[Rsiena-commits] r346 - in pkg: RSiena RSiena/R RSiena/man RSiena/src RSiena/tests RSienaTest RSienaTest/R RSienaTest/doc RSienaTest/man RSienaTest/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 15 11:26:04 CET 2020
Author: tomsnijders
Date: 2020-01-15 11:26:04 +0100 (Wed, 15 Jan 2020)
New Revision: 346
Modified:
pkg/RSiena/ChangeLog
pkg/RSiena/DESCRIPTION
pkg/RSiena/R/globals.r
pkg/RSiena/R/print01Report.r
pkg/RSiena/R/siena08.r
pkg/RSiena/R/sienaModelCreate.r
pkg/RSiena/cran-comments.md
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/man/Wald.Rd
pkg/RSiena/man/print.sienaMeta.Rd
pkg/RSiena/man/print.sienaTest.Rd
pkg/RSiena/man/print01Report.Rd
pkg/RSiena/man/siena07.Rd
pkg/RSiena/man/siena08.Rd
pkg/RSiena/man/sienaAlgorithmCreate.Rd
pkg/RSiena/man/sienaFit.Rd
pkg/RSiena/man/sienaGOF-auxiliary.Rd
pkg/RSiena/man/sienaGOF.Rd
pkg/RSiena/man/sienaRI.Rd
pkg/RSiena/man/sienaTimeTest.Rd
pkg/RSiena/man/simstats0c.Rd
pkg/RSiena/man/updateTheta.Rd
pkg/RSiena/src/Makevars.win
pkg/RSiena/tests/parallel.R
pkg/RSiena/tests/parallel.Rout.save
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/globals.r
pkg/RSienaTest/R/print01Report.r
pkg/RSienaTest/R/siena08.r
pkg/RSienaTest/R/sienaModelCreate.r
pkg/RSienaTest/doc/RSiena.bib
pkg/RSienaTest/doc/RSiena_Manual.pdf
pkg/RSienaTest/doc/RSiena_Manual.tex
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/Wald.Rd
pkg/RSienaTest/man/print.sienaMeta.Rd
pkg/RSienaTest/man/print01Report.Rd
pkg/RSienaTest/man/siena07.Rd
pkg/RSienaTest/man/siena08.Rd
pkg/RSienaTest/man/sienaAlgorithmCreate.Rd
pkg/RSienaTest/man/sienaGOF-auxiliary.Rd
pkg/RSienaTest/man/sienaGOF.Rd
pkg/RSienaTest/man/sienaRI.Rd
pkg/RSienaTest/man/sienaTimeTest.Rd
pkg/RSienaTest/tests/parallel.R
pkg/RSienaTest/tests/parallel.Rout.save
Log:
As CRAN RSiena version 1.2.23.
Modified: pkg/RSiena/ChangeLog
===================================================================
--- pkg/RSiena/ChangeLog 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/ChangeLog 2020-01-15 10:26:04 UTC (rev 346)
@@ -1,3 +1,16 @@
+2020-01-15 R-Forge Revision 346, version 1.2-23 same as CRAN version
+(except that one error in dontrun part of sienaGOF-auxiliary.Rd was corrected).
+
+2020-01-12 Package version 1.2-23 submitted to CRAN.
+ * Changes in RSiena and RSienaTest:
+ Option projname=NULL in sienaAlgorithmCreate.
+ This option is used for all examples in RSiena where siena07 is called,
+ to restrict file writing for examples to the temporary directory.
+
+2020-01-10 Package version 1.2-22.
+ * Changes in RSiena and RSienaTest:
+ Changed extension names of output files from .out to .txt.
+
2020-01-04 R-Forge Revision 345, package version 1.2-22.
Changes in RSiena and RSienaTest:
* Tested effects reported in print of Multipar.RSiena and score.Test.
