[Rsiena-commits] r283 - in pkg: RSiena RSiena/R RSiena/data RSiena/inst/doc RSiena/man RSiena/src RSiena/src/model/effects RSiena/src/model/tables RSienaTest RSienaTest/R RSienaTest/data RSienaTest/doc RSienaTest/inst/doc RSienaTest/man RSienaTest/po RSienaTest/src RSienaTest/src/model/effects RSienaTest/src/model/tables
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 11 23:09:10 CET 2014
Author: tomsnijders
Date: 2014-12-11 23:09:09 +0100 (Thu, 11 Dec 2014)
New Revision: 283
Added:
pkg/RSiena/src/model/effects/MaxAlterEffect.cpp
pkg/RSiena/src/model/effects/MaxAlterEffect.h
pkg/RSiena/src/model/effects/RecipdegreeActivityEffect.cpp
pkg/RSiena/src/model/effects/RecipdegreeActivityEffect.h
pkg/RSiena/src/model/effects/RecipdegreePopularityEffect.cpp
pkg/RSiena/src/model/effects/RecipdegreePopularityEffect.h
pkg/RSienaTest/src/model/effects/MaxAlterEffect.cpp
pkg/RSienaTest/src/model/effects/MaxAlterEffect.h
pkg/RSienaTest/src/model/effects/RecipdegreeActivityEffect.cpp
pkg/RSienaTest/src/model/effects/RecipdegreeActivityEffect.h
pkg/RSienaTest/src/model/effects/RecipdegreePopularityEffect.cpp
pkg/RSienaTest/src/model/effects/RecipdegreePopularityEffect.h
Modified:
pkg/RSiena/ChangeLog
pkg/RSiena/DESCRIPTION
pkg/RSiena/R/initializeFRAN.r
pkg/RSiena/R/phase3.r
pkg/RSiena/R/sienaRI.r
pkg/RSiena/R/sienaRIDynamics.r
pkg/RSiena/R/sienaprint.r
pkg/RSiena/data/allEffects.csv
pkg/RSiena/inst/doc/RSiena.bib
pkg/RSiena/inst/doc/RSiena_Manual.pdf
pkg/RSiena/inst/doc/RSiena_Manual.tex
pkg/RSiena/man/RSiena-package.Rd
pkg/RSiena/man/sienaCompositionChange.Rd
pkg/RSiena/man/sienaFit.Rd
pkg/RSiena/man/sienaGOF.Rd
pkg/RSiena/man/sienaRI.Rd
pkg/RSiena/man/sienaRIDynamics.Rd
pkg/RSiena/src/model/effects/AllEffects.h
pkg/RSiena/src/model/effects/AntiIsolateEffect.cpp
pkg/RSiena/src/model/effects/AntiIsolateEffect.h
pkg/RSiena/src/model/effects/EffectFactory.cpp
pkg/RSiena/src/model/effects/OutdegreeActivityEffect.cpp
pkg/RSiena/src/model/effects/TransitiveTripletsEffect.cpp
pkg/RSiena/src/model/effects/TransitiveTripletsEffect.h
pkg/RSiena/src/model/tables/MixedTwoPathTable.cpp
pkg/RSiena/src/siena07setup.cpp
pkg/RSienaTest/ChangeLog
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/initializeFRAN.r
pkg/RSienaTest/R/phase3.r
pkg/RSienaTest/R/robmon.r
pkg/RSienaTest/R/sienaBayes.r
pkg/RSienaTest/R/sienaRI.r
pkg/RSienaTest/R/sienaRIDynamics.r
pkg/RSienaTest/R/sienaprint.r
pkg/RSienaTest/data/allEffects.csv
pkg/RSienaTest/doc/Siena_algorithms.tex
pkg/RSienaTest/inst/doc/RSiena.bib
pkg/RSienaTest/inst/doc/RSiena_Manual.pdf
pkg/RSienaTest/inst/doc/RSiena_Manual.tex
pkg/RSienaTest/man/RSiena-package.Rd
pkg/RSienaTest/man/sienaBayes.Rd
pkg/RSienaTest/man/sienaFit.Rd
pkg/RSienaTest/man/sienaRI.Rd
pkg/RSienaTest/man/sienaRIDynamics.Rd
pkg/RSienaTest/po/R-RSienaTest.pot
pkg/RSienaTest/src/model/effects/AllEffects.h
pkg/RSienaTest/src/model/effects/AntiIsolateEffect.cpp
pkg/RSienaTest/src/model/effects/AntiIsolateEffect.h
pkg/RSienaTest/src/model/effects/EffectFactory.cpp
pkg/RSienaTest/src/model/effects/OutdegreeActivityEffect.cpp
pkg/RSienaTest/src/model/effects/TransitiveTripletsEffect.cpp
pkg/RSienaTest/src/model/effects/TransitiveTripletsEffect.h
pkg/RSienaTest/src/model/tables/MixedTwoPathTable.cpp
pkg/RSienaTest/src/siena07setup.cpp
Log:
Version 1.1-282, see changelog.
