[Rsiena-commits] r102 - in pkg/RSienaTest: . R doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 10 17:27:49 CEST 2010
Author: jalospinoso
Date: 2010-06-10 17:27:48 +0200 (Thu, 10 Jun 2010)
New Revision: 102
Removed:
pkg/RSienaTest/man/includeTimeDummy.Rd
Modified:
pkg/RSienaTest/NAMESPACE
pkg/RSienaTest/R/sienaTimeTest.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/s_man400.tex
pkg/RSienaTest/man/plot.sienaTimeTest.Rd
pkg/RSienaTest/man/setEffect.Rd
pkg/RSienaTest/man/sienaTimeTest.Rd
Log:
Removed includeTimeDummy
Modified: pkg/RSienaTest/NAMESPACE
===================================================================
--- pkg/RSienaTest/NAMESPACE 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/NAMESPACE 2010-06-10 15:27:48 UTC (rev 102)
@@ -5,7 +5,7 @@
sienaGroupCreate, sienaModelCreate, sienaNet, sienaNodeSet, #simstats0c,
varCovar, varDyadCovar, setEffect, includeEffects, includeInteraction,
effectsDocumentation, sienaDataConstraint, #maxlikefn,
- installGui, siena08, iwlsm, sienaTimeTest, includeTimeDummy)
+ installGui, siena08, iwlsm, sienaTimeTest)
import(Matrix)
import(xtable)
Modified: pkg/RSienaTest/R/sienaTimeTest.r
===================================================================
--- pkg/RSienaTest/R/sienaTimeTest.r 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/R/sienaTimeTest.r 2010-06-10 15:27:48 UTC (rev 102)
@@ -760,40 +760,4 @@
}
list(effects=effects, data=data)
}
-}
-##@includeTimeDummy DataCreate
-includeTimeDummy <- function(myeff, ..., timeDummy="all", name=myeff$name[1],
- type="eval", interaction1="", interaction2="", include=TRUE,
- character=FALSE)
-{
-
- if (character)
- {
- dots <- sapply(list(...), function(x)x)
- }
- else
- {
- dots <- substitute(list(...))[-1] ##first entry is the word 'list'
- }
- if (length(dots) == 0)
- {
- stop("need some effect short names")
- }
- if (!character)
- {
- effectNames <- sapply(dots, function(x)deparse(x))
- }
- else
- {
- effectNames <- dots
- }
- use <- myeff$shortName %in% effectNames &
- myeff$type==type &
- myeff$name==name &
- myeff$interaction1 == interaction1 &
- myeff$interaction2 == interaction2
- myeff[use, "timeDummy"] <- timeDummy
- myeff[use, "include"] <- include
- print.data.frame(myeff[use,])
- myeff
-}
+}
\ No newline at end of file
Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/changeLog 2010-06-10 15:27:48 UTC (rev 102)
@@ -1,3 +1,12 @@
+2010-06-08 R-forge revision 100/101
+
+ * R/sienaTimeTest.r: added changing covariate functionality to
+ sienaTimeFix for RateX effects. Deleted includeTimeDummy.
+ * man/includeTimeDummy.r: deleted.
+ * man/sienaTimeTest.r: changed includeTimeDummy to setEffects
+ * man/plot.sienaTimeTest.r: changed includeTimeDummy to setEffects
+ * doc/s_man400.tex: changed includeTimeDummy to setEffects
+
2010-06-08 R-forge revision 99
* R/simstatsc.r: fixed bug that bipartite networks not allowed 'loops'
Modified: pkg/RSienaTest/doc/s_man400.tex
===================================================================
--- pkg/RSienaTest/doc/s_man400.tex 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/doc/s_man400.tex 2010-06-10 15:27:48 UTC (rev 102)
@@ -1491,7 +1491,7 @@
# Add a few time dummy terms:
- myeff3<- includeTimeDummy(myeff2, recip, balance, timeDummy="2")
+ myeff3<- setEffect(myeff2, recip, balance, timeDummy="2")
# And estimate the new model:
@@ -3756,7 +3756,7 @@
with time dummies. You
can include these in your model simply via the function
\begin{verbatim}
-myeffects <- includeTimeDummy(myeffects, density, reciprocity, timeDummy="2,3,6")
+myeffects <- setEffect(myeffects, density, reciprocity, timeDummy="2,3,6")
\end{verbatim}
which would add three time dummy terms to each effect listed in the function.
