Author: Mark S. Handcock
Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis. For a list of functions type: help(package='ergm')
Diff between ergm versions 2.1 dated 2008-04-28 and 2.2-0 dated 2009-03-01
ergm-2.1/ergm/.atexfile |only ergm-2.1/ergm/LICENSE.122207 |only ergm-2.1/ergm/LICENSE.2006 |only ergm-2.1/ergm/R/ergm.geodist.R |only ergm-2.1/ergm/Rd2.pdf |only ergm-2.1/ergm/ergm-internal.Rd |only ergm-2.1/ergm/inst/license.statnet.R |only ergm-2.2-0/ergm/DESCRIPTION | 9 ergm-2.2-0/ergm/R/InitConstraint.R | 24 ergm-2.2-0/ergm/R/InitErgm.R | 649 ++++---- ergm-2.2-0/ergm/R/InitErgmTerm.R | 626 ++++++- ergm-2.2-0/ergm/R/InitMHP.R | 14 ergm-2.2-0/ergm/R/anova.ergm.R | 14 ergm-2.2-0/ergm/R/anova.ergmlist.R | 16 ergm-2.2-0/ergm/R/as.directed.R | 14 ergm-2.2-0/ergm/R/as.edgelist.R | 14 ergm-2.2-0/ergm/R/as.network.numeric.R | 14 ergm-2.2-0/ergm/R/check.ErgmTerm.R | 31 ergm-2.2-0/ergm/R/coef.ergm.R | 14 ergm-2.2-0/ergm/R/control.ergm.R | 22 ergm-2.2-0/ergm/R/control.gof.R | 14 ergm-2.2-0/ergm/R/control.san.R |only ergm-2.2-0/ergm/R/control.simulate.R | 14 ergm-2.2-0/ergm/R/edgelist.ergm.R |only ergm-2.2-0/ergm/R/ergm.Cprepare.R | 18 ergm-2.2-0/ergm/R/ergm.MCMCacf.R | 14 ergm-2.2-0/ergm/R/ergm.MCMCse.R | 68 ergm-2.2-0/ergm/R/ergm.R | 153 + ergm-2.2-0/ergm/R/ergm.bounddeg.R | 14 ergm-2.2-0/ergm/R/ergm.check.R | 14 ergm-2.2-0/ergm/R/ergm.curved.R | 14 ergm-2.2-0/ergm/R/ergm.curved.statsmatrix.R | 14 ergm-2.2-0/ergm/R/ergm.curved.update.R | 14 ergm-2.2-0/ergm/R/ergm.degeneracy.R | 14 ergm-2.2-0/ergm/R/ergm.degenerate.R | 14 ergm-2.2-0/ergm/R/ergm.design.R |only ergm-2.2-0/ergm/R/ergm.estimate.R | 80 ergm-2.2-0/ergm/R/ergm.eta.R | 14 ergm-2.2-0/ergm/R/ergm.etagrad.R | 14 ergm-2.2-0/ergm/R/ergm.etagradmult.R | 14 ergm-2.2-0/ergm/R/ergm.etamap.R | 14 ergm-2.2-0/ergm/R/ergm.geodistn.R | 83 - ergm-2.2-0/ergm/R/ergm.getMCMCsample.R | 84 - ergm-2.2-0/ergm/R/ergm.getglobalstats.R | 229 -- ergm-2.2-0/ergm/R/ergm.getmodel.R | 49 ergm-2.2-0/ergm/R/ergm.getnetwork.R | 26 ergm-2.2-0/ergm/R/ergm.getterms.R | 14 ergm-2.2-0/ergm/R/ergm.independencemodel.R | 14 ergm-2.2-0/ergm/R/ergm.initialfit.R | 48 ergm-2.2-0/ergm/R/ergm.llik.R | 14 ergm-2.2-0/ergm/R/ergm.llik.miss.R |only ergm-2.2-0/ergm/R/ergm.logitreg.R | 14 ergm-2.2-0/ergm/R/ergm.mainfitloop.R | 54 ergm-2.2-0/ergm/R/ergm.mple.R | 43 ergm-2.2-0/ergm/R/ergm.pen.glm.R | 50 ergm-2.2-0/ergm/R/ergm.phase12.R | 18 ergm-2.2-0/ergm/R/ergm.pl.R | 62 ergm-2.2-0/ergm/R/ergm.revisetheta0.R | 14 ergm-2.2-0/ergm/R/ergm.robmon.R | 24 ergm-2.2-0/ergm/R/ergm.san.R |only ergm-2.2-0/ergm/R/ergm.stocapprox.R | 22 ergm-2.2-0/ergm/R/ergm.sufftoprob.R | 14 ergm-2.2-0/ergm/R/ergm.utility.R | 26 ergm-2.2-0/ergm/R/get.node.attr.R | 