Modified: pkg/RSiena/ChangeLog
===================================================================
--- pkg/RSiena/ChangeLog 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/ChangeLog 2014-12-11 22:09:09 UTC (rev 283)
@@ -1,3 +1,44 @@
+2014-12-11 R-Forge Revision 282
+Changes in RSiena and RSienaTest:
+ * Effects cl.XWX and cl2.XWX corrected (thanks to Christoph Stadtfeld)
+ (MixedTwoPathTable.cpp).
+ * interactionType of gwesp.. effects was made dyadic (allEffects.csv)
+ * Some layout changes in warning message, phase3.r.
+ * New effects reciPop, reciAct, in3Plus, maxAlt, minAlt, transTrip1,
+ transTrip2.
+ * Effect antiInIsolate2 got alias in2Plus.
+ * inPop is dyadic effect (except for symmetric networks)
+ (it is sum_j x_{ij} (sum_{h \neq i} x_{hj} + 1)).
+ * egoX added as effect for non-directed networks
+ (can be important for representing effects of group-level covariates
+ in multi-group analyses).
+ * Components IActors and expectedI added to sienaRI() and print.sienaRI().
+ * The check for MaxDegree when running siena07 now works properly also
+ for sienaGroup objects (initializeFRAN).
+ * Manual introduces the term 'elementary effects'.
+Changes in RSienaTest:
+ * sienaBayes: the stop caused by singularity of the precision
+ matrix after the multi-group estimation now is circumvented;
+ still a warning is printed to the screen. This allows the use of
+ more than one elementary effects having the same target statistic.
+ * sienaBayes: option priorRatesFromData changed to values 0-1-2,
+ with 0 = former FALSE, 1 = former TRUE, 2 = robust estimation of prior
+ for rate parameters from estimates at the end of initialization phase.
+ * sienaBayes: correction thetaMati (not important,
+ only for output to screen).
+ * sienaprint: correction of print.summary.sienaBayesFit for models
+ with more than one dependent variable.
+
+2014-11-22 R-Forge Revision 281
+Changes in RSiena:
+ * Translation of R messages was updated: changed file
+ \pkg\RSiena\po\R-RSiena.pot
+
+2014-11-19 R-Forge Revision 280
+Changes in RSienaTest:
+ * Small changes in help pages for sienaGOF and for sienaCompositionChange.
+ * New parameters nSampVarying and nSampConst in sienaBayes().
+
2014-11-13 R-Forge Revision 279
Changes in RSiena and RSienaTest:
* Effect AltsAvAlt renamed to avXAlt (with error message).
@@ -6,10 +47,10 @@
* New effects sameXInPop, transRecTrip2,
totAlt, avInAlt, totInAlt, totRecAlt,
totXAlt, avXInAlt, totXInAlt,
- avAltDist2, totAltDist2, avTAltDist, totAAltDist2,
- avXAltDist, totXAltDist2, avTXAltDist, totAXAltDist2,
- avInAltDist2, totInAltDist2, avTInAltDist, totAInAltDist2,
- avXInAltDist2, totXInAltDist2, avTXInAltDist, totAXInAltDist2,
+ avAltDist2, totAltDist2, avTAltDist2, totAAltDist2,
+ avXAltDist, totXAltDist2, avTXAltDist2, totAXAltDist2,
+ avInAltDist2, totInAltDist2, avTInAltDist2, totAInAltDist2,
+ avXInAltDist2, totXInAltDist2, avTXInAltDist2, totAXInAltDist2,
XWX1, XWX2, cl.XWX1, cl.XWX2.
* gwesp.. effects get endowment=TRUE in allEffects.csv, and thereby
obtain endowment and creation effects.