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/DESCRIPTION 2020-01-15 10:26:04 UTC (rev 346)
@@ -2,8 +2,8 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.2-22
-Date: 2020-01-04
+Version: 1.2-23
+Date: 2020-01-12
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger,
Nynke Niezink
Depends: R (>= 2.15.0)
Modified: pkg/RSiena/R/globals.r
===================================================================
--- pkg/RSiena/R/globals.r 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/R/globals.r 2020-01-15 10:26:04 UTC (rev 346)
@@ -8,7 +8,7 @@
## * Description: This file contains the code to create and use global objects
## *
## ****************************************************************************/
-##@outf Objects/File project .out file
+##@outf Objects/File project .txt file
outf <- NULL
##@lf Objects/File suppressed or to console
lf <- NULL
@@ -36,11 +36,11 @@
noReportFile <<- FALSE
if (type =='w')
{
- x$outf <<- file(paste(projname, ".out", sep=""), open="w")
+ x$outf <<- file(paste(projname, ".txt", sep=""), open="w")
}
else if (type =="a")
{
- x$outf <<- file(paste(projname, ".out", sep=""), open="a")
+ x$outf <<- file(paste(projname, ".txt", sep=""), open="a")
}
else if (type == "n")
{
Modified: pkg/RSiena/R/print01Report.r
===================================================================
--- pkg/RSiena/R/print01Report.r 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/R/print01Report.r 2020-01-15 10:26:04 UTC (rev 346)
@@ -894,10 +894,10 @@
}
Report(openfiles=TRUE, type="w", projname=modelname)
Report(" ************************\n", outf)
- Report(c(" ", modelname, ".out\n"),
+ Report(c(" ", modelname, ".txt\n"),
sep='', outf)
Report(" ************************\n\n", outf)
- Report(c("Filename is ", modelname, ".out.\n\n"), sep="", outf)
+ Report(c("Filename is ", modelname, ".txt.\n\n"), sep="", outf)
Report(c("This file contains primary output for SIENA project <<",
modelname, ">>.\n\n"), sep="", outf)
Report(c("Date and time:", format(Sys.time(), "%d/%m/%Y %X"), "\n\n"), outf)
Modified: pkg/RSiena/R/siena08.r
===================================================================
--- pkg/RSiena/R/siena08.r 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/R/siena08.r 2020-01-15 10:26:04 UTC (rev 346)
@@ -498,9 +498,9 @@
0
}
Report(c(rep(" ", nBlanks), rep("*", astlen), "\n"), sep="", outf)
- Report(c(rep(" ", nBlanks2), projname, ".out\n"), sep="", outf)
+ Report(c(rep(" ", nBlanks2), projname, ".txt\n"), sep="", outf)
Report(c(rep(" ", nBlanks), rep("*", astlen), "\n"), sep="", outf)
- Report(c("Filename is ", projname, ".out.\n\n"), sep="", outf)
+ Report(c("Filename is ", projname, ".txt.\n\n"), sep="", outf)
Report(c("This file contains primary output for SIENA project <<",
projname, ">>.\n\n"), sep="", outf)
Report(c("Date and time:", format(Sys.time(),
Modified: pkg/RSiena/R/sienaModelCreate.r
===================================================================
--- pkg/RSiena/R/sienaModelCreate.r 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/R/sienaModelCreate.r 2020-01-15 10:26:04 UTC (rev 346)
@@ -25,7 +25,26 @@
lessMem=FALSE)
{
model <- NULL
- model$projname <- projname
+ if (is.null(projname))
+ {
+ model$projname <- tempfile("Siena")
+ cat('siena07 will create an output file',
+ paste(model$projname,'.txt',sep=''),'.\n')
+ cat('This is a temporary file for this R session.\n')
+ }
+ else
+ {
+ if (is.character(projname))
+ {
+ model$projname <- projname
+ cat('siena07 will create an output file',
+ paste(model$projname,'.txt',sep=''),'.\n')
+ }
+ else
+ {
+ stop('projname should be a character string.')
+ }
+ }
model$useStdInits <- useStdInits
model$checktime <- TRUE
model$n3 <- n3
Modified: pkg/RSiena/cran-comments.md
===================================================================
--- pkg/RSiena/cran-comments.md 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/cran-comments.md 2020-01-15 10:26:04 UTC (rev 346)
@@ -1,29 +1,5 @@
-# RSiena new version 1.2-21 (2019-12-18)
+# RSiena new version 1.2-23 (2020-01-12)
-## The only remaining NOTE was that on x86_64-pc-linux-gnu (64-bit)
- apparently the file Siena.out was not deleted. This now is done
- by calling unlink().
-
-# RSiena new version 1.2-20 (2019-12-16)
-
-## The note in Debian about existence of file Siena.out in the
- check directory was fixed, using file.remove().
-
-## The additional issue for the earlier version 1.2-12 in LTO
- (about getChainProbabilities) was fixed by dropping this function
- which was not used anyway.
-
-## The additional issue for the earlier version 1.2-12 in rchk (about DumpChain)
- was fixed by dropping this function which was not used anyway.
