Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.0.1 dated 2017-05-01 and 1.1.0 dated 2017-09-08
PhylogeneticEM-1.0.1/PhylogeneticEM/man/optimize_costs_given_shift_position.OU.specialCase.Rd |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-handling_parameters.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-initialization.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-log_likelihood.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-model_selection.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-parsimonyNumber.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-partitionsNumber.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test-simulate.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test_compute_variance_covariance.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test_impute-traits.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test_independent_multivariate.R |only PhylogeneticEM-1.0.1/PhylogeneticEM/tests/testthat/test_no_missing.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/DESCRIPTION | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/MD5 | 238 ++-- PhylogeneticEM-1.1.0/PhylogeneticEM/NEWS.md | 23 PhylogeneticEM-1.1.0/PhylogeneticEM/R/E_step.R | 38 PhylogeneticEM-1.1.0/PhylogeneticEM/R/M_step.R | 191 +-- PhylogeneticEM-1.1.0/PhylogeneticEM/R/RcppExports.R | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/R/estimateEM.R | 106 + PhylogeneticEM-1.1.0/PhylogeneticEM/R/generic_functions.R | 28 PhylogeneticEM-1.1.0/PhylogeneticEM/R/init_EM.R | 560 ++++++---- PhylogeneticEM-1.1.0/PhylogeneticEM/R/model_selection.R | 24 PhylogeneticEM-1.1.0/PhylogeneticEM/R/parsimonyNumber.R | 109 + PhylogeneticEM-1.1.0/PhylogeneticEM/R/partitionsNumber.R | 66 - PhylogeneticEM-1.1.0/PhylogeneticEM/R/plot_functions.R | 75 - PhylogeneticEM-1.1.0/PhylogeneticEM/R/shifts_manipulations.R | 32 PhylogeneticEM-1.1.0/PhylogeneticEM/R/shutoff.R | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/R/simulate.R | 40 PhylogeneticEM-1.1.0/PhylogeneticEM/build/vignette.rds |binary PhylogeneticEM-1.1.0/PhylogeneticEM/inst/CITATION | 14 PhylogeneticEM-1.1.0/PhylogeneticEM/inst/doc/tutorial.Rmd | 16 PhylogeneticEM-1.1.0/PhylogeneticEM/inst/doc/tutorial.html | 24 PhylogeneticEM-1.1.0/PhylogeneticEM/man/PhyloEM.Rd | 34 PhylogeneticEM-1.1.0/PhylogeneticEM/man/check.selection.strength.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/check_dimensions.Rd | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/man/check_parsimony.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/check_parsimony_clusters.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_E.simple.Rd | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_actualization_matrix_ultrametric.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_betas_from_shifts.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_expectations.BM.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_expectations.scOU.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_gauss_lasso.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_mahalanobis_distance.simple.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_mean_variance.simple.Rd | 7 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_times_ca.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_tree_correlations_matrix.scOU.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/compute_variance_covariance.scOU.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/enumerate_parsimony.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/equivalent_shifts.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/equivalent_shifts_values.Rd | 12 PhylogeneticEM-1.1.0/PhylogeneticEM/man/estimate.alpha.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/estimateEM.Rd | 20 PhylogeneticEM-1.1.0/PhylogeneticEM/man/extract.enumerate_parsimony.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/extract.parsimonyNumber.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/extract.partitionsNumber.Rd | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/man/extract.simul_process.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/find_grid_alpha.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/find_independent_regression_vectors.glmnet_multivariate.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/find_shift_values.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/format_output.Rd | 20 PhylogeneticEM-1.1.0/PhylogeneticEM/man/get_variance_node.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/go_back_to_original_process.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/impute.data.Rphylopars.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/imputed_traits.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.EM.lasso.Rd | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.allocate_regimes_from_shifts.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.alpha.gamma.estimation.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.compute_betas_from_shifts.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.enumerate_parsimony.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.simulate.BM.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.simulate.OU.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/init.simulate.StateAndExp.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/is.in.ranges.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/lasso_regression_K_fixed.glmnet_multivariate.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/log_likelihood.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/matrix_of_possibles.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/merge_complementary_vectors.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/model_selection.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/params_BM.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/params_OU.Rd | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/man/params_process.PhyloEM.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/params_process.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/params_process.character.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/parsimonyNumber.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/partitionsNumber.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/penalty_BaraudGiraudHuet_likelihood.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/penalty_BirgeMassart_shape1.Rd | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/man/penalty_BirgeMassart_shape2.