_m)) \big) ,
\end{equation}
where $M$ is the number of observations, $x(t_m)$ is the observed situation
@@ -6475,26 +6535,35 @@
(Programmers should consult the changeLog file on CRAN or in the R-forge
repository.)
\begin{itemize}
+\item 2010-01-19 R-forge revision 45
+ New documentation for the effects object.
+\item 2010-01-18 R-forge revision 43 (RSiena)
+\begin{itemize}
+\item new behavior effects
+\item user specified interactions
+\item new utilities to update the effects object
+\end{itemize}
\item 2010-01-15 R-forge revision 41 (RSienaTest only)
\begin{itemize}
\item
new effect: Popularity Alter, and altered effect1-3 to integers to correct
- bug in fix(myeff)
- \item new utility functions to update effects object * no longer
- necessary to include underlying effects for interactions.
- \item user parameter for number of unspecified behavior interactions
+ bug in fix(myeff)
+ \item new utility functions to update effects object
+ \item no longer
+ necessary to include underlying effects for interactions.
+ \item user parameter for number of unspecified behavior interactions
\item remove extra sqrt roots in standard error of rates for conditional
estimation (see revision 31)
\end{itemize}
\item 2010-01-15 R-forge revision 40: RSiena only
-
+
remove extra sqrt roots in standard error of rates for conditional
estimation (see revision 32)
-
-
+
+
\item 2010-01-02 R-forge revision 34
-
+
Corrected layout of print and xtable for SienaFit objects with both behavior and
network variables.
@@ -6830,6 +6899,12 @@
edited by Kees van Montfort, Han Oud and Albert Satorra, pp.\ 41--71.
Mahwah, NJ: Lawrence Erlbaum.
+\bibitem{}
+Snijders, T.A.B., van de Bunt, G.G., and Steglich, C.E.G. (2010).
+Introduction to actor-based models for network dynamics.
+\textit{Social Networks}, 32, 44--60.
+
+
\bibitem{} Snijders, T.A.B., and M.A.J.\ Van Duijn. 1997.
Simulation for statistical inference in dynamic network models.
Pp.\ 493 -- 512 in {\em Simulating Social Phenomena}, edited by
Added: pkg/RSienaTest/inst/doc/effects.pdf
===================================================================
(Binary files differ)
Property changes on: pkg/RSienaTest/inst/doc/effects.pdf
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: pkg/RSienaTest/inst/doc/s_man400.pdf
===================================================================
--- pkg/RSienaTest/inst/doc/s_man400.pdf 2010-01-19 16:26:19 UTC (rev 45)
+++ pkg/RSienaTest/inst/doc/s_man400.pdf 2010-01-19 16:36:27 UTC (rev 46)
@@ -469,19 +469,17 @@
(References)
endobj
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-/Length 1076
+/Length 1077
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[TRUNCATED]
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