@@ -58,7 +99,7 @@
* Small improvement in print.summary.sienaBayesFit().
* multipleBayesTest now allows matrix parameter to test
linear combinations.
- * Improved plot.multipleBayesTest (show truncation at 0).
+ * Improved plot.multipleBayesTest (shows truncation at 0).
2014-07-24 R-Forge Revision 278
Changes in RSiena and RSienaTest:
@@ -184,7 +225,8 @@
2014-03-30 R-Forge Revision 267
Changes in RSiena:
-Added R-files that contain functionalities to calculate, print and plot relative importances of effects
+Added R-files that contain functionalities to calculate, print and plot
+ relative importances of effects
* sienaRI.r: new
* sienaRIDynamics.r: new
Changes in RSiena and RSienaTest:
@@ -204,16 +246,19 @@
2014-03-14 R-Forge Revisions 255-260
Changes in RSienaTest:
- * Modified getTargets(...) such that it is possible to return target statistics of individual actors
- as well as change contributions necessary for calculating relative importances of effects (siena07setup.cpp).
+ * Modified getTargets(...) such that it is possible to return target
+ statistics of individual actors
+ as well as change contributions necessary for calculating relative
+ importances of effects (siena07setup.cpp).
* Call of getTargets(...) is correspondingly adapted (initializeFRAN.r).
* Modified simstats0c(...) such that it is possible to return
statistics of individual actors in simulated networks
- as well as statistic contributions of all potential tie flips or behavior changes
- for all simulated micro-steps (simstatsc.r).
- * Modified model(...) such that it calculates and returns the statistics newly needed in
- simstats0c(...) (siena07model.cpp)
- * Added methods, functions, constructors, and fields needed due to changes in getTargets(...) and model(...):
+ as well as statistic contributions of all potential tie flips or
+ behavior changes for all simulated micro-steps (simstatsc.r).
+ * Modified model(...) such that it calculates and returns the statistics
+ newly needed in simstats0c(...) (siena07model.cpp)
+ * Added methods, functions, constructors, and fields needed due to changes
+ in getTargets(...) and model(...):
public void needChangeContributions(bool flag) (Model.h, Model.cpp)
public bool needChangeContributions() (Model.h, Model.cpp)
private bool lneedChangeContributions2 (Model.h)
@@ -243,11 +288,15 @@
protected map<const EffectInfo *, vector<double> > * lpChangeContribution;
* Modifications of functions makeChange() and calculateTieFlipProbabilities()
in class NetworkVariable (NetworkVariable.cpp)
- calculateProbabilities(), totalEvaluationContribution(), totalEndowmentContribution(), and totalCreationContribution()
+ calculateProbabilities(), totalEvaluationContribution(),
+ totalEndowmentContribution(), and totalCreationContribution()
in class BehaviorVariable (BehaviorVariable.cpp)
- in order to store statistic contributions of effects to all possible choices od an actor in the current micro-step
- * Added functions to classes NetworkEffect and BehaviorEffect (NetworkEffect.h, NetworkEffect.cpp, BehaviorEffect.h, BehaviorEffect.cpp)
- such that, in addition to the sum of statistics ovar all actors, individual actor statistics can be returned
+ in order to store statistic contributions of effects to all possible
+ choices of an actor in the current micro-step
+ * Added functions to classes NetworkEffect and BehaviorEffect
+ (NetworkEffect.h, NetworkEffect.cpp, BehaviorEffect.h, BehaviorEffect.cpp)
+ such that, in addition to the sum of statistics ovar all actors,
+ individual actor statistics can be returned
public virtual pair <double, double * > statistic(..., bool needActorStatistics)