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/penalty_pBIC.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/plot.PhyloEM.Rd | 14 PhylogeneticEM-1.1.0/PhylogeneticEM/man/plot.equivalent_shifts.Rd | 21 PhylogeneticEM-1.1.0/PhylogeneticEM/man/plot.params_process.Rd | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/man/prod.index.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/recursionDown.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/residuals.PhyloEM.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/sample_edges_intervals.Rd | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/man/sample_shifts_edges.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/scale_params.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/segmentation.OU.specialCase.same_shifts.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/shifts.list_to_matrix.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/shifts.list_to_vector.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/shifts_to_simmap.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/simul_process.Rd | 6 PhylogeneticEM-1.1.0/PhylogeneticEM/man/simulate_internal.Rd | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/man/sum.partitions.Rd | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/man/sum.partitions.cardFixed.Rd | 10 PhylogeneticEM-1.1.0/PhylogeneticEM/man/sum.prod.comb.Rd | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/man/sum.simplex.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/test.root.state.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/transform_shifts_values.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/update.compute_betas_from_shifts.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/man/update.partitionsNumber.gen.Rd | 4 PhylogeneticEM-1.1.0/PhylogeneticEM/man/wrapper_E_step.Rd | 2 PhylogeneticEM-1.1.0/PhylogeneticEM/src/RcppExports.cpp | 8 PhylogeneticEM-1.1.0/PhylogeneticEM/src/init.c | 26 PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-EM-initialization.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-EM-no_missing.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-core-compute_variance_covariance.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-core-log_likelihood.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-independent_multivariate.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-shifts-model_selection.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-shifts-parsimonyNumber.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-shifts-partitionsNumber.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-utilities-handling_parameters.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-utilities-impute-traits.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat/test-utilities-simulate.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat_EM.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat_core.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat_independent.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat_shifts.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat_upward.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/tests/testthat_utilities.R |only PhylogeneticEM-1.1.0/PhylogeneticEM/vignettes/tutorial.Rmd | 16 135 files changed, 1148 insertions(+), 946 deletions(-)
More information about PhylogeneticEM at CRAN
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Title: Dynamic Modeling and Parameter Estimation in ODE Models
Description: The framework provides functions to generate ODEs of reaction
networks, parameter transformations, observation functions, residual functions,
etc. The framework follows the paradigm that derivative information should be
used for optimization whenever possible. Therefore, all major functions produce
and can handle expressions for symbolic derivatives.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>
Diff between dMod versions 0.3.2 dated 2016-09-30 and 0.4 dated 2017-09-08
dMod-0.3.2/dMod/R/sparseMatrix.R |only dMod-0.3.2/dMod/R/testing.R |only dMod-0.3.2/dMod/inst/examples/plotArray.R |only dMod-0.3.2/dMod/man/createExample.Rd |only dMod-0.3.2/dMod/man/exmpextr.Rd |only dMod-0.3.2/dMod/man/extractExamples.Rd |only dMod-0.3.2/dMod/man/loadTemplate.Rd |only dMod-0.3.2/dMod/man/plotArray.Rd |only dMod-0.3.2/dMod/man/quasiSteadyStates.Rd |only dMod-0.3.2/dMod/man/runbg.install.Rd |only dMod-0.3.2/dMod/vignettes/framework.Rmd |only dMod-0.3.2/dMod/vignettes/pnas_data_original.csv |only dMod-0.3.2/dMod/vignettes/topology_linchain.csv |only dMod-0.4/dMod/DESCRIPTION | 15 - dMod-0.4/dMod/MD5 | 153 +++++++----- dMod-0.4/dMod/NAMESPACE | 37 ++- dMod-0.4/dMod/R/classes.R | 275 ++++++++++++++++++----- dMod-0.4/dMod/R/dMod.R | 2 dMod-0.4/dMod/R/data.R | 10 dMod-0.4/dMod/R/dataClass.R | 27 ++ dMod-0.4/dMod/R/eqnClass.R | 48 ++-- dMod-0.4/dMod/R/objClass.R | 256 +++++++++++++++++---- dMod-0.4/dMod/R/parClass.R | 12 + dMod-0.4/dMod/R/parameters.R | 112 +++++---- dMod-0.4/dMod/R/plots.R | 248 ++++++++++---------- dMod-0.4/dMod/R/prdClass.R | 46 +++ dMod-0.4/dMod/R/prediction.R | 99 ++++---- dMod-0.4/dMod/R/remoteComputing.R | 252 +++++++++++++++++++-- dMod-0.4/dMod/R/statistics.R | 129 +++++++++- dMod-0.4/dMod/R/tools.R | 129 +++++++++- dMod-0.4/dMod/R/toolsDaniel.R | 154 ++++++++++++ dMod-0.4/dMod/R/toolsMarcus.R | 74 ------ dMod-0.4/dMod/R/toolsMirjam.R | 13 - dMod-0.4/dMod/R/toolsWolfgang.R | 15 - dMod-0.4/dMod/R/trustL1.R |only dMod-0.4/dMod/build/vignette.rds |binary dMod-0.4/dMod/data |only dMod-0.4/dMod/inst/doc/dMod.R | 56 ++-- dMod-0.4/dMod/inst/doc/dMod.Rmd | 60 +++-- dMod-0.4/dMod/inst/doc/dMod.html | 97 ++++---- dMod-0.4/dMod/inst/examples/errmodel.R |only dMod-0.4/dMod/inst/examples/parlist.R | 3 dMod-0.4/dMod/inst/examples/plotting.R | 6 dMod-0.4/dMod/inst/examples/profiles.R | 2 dMod-0.4/dMod/inst/examples/test_blocks.R | 1 dMod-0.4/dMod/inst/testing |only dMod-0.4/dMod/inst/tests |only dMod-0.4/dMod/man/P.Rd | 9 dMod-0.4/dMod/man/Pexpl.Rd | 7 dMod-0.4/dMod/man/Xs.Rd | 1 dMod-0.4/dMod/man/Y.Rd | 3 dMod-0.4/dMod/man/as.data.frame.dMod.Rd |only dMod-0.4/dMod/man/as.parframe.Rd | 3 dMod-0.4/dMod/man/compile.Rd |only dMod-0.4/dMod/man/confint.parframe.Rd |only dMod-0.4/dMod/man/constraintExp2.Rd |only dMod-0.4/dMod/man/constraintL2.Rd | 28 ++ dMod-0.4/dMod/man/funC0.Rd | 6 dMod-0.4/dMod/man/getLocalDLLs.Rd |only dMod-0.4/dMod/man/getParameters.Rd | 16 - dMod-0.4/dMod/man/grapes-.-times-grapes.Rd |only dMod-0.4/dMod/man/jakstat.Rd |only dMod-0.4/dMod/man/load.parlist.Rd | 2 dMod-0.4/dMod/man/loadDLL.Rd |only dMod-0.4/dMod/man/lsdMod.Rd | 4 dMod-0.4/dMod/man/mname.Rd |only dMod-0.4/dMod/man/modelname.Rd |only dMod-0.4/dMod/man/mstrust.Rd | 1 dMod-0.4/dMod/man/odemodel.Rd | 5 dMod-0.4/dMod/man/parframe.Rd | 3 dMod-0.4/dMod/man/parlist.Rd | 3 dMod-0.4/dMod/man/parvec.Rd | 4 dMod-0.4/dMod/man/plotCombined.Rd | 6 dMod-0.4/dMod/man/plotData.Rd | 6 dMod-0.4/dMod/man/plotPars.Rd | 5 dMod-0.4/dMod/man/plotPrediction.Rd | 6 dMod-0.4/dMod/man/plotResiduals.Rd |only dMod-0.4/dMod/man/plotValues.Rd | 5 dMod-0.4/dMod/man/predict.prdfn.Rd |only dMod-0.4/dMod/man/profile.Rd | 4 dMod-0.4/dMod/man/repar.Rd |only dMod-0.4/dMod/man/runbg.Rd | 4 dMod-0.4/dMod/man/runbgInstall.Rd |only dMod-0.4/dMod/man/runbg_bwfor.Rd |only dMod-0.4/dMod/man/scale_color_dMod.Rd | 1 dMod-0.4/dMod/man/trust.Rd |only dMod-0.4/dMod/man/wide2long.Rd | 2 dMod-0.4/dMod/vignettes/dMod.Rmd | 60 +++-- 88 files changed, 1811 insertions(+), 714 deletions(-)
