[Rsiena-commits] r252 - in pkg: RSiena RSiena/man RSiena/src/model/effects RSienaTest RSienaTest/R RSienaTest/inst/doc RSienaTest/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Feb 15 16:16:04 CET 2014
Author: tomsnijders
Date: 2014-02-15 16:16:03 +0100 (Sat, 15 Feb 2014)
New Revision: 252
Modified:
pkg/RSiena/DESCRIPTION
pkg/RSiena/changeLog
pkg/RSiena/man/siena01Gui.Rd
pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.cpp
pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.h
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/inst/doc/RSiena.bib
pkg/RSienaTest/man/siena01Gui.Rd
Log:
Version 1.1-252. The previous version (251) did not build on R-Forge; my only possible diagnosis was the lack of eoln-native property on HomCovariateTransitiveTripletsEffect.h and .cpp.
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSiena/DESCRIPTION 2014-02-15 15:16:03 UTC (rev 252)
@@ -1,8 +1,8 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-251
-Date: 2014-02-13
+Version: 1.1-252
+Date: 2014-02-15
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders
Depends: R (>= 2.15.0)
Imports: Matrix
Modified: pkg/RSiena/changeLog
===================================================================
--- pkg/RSiena/changeLog 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSiena/changeLog 2014-02-15 15:16:03 UTC (rev 252)
@@ -1,3 +1,10 @@
+2014-02-15 R-Forge Revision 252
+Changes in RSiena:
+ * Set eoln property to "native" for HomCovariateTransitiveTripletsEffect.h
+ and HomCovariateTransitiveTripletsEffect.cpp.
+Changes in RSienaTest:
+ * Small change to sienaBayes (mustUpdate).
+
2014-02-13 R-Forge Revision 251
Changes in RSiena and RSienaTest:
* Also cater for behavior user-specified interactions in includeInteraction
@@ -25,7 +32,8 @@
by maximum likelihood estimation.
Changes in RSiena:
* Ported effects outRateLog and outTrunc2 from RSienaTest.
- * Ported changes (new folders and files) in \src\network\ from RSienaTest.
+ * Ported changes (new folders and files: \layers, \iterators, etc.)#
+ in \src\network\ from RSienaTest.
Changes in RSienaTest:
* Major changes to sienaBayes and print.sienaBayes,
to permit estimation of multilevel stochastic actor-oriented model with
Modified: pkg/RSiena/man/siena01Gui.Rd
===================================================================
--- pkg/RSiena/man/siena01Gui.Rd 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSiena/man/siena01Gui.Rd 2014-02-15 15:16:03 UTC (rev 252)
@@ -13,9 +13,12 @@
}
\details{
- This function provides a graphical user interface for fitting Siena
+ This function provides a graphical user interface (gui) for fitting Siena
models.
- Note that this is less flexible and has fewer possibilities than
+ More documentation can be obtained by requesting
+ \code{RShowDoc("rsiena01gui", package="RSiena")}.
+
+ Note that this gui is less flexible and has fewer possibilities than
creating data objects from matrices and
vectors using \code{\link{sienaDependent}}, \code{\link{coCovar}} etc.,
and finally \code{\link{sienaDataCreate}}.
@@ -58,7 +61,8 @@
None, although various objects made will still be in the directory if you
are using this within an R session.
}
-\references{See \url{http://www.stats.ox.ac.uk/~snijders/siena/}}
+\references{See \url{http://www.stats.ox.ac.uk/~snijders/siena/}
+ or \code{RShowDoc("rsiena01gui", package="RSiena")}.}
\author{Ruth Ripley}
\seealso{ \code{\link{sienaDataCreateFromSession}},
\code{\link{sienaDataCreate}}.}
Modified: pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.cpp
===================================================================
--- pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.cpp 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.cpp 2014-02-15 15:16:03 UTC (rev 252)
@@ -1,137 +1,137 @@
-/******************************************************************************
- * SIENA: Simulation Investigation for Empirical Network Analysis
- *
- * Web: http://www.stats.ox.ac.uk/~snijders/siena/
- *
- * File: HomCovariateTransitiveTripletsEffect.cpp
- *
- * Description: This file contains the implementation of the class
- * HomCovariateTransitiveTripletsEffect.