public virtual pair <double, double * > evaluationStatistic(...,bool needActorStatistics)
public virtual pair <double, double * > endowmentStatistic(..., bool needActorStatistics)
Modified: pkg/RSiena/DESCRIPTION
===================================================================
--- pkg/RSiena/DESCRIPTION 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/DESCRIPTION 2014-12-11 22:09:09 UTC (rev 283)
@@ -1,8 +1,8 @@
Package: RSiena
Type: Package
Title: Siena - Simulation Investigation for Empirical Network Analysis
-Version: 1.1-279
-Date: 2014-11-13
+Version: 1.1-282
+Date: 2014-12-11
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders
Depends: R (>= 2.15.0)
Imports: Matrix
Modified: pkg/RSiena/R/initializeFRAN.r
===================================================================
--- pkg/RSiena/R/initializeFRAN.r 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/R/initializeFRAN.r 2014-12-11 22:09:09 UTC (rev 283)
@@ -72,7 +72,10 @@
}
effects$initialValue <- defaultEffects$initialValue
}
- if (!all(names(x$MaxDegree) %in% names(data$depvars)))
+ if (((inherits(data, "sienaGroup")) &&
+ (!all(names(x$MaxDegree) %in% names(data[[1]]$depvars)))) ||
+ ((!inherits(data, "sienaGroup")) &&
+ (!all(names(x$MaxDegree) %in% names(data$depvars)))))
{
cat(' MaxDegree in the algorithm should be a named vector\n')
cat(' with only names of dependent variables in the data set.\n')
Modified: pkg/RSiena/R/phase3.r
===================================================================
--- pkg/RSiena/R/phase3.r 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/R/phase3.r 2014-12-11 22:09:09 UTC (rev 283)
@@ -293,9 +293,9 @@
Report(thetext, outf)
Report('\n',outf)
cat('*** Warning: Covariance matrix not positive definite *** \n')
- cat('*** Standard errors not reliable ***')
+ cat('*** Standard errors not reliable ***\n')
cat('The following is approximately a linear combination \n')
- cat('For which the data carries no information:\n',
+ cat('for which the data carries no information:\n',
thetext,'\n')
cat('It is advisable to drop one or more of these effects.\n')
if (any(z$fixed || any(z$newfixed)))
Modified: pkg/RSiena/R/sienaRI.r
===================================================================
--- pkg/RSiena/R/sienaRI.r 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/R/sienaRI.r 2014-12-11 22:09:09 UTC (rev 283)
@@ -9,7 +9,7 @@
# * in for potential desicions of actors at observation moments.
# *****************************************************************************/
-##@sienaRI. Use as RSiena:::sienaRI()
+##@sienaRI
sienaRI <- function(data, ans=NULL, theta=NULL, algorithm=NULL, effects=NULL)
{
if (!inherits(data, "siena"))
@@ -184,7 +184,9 @@
# effects$type[!currentDepEffs],effects$interaction1[!currentDepEffs],sep=".")
expectedRI <- list()
+ expectedI <- list()
RIActors <- list()
+ IActors <- list()
absoluteSumActors <- list()
entropyActors <-list()
for(w in 1:waves)
@@ -214,11 +216,15 @@
absoluteSumActors[[w]] <- colSums(RIs_matrix)
entropyActors[[w]] <- entropies
expectedRI[[w]] <- rowSums(RIActors[[w]] )/dim(RIActors[[w]])[2]
+ IActors[[w]] <- RIs_matrix
+ expectedI[[w]] <- rowMeans(RIs_matrix)
}
RItmp <- NULL
RItmp$dependentVariable <- currentDepName
RItmp$expectedRI <- expectedRI
RItmp$RIActors <- RIActors
+ RItmp$expectedI <- expectedI
+ RItmp$IActors <- IActors
RItmp$absoluteSumActors <- absoluteSumActors
RItmp$entropyActors <- entropyActors
if(!is.null(effectNames))
@@ -306,6 +312,12 @@
print.sienaRI <- function(x, ...){
if (!inherits(x, "sienaRI"))
{
+ if (inherits(x[[1]], "sienaRI"))
+ {
+ cat("The components of this object ")
+ cat("are Siena relative importance of effects objects.\n")
+ cat("Apply the print function to the separate components.\n")