Title: Analyzing Remotely Sensed Forest Data
Description: Provides tools for analyzing remotely sensed forest data, including functions for detecting treetops from canopy models, outlining tree crowns and generating spatial statistics.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between ForestTools versions 0.1.4 dated 2017-04-17 and 0.1.5 dated 2017-09-08
DESCRIPTION | 14 +++++----- MD5 | 46 ++++++++++++++++++------------------ NEWS.md | 4 +++ R/ForestTools.R | 2 - R/SegmentCrowns.R | 2 - R/SpatialStatistics.R | 2 - R/TreeTopFinder.R | 32 ++++++++++++++----------- build/vignette.rds |binary inst/doc/inventoryAttributes.html | 16 ++++++------ inst/doc/polygonalCrownMaps.html | 8 +++--- inst/doc/treetopAnalysis.html | 22 ++++++++--------- man/CHMdemo.Rd | 1 man/ForestTools.Rd | 3 -- man/SegmentCrowns.Rd | 3 -- man/SpatialStatistics.Rd | 3 -- man/TreeTopFinder.Rd | 1 man/kootenayBlocks.Rd | 1 man/kootenayCHM.Rd | 1 man/kootenayCrowns.Rd | 1 man/kootenayTrees.Rd | 1 man/quesnelBlocks.Rd | 1 man/quesnelCHM.Rd | 1 man/quesnelTrees.Rd | 1 tests/testthat/test_TreeTopFinder.R | 26 ++++++++++---------- 24 files changed, 94 insertions(+), 98 deletions(-)
Title: Large-Scale Bayesian Variable Selection Using Variational
Methods
Description: Fast algorithms for fitting Bayesian variable selection
models and computing Bayes factors, in which the outcome (or
response variable) is modeled using a linear regression or a
logistic regression. The algorithms are based on the variational
approximations described in "Scalable variational inference for
Bayesian variable selection in regression, and its accuracy in
genetic association studies" (P. Carbonetto & M. Stephens, 2012,
<DOI:10.1214/12-BA703>). This software has been applied to large
data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto [aut, cre],
Matthew Stephens [aut],
David Gerard [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between varbvs versions 2.0-8 dated 2017-03-24 and 2.4-0 dated 2017-09-08
varbvs-2.0-8/varbvs/man/bayesfactor.Rd |only varbvs-2.4-0/varbvs/DESCRIPTION | 23 - varbvs-2.4-0/varbvs/MD5 | 133 +++--- varbvs-2.4-0/varbvs/NAMESPACE | 8 varbvs-2.4-0/varbvs/R/RcppExports.R | 13 varbvs-2.4-0/varbvs/R/bayesfactor.R | 26 + varbvs-2.4-0/varbvs/R/misc.R | 51 ++ varbvs-2.4-0/varbvs/R/plot.varbvs.R | 18 varbvs-2.4-0/varbvs/R/predict.varbvs.R | 17 varbvs-2.4-0/varbvs/R/subset.varbvs.R | 18 varbvs-2.4-0/varbvs/R/summary.varbvs.R | 37 + varbvs-2.4-0/varbvs/R/varbvs.R | 94 ++-- varbvs-2.4-0/varbvs/R/varbvsbin.R | 17 varbvs-2.4-0/varbvs/R/varbvsbinupdate.R | 13 varbvs-2.4-0/varbvs/R/varbvsbinz.R | 17 varbvs-2.4-0/varbvs/R/varbvsbinzupdate.R | 13 varbvs-2.4-0/varbvs/R/varbvscoefcred.R | 20 - varbvs-2.4-0/varbvs/R/varbvsindep.R | 13 varbvs-2.4-0/varbvs/R/varbvsmix.R |only varbvs-2.4-0/varbvs/R/varbvsmixupdate.R |only varbvs-2.4-0/varbvs/R/varbvsnorm.R | 19 varbvs-2.4-0/varbvs/R/varbvsnormupdate.R | 13 varbvs-2.4-0/varbvs/R/varbvspve.R | 24 + varbvs-2.4-0/varbvs/README.md | 92 ++-- varbvs-2.4-0/varbvs/build/vignette.rds |binary varbvs-2.4-0/varbvs/inst/doc/cd.R | 8 varbvs-2.4-0/varbvs/inst/doc/cd.Rmd | 8 varbvs-2.4-0/varbvs/inst/doc/cd.html | 8 varbvs-2.4-0/varbvs/inst/doc/cfw.R | 18 varbvs-2.4-0/varbvs/inst/doc/cfw.Rmd | 24 - varbvs-2.4-0/varbvs/inst/doc/cfw.html | 23 - varbvs-2.4-0/varbvs/inst/doc/cytokine.R | 9 varbvs-2.4-0/varbvs/inst/doc/cytokine.Rmd | 13 varbvs-2.4-0/varbvs/inst/doc/cytokine.html | 13 varbvs-2.4-0/varbvs/inst/doc/leukemia.R | 167 +++----- varbvs-2.4-0/varbvs/inst/doc/leukemia.Rmd | 215 ++++------- varbvs-2.4-0/varbvs/inst/doc/leukemia.html | 251 ++++++------- varbvs-2.4-0/varbvs/man/plot.varbvs.Rd | 5 varbvs-2.4-0/varbvs/man/predict.varbvs.Rd | 2 varbvs-2.4-0/varbvs/man/subset.varbvs.Rd | 2 varbvs-2.4-0/varbvs/man/summary.varbvs.Rd | 2 varbvs-2.4-0/varbvs/man/varbvs-internal.Rd | 8 varbvs-2.4-0/varbvs/man/varbvs.Rd | 117 +++--- varbvs-2.4-0/varbvs/man/varbvsbf.Rd |only varbvs-2.4-0/varbvs/man/varbvscoefcred.Rd | 2 varbvs-2.4-0/varbvs/man/varbvsindep.Rd | 4 varbvs-2.4-0/varbvs/man/varbvsmix.Rd |only varbvs-2.4-0/varbvs/src/diagsq.c | 13 varbvs-2.4-0/varbvs/src/diagsq.h | 13 varbvs-2.4-0/varbvs/src/diagsqr.c | 13 varbvs-2.4-0/varbvs/src/init.c | 15 varbvs-2.4-0/varbvs/src/misc.c | 44 ++ varbvs-2.4-0/varbvs/src/misc.h | 23 + varbvs-2.4-0/varbvs/src/types.h | 13 varbvs-2.4-0/varbvs/src/varbvs.c | 58 ++- varbvs-2.4-0/varbvs/src/varbvs.h | 41 ++ varbvs-2.4-0/varbvs/src/varbvsnormupdate_rcpp.cpp | 13 varbvs-2.4-0/varbvs/src/varbvsr.c | 67 +++ varbvs-2.4-0/varbvs/src/varbvsr.h | 19 varbvs-2.4-0/varbvs/tests/testthat.R | 13 varbvs-2.4-0/varbvs/tests/testthat/data.singular.cov.RData |only varbvs-2.4-0/varbvs/tests/testthat/demo.cc.R | 7 varbvs-2.4-0/varbvs/tests/testthat/demo.mix.R |only varbvs-2.4-0/varbvs/tests/testthat/demo.mix.dense.R |only varbvs-2.4-0/varbvs/tests/testthat/demo.qtl.R | 9 varbvs-2.4-0/varbvs/tests/testthat/demo.test.mix.R |only varbvs-2.4-0/varbvs/tests/testthat/test_varbvs.R | 56 ++ varbvs-2.4-0/varbvs/tests/testthat/test_varbvsnormupdate.R | 13 varbvs-2.4-0/varbvs/vignettes/cd.Rmd | 8 varbvs-2.4-0/varbvs/vignettes/cfw.Rmd | 24 - varbvs-2.4-0/varbvs/vignettes/cytokine.Rmd | 13 varbvs-2.4-0/varbvs/vignettes/leukemia.Rmd | 215 ++++------- 72 files changed, 1457 insertions(+), 811 deletions(-)
Title: Regularized Structural Equation Modeling
Description: Uses both ridge and lasso penalties (and extensions) to penalize
specific parameters in structural equation models. The package offers additional
cost functions, cross validation, and other extensions beyond traditional structural
equation models.