@@ -4804,7 +4804,7 @@
If as a consequence of this analysis you wish to add time dummy terms,
this may be done via
\begin{verbatim}
-myeff <- includeTimeDummy(myeff, recip, balance, timeDummy="2")
+myeff <- setEffect(myeff, recip, balance, timeDummy="2")
ans3 <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE)
\end{verbatim}
and testing again,
@@ -7851,6 +7851,7 @@
(Programmers should consult the changeLog file on CRAN or in the R-forge
repository.)
\begin{itemize}
+\item 2010-06-10 R-forge revision 100/101: Removed includeTimeDummy, as it duplicates functionality for setEffects. Fixed RateX so that it works with changing actor covariates as well.
\item 2010-06-08 R-forge revision 99
Fix to bug introduced in revision 98: bipartite networks could not have 'loops'
\item 2010-06-08 R-forge revision 98
Deleted: pkg/RSienaTest/man/includeTimeDummy.Rd
===================================================================
--- pkg/RSienaTest/man/includeTimeDummy.Rd 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/man/includeTimeDummy.Rd 2010-06-10 15:27:48 UTC (rev 102)
@@ -1,95 +0,0 @@
-\name{includeTimeDummy}
-\alias{includeTimeDummy}
-\title{Functions to include time dummy effects in a Siena model}
-\description{
- This function provides an interface to set the TimeDummy column on
- selected rows of a Siena effects object.
- }
-
-\usage{
-includeTimeDummy(myeff, ..., timeDummy="all", name=myeff$name[1],
-type="eval", interaction1="", interaction2="", include=TRUE,
-character=FALSE)
-}
-\arguments{
- \item{myeff}{a Siena effects object as created by \code{\link{getEffects}}
-}
- \item{\dots}{
-short names to identify the effects which should be included or excluded.
-}
-\item{timeDummy}{character string. Either "all" or the periods for which
- to create dummies, space delimited.}
- \item{include}{Boolean. default TRUE, but can be switched to FALSE to
- turn off an effect.
- }
- \item{name}{Name of network for which effects are being
- included. Defaults to the first in the effects object.
-}
- \item{type}{
- Type of effects to be included.
-}
- \item{interaction1}{
- Name of siena object where needed to completely identify the
- effects e.g. covariate name or behavior variable name.
-}
- \item{interaction2}{
- Name of siena object where needed to completely identify the
- effects e.g. covariate name or behavior variable name.
-}
-\item{character}{Boolean: are the effect names character strings or not}
-}
-\details{
-The arguments should identify the effects completely. The
- include column will be set to the value requested (TRUE or FALSE)}
-\value{
- An updated version of the input effects object, with the include
- columns for one or more rows
- updated.
- Details of the rows altered will be printed.
-}
-
-\references{See \url{http://www.stats.ox.ac.uk/~snijders/siena/}
- for general information on RSiena.
-
-}
-\author{Josh Lospinoso}
-\seealso{\code{\link{sienaTimeTest}}, \code{\link{getEffects}},
- \code{\link{siena07}}}
-\examples{
-## Estimate a restricted model
-mymodel <- sienaModelCreate(fn=simstats0c, nsub=2, n3=100)
-mynet1 <- sienaNet(array(c(s501, s502, s503), dim=c(50, 50, 3)))
-mydata <- sienaDataCreate(mynet1)
-myeff <- getEffects(mydata)
-myeff <- includeEffects(myeff, transTrip, balance)
-ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE)
-
-## Conduct the score type test to assess whether heterogeneity is present.
-tt <- sienaTimeTest(ans)
-
-## Suppose that we wish to include two time dummies.
-## Add them in the following way:
-myeff <- includeTimeDummy(myeff, recip, balance, timeDummy="2")
-ans2 <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE)
-
-## Re-assess the time heterogeneity
-tt2 <- sienaTimeTest(ans2)
-
-## And so on..
-
-## A demonstration of RateX heterogeneity. Note that rate
-## interactions are not implemented in general, just for
-## Rate x cCovar.