-
-
-# RSiena new version 1.2-19 (2019-12-16)
-
-## Kurt Hornik sent me a message that it was necessary to replace the use of
- (class(..) == ... ) by (inherits(...)).
- This was done, and fixes the error in the earlier version 1.2-12 occurring
- for r-devel-linux-x86_64-debian-clang.
-
## Passed checks on Windows, Mac, and Linux for R-release and R-devel.
* No ERRORs or WARNINGs.
* On some systems there is a NOTE about the installed package size,
@@ -31,6 +7,17 @@
* Sometimes NOTEs about computation times of examples.
These require simulations, and times are barely over 5s.
+## Kurt Hornik sent me a message that it was necessary to replace the use of
+ (class(..) == ... ) by (inherits(...)).
+ This was done, and fixes the error in the earlier version 1.2-12 occurring
+ for r-devel-linux-x86_64-debian-clang.
+
+## Brian Ripley sent me a message that there may be minor changes in output
+ depending on the platform. This now is avoided by minor changes in the tests.
+ Brian also sent me a message about strange things in the Configure files.
+ Since tests are passed (as above) on various R-hub platforms
+ I think this is not a major obstacle for now, and will look into it later.
+
## There are quite some parts in the .Rd files with donttest.
This is because executing them is too time-consuming.
* R CMD check --run-donttest on Windows OK.
Modified: pkg/RSiena/man/RSiena-package.Rd
===================================================================
--- pkg/RSiena/man/RSiena-package.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/RSiena-package.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -44,8 +44,8 @@
\tabular{ll}{
Package: \tab RSiena\cr
Type: \tab Package\cr
- Version: \tab 1.2-22\cr
- Date: \tab 2020-01-02\cr
+ Version: \tab 1.2-23\cr
+ Date: \tab 2020-01-12\cr
Depends: \tab R (>= 3.0.0)\cr
Imports: \tab Matrix\cr
Suggests: \tab tcltk, network, codetools, lattice, MASS, parallel,
@@ -103,7 +103,7 @@
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTrip)
myeff
-myalgorithm <- sienaAlgorithmCreate(nsub=3, n3=200)
+myalgorithm <- sienaAlgorithmCreate(nsub=3, n3=200, projname=NULL)
ans <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE)
summary(ans)
}
Modified: pkg/RSiena/man/Wald.Rd
===================================================================
--- pkg/RSiena/man/Wald.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/Wald.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -70,7 +70,7 @@
mynet <- sienaDependent(array(c(s501, s502), dim=c(50, 50, 2)))
mydata <- sienaDataCreate(mynet)
myeff <- getEffects(mydata)
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=40, seed=123)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=40, seed=1777, projname=NULL)
# nsub=1 and n3=40 is used here for having a brief computation,
# not for practice.
myeff <- includeEffects(myeff, transTrip, transTies)
Modified: pkg/RSiena/man/print.sienaMeta.Rd
===================================================================
--- pkg/RSiena/man/print.sienaMeta.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/print.sienaMeta.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -24,7 +24,7 @@
\item{x}{An object of class \code{sienaMeta}, or
\code{summary.sienaMeta} as appropriate.}
\item{file}{Boolean: if TRUE, sends output to file named
- \code{x$projname.out}. If FALSE, output is to the terminal.}
+ \code{x$projname.txt}. If FALSE, output is to the terminal.}
\item{reportEstimates}{Boolean: whether to report all estimates and standard errors.}
\item{extra}{Boolean: if TRUE, prints more information.}
\item{which}{Set of effects contained in the plot (given by sequence numbers).}
@@ -47,7 +47,7 @@
Output from either can be directed to a file by using the argument
\code{file}. It will be appended to any existing file of the same
- name: \code{projname.out} where \code{projname} is the value of the
+ name: \code{projname.txt} where \code{projname} is the value of the
argument to \code{siena08}.
The function \code{plot.sienaMeta} plots estimates against standard
Modified: pkg/RSiena/man/print.sienaTest.Rd
===================================================================
--- pkg/RSiena/man/print.sienaTest.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/print.sienaTest.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -31,7 +31,7 @@
mynet <- sienaDependent(array(c(s501, s502), dim=c(50, 50, 2)))
mydata <- sienaDataCreate(mynet)
myeff <- getEffects(mydata)
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=40, seed=123)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=40, seed=123, projname=NULL)
# nsub=1 and n3=40 is used here for having a brief computation,
# not for practice.
myeff <- includeEffects(myeff, transTrip, transTies)
Modified: pkg/RSiena/man/print01Report.Rd
===================================================================
--- pkg/RSiena/man/print01Report.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/print01Report.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -13,13 +13,13 @@
\item{data}{a Siena data object
}
\item{modelname}{
- Character string used to name the output file "modelname.out"
+ Character string used to name the output file "modelname.txt"
}
\item{getDocumentation}{Flag to allow documentation of internal
functions, not for use by users.}
}
\details{
- First deletes any file of the name "modelname.out", then prints a new one.