Author: Ross Jacobucci[aut,cre],
Kevin J. Grimm [ctb],
Andreas M. Brandmaier [ctb],
Sarfaraz Serang [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Diff between regsem versions 0.8.1 dated 2017-06-08 and 0.9.2 dated 2017-09-08
DESCRIPTION | 11 +- MD5 | 36 ++++----- NAMESPACE | 2 R/RcppExports.R | 8 +- R/coord_desc.R | 113 ++++++++++++++++-------------- R/cv_regsem.R | 95 +++++++++++++++++++++---- R/multi_optim.R | 19 +++-- R/parse_parameters.R | 2 R/plot.R | 77 +++++++++++++------- R/regsem.R | 47 +++++++----- R/summary.cvregsem.R | 29 +++++-- R/xmed_cat.R | 165 ++++++++++++++++++-------------------------- man/cv_regsem.Rd | 60 ++++++++++++---- man/multi_optim.Rd | 21 +++-- man/plot.cvregsem.Rd | 7 + man/regsem.Rd | 21 +++-- man/summary.cvregsem.Rd | 2 man/xmed_cat.Rd | 7 + src/regsem_rcpp_fit_fun.cpp | 2 19 files changed, 439 insertions(+), 285 deletions(-)
Title: Gaussian Process Fitting
Description: Fits a Gaussian process model to data. Gaussian processes
are commonly used in computer experiments to fit an interpolating model.
The model is stored as an 'R6' object and can be easily updated with new
data. There are options to run in parallel (not for Windows), and 'Rcpp'
has been used to speed up calculations. Other R packages that perform
similar calculations include 'laGP', 'DiceKriging', 'GPfit', and 'mlegp'.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between GauPro versions 0.2.0 dated 2017-08-16 and 0.2.1 dated 2017-09-08
DESCRIPTION | 8 ++-- MD5 | 46 +++++++++++++-------------- NEWS.md | 5 ++ R/GauPro_S3.R | 5 ++ R/kernel_Matern52.R | 18 ---------- R/kernel_RatQuad.R | 18 ---------- R/kernel_model.R | 3 + R/kernel_product.R | 18 ---------- R/kernel_sum.R | 18 ---------- inst/doc/CrossValidationErrorCorrection.R | 8 +++- inst/doc/CrossValidationErrorCorrection.Rmd | 8 +++- inst/doc/CrossValidationErrorCorrection.html | 28 +++++++++------- inst/doc/GauPro.R | 16 +++++++-- inst/doc/GauPro.Rmd | 16 +++++++-- inst/doc/GauPro.html | 20 ++++++++--- inst/doc/IntroductionToGPs.html | 4 +- inst/doc/derivatives.html | 4 +- inst/doc/surface_derivatives.html | 4 +- man/GauPro_kernel_model.Rd | 3 + man/plot.GauPro.Rd | 5 ++ src/Gaussian_hessian.cpp | 8 ++-- tests/testthat/test_kernel_model_grad.R | 5 +- vignettes/CrossValidationErrorCorrection.Rmd | 8 +++- vignettes/GauPro.Rmd | 16 +++++++-- 24 files changed, 142 insertions(+), 150 deletions(-)
Title: Tools for Reshaping Text
Description: Tools that can be used to reshape and restructure text data.
Author: Tyler Rinker [aut, cre],
Joran Elias [ctb],
Matthew Flickinger [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between textshape versions 1.3.0 dated 2017-07-27 and 1.5.0 dated 2017-09-08
textshape-1.3.0/textshape/tools/figure/unnamed-chunk-11-1.png |only textshape-1.3.0/textshape/tools/figure/unnamed-chunk-13-1.png |only textshape-1.3.0/textshape/tools/figure/unnamed-chunk-15-1.png |only textshape-1.3.0/textshape/tools/figure/unnamed-chunk-30-1.png |only textshape-1.3.0/textshape/tools/figure/unnamed-chunk-31-1.png |only textshape-1.3.0/textshape/tools/figure/unnamed-chunk-7-1.png |only textshape-1.5.0/textshape/DESCRIPTION | 14 textshape-1.5.0/textshape/MD5 | 48 +- textshape-1.5.0/textshape/NAMESPACE | 6 textshape-1.5.0/textshape/NEWS | 29 + textshape-1.5.0/textshape/R/cluster_matrix.R |only textshape-1.5.0/textshape/R/mtabulate.R | 2 textshape-1.5.0/textshape/R/split_run.R | 2 textshape-1.5.0/textshape/R/split_sentence.R | 21 - textshape-1.5.0/textshape/R/split_sentence_token.R |only textshape-1.5.0/textshape/R/split_speaker.R | 6 textshape-1.5.0/textshape/R/split_token.R | 2 textshape-1.5.0/textshape/R/split_word.R | 2 textshape-1.5.0/textshape/R/tidy_matrix.R |only textshape-1.5.0/textshape/README.md | 202 ++++++---- textshape-1.5.0/textshape/data/DATA.rda |binary textshape-1.5.0/textshape/data/golden_rules.rda |binary textshape-1.5.0/textshape/data/hamlet.rda |binary textshape-1.5.0/textshape/data/simple_dtm.rda |binary textshape-1.5.0/textshape/inst/CITATION | 9 textshape-1.5.0/textshape/man/cluster_matrix.Rd |only textshape-1.5.0/textshape/man/split_sentence_token.Rd |only textshape-1.5.0/textshape/man/tidy_matrix.Rd |only textshape-1.5.0/textshape/tools/figure/unnamed-chunk-10-1.png |only textshape-1.5.0/textshape/tools/figure/unnamed-chunk-17-1.png |only textshape-1.5.0/textshape/tools/figure/unnamed-chunk-8-1.png |binary textshape-1.5.0/textshape/tools/figure/unnamed-chunk-9-1.png |binary 32 files changed, 229 insertions(+), 114 deletions(-)
Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts
<https://fonts.google.com/> into R, in order to
support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between sysfonts versions 0.6 dated 2017-07-09 and 0.7 dated 2017-09-08
sysfonts-0.6/sysfonts/man/font.add.Rd |only sysfonts-0.6/sysfonts/man/font.add.google.Rd |only sysfonts-0.6/sysfonts/man/font.families.Rd |only sysfonts-0.6/sysfonts/man/font.families.google.Rd |only sysfonts-0.6/sysfonts/man/font.files.Rd |only sysfonts-0.6/sysfonts/man/font.paths.Rd |only sysfonts-0.7/sysfonts/DESCRIPTION | 8 - sysfonts-0.7/sysfonts/MD5 | 25 ++--- sysfonts-0.7/sysfonts/NAMESPACE | 4 sysfonts-0.7/sysfonts/R/deprecate.R |only sysfonts-0.7/sysfonts/R/font.R | 103 ++++++++++++++++------ sysfonts-0.7/sysfonts/R/google.R | 55 ++++++++--- sysfonts-0.7/sysfonts/inst/NEWS.Rd | 21 ++++ sysfonts-0.7/sysfonts/man/font_add.Rd |only sysfonts-0.7/sysfonts/man/font_add_google.Rd |only sysfonts-0.7/sysfonts/man/font_families.Rd |only sysfonts-0.7/sysfonts/man/font_families_google.Rd |only sysfonts-0.7/sysfonts/man/font_files.Rd |only sysfonts-0.7/sysfonts/man/font_paths.Rd |only sysfonts-0.7/sysfonts/src/Makevars.win | 2 20 files changed, 159 insertions(+), 59 deletions(-)
Title: Simple Key Value Stores
Description: Creates and manages simple key-value stores. These can
use a variety of approaches for storing the data. This package
implements the base methods and support for file system, in-memory
and DBI-based database stores.