- *****************************************************************************/
-#include <cmath>
-
-#include "HomCovariateTransitiveTripletsEffect.h"
-#include "utils/Utils.h"
-#include "network/Network.h"
-#include "network/IncidentTieIterator.h"
-#include "network/CommonNeighborIterator.h"
-#include "network/OneModeNetwork.h"
-#include "network/TieIterator.h"
-#include "model/variables/NetworkVariable.h"
-#include "model/tables/ConfigurationTable.h"
-
-namespace siena
-{
-
-/**
- * Constructor.
- */
-
-HomCovariateTransitiveTripletsEffect::HomCovariateTransitiveTripletsEffect(
- const EffectInfo * pEffectInfo, bool reciprocal) :
- CovariateDependentNetworkEffect(pEffectInfo)
-{
-// currently not used:
- {
- this->lreciprocal = reciprocal;
- }
-}
-
-/**
- * Calculates the contribution of a tie flip to the given actor.
- */
-double HomCovariateTransitiveTripletsEffect::calculateContribution(
- int alter) const
-{
- // If we are introducing a tie from the ego i to the alter j, then each
- // two-path from i to j via h with v_i = v_h != v_j contributes one unit;
- // in addition, each in-star i -> h <- j with v_i = v_j != v_h
- // also contributes one unit.
- // This number is not stored in a table and is calculated from scratch.
-
- int contribution1 = 0;
- const Network * pNetwork = this->pNetwork();
-
- // The following probably can be done more efficiently
- // using CommonNeighborIterator.
- // Iterate over ego's outgoing ties
- if (fabs(this->value(alter) - this->value(this->ego())) < EPSILON)
- {
- for (IncidentTieIterator iter = pNetwork->outTies(this->ego());
- iter.valid();
- iter.next())
- {
-
-// HERE THE COVAR OF THE MEDIATING ACTOR IS IDENTIFIED!!!!
-
- // Get the receiver of the outgoing tie.
- int h = iter.actor();
- // in 2-stars:
- if (fabs( this->value(h) - this->value( this->ego() ) ) < EPSILON &&
- pNetwork->tieValue(alter, h) >= 1)
- {
- contribution1++ ;
- }
- }
- }
- else
- {
- for (IncidentTieIterator iter = pNetwork->outTies(this->ego());
- iter.valid();
- iter.next())
- {
- // Get the receiver of the outgoing tie.
- int h = iter.actor();
- // 2-paths:
- if (fabs(this->value(h) - this->value(this->ego())) < EPSILON &&
- pNetwork->tieValue(h, alter) >= 1)
- {
- contribution1++ ;
- }
- }
- }
-
-
-
-
-
-
- return contribution1;
-}
-
-
-/**
- * The contribution of the tie from the implicit ego to the given alter
- * to the statistic. It is assumed that preprocessEgo(ego) has been
- * called before.
- */
-double HomCovariateTransitiveTripletsEffect::tieStatistic(int alter)
-{
-
- int statistic = 0;
- const Network * pNetwork = this->pNetwork();
-
- if (!this->missing(this->ego()) && !this->missing(alter) &&
- fabs(this->value(alter) - this->value(this->ego())) < EPSILON)
- {
- // The following probably can be done more efficiently
- // using CommonNeighborIterator.
- // Iterate over ego's outgoing ties
- for (IncidentTieIterator iter = pNetwork->outTies(this->ego());
- iter.valid();
- iter.next())
- {
- // Get the receiver of the outgoing tie.