+ First deletes any file of the name "modelname.txt", then prints a new one.
}
\value{
No value returned.
Modified: pkg/RSiena/man/siena07.Rd
===================================================================
--- pkg/RSiena/man/siena07.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/siena07.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -183,7 +183,7 @@
\item{Phase3nits}{Number of iterations actually performed in phase 3.}
\item{thetaUsed}{If \code{thetaValues} is not \code{NULL}, the matrix
of parameter values actually used in the simulations of Phase 3.}
- Writes text output to the file named "projname.out", where projname is defined
+ Writes text output to the file named "projname.txt", where projname is defined
in the \code{\link{sienaAlgorithm}} object \code{x}.
}
\references{\itemize{
@@ -223,7 +223,7 @@
There are print, summary and xtable methods for \code{\link{sienaFit}}
objects: \code{\link{xtable}}, \code{\link{print.sienaFit}}.}
\examples{
-myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=100, seed=123)
+myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=100, seed=1293, projname=NULL)
# nsub=2 and n3=100 is used here for having a brief computation, not for practice.
mynet1 <- sienaDependent(array(c(tmp3, tmp4), dim=c(32, 32, 2)))
mydata <- sienaDataCreate(mynet1)
@@ -232,7 +232,7 @@
# or for non-conditional estimation --------------------------------------------
\dontrun{
-model <- sienaModelCreate(nsub=2, n3=100, cond=FALSE, seed=123)
+model <- sienaAlgorithmCreate(nsub=2, n3=100, cond=FALSE, seed=1283)
ans <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE)
}
@@ -294,7 +294,7 @@
mats <- array(c(mat1,mat2,mat3), dim=c(4,4,3))
net <- sienaDependent(mats, allowOnly=FALSE)
sdat <- sienaDataCreate(net)
-alg <- sienaAlgorithmCreate(maxlike=TRUE, nsub=3, n3=100, seed=1234)
+alg <- sienaAlgorithmCreate(maxlike=TRUE, nsub=3, n3=100, seed=12534, projname=NULL)
effs <- getEffects(sdat)
(ans <- siena07(alg, data=sdat, effects=effs, returnDeps=TRUE, batch=TRUE))
# See manual Section 9.1 for information about the following functions
Modified: pkg/RSiena/man/siena08.Rd
===================================================================
--- pkg/RSiena/man/siena08.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/siena08.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -125,7 +125,7 @@
dataset.1 <- sienaDataCreate(Friends = Group1)
dataset.3 <- sienaDataCreate(Friends = Group3)
dataset.4 <- sienaDataCreate(Friends = Group4)
-OneAlgorithm <- sienaAlgorithmCreate(projname = "SingleGroups", seed=1234)
+OneAlgorithm <- sienaAlgorithmCreate(projname = "SingleGroups", seed=128)
effects.1 <- getEffects(dataset.1)
effects.3 <- getEffects(dataset.3)
effects.4 <- getEffects(dataset.4)
Modified: pkg/RSiena/man/sienaAlgorithmCreate.Rd
===================================================================
--- pkg/RSiena/man/sienaAlgorithmCreate.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/sienaAlgorithmCreate.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -43,7 +43,9 @@
\item{fn}{Function to do one simulation in the Robbins-Monro
algorithm. Not to be touched.}
\item{projname}{Character string name of project; the output file will be
- called projname.out. No embedded spaces!!!}
+ called projname.txt. No embedded spaces!!!\cr
+ If \code{projname=NULL}, output will be written to a file in the temporary
+ session directory, created as \code{\link{tempfile}(Siena)}.}
\item{MaxDegree}{Named vector of maximum degree values for
corresponding networks. Allows to restrict the model to networks
with degrees not higher than this maximum.
@@ -177,7 +179,9 @@
Robbins-Monro algorithm. Those not
available as arguments can be changed manually where desired.\cr
Further information about the implementation of the algorithm is in \cr
- http://www.stats.ox.ac.uk/~snijders/siena/Siena_algorithms.pdf.