Author: Rich FitzJohn
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between storr versions 1.1.1 dated 2017-06-02 and 1.1.2 dated 2017-09-08
storr-1.1.1/storr/R/driver_redis_api.R |only storr-1.1.1/storr/man/storr_redis_api.Rd |only storr-1.1.1/storr/tests/testthat/test-driver-redis-api.R |only storr-1.1.2/storr/DESCRIPTION | 12 +-- storr-1.1.2/storr/MD5 | 48 +++++++-------- storr-1.1.2/storr/NAMESPACE | 1 storr-1.1.2/storr/NEWS.md | 11 +++ storr-1.1.2/storr/R/defunct.R |only storr-1.1.2/storr/R/driver_rds.R | 2 storr-1.1.2/storr/R/spec.R | 8 ++ storr-1.1.2/storr/R/storr.R | 23 +++++-- storr-1.1.2/storr/R/utils.R | 4 - storr-1.1.2/storr/inst/doc/external.html | 34 +++++----- storr-1.1.2/storr/inst/doc/storr.html | 38 +++++------ storr-1.1.2/storr/man/encode64.Rd | 3 storr-1.1.2/storr/man/fetch_hook_read.Rd | 1 storr-1.1.2/storr/man/join_key_namespace.Rd |only storr-1.1.2/storr/man/storr-defunct.Rd |only storr-1.1.2/storr/man/storr.Rd | 13 +--- storr-1.1.2/storr/man/storr_dbi.Rd | 3 storr-1.1.2/storr/man/storr_environment.Rd | 3 storr-1.1.2/storr/man/storr_external.Rd | 1 storr-1.1.2/storr/man/storr_rds.Rd | 3 storr-1.1.2/storr/man/test_driver.Rd | 1 storr-1.1.2/storr/tests/testthat/test-auto.R | 16 ----- storr-1.1.2/storr/tests/testthat/test-driver-dbi.R | 13 +++- storr-1.1.2/storr/tests/testthat/test-driver-rds.R | 14 ++++ storr-1.1.2/storr/tests/testthat/test-util.R | 4 - 28 files changed, 136 insertions(+), 120 deletions(-)
Title: Siena - Simulation Investigation for Empirical Network Analysis
Description: Statistical modelling for longitudinal network data
using stochastic actor-oriented models.
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders, Felix Schoenenberger
Maintainer: Tom A.B. Snijders <tom.snijders@nuffield.ox.ac.uk>
Diff between RSiena versions 1.1-232 dated 2013-06-19 and 1.2-3 dated 2017-09-08
RSiena-1.1-232/RSiena/R/siena01.r |only RSiena-1.1-232/RSiena/R/sienaDataCreateFromSession.r |only RSiena-1.1-232/RSiena/changeLog |only RSiena-1.1-232/RSiena/inst/doc/RSiena.bib |only RSiena-1.1-232/RSiena/inst/doc/RSiena_Manual.pdf |only RSiena-1.1-232/RSiena/inst/doc/RSiena_Manual.tex |only RSiena-1.1-232/RSiena/inst/doc/effects.pdf |only RSiena-1.1-232/RSiena/inst/doc/siena1.png |only RSiena-1.1-232/RSiena/inst/doc/siena2.png |only RSiena-1.1-232/RSiena/inst/doc/siena3.png |only RSiena-1.1-232/RSiena/man/installGui.Rd |only RSiena-1.1-232/RSiena/man/siena01Gui.Rd |only RSiena-1.1-232/RSiena/man/sienaDataCreateFromSession.Rd |only RSiena-1.1-232/RSiena/man/sienaModelOptions.Rd |only RSiena-1.1-232/RSiena/po/R-ko.mo |only RSiena-1.1-232/RSiena/src/Makevars |only RSiena-1.1-232/RSiena/src/Makevars.win |only RSiena-1.1-232/RSiena/tests/scriptfile.Rout.save |only RSiena-1.1-232/RSiena/tests/scriptfile.Rout.win |only RSiena-1.1-232/RSiena/tests/scripts.R |only RSiena-1.1-232/RSiena/tests/scripts.Rout.save |only RSiena-1.2-3/RSiena/.Rinstignore | 1 RSiena-1.2-3/RSiena/ChangeLog |only RSiena-1.2-3/RSiena/DESCRIPTION | 23 RSiena-1.2-3/RSiena/MD5 | 616 +++-- RSiena-1.2-3/RSiena/NAMESPACE | 42 RSiena-1.2-3/RSiena/R/RSienaRDocumentation.r | 16 RSiena-1.2-3/RSiena/R/Sienatest.r | 145 - RSiena-1.2-3/RSiena/R/checkImpossibleChanges.r |only RSiena-1.2-3/RSiena/R/effects.r | 400 ++- RSiena-1.2-3/RSiena/R/effectsDocumentation.r | 31 RSiena-1.2-3/RSiena/R/effectsMethods.r | 137 + RSiena-1.2-3/RSiena/R/getActorStatistics.r |only RSiena-1.2-3/RSiena/R/getTargets.r | 117 - RSiena-1.2-3/RSiena/R/globals.r | 4 RSiena-1.2-3/RSiena/R/initializeFRAN.r | 476 ++-- RSiena-1.2-3/RSiena/R/maxlike.r | 4 RSiena-1.2-3/RSiena/R/maxlikec.r | 4 RSiena-1.2-3/RSiena/R/phase1.r | 121 - RSiena-1.2-3/RSiena/R/phase2.r | 164 + RSiena-1.2-3/RSiena/R/phase3.r | 395 ++- RSiena-1.2-3/RSiena/R/print01Report.r | 541 ++-- RSiena-1.2-3/RSiena/R/print07Report.r | 393 +-- RSiena-1.2-3/RSiena/R/printDataReport.r | 77 RSiena-1.2-3/RSiena/R/printInitialDescription.r | 12 RSiena-1.2-3/RSiena/R/robmon.r | 60 RSiena-1.2-3/RSiena/R/siena07.r | 59 RSiena-1.2-3/RSiena/R/siena07gui.r | 2 RSiena-1.2-3/RSiena/R/siena08.r | 33 RSiena-1.2-3/RSiena/R/sienaDataCreate.r | 117 - RSiena-1.2-3/RSiena/R/sienaGOF.r | 656 +++-- RSiena-1.2-3/RSiena/R/sienaModelCreate.r | 243 +- RSiena-1.2-3/RSiena/R/sienaRI.r |only RSiena-1.2-3/RSiena/R/sienaRIDynamics.r |only RSiena-1.2-3/RSiena/R/sienaTimeTest.r | 49 RSiena-1.2-3/RSiena/R/sienaeffects.r | 491 ++-- RSiena-1.2-3/RSiena/R/sienaprint.r | 726 +++++- RSiena-1.2-3/RSiena/R/sienatable.r | 52 RSiena-1.2-3/RSiena/R/sienautils.r | 50 RSiena-1.2-3/RSiena/R/simstatsc.r | 36 RSiena-1.2-3/RSiena/R/terminateFRAN.r | 3 RSiena-1.2-3/RSiena/R/zzz.R | 2 RSiena-1.2-3/RSiena/cleanup | 20 RSiena-1.2-3/RSiena/cleanup.win | 15 RSiena-1.2-3/RSiena/configure |only RSiena-1.2-3/RSiena/configure.ac |only RSiena-1.2-3/RSiena/configure.win |only RSiena-1.2-3/RSiena/data/RSiena.rda |binary RSiena-1.2-3/RSiena/data/allEffects.R | 2 RSiena-1.2-3/RSiena/data/allEffects.csv | 675 +++-- RSiena-1.2-3/RSiena/inst/scripts/Rscript02SienaVariableFormat.R | 5 RSiena-1.2-3/RSiena/inst/scripts/Rscript03SienaRunModel.R | 2 RSiena-1.2-3/RSiena/inst/scripts/Rscript04SienaBehaviour.R | 2 RSiena-1.2-3/RSiena/inst/sienascript | 1 RSiena-1.2-3/RSiena/man/RSiena-package.Rd | 64 RSiena-1.2-3/RSiena/man/Wald.Rd |only RSiena-1.2-3/RSiena/man/allEffects.Rd | 6 RSiena-1.2-3/RSiena/man/coCovar.Rd | 19 RSiena-1.2-3/RSiena/man/coDyadCovar.Rd | 3 RSiena-1.2-3/RSiena/man/edit.sienaEffects.Rd | 4 RSiena-1.2-3/RSiena/man/effectsDocumentation.Rd | 10 RSiena-1.2-3/RSiena/man/getEffects.Rd | 33 RSiena-1.2-3/RSiena/man/hn3401.Rd | 2 RSiena-1.2-3/RSiena/man/includeEffects.Rd | 42 RSiena-1.2-3/RSiena/man/includeInteraction.Rd | 60 RSiena-1.2-3/RSiena/man/includeTimeDummy.Rd | 2 RSiena-1.2-3/RSiena/man/iwlsm.Rd | 2 RSiena-1.2-3/RSiena/man/maxlikefn.Rd | 4 RSiena-1.2-3/RSiena/man/n3401.Rd | 2 RSiena-1.2-3/RSiena/man/print.sienaEffects.Rd | 7 RSiena-1.2-3/RSiena/man/print.sienaMeta.Rd | 17 RSiena-1.2-3/RSiena/man/print01Report.Rd | 19 RSiena-1.2-3/RSiena/man/s50.Rd | 19 RSiena-1.2-3/RSiena/man/s501.Rd | 4 RSiena-1.2-3/RSiena/man/s502.Rd | 5 RSiena-1.2-3/RSiena/man/s503.Rd | 6 RSiena-1.2-3/RSiena/man/s50a.Rd | 7 RSiena-1.2-3/RSiena/man/s50s.Rd |only RSiena-1.2-3/RSiena/man/setEffect.Rd | 81 RSiena-1.2-3/RSiena/man/siena07.Rd | 135 - RSiena-1.2-3/RSiena/man/siena08.Rd | 56 RSiena-1.2-3/RSiena/man/sienaAlgorithmCreate.Rd | 197 - RSiena-1.2-3/RSiena/man/sienaCompositionChange.Rd | 53 RSiena-1.2-3/RSiena/man/sienaDataCreate.Rd | 32 RSiena-1.2-3/RSiena/man/sienaDependent.Rd | 25 RSiena-1.2-3/RSiena/man/sienaFit.Rd | 50 RSiena-1.2-3/RSiena/man/sienaGOF-auxiliary.Rd | 73 RSiena-1.2-3/RSiena/man/sienaGOF.Rd | 156 + RSiena-1.2-3/RSiena/man/sienaGroupCreate.Rd | 17 RSiena-1.2-3/RSiena/man/sienaNodeSet.Rd | 6 RSiena-1.2-3/RSiena/man/sienaRI.Rd |only RSiena-1.2-3/RSiena/man/sienaTimeTest.Rd | 81 RSiena-1.2-3/RSiena/man/simstats0c.Rd | 3 RSiena-1.2-3/RSiena/man/tmp3.Rd | 5 RSiena-1.2-3/RSiena/man/tmp4.Rd | 5 RSiena-1.2-3/RSiena/man/updateTheta.Rd | 90 RSiena-1.2-3/RSiena/man/varCovar.Rd | 19 RSiena-1.2-3/RSiena/man/varDyadCovar.Rd | 9 RSiena-1.2-3/RSiena/man/xtable.Rd | 8 RSiena-1.2-3/RSiena/po/R-RSiena.pot | 331 ++ RSiena-1.2-3/RSiena/po/R-ko.po | 468 ++-- RSiena-1.2-3/RSiena/src/Makevars.in |only RSiena-1.2-3/RSiena/src/data/BehaviorLongitudinalData.cpp | 17 RSiena-1.2-3/RSiena/src/data/BehaviorLongitudinalData.h | 7 RSiena-1.2-3/RSiena/src/data/ChangingDyadicCovariate.cpp | 4 RSiena-1.2-3/RSiena/src/data/ChangingDyadicCovariate.h | 14 RSiena-1.2-3/RSiena/src/data/ConstantDyadicCovariate.cpp | 2 RSiena-1.2-3/RSiena/src/data/ConstantDyadicCovariate.h | 12 RSiena-1.2-3/RSiena/src/data/Covariate.cpp | 19 RSiena-1.2-3/RSiena/src/data/Covariate.h | 14 RSiena-1.2-3/RSiena/src/data/Data.cpp | 2 RSiena-1.2-3/RSiena/src/data/Data.h | 12 RSiena-1.2-3/RSiena/src/data/DyadicCovariateValueIterator.cpp | 2 RSiena-1.2-3/RSiena/src/data/DyadicCovariateValueIterator.h | 14 RSiena-1.2-3/RSiena/src/data/NetworkConstraint.cpp | 5 RSiena-1.2-3/RSiena/src/data/NetworkConstraint.h | 18 RSiena-1.2-3/RSiena/src/data/NetworkLongitudinalData.cpp | 76 RSiena-1.2-3/RSiena/src/data/NetworkLongitudinalData.h | 31 RSiena-1.2-3/RSiena/src/init.c |only RSiena-1.2-3/RSiena/src/model/EffectInfo.cpp | 7 RSiena-1.2-3/RSiena/src/model/EffectInfo.h | 47 RSiena-1.2-3/RSiena/src/model/EpochSimulation.cpp | 803 ++---- RSiena-1.2-3/RSiena/src/model/EpochSimulation.h | 147 - RSiena-1.2-3/RSiena/src/model/Model.cpp | 79 RSiena-1.2-3/RSiena/src/model/Model.h | 97 RSiena-1.2-3/RSiena/src/model/State.cpp | 2 RSiena-1.2-3/RSiena/src/model/State.h | 14 RSiena-1.2-3/RSiena/src/model/StatisticCalculator.cpp | 516 +++- RSiena-1.2-3/RSiena/src/model/StatisticCalculator.h | 36 RSiena-1.2-3/RSiena/src/model/effects/AllEffects.h | 31 RSiena-1.2-3/RSiena/src/model/effects/AlterCovariateActivityEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AlterCovariateActivityEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateAvAltEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateAvAltEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateAvSimEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateAvSimEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateAverageEffect.cpp | 36 RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateAverageEffect.h | 4 RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateTotSimEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AltersCovariateTotSimEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AltersDist2CovariateAverageEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AltersDist2CovariateAverageEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AltersInDist2CovariateAverageEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AltersInDist2CovariateAverageEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AntiIsolateEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AntiIsolateEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AverageAlterDist2Effect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AverageAlterDist2Effect.h |only RSiena-1.2-3/RSiena/src/model/effects/AverageAlterEffect.cpp | 78 RSiena-1.2-3/RSiena/src/model/effects/AverageAlterEffect.h | 9 