+ }
stop("not a legitimate Siena relative importance of effects object")
}
cat(paste("\n Expected relative importance of effects for dependent variable '",
@@ -313,16 +325,27 @@
waves <- length(x$expectedRI)
effs <- length(x$effectNames)
colNames = paste("wave ", 1:waves, sep="")
- line1 <- paste(format("", width =63), sep="")
+ line1 <- format("", width =63)
line2 <- paste(format(1:effs,width=3), '. ', format(x$effectNames, width = 56),sep="")
+ line3 <- line2
+ line4 <- format(" Entropy", width = 61)
for(w in 1:length(colNames))
{
line1 <- paste(line1, format(colNames[w], width=8)," ", sep = "")
- line2 <- paste(line2, format(round(x$expectedRI[[w]], 4), width=8, nsmall=4)," ",sep="")
+ line2 <- paste(line2, format(round(x$expectedRI[[w]], 4),
+ width=8, nsmall=4)," ",sep="")
+ line3 <- paste(line3, format(round(x$expectedI[[w]], 4),
+ width=8, nsmall=4)," ",sep="")
+ line4 <- paste(line4, format(round(mean(x$entropyActors[[w]]), 4),
+ width=8, nsmall=4)," ",sep="")
}
line2 <- paste(line2, rep('\n',effs), sep="")
+ line3 <- paste(line3, rep('\n',effs), sep="")
cat(as.matrix(line1),'\n \n', sep='')
cat(as.matrix(line2),'\n', sep='')
+ cat("\n Expected importance of effects for this dependent variable:\n\n")
+ cat(as.matrix(line3),'\n\n', sep='')
+ cat(as.matrix(line4),'\n', sep='')
invisible(x)
}
@@ -388,7 +411,7 @@
}
if(is.null(legendHeight))
{
- legendHeight <- max(0.6,ceiling(length(x$effectNames)/legendColumns)*0.2)
+ legendHeight <- max(0.8,ceiling(length(x$effectNames)/legendColumns)*0.2)
}
}
if(!is.null(height))
@@ -519,8 +542,8 @@
layoutMatrix <- matrix(c(1:(2*waves)), byrow= TRUE, ncol=2, nrow=waves)
layout(layoutMatrix,widths=c((actors/3),2),heights=rep(1,waves))
}
- par( oma = c( 0, 0, 2, 0 ),
- mar = par()$mar+c(4.1, 4.1, 1.1, 0.1), xpd=T , cex = 0.75, no.readonly = TRUE )
+# par( oma = c( 0, 0, 2, 0 ),
+# mar = par()$mar+c(4.1, 4.1, 1.1, 0.1), xpd=T , cex = 0.75, no.readonly = TRUE )
}else{
if(legend)
{
@@ -530,8 +553,8 @@
layoutMatrix <- matrix(c(1:waves), byrow= TRUE, ncol=1, nrow=waves)
layout(layoutMatrix,widths=c((actors/3)),heights=rep(1,waves))
}
- par( oma = c( 0, 0, 2, 0 ),mar = par()$mar+c(4.1,4.1,1.1,3), xpd=T ,
- cex = 0.75, no.readonly = TRUE )
+# par( oma = c( 0, 0, 2, 0 ),mar = par()$mar+c(4.1,4.1,1.1,3), xpd=T ,
+# cex = 0.75, no.readonly = TRUE )
}
for(w in 1:waves)
{
Modified: pkg/RSiena/R/sienaRIDynamics.r
===================================================================
--- pkg/RSiena/R/sienaRIDynamics.r 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/R/sienaRIDynamics.r 2014-12-11 22:09:09 UTC (rev 283)
@@ -9,7 +9,7 @@
# * in sequences of simulated micro-steps
# *****************************************************************************/
-##@sienaRIDynamics. Use as RSiena:::sienaRIDynamics()
+##@sienaRIDynamics
sienaRIDynamics <- function(data, ans=NULL, theta=NULL, algorithm=NULL, effects=NULL, depvar=NULL, intervalsPerPeriod=NULL)
{
if(length(data$depvars)>1){
Modified: pkg/RSiena/R/sienaprint.r
===================================================================
--- pkg/RSiena/R/sienaprint.r 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/R/sienaprint.r 2014-12-11 22:09:09 UTC (rev 283)
@@ -1205,7 +1205,9 @@
cat("\nBasic rates parameters are treated as incidental parameters.\n\n")
}
cat("\nAlgorithm specifications were nwarm =",x$nwarm,", nmain =", x$nmain,
- ", nrunMHBatches =", x$nrunMHBatches, ", mult =", x$mult, ".\n")
+ ", nrunMHBatches =", x$nrunMHBatches,
+ ",\n nSampVarying =", x$nSampVarying, ", nSampConst =", x$nSampConst,
+ ", mult =", x$mult, ".\n")
if (!is.null(nfirst))
{
cat("For the results, nwarm is superseded by nfirst = ", nfirst, ".")