- int h = iter.actor();
- // 2-paths:
- if (fabs(this->value(h) - this->value(this->ego())) < EPSILON &&
- pNetwork->tieValue(h, alter) >= 1)
- {
- statistic++ ;
- }
- }
- }
- return statistic;
-}
-
-}
+/******************************************************************************
+ * SIENA: Simulation Investigation for Empirical Network Analysis
+ *
+ * Web: http://www.stats.ox.ac.uk/~snijders/siena/
+ *
+ * File: HomCovariateTransitiveTripletsEffect.cpp
+ *
+ * Description: This file contains the implementation of the class
+ * HomCovariateTransitiveTripletsEffect.
+ *****************************************************************************/
+#include <cmath>
+
+#include "HomCovariateTransitiveTripletsEffect.h"
+#include "utils/Utils.h"
+#include "network/Network.h"
+#include "network/IncidentTieIterator.h"
+#include "network/CommonNeighborIterator.h"
+#include "network/OneModeNetwork.h"
+#include "network/TieIterator.h"
+#include "model/variables/NetworkVariable.h"
+#include "model/tables/ConfigurationTable.h"
+
+namespace siena
+{
+
+/**
+ * Constructor.
+ */
+
+HomCovariateTransitiveTripletsEffect::HomCovariateTransitiveTripletsEffect(
+ const EffectInfo * pEffectInfo, bool reciprocal) :
+ CovariateDependentNetworkEffect(pEffectInfo)
+{
+// currently not used:
+ {
+ this->lreciprocal = reciprocal;
+ }
+}
+
+/**
+ * Calculates the contribution of a tie flip to the given actor.
+ */
+double HomCovariateTransitiveTripletsEffect::calculateContribution(
+ int alter) const
+{
+ // If we are introducing a tie from the ego i to the alter j, then each
+ // two-path from i to j via h with v_i = v_h != v_j contributes one unit;
+ // in addition, each in-star i -> h <- j with v_i = v_j != v_h
+ // also contributes one unit.
+ // This number is not stored in a table and is calculated from scratch.
+
+ int contribution1 = 0;
+ const Network * pNetwork = this->pNetwork();
+
+ // The following probably can be done more efficiently
+ // using CommonNeighborIterator.
+ // Iterate over ego's outgoing ties
+ if (fabs(this->value(alter) - this->value(this->ego())) < EPSILON)
+ {
+ for (IncidentTieIterator iter = pNetwork->outTies(this->ego());
+ iter.valid();
+ iter.next())
+ {
+
+// HERE THE COVAR OF THE MEDIATING ACTOR IS IDENTIFIED!!!!
+
+ // Get the receiver of the outgoing tie.
+ int h = iter.actor();
+ // in 2-stars:
+ if (fabs( this->value(h) - this->value( this->ego() ) ) < EPSILON &&
+ pNetwork->tieValue(alter, h) >= 1)
+ {
+ contribution1++ ;
+ }
+ }
+ }
+ else
+ {
+ for (IncidentTieIterator iter = pNetwork->outTies(this->ego());
+ iter.valid();
+ iter.next())
+ {
+ // Get the receiver of the outgoing tie.
+ int h = iter.actor();
+ // 2-paths:
+ if (fabs(this->value(h) - this->value(this->ego())) < EPSILON &&
+ pNetwork->tieValue(h, alter) >= 1)
+ {
+ contribution1++ ;
+ }
+ }
+ }
+
+
+
+
+
+
+ return contribution1;
+}
+
+
+/**
+ * The contribution of the tie from the implicit ego to the given alter
+ * to the statistic. It is assumed that preprocessEgo(ego) has been
+ * called before.
+ */
+double HomCovariateTransitiveTripletsEffect::tieStatistic(int alter)
+{
+
+ int statistic = 0;
+ const Network * pNetwork = this->pNetwork();
+
+ if (!this->missing(this->ego()) && !this->missing(alter) &&
+ fabs(this->value(alter) - this->value(this->ego())) < EPSILON)
+ {
+ // The following probably can be done more efficiently
+ // using CommonNeighborIterator.
+ // Iterate over ego's outgoing ties
+ for (IncidentTieIterator iter = pNetwork->outTies(this->ego());
+ iter.valid();
+ iter.next())
+ {
+ // Get the receiver of the outgoing tie.