+ http://www.stats.ox.ac.uk/~snijders/siena/Siena_algorithms.pdf.\cr
+ Some of the examples use \code{projname=NULL}; this is just for the sake of
+ checking the examples, not necessarily intended for normal use.
}
\value{Returns an object of class \code{sienaAlgorithm} containing
values implied by the parameters.}
Modified: pkg/RSiena/man/sienaFit.Rd
===================================================================
--- pkg/RSiena/man/sienaFit.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/sienaFit.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -92,7 +92,7 @@
\seealso{\code{\link[xtable]{xtable}}, \code{\link[xtable]{print.xtable}},
\code{\link{siena07}}}
\examples{
-myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=100)
+myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=100, projname=NULL)
mynet1 <- sienaDependent(array(c(tmp3, tmp4), dim=c(32, 32, 2)))
mydata <- sienaDataCreate(mynet1)
myeff <- getEffects(mydata)
Modified: pkg/RSiena/man/sienaGOF-auxiliary.Rd
===================================================================
--- pkg/RSiena/man/sienaGOF-auxiliary.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/sienaGOF-auxiliary.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -181,7 +181,7 @@
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTies, cycle3)
# Shorter phases 2 and 3, just for example:
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50, seed=1234)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50, seed=122, projname=NULL)
(ans <- siena07(myalgorithm, data=mydata, effects=myeff, returnDeps=TRUE,
batch=TRUE))
@@ -243,7 +243,8 @@
interaction1="onemodenet")
twoeff
# Shorter phases 2 and 3, just for example:
-twoalgorithm <- sienaAlgorithmCreate(projname="twomode", nsub=1, n3=100, seed=1234)
+twoalgorithm <- sienaAlgorithmCreate(projname="twomode", nsub=1, n3=100,
+ seed=5634)
(ans <- siena07(twoalgorithm, data=twodata, effects=twoeff, returnDeps=TRUE,
batch=TRUE))
(gof.two <- sienaGOF(ans, mixedTriadCensus,
@@ -382,7 +383,7 @@
myeff <- includeEffects(myeff, outdeg, name="mybeh", interaction1="mynet1")
myeff <- includeEffects(myeff, outdeg, name="mybeh", interaction1="mynet1")
# Shorter phases 2 and 3, just for example:
-myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=200, seed=1234)
+myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=200, seed=765, projname=NULL)
(ans2 <- siena07(myalgorithm, data=mydata, effects=myeff, returnDeps=TRUE,
batch=TRUE))
gofc <- sienaGOF(ans2, EigenvalueDistribution, varName="mynet1",
Modified: pkg/RSiena/man/sienaGOF.Rd
===================================================================
--- pkg/RSiena/man/sienaGOF.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/sienaGOF.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -233,7 +233,7 @@
myeff <- includeEffects(myeff, transTrip)
myeff <- setEffect(myeff, cycle3, fix=TRUE, test=TRUE)
myeff <- setEffect(myeff, transTies, fix=TRUE, test=TRUE)
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=25)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=10, projname=NULL)
# Shorter phases 2 and 3, just for example.
ans <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE, returnDeps=TRUE)
gofi <- sienaGOF(ans, IndegreeDistribution, verbose=TRUE, join=TRUE,
@@ -250,6 +250,7 @@
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTrip)
myeff <- includeEffects(myeff, recip, name="mynet2")
+# Shorter phases 2 and 3, just for example.