@@ -1240,7 +1242,7 @@
print.sienaBayesFit(x, nfirst)
if (ntot > first+2)
{
- cat("Posterior means and standard deviations per group\n")
+ cat("Posterior means and standard deviations of varying parameters per group\n")
for (h in 1:length(x$f$groupNames))
{
cat("\n", x$f$groupNames[h], "\n")
@@ -1250,7 +1252,7 @@
addtorow <- tmp$addtorow
# first two lines are the header
lines.thisgroup <-
- union(c(1,2), 2 + unlist(x$ratePositions)[h])
+ union(c(1,2), 2 + x$ratePositions[[h]])
lines.thisgroup <- union(lines.thisgroup,
2 + which(x$varyingObjectiveParameters))
lines.thisgroup <- sort(union(lines.thisgroup, 2 + which(x$set2)))
Modified: pkg/RSiena/data/allEffects.csv
===================================================================
--- pkg/RSiena/data/allEffects.csv 2014-11-22 05:02:46 UTC (rev 282)
+++ pkg/RSiena/data/allEffects.csv 2014-12-11 22:09:09 UTC (rev 283)
@@ -24,6 +24,8 @@
behaviorOneModeObjective,behavior xxxxxx av. in-alt.dist. 2,beh. xxxxxx av. in-alt. dist. 2,avInAltDist2,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorOneModeObjective,behavior xxxxxx tot. in-alt. dist. 2,beh. xxxxxx tot. in-alt. dist. 2,totInAltDist2,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorOneModeObjective,behavior xxxxxx av. in-alt. tot. dist. 2,beh. xxxxxx av. in-alt. tot. dist. 2,avTInAltDist2,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
+behaviorOneModeObjective,behavior xxxxxx max. alter,beh. xxxxxx max. alters,maxAlt,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
+behaviorOneModeObjective,behavior xxxxxx min. alter,beh. xxxxxx min. alters,minAlt,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorOneModeObjective,behavior xxxxxx tot. in-alt. av. dist. 2,beh. xxxxxx tot. in-alt. av. dist. 2,totAInAltDist2,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorOneModeObjective,behavior xxxxxx dense triads,beh. xxxxxx dense triads ,behDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorOneModeObjective,behavior xxxxxx similarity in dense triads,beh. xxxxxx homogeneity of dense triads ,simDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK,FALSE
@@ -44,6 +46,8 @@
behaviorSymmetricObjective,behavior xxxxxx average rec. alters,beh. xxxxxx average rec. alters,avRecAlt,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorSymmetricObjective,behavior xxxxxx av. alter dist. 2,beh. xxxxxx av. alters dist. 2,avAltDist2,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorSymmetricObjective,behavior xxxxxx tot. alter dist. 2,beh. xxxxxx tot. alters dist. 2,totAltDist2,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
+behaviorSymmetricObjective,behavior xxxxxx max. alter,beh. xxxxxx max. alters,maxAlt,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
+behaviorSymmetricObjective,behavior xxxxxx min. alter,beh. xxxxxx min. alters,minAlt,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorSymmetricObjective,behavior xxxxxx dense triads,beh. xxxxxx dense triads ,behDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorSymmetricObjective,behavior xxxxxx similarity in dense triads,beh. xxxxxx homogeneity of dense triads ,simDenseTriads,FALSE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,OK,FALSE
behaviorSymmetricObjective,behavior xxxxxx ave. sim. x popularity ego,beh. xxxxxx ave. sim. x indegrees ego,avSimPopEgo,TRUE,yyyyyy,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
@@ -123,6 +127,7 @@
covarBBehaviorBipartiteObjective,behavior xxxxxx: alter's (zzzzzz) yyyyyy total,beh. xxxxxx alter's (zzzzzz) yyyyyy total,totXAlt,TRUE,yyyyyy,zzzzzz,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,OK,FALSE
covarSymmetricObjective,xxxxxx,Sum of degrees x xxxxxx,altX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarSymmetricObjective,xxxxxx squared,Sum of degrees x squared xxxxxx,altSqX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
+covarSymmetricObjective,xxxxxx,Sum of degrees x xxxxxx,egoX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarSymmetricObjective,xxxxxx similarity,xxxxxx similarity,simX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarSymmetricObjective,same xxxxxx,same xxxxxx,sameX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarSymmetricObjective,transitive triads same xxxxxx,Number of transitive triads same on xxxxxx,sameXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
@@ -148,7 +153,7 @@
covarNonSymmetricObjective,transitive triplets xxxxxx similarity,Number of trans trip similar on xxxxxx,simXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,same xxxxxx,Same values on xxxxxx,sameX,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,same xxxxxx x reciprocity,Same values on xxxxxx x reciprocity,sameXRecip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
-covarNonSymmetricObjective,ind. pop. from same xxxxxx,indegree pop. from same values on xxxxxx,sameXInPop,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
+covarNonSymmetricObjective,ind. pop. from same xxxxxx,indegree pop. from same values on xxxxxx,sameXInPop,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