-\dontrun{
-mymodel <- sienaModelCreate(fn=simstats0c, nsub=2, n3=100)
-mynet1 <- sienaNet(array(c(s501, s502, s503), dim=c(50, 50, 3)))
-myccov <- coCovar(s50a[,1])
-mydata <- sienaDataCreate(mynet1, myccov)
-myeff <- getEffects(mydata)
-myeff <- includeEffects(myeff, transTrip, balance)
-myeff <- includeTimeDummy(myeff, RateX, type="rate",
- interaction1="myccov")
-ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE)
-}
-}
-\keyword{models}
Modified: pkg/RSienaTest/man/plot.sienaTimeTest.Rd
===================================================================
--- pkg/RSienaTest/man/plot.sienaTimeTest.Rd 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/man/plot.sienaTimeTest.Rd 2010-06-10 15:27:48 UTC (rev 102)
@@ -73,9 +73,9 @@
mydata <- sienaDataCreate(mynet1)
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTrip, balance)
-myeff <- includeTimeDummy(myeff, recip, timeDummy="2,3,5")
-myeff <- includeTimeDummy(myeff, balance, timeDummy="4")
-myeff <- includeTimeDummy(myeff, density, timeDummy="all")
+myeff <- setEffect(myeff, recip, timeDummy="2,3,5")
+myeff <- setEffect(myeff, balance, timeDummy="4")
+myeff <- setEffect(myeff, density, timeDummy="all")
ansp <- siena07(mymodel, data=mydata, effects=myeff, batch=FALSE)
ttp <- sienaTimeTest(ansp)
Modified: pkg/RSienaTest/man/setEffect.Rd
===================================================================
--- pkg/RSienaTest/man/setEffect.Rd 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/man/setEffect.Rd 2010-06-10 15:27:48 UTC (rev 102)
@@ -29,7 +29,7 @@
\item{initialValue}{Initial value required. Default 0.
}
\item{timeDummy}{string: Comma delimited string of which periods to
-dummy. Alternately, use \code{\link{includeTimeDummy}}.
+dummy. Alternately, use the corresponding column on your effect object}.
}
\item{include}{Boolean. default TRUE, but can be switched to FALSE to
turn off an effect.}
Modified: pkg/RSienaTest/man/sienaTimeTest.Rd
===================================================================
--- pkg/RSienaTest/man/sienaTimeTest.Rd 2010-06-09 19:50:02 UTC (rev 101)
+++ pkg/RSienaTest/man/sienaTimeTest.Rd 2010-06-10 15:27:48 UTC (rev 102)
@@ -45,7 +45,7 @@
time periods or effects (or any combination therein), the
\code{timeDummy} column provides facilities within a sienaFit object to
quickly adjust the model and re-estimate in the usual way. Alternately,
- the includeTimeDummy function can be used to add the desired dummies.
+ the setEffect function can be used to add the desired dummies.
}
\value{
\code{sienaTimeTest} Returns a list containing many items,
@@ -76,7 +76,7 @@
}
\author{Josh Lospinoso}
\seealso{\code{\link{siena07}}, \code{\link{plot.sienaTimeTest}},
- \code{\link{includeTimeDummy}}}
+ \code{\link{setEffect}}}
\examples{
## Estimate a restricted model
mymodel <- sienaModelCreate(fn=simstats0c, nsub=2, n3=100)
@@ -91,7 +91,7 @@
## Suppose that we wish to include two time dummies.
## Add them in the following way:
-myeff <- includeTimeDummy(myeff, recip, balance, timeDummy="2")
+myeff <- setEffect(myeff, recip, balance, timeDummy="2")
ans2 <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE)
## Re-assess the time heterogeneity
@@ -106,9 +106,9 @@
mydata <- sienaDataCreate(mynet1)
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTrip, balance)
-myeff <- includeTimeDummy(myeff, recip, timeDummy="2,3,5")
-myeff <- includeTimeDummy(myeff, balance, timeDummy="4")
-myeff <- includeTimeDummy(myeff, density, timeDummy="all")
+myeff <- setEffect(myeff, recip, timeDummy="2,3,5")
+myeff <- setEffect(myeff, balance, timeDummy="4")
+myeff <- setEffect(myeff, density, timeDummy="all")
ansp <- siena07(mymodel, data=mydata, effects=myeff, batch=FALSE)
ttp <- sienaTimeTest(ansp)
@@ -128,8 +128,8 @@
mydata <- sienaDataCreate(mynet1, myccov)
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTrip, balance)
-myeff <- includeTimeDummy(myeff, RateX, type="rate",
- interaction1="myccov")
+myeff <- setEffect(myeff, RateX, type="rate",
+ interaction1="myccov", timeDummy="all")
ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE)
}
}
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