+ int h = iter.actor();
+ // 2-paths:
+ if (fabs(this->value(h) - this->value(this->ego())) < EPSILON &&
+ pNetwork->tieValue(h, alter) >= 1)
+ {
+ statistic++ ;
+ }
+ }
+ }
+ return statistic;
+}
+
+}
Property changes on: pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.cpp
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.h
===================================================================
--- pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.h 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.h 2014-02-15 15:16:03 UTC (rev 252)
@@ -1,42 +1,42 @@
-/******************************************************************************
- * SIENA: Simulation Investigation for Empirical Network Analysis
- *
- * Web: http://www.stats.ox.ac.uk/~snijders/siena/
- *
- * File: HomCovariateTransitiveTripletsEffect.h
- *
- * Description: This file contains the declaration of the class
- * HomCovariateTransitiveTripletsEffect.
- * Contributed by Robert Hellpap.
- *****************************************************************************/
-
-#ifndef HOMCOVARIATETRANSITIVETRIPLETSEFFECT_H_
-#define HOMCOVARIATETRANSITIVETRIPLETSEFFECT_H_
-
-#include "model/effects/NetworkEffect.h"
-#include "CovariateDependentNetworkEffect.h"
-
-namespace siena
-{
-
-class HomCovariateTransitiveTripletsEffect :
- public CovariateDependentNetworkEffect
-{
-public:
- HomCovariateTransitiveTripletsEffect(
- const EffectInfo * pEffectInfo, bool reciprocal);
- virtual double calculateContribution(int alter) const;
-
-protected:
- virtual double tieStatistic(int alter);
-
-private:
- // Indicates if a reciprocal version of the effect is required;
- // currently not implemented.
-
- bool lreciprocal;
-};
-
-}
-
-#endif /*HOMCOVARIATETRANSITIVETRIPLETSEFFECT_H_*/
+/******************************************************************************
+ * SIENA: Simulation Investigation for Empirical Network Analysis
+ *
+ * Web: http://www.stats.ox.ac.uk/~snijders/siena/
+ *
+ * File: HomCovariateTransitiveTripletsEffect.h
+ *
+ * Description: This file contains the declaration of the class
+ * HomCovariateTransitiveTripletsEffect.
+ * Contributed by Robert Hellpap.
+ *****************************************************************************/
+
+#ifndef HOMCOVARIATETRANSITIVETRIPLETSEFFECT_H_
+#define HOMCOVARIATETRANSITIVETRIPLETSEFFECT_H_
+
+#include "model/effects/NetworkEffect.h"
+#include "CovariateDependentNetworkEffect.h"
+
+namespace siena
+{
+
+class HomCovariateTransitiveTripletsEffect :
+ public CovariateDependentNetworkEffect
+{
+public:
+ HomCovariateTransitiveTripletsEffect(
+ const EffectInfo * pEffectInfo, bool reciprocal);
+ virtual double calculateContribution(int alter) const;
+
+protected:
+ virtual double tieStatistic(int alter);
+
+private:
+ // Indicates if a reciprocal version of the effect is required;
+ // currently not implemented.