covarNonSymmetricObjective,transitive triplets same xxxxxx,Number of transitive triplets same on xxxxxx,sameXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
covarNonSymmetricObjective,transitive triplets homog. xxxxxx,Number of transitive triplets homogeneous on xxxxxx,homXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
covarNonSymmetricObjective,transitive triplets jumping xxxxxx,Number of transitive triplets jumping xxxxxx,jumpXTransTrip,TRUE,xxxxxx,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
@@ -167,7 +172,7 @@
covarBehaviorRate,effect yyyyyy on rate xxxxxx,Amount of change on xxxxxx x yyyyyy,RateX,NA,yyyyyy,,rate,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,rate,NA,covariate,0,0,0,0,,FALSE
bipartiteObjective,outdegree (density),Number of ties,density,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
bipartiteObjective,4-cycles,(Number 4-cycles)^1/#),cycle4,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
-bipartiteObjective,indegree - popularity,Sum of squared indegrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
+bipartiteObjective,indegree - popularity,Sum of squared indegrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
bipartiteObjective,indegree - popularity (sqrt),Sum of indegrees x sqrt(indegree),inPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
bipartiteObjective,outdegree - activity,Sum of squared outdegrees,outAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
bipartiteObjective,outdegree - activity (sqrt),Sum of outdegrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
@@ -177,10 +182,14 @@
bipartiteObjective,1/(outdegree+#)(outdegree+1+#),Sum 1/(outdegrees + #)(outdegrees + 1 + #),outSqInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
bipartiteObjective,anti in-isolates,Number of indegrees at least 1,antiInIso,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
bipartiteObjective,anti in-near-isolates,Number of indegrees at least 2,antiInIso2,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
+bipartiteObjective,indegree at least 2,Number of indegrees at least 2,in2Plus,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
+bipartiteObjective,indegree at least 3,Number of indegrees at least 3,in3Plus,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
bipartiteObjective,out-in degree^(1/2) assortativity,Sum of out-in degree^(1/2) products,outInAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,,FALSE
nonSymmetricObjective,outdegree (density),Number of ties,density,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,TRUE
nonSymmetricObjective,reciprocity,Number of reciprocated ties,recip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,TRUE
nonSymmetricObjective,transitive triplets,Number of transitive triplets,transTrip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
+nonSymmetricObjective,transitive triplets (1),Number of transitive triplets,transTrip1,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,TRUE
+nonSymmetricObjective,transitive triplets (2),Number of transitive triplets,transTrip2,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,TRUE
nonSymmetricObjective,transitive mediated triplets,Number of transitive triplets,transMedTrip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,transitive recipr. triplets,Number of transitive recipr. triplets,transRecTrip,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,trans. recipr. triplets type 2,Number of trans. recipr. triplets type 2,transRecTrip2,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
@@ -188,23 +197,26 @@
nonSymmetricObjective,transitive ties,Number of ties with transitive closure,transTies,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,betweenness,betweenness count,between,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,balance,Amount of balance,balance,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
-nonSymmetricObjective,number of actors at dist 2,Number of directed dists equal to 2,nbrDist2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE,FALSE
+nonSymmetricObjective,number of actors at dist 2,Number of directed dists equal to 2,nbrDist2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
nonSymmetricObjective,number pairs at doubly achieved dist 2,Number of doubly achieved dists 2,nbrDist2twice,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
nonSymmetricObjective,dense triads,Sum of triads with # or more ties,denseTriads,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,,TRUE
-nonSymmetricObjective,GWESP I -> K -> J (#),Number of edgewise shared partners by two path (#),gwespFF,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,,FALSE
-nonSymmetricObjective,GWESP I <- K <- J (#),Number of edgewise shared partners by reverse two path (#),gwespBB,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,,FALSE
-nonSymmetricObjective,GWESP I <- K -> J (#),Number of edgewise shared partners by out two stars (#),gwespFB,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,,FALSE