ans <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE, returnDeps=TRUE)
gofi <- sienaGOF(ans, IndegreeDistribution, verbose=TRUE, join=TRUE,
varName="mynet1")
@@ -279,7 +280,7 @@
\dontrun{
library(parallel)
(n.clus <- detectCores() - 1) # subtract 1 to keep time for other processes
-myalgorithm.c <- sienaAlgorithmCreate(nsub=4, n3=1000, seed=12345)
+myalgorithm.c <- sienaAlgorithmCreate(nsub=4, n3=1000, seed=1265)
(ans.c <- siena07(myalgorithm.c, data=mydata, effects=myeff, batch=TRUE,
returnDeps=TRUE, useCluster=TRUE, nbrNodes=n.clus))
gofi.1 <- sienaGOF(ans.c, TriadCensus, verbose=TRUE, varName="mynet1")
Modified: pkg/RSiena/man/sienaRI.Rd
===================================================================
--- pkg/RSiena/man/sienaRI.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/sienaRI.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -187,7 +187,7 @@
}
\author{Natalie Indlekofer, some additions by Tom Snijders}
\examples{
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50, projname=NULL)
mynet1 <- sienaDependent(array(c(tmp3, tmp4), dim=c(32, 32, 2)))
mydata <- sienaDataCreate(mynet1)
myeff <- getEffects(mydata)
@@ -201,7 +201,7 @@
plot(RI, actors=1:20, addPieChart=TRUE, radius=1.08)
}
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50, projname=NULL)
mynet2 <- sienaDependent(array(c(s502, s503), dim=c(50, 50, 2)))
mybeh <- sienaDependent(s50a[,2:3], type="behavior")
mydata2 <- sienaDataCreate(mynet2, mybeh)
Modified: pkg/RSiena/man/sienaTimeTest.Rd
===================================================================
--- pkg/RSiena/man/sienaTimeTest.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/sienaTimeTest.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -109,7 +109,7 @@
\code{\link{includeTimeDummy}}}
\examples{
## Estimate a restricted model
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=50, projname=NULL)
# Short estimation not for practice, just for having a quick demonstration
mynet1 <- sienaDependent(array(c(s501, s502, s503), dim=c(50, 50, 3)))
mydata <- sienaDataCreate(mynet1)
@@ -135,7 +135,7 @@
## (Of course pasting these identical sets of three waves after each other
## in a sequence of six is not really meaningful. It's just a demonstration.)
-myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=50, seed=1234)
+myalgorithm <- sienaAlgorithmCreate(nsub=2, n3=50, seed=654, projname=NULL)
mynet1 <- sienaDependent(array(c(s501, s502, s503, s501, s503, s502),
dim=c(50, 50, 6)))
mydata <- sienaDataCreate(mynet1)
Modified: pkg/RSiena/man/simstats0c.Rd
===================================================================
--- pkg/RSiena/man/simstats0c.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/simstats0c.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -121,7 +121,7 @@
mydata <- sienaDataCreate(mynet1)
myeff <- getEffects(mydata)
myeff <- includeEffects(myeff, transTrip)
-myalgorithm <- sienaAlgorithmCreate(fn=simstats0c, nsub=2, n3=100)
+myalgorithm <- sienaAlgorithmCreate(fn=simstats0c, nsub=2, n3=100, projname=NULL)
ans <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE)
}
\keyword{models}
Modified: pkg/RSiena/man/updateTheta.Rd
===================================================================
--- pkg/RSiena/man/updateTheta.Rd 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/man/updateTheta.Rd 2020-01-15 10:26:04 UTC (rev 346)
@@ -71,7 +71,7 @@
mydata <- sienaDataCreate(mynet1)
myeff1 <- getEffects(mydata)
myeff1 <- includeEffects(myeff1, transTrip)
-myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=100)
+myalgorithm <- sienaAlgorithmCreate(nsub=1, n3=100, projname=NULL)
ans <- siena07(myalgorithm, data=mydata, effects=myeff1, batch=TRUE)
ans$theta
(myeff <- updateTheta(myeff1, ans))
Modified: pkg/RSiena/src/Makevars.win
===================================================================
--- pkg/RSiena/src/Makevars.win 2020-01-06 15:55:32 UTC (rev 345)
+++ pkg/RSiena/src/Makevars.win 2020-01-15 10:26:04 UTC (rev 346)
@@ -1,30 +1,12 @@
-##split sources to ensure the commands for linking are not too long!
-SOURCES1=$(wildcard data/*.cpp network/*.cpp network/*/*.cpp utils/*.cpp)
-SOURCES2=$(wildcard model/*.cpp model/tables/*.cpp model/variables/*.cpp model/ml/*.cpp model/filters/*.cpp)
-SOURCES3=$(wildcard model/effects/*.cpp)
-SOURCES4=$(wildcard model/effects/generic/*.cpp)
+# -*- Makefile -*-
+# vim:ft=make:
-OBJECTS = siena07models.o siena07utilities.o siena07setup.o siena07internals.o
-OBJS1 = $(SOURCES1:.cpp=.o)
-OBJS2 = $(SOURCES2:.cpp=.o)
-OBJS3 = $(SOURCES3:.cpp=.o)
-OBJS4 = $(SOURCES4:.cpp=.o)
-PKG_CPPFLAGS=-I.
-PKG_LIBS = libSn1.a libSn2.a libSn3.a libSn4.a libSn1.a libSn2.a libSn3.a libSn4.a
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 346
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