14 ergm-2.2-0/ergm/R/getMHproposal.R | 22 ergm-2.2-0/ergm/R/gof.ergm.R | 35 ergm-2.2-0/ergm/R/license.statnet.R | 14 ergm-2.2-0/ergm/R/mcmc.diagnostics.ergm.R | 14 ergm-2.2-0/ergm/R/midarrow.R | 14 ergm-2.2-0/ergm/R/mixingmatrix.R | 14 ergm-2.2-0/ergm/R/network.update.R | 14 ergm-2.2-0/ergm/R/plot.ergm.R | 14 ergm-2.2-0/ergm/R/print.ergm.R | 14 ergm-2.2-0/ergm/R/print.network.series.R | 14 ergm-2.2-0/ergm/R/print.summary.ergm.R | 14 ergm-2.2-0/ergm/R/robust.inverse.R | 14 ergm-2.2-0/ergm/R/simulate.ergm.R | 262 +-- ergm-2.2-0/ergm/R/statnetShowDoc.R | 14 ergm-2.2-0/ergm/R/summary.ergm.R | 16 ergm-2.2-0/ergm/R/summary.network.series.R | 14 ergm-2.2-0/ergm/R/summary.statistics.network.R | 18 ergm-2.2-0/ergm/R/zzz.R | 13 ergm-2.2-0/ergm/inst/CITATION | 83 - ergm-2.2-0/ergm/man/Getting.Started.Rd | 103 - ergm-2.2-0/ergm/man/anova.ergm.Rd | 12 ergm-2.2-0/ergm/man/as.network.numeric.Rd | 12 ergm-2.2-0/ergm/man/coef.ergm.Rd | 12 ergm-2.2-0/ergm/man/control.ergm.Rd | 62 ergm-2.2-0/ergm/man/control.gof.Rd | 12 ergm-2.2-0/ergm/man/control.simulate.Rd | 12 ergm-2.2-0/ergm/man/edgelist.ergm.Rd |only ergm-2.2-0/ergm/man/ergm-internal.Rd | 34 ergm-2.2-0/ergm/man/ergm-package.Rd | 94 - ergm-2.2-0/ergm/man/ergm-terms.Rd | 647 ++++---- ergm-2.2-0/ergm/man/ergm.Rd | 139 + ergm-2.2-0/ergm/man/ergmuserterms.Rd | 45 ergm-2.2-0/ergm/man/faux.magnolia.high.Rd | 12 ergm-2.2-0/ergm/man/faux.mesa.high.Rd | 200 +- ergm-2.2-0/ergm/man/flobusiness.Rd | 12 ergm-2.2-0/ergm/man/flomarriage.Rd | 12 ergm-2.2-0/ergm/man/florentine.Rd | 12 ergm-2.2-0/ergm/man/g4.Rd | 12 ergm-2.2-0/ergm/man/gof.ergm.Rd | 12 ergm-2.2-0/ergm/man/mcmc.diagnostics.ergm.Rd | 12 ergm-2.2-0/ergm/man/molecule.Rd | 12 ergm-2.2-0/ergm/man/network.update.Rd | 12 ergm-2.2-0/ergm/man/plot.ergm.Rd | 12 ergm-2.2-0/ergm/man/plot.gofobject.Rd | 12 ergm-2.2-0/ergm/man/print.ergm.Rd | 12 ergm-2.2-0/ergm/man/samplk.Rd | 12 ergm-2.2-0/ergm/man/sampson.Rd | 12 ergm-2.2-0/ergm/man/simulate.ergm.Rd | 18 ergm-2.2-0/ergm/man/summary.ergm.Rd | 12 ergm-2.2-0/ergm/man/summary.gofobject.Rd | 12 ergm-2.2-0/ergm/man/summary.statistics.Rd | 13 ergm-2.2-0/ergm/src/MCMC.c | 15 ergm-2.2-0/ergm/src/MCMC.h | 15 ergm-2.2-0/ergm/src/MHproposals.c | 26 ergm-2.2-0/ergm/src/MHproposals.h | 15 ergm-2.2-0/ergm/src/MHproposals_bipartite.c | 15 ergm-2.2-0/ergm/src/MHproposals_bipartite.h | 15 ergm-2.2-0/ergm/src/MPLE.c | 19 ergm-2.2-0/ergm/src/MPLE.h | 15 ergm-2.2-0/ergm/src/SAN.c |only ergm-2.2-0/ergm/src/SAN.h |only ergm-2.2-0/ergm/src/changestats.c | 2007 +++++++++++++++++-------- ergm-2.2-0/ergm/src/changestats.h | 29 ergm-2.2-0/ergm/src/edgetree.c | 46 ergm-2.2-0/ergm/src/edgetree.h | 25 ergm-2.2-0/ergm/src/geodist.c | 16 ergm-2.2-0/ergm/src/geodist.h | 16 ergm-2.2-0/ergm/src/model.c | 15 ergm-2.2-0/ergm/src/model.h | 15 ergm-2.2-0/ergm/src/netstats.c | 39 ergm-2.2-0/ergm/src/netstats.h | 15 ergm-2.2-0/ergm/src/wtedgetree.c |only ergm-2.2-0/ergm/src/wtedgetree.h |only ergm-2.2-0/ergm/tests/ALLTERMTESTS | 1 ergm-2.2-0/ergm/tests/constrain_observed.R |only ergm-2.2-0/ergm/tests/hamming_termtests.R |only 140 files changed, 5352 insertions(+), 2123 deletions(-)
Author: Gopal, V. and Fuentes, C. and Casella, G.
Title: Tests/Searches for significant clusters in genetic data.
Description: Bayes Clustering Package
Diff between bayesclust versions 1.1 dated 2009-02-03 and 2.1 dated 2009-03-01
DESCRIPTION | 6 ++-- R/cluster.optimal.R | 68 ++++++++++++++++++++-------------------------- R/cluster.test.R | 11 +++---- R/fdr.test.R | 11 +++---- R/nulldensity.R | 4 -- man/bayesclust-package.Rd | 2 - man/cluster.optimal.Rd | 4 +- man/cluster.test.Rd | 4 +- man/fdr.test.Rd | 9 ++---- man/nulldensity.Rd | 8 ++--- src/GroupMH.c | 40 ++++----------------------- src/nullsum.c | 19 +----------- 12 files changed, 64 insertions(+), 122 deletions(-)
Author: Yaqian Guo
Title: Shrunken Centroids Regularized Discriminant Analysis
Description: Shrunken Centroids Regularized Discriminant Analysis
for the classification purpose in high dimensional data.
Diff between rda versions 1.0 dated 2006-02-14 and 1.0.1 dated 2009-03-01
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Stefan Hengl
Title: Mean Optimal Transformation Approach
Description: Detect nonlinear functional relations. This package was originally
designed for the identifiability analysis of nonlinear dynamical models. However,
the concept is very general and allows to detect groups of functionally related
variables whenever there are multiple estimates for each variable, which can be written
in matrix K. The essence of the algorithm is the calculation of mean optimal
transformations estimated from bootstrap samples drawn from K.
Diff between mota versions 1.2 dated 2007-09-07 and 1.2.1 dated 2009-03-01
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Amy Kapp
Title: Reproducibility of gene expression clusters
Description: A function for validating microarry clusters via reproducibility
Diff between clusterRepro versions 0.5-1 dated 2006-02-22 and 0.5-1.1 dated 2009-03-01
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Andrew Gelman
Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing lm, glm, mer and polr outputs.
Diff between arm versions 1.2-6 dated 2009-02-28 and 1.2-7 dated 2009-03-01
CHANGELOG | 5 +++++ DESCRIPTION | 7 +++---- R/display.R | 24 +++++++++++++++++------- 3 files changed, 25 insertions(+), 11 deletions(-)