-nonSymmetricObjective,GWESP I -> K <- J (#),Number of edgewise shared partners by in two stars (#),gwespBF,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,,FALSE
-nonSymmetricObjective,GWESP I <> K <> J (#),Number of edgewise shared partners both in AND out two stars (#),gwespRR,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,,FALSE
+nonSymmetricObjective,GWESP I -> K -> J (#),Number of edgewise shared partners by two path (#),gwespFF,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,dyadic,FALSE
+nonSymmetricObjective,GWESP I <- K <- J (#),Number of edgewise shared partners by reverse two path (#),gwespBB,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,dyadic,FALSE
+nonSymmetricObjective,GWESP I <- K -> J (#),Number of edgewise shared partners by out two stars (#),gwespFB,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,dyadic,FALSE
+nonSymmetricObjective,GWESP I -> K <- J (#),Number of edgewise shared partners by in two stars (#),gwespBF,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,dyadic,FALSE
+nonSymmetricObjective,GWESP I <> K <> J (#),Number of edgewise shared partners both in AND out two stars (#),gwespRR,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,69,objective,NA,NA,0,0,0,0,dyadic,FALSE
nonSymmetricObjective,shared popularity,(Number 2-2PU)^1/#),sharedPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,FALSE
-nonSymmetricObjective,indegree - popularity,Sum of squared indegrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
+nonSymmetricObjective,indegree - popularity,Sum of squared indegrees,inPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
nonSymmetricObjective,indegree - popularity (sqrt),Sum of indegrees x sqrt(indegree),inPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
nonSymmetricObjective,outdegree - popularity,Sum of crossproducts indegree x outdegree,outPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
nonSymmetricObjective,outdegree - popularity (sqrt),Sum of indegrees x sqrt(outdegree),outPopSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
-nonSymmetricObjective,indegree - activity,Sum of crossproducts indegree x outdegree,inAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,TRUE
+nonSymmetricObjective,rec.degree - popularity,Sum rec.degr x indegr,reciPop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
+nonSymmetricObjective,rec.degree - popularity (sqrt),Sum sqrt(rec.degr) x indegr,reciPopSqrt,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,dyadic,FALSE
nonSymmetricObjective,indegree - activity (sqrt),Sum of outdegrees x sqrt(indegree),inActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,TRUE
nonSymmetricObjective,outdegree - activity,Sum of squared outdegrees,outAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,outdegree - activity (sqrt),Sum of outdegrees^(1.5),outActSqrt,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
+nonSymmetricObjective,rec.degree - activity,Sum rec.degr x outdegr,reciAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,TRUE
+nonSymmetricObjective,indegree - activity,Sum of crossproducts indegree x outdegree,inAct,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,TRUE
nonSymmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,outdegree-trunc(#),Sum of outdegrees trunc(#),outTrunc2,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,5,objective,NA,NA,0,0,0,0,,TRUE
nonSymmetricObjective,1/(outdegree + #),Sum 1/(outdegrees + #),outInv,FALSE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,1,objective,NA,NA,0,0,0,0,,TRUE
@@ -214,6 +226,8 @@
nonSymmetricObjective,anti isolates,N. of act.(od.=0 and id.>=1),antiIso,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
nonSymmetricObjective,anti in-isolates,Number of indegrees at least 1,antiInIso,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
nonSymmetricObjective,anti in-near-isolates,Number of indegrees at least 2,antiInIso2,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
+nonSymmetricObjective,indegree at least 2,Number of indegrees at least 2,in2Plus,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
+nonSymmetricObjective,indegree at least 3,Number of indegrees at least 3,in3Plus,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
nonSymmetricObjective,isolate - popularity,N. actors (ind.=1 and outd.=0),isolatePop,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,ego,FALSE
nonSymmetricObjective,out-out degree^(1/#) assortativity,Sum of out-out degree^(1/#) products,outOutAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,,FALSE
nonSymmetricObjective,out-in degree^(1/#) assortativity,Sum of out-in degree^(1/#) products,outInAss,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,2,objective,NA,NA,0,0,0,0,,FALSE
@@ -227,7 +241,7 @@
symmetricObjective,balance,Amount of balance,balance,TRUE,,,eval,FALSE,FALSE,FALSE,FALSE,FALSE,",",0,0,objective,NA,NA,0,0,0,0,,FALSE
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 283
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