+
+ bool lreciprocal;
+};
+
+}
+
+#endif /*HOMCOVARIATETRANSITIVETRIPLETSEFFECT_H_*/
Property changes on: pkg/RSiena/src/model/effects/HomCovariateTransitiveTripletseffect.h
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSienaTest/DESCRIPTION 2014-02-15 15:16:03 UTC (rev 252)
@@ -1,8 +1,8 @@
Package: RSienaTest
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-251
-Date: 2014-02-13
+Version: 1.1-252
+Date: 2014-02-15
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders
Depends: R (>= 2.15.0)
Imports: Matrix
Modified: pkg/RSienaTest/R/sienaBayes.r
===================================================================
--- pkg/RSienaTest/R/sienaBayes.r 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSienaTest/R/sienaBayes.r 2014-02-15 15:16:03 UTC (rev 252)
@@ -164,7 +164,8 @@
mustUpdate <- (number < 3)
if (any(is.na(mustUpdate)))
{
- stop("is.na(mustUpdate) in improveMH")
+ cat("is.na(mustUpdate) in improveMH\n")
+ mustUpdate[is.na(mustUpdate)] <- FALSE
# Can happen in case of divergence: logLik = -Infty
}
z$scaleFactors[mustUpdate[groups]] <<-
Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSienaTest/changeLog 2014-02-15 15:16:03 UTC (rev 252)
@@ -1,3 +1,10 @@
+2014-02-15 R-Forge Revision 252
+Changes in RSiena:
+ * Set eoln property to "native" for HomCovariateTransitiveTripletsEffect.h
+ and HomCovariateTransitiveTripletsEffect.cpp.
+Changes in RSienaTest:
+ * Small change to sienaBayes (mustUpdate).
+
2014-02-13 R-Forge Revision 251
Changes in RSiena and RSienaTest:
* Also cater for behavior user-specified interactions in includeInteraction
@@ -25,7 +32,8 @@
by maximum likelihood estimation.
Changes in RSiena:
* Ported effects outRateLog and outTrunc2 from RSienaTest.
- * Ported changes (new folders and files) in \src\network\ from RSienaTest.
+ * Ported changes (new folders and files: \layers, \iterators, etc.)#
+ in \src\network\ from RSienaTest.
Changes in RSienaTest:
* Major changes to sienaBayes and print.sienaBayes,
to permit estimation of multilevel stochastic actor-oriented model with
Modified: pkg/RSienaTest/inst/doc/RSiena.bib
===================================================================
--- pkg/RSienaTest/inst/doc/RSiena.bib 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSienaTest/inst/doc/RSiena.bib 2014-02-15 15:16:03 UTC (rev 252)
@@ -1649,6 +1649,15 @@
pages ={109 -- 137}}
+ at ARTICLE{HollandLeinhardt1970,
+ AUTHOR = "Paul W. {Holland} and Samuel {Leinhardt}",
+ TITLE = "A method for detecting structure in sociometric data",
+ YEAR = "1970",
+ JOURNAL = "American Journal of Sociology",
+ VOLUME = "70",
+ PAGES = "492 -- 513" }
+
+
@ARTICLE{HollandLeinhardt1971,
AUTHOR = "Paul W. {Holland} and Samuel {Leinhardt}",
TITLE = "Transitivity in structural models of small groups",
Modified: pkg/RSienaTest/man/siena01Gui.Rd
===================================================================
--- pkg/RSienaTest/man/siena01Gui.Rd 2014-02-13 23:03:20 UTC (rev 251)
+++ pkg/RSienaTest/man/siena01Gui.Rd 2014-02-15 15:16:03 UTC (rev 252)
@@ -13,9 +13,12 @@
}
\details{
- This function provides a graphical user interface for fitting Siena
+ This function provides a graphical user interface (gui) for fitting Siena
models.
- Note that this is less flexible and has fewer possibilities than
+ More documentation can be obtained by requesting
+ \code{RShowDoc("rsiena01gui", package="RSienaTest")}.
+
+ Note that this gui is less flexible and has fewer possibilities than
creating data objects from matrices and
vectors using \code{\link{sienaDependent}}, \code{\link{coCovar}} etc.,
and finally \code{\link{sienaDataCreate}}.
@@ -58,7 +61,8 @@
None, although various objects made will still be in the directory if you
are using this within an R session.
}
-\references{See \url{http://www.stats.ox.ac.uk/~snijders/siena/}}
+\references{See \url{http://www.stats.ox.ac.uk/~snijders/siena/}
+ or \code{RShowDoc("rsiena01gui", package="RSienaTest")}.}
\author{Ruth Ripley}
\seealso{ \code{\link{sienaDataCreateFromSession}},
\code{\link{sienaDataCreate}}.}
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