RSiena-1.2-3/RSiena/src/model/effects/AverageAlterInDist2Effect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AverageAlterInDist2Effect.h |only RSiena-1.2-3/RSiena/src/model/effects/AverageInAlterEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/AverageInAlterEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/AverageReciprocatedAlterEffect.cpp | 17 RSiena-1.2-3/RSiena/src/model/effects/AverageReciprocatedAlterEffect.h | 5 RSiena-1.2-3/RSiena/src/model/effects/BehaviorEffect.cpp | 108 RSiena-1.2-3/RSiena/src/model/effects/BehaviorEffect.h | 26 RSiena-1.2-3/RSiena/src/model/effects/BothDegreesEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/BothDegreesEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/CovariateAlterEffect.cpp | 50 RSiena-1.2-3/RSiena/src/model/effects/CovariateAlterEffect.h | 6 RSiena-1.2-3/RSiena/src/model/effects/CovariateAndNetworkBehaviorEffect.cpp | 105 RSiena-1.2-3/RSiena/src/model/effects/CovariateAndNetworkBehaviorEffect.h | 8 RSiena-1.2-3/RSiena/src/model/effects/CovariateDependentBehaviorEffect.cpp | 22 RSiena-1.2-3/RSiena/src/model/effects/CovariateDependentBehaviorEffect.h | 1 RSiena-1.2-3/RSiena/src/model/effects/CovariateDependentNetworkEffect.cpp | 109 RSiena-1.2-3/RSiena/src/model/effects/CovariateDependentNetworkEffect.h | 12 RSiena-1.2-3/RSiena/src/model/effects/CovariateDiffEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/CovariateDiffEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/CovariateDiffEgoEffect.cpp 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RSiena-1.2-3/RSiena/src/model/effects/IsolatePopEffect.h | 10 RSiena-1.2-3/RSiena/src/model/effects/MaxAlterEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/MaxAlterEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/MixedNetworkEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/MixedNetworkEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/NetworkDependentBehaviorEffect.cpp | 142 + RSiena-1.2-3/RSiena/src/model/effects/NetworkDependentBehaviorEffect.h | 16 RSiena-1.2-3/RSiena/src/model/effects/NetworkEffect.cpp | 55 RSiena-1.2-3/RSiena/src/model/effects/NetworkEffect.h | 8 RSiena-1.2-3/RSiena/src/model/effects/OutdegreeActivityEffect.cpp | 20 RSiena-1.2-3/RSiena/src/model/effects/OutdegreeActivityEffect.h | 13 RSiena-1.2-3/RSiena/src/model/effects/OutdegreeActivitySqrtEffect.cpp | 18 RSiena-1.2-3/RSiena/src/model/effects/OutdegreeActivitySqrtEffect.h | 4 RSiena-1.2-3/RSiena/src/model/effects/RecipdegreeActivityEffect.cpp |only 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RSiena-1.2-3/RSiena/src/model/effects/StructuralRateEffect.h | 3 RSiena-1.2-3/RSiena/src/model/effects/ThresholdShapeEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/ThresholdShapeEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/TransitiveReciprocatedTriplets2Effect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/TransitiveReciprocatedTriplets2Effect.h |only RSiena-1.2-3/RSiena/src/model/effects/TransitiveTripletsEffect.cpp | 12 RSiena-1.2-3/RSiena/src/model/effects/TransitiveTripletsEffect.h | 9 RSiena-1.2-3/RSiena/src/model/effects/TwoNetworkDependentBehaviorEffect.cpp |only RSiena-1.2-3/RSiena/src/model/effects/TwoNetworkDependentBehaviorEffect.h |only RSiena-1.2-3/RSiena/src/model/effects/XWXClosureEffect.cpp | 9 RSiena-1.2-3/RSiena/src/model/effects/XWXClosureEffect.h | 5 RSiena-1.2-3/RSiena/src/model/effects/generic/AlterFunction.cpp | 1 RSiena-1.2-3/RSiena/src/model/effects/generic/AlterFunction.h | 4 RSiena-1.2-3/RSiena/src/model/effects/generic/AlterPredicate.cpp | 2 RSiena-1.2-3/RSiena/src/model/effects/generic/AlterPredicate.h | 5 RSiena-1.2-3/RSiena/src/model/effects/generic/ConstantFunction.h | 2 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDegreeFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDegreeFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.cpp | 34 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2AlterNetworkFunction.h | 5 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2EgoAltSimNetworkFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2EgoAltSimNetworkFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2InAlterNetworkFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2NetworkFunction.cpp | 232 +- RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2NetworkFunction.h | 16 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.cpp | 2 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateDistance2SimilarityNetworkFunction.h | 2 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateMixedNetworkAlterFunction.h | 10 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateNetworkAlterFunction.cpp | 22 RSiena-1.2-3/RSiena/src/model/effects/generic/CovariateNetworkAlterFunction.h | 10 RSiena-1.2-3/RSiena/src/model/effects/generic/DifferentCovariateInStarFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/DifferentCovariateInStarFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/DifferentCovariateOutStarFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/DifferentCovariateOutStarFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/DoubleOutActFunction.cpp |only 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RSiena-1.2-3/RSiena/src/model/effects/generic/MixedInStarFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/MixedNetworkAlterFunction.cpp | 34 RSiena-1.2-3/RSiena/src/model/effects/generic/MixedNetworkAlterFunction.h | 17 RSiena-1.2-3/RSiena/src/model/effects/generic/MixedOutStarFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/MixedOutStarFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/MixedThreeCyclesFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/MixedThreeCyclesFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/NetworkAlterFunction.cpp | 18 RSiena-1.2-3/RSiena/src/model/effects/generic/NetworkAlterFunction.h | 8 RSiena-1.2-3/RSiena/src/model/effects/generic/OutActDistance2Function.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/OutActDistance2Function.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/OutJaccardFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/OutJaccardFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateInStarFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateInStarFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateInTiesFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateInTiesFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateMixedTwoPathFunction.h | 8 RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateOutStarFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateOutStarFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateOutTiesFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/SameCovariateOutTiesFunction.h |only RSiena-1.2-3/RSiena/src/model/effects/generic/SumFunction.cpp |only RSiena-1.2-3/RSiena/src/model/effects/generic/SumFunction.h |only RSiena-1.2-3/RSiena/src/model/ml/Chain.cpp | 2 RSiena-1.2-3/RSiena/src/model/ml/Chain.h | 22 RSiena-1.2-3/RSiena/src/model/ml/MLSimulation.cpp | 1123 ++++++--- RSiena-1.2-3/RSiena/src/model/ml/MLSimulation.h | 13 RSiena-1.2-3/RSiena/src/model/ml/MiniStep.cpp | 25 RSiena-1.2-3/RSiena/src/model/ml/MiniStep.h | 14 RSiena-1.2-3/RSiena/src/model/tables/Cache.cpp | 1 RSiena-1.2-3/RSiena/src/model/tables/Cache.h | 6 RSiena-1.2-3/RSiena/src/model/tables/MixedTwoPathTable.cpp | 40 RSiena-1.2-3/RSiena/src/model/tables/TwoNetworkCache.cpp | 31 RSiena-1.2-3/RSiena/src/model/tables/TwoNetworkCache.h | 37 RSiena-1.2-3/RSiena/src/model/variables/BehaviorVariable.cpp | 197 + RSiena-1.2-3/RSiena/src/model/variables/BehaviorVariable.h | 7 RSiena-1.2-3/RSiena/src/model/variables/DependentVariable.cpp | 520 ++-- RSiena-1.2-3/RSiena/src/model/variables/DependentVariable.h | 99 RSiena-1.2-3/RSiena/src/model/variables/DiffusionEffectValueTable.cpp | 36 RSiena-1.2-3/RSiena/src/model/variables/EffectValueTable.cpp | 31 RSiena-1.2-3/RSiena/src/model/variables/NetworkVariable.cpp | 466 ++-- RSiena-1.2-3/RSiena/src/model/variables/NetworkVariable.h | 14 RSiena-1.2-3/RSiena/src/network/CommonNeighborIterator.cpp | 69 RSiena-1.2-3/RSiena/src/network/CommonNeighborIterator.h | 20 RSiena-1.2-3/RSiena/src/network/INetworkChangeListener.h |only RSiena-1.2-3/RSiena/src/network/IncidentTieIterator.cpp | 89 RSiena-1.2-3/RSiena/src/network/IncidentTieIterator.h | 62 RSiena-1.2-3/RSiena/src/network/Network.cpp | 390 +-- RSiena-1.2-3/RSiena/src/network/Network.h | 32 RSiena-1.2-3/RSiena/src/network/OneModeNetwork.cpp | 241 -- RSiena-1.2-3/RSiena/src/network/OneModeNetwork.h | 1 RSiena-1.2-3/RSiena/src/network/iterators |only RSiena-1.2-3/RSiena/src/network/layers |only RSiena-1.2-3/RSiena/src/siena07internals.cpp | 416 ++- RSiena-1.2-3/RSiena/src/siena07internals.h | 46 RSiena-1.2-3/RSiena/src/siena07models.cpp | 81 RSiena-1.2-3/RSiena/src/siena07models.h | 6 RSiena-1.2-3/RSiena/src/siena07setup.cpp | 262 ++ RSiena-1.2-3/RSiena/src/siena07setup.h | 12 RSiena-1.2-3/RSiena/src/siena07utilities.cpp | 238 ++ RSiena-1.2-3/RSiena/src/siena07utilities.h | 15 RSiena-1.2-3/RSiena/src/sources.list |only RSiena-1.2-3/RSiena/src/utils/NamedObject.h | 8 RSiena-1.2-3/RSiena/src/utils/Random.h | 4 RSiena-1.2-3/RSiena/src/utils/Utils.cpp | 9 RSiena-1.2-3/RSiena/src/utils/Utils.h | 2 RSiena-1.2-3/RSiena/tests/parallel.R | 55 RSiena-1.2-3/RSiena/tests/parallel.Rout.save | 522 ++-- 377 files changed, 13353 insertions(+), 6062 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Manjunath B G [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.7.16 dated 2017-08-13 and 2.7.17 dated 2017-09-08
DESCRIPTION | 10 - MD5 | 77 +++++----- NEWS | 13 - R/MxCompare.R | 6 R/MxDataWLS.R | 53 +++++- R/MxFitFunctionWLS.R | 12 + R/MxRun.R | 4 R/MxUnitTesting.R | 22 ++ R/MxVersion.R | 2 configure | 5 inst/CITATION | 2 inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitionsAllFixed.R | 2 inst/models/nightly/ifa-fisher-info.R | 2 inst/models/nightly/ifa-latent-2d.R | 2 inst/models/nightly/ifa-meat-2tier.R | 2 inst/models/nightly/ifa-ms.R | 10 - inst/models/passing/NA-defvar.R |only inst/models/passing/StateSpaceInputs.R | 2 inst/models/passing/SummaryCheck.R | 25 +++ inst/models/passing/fm-example2-2.R | 2 inst/models/passing/ifa-allna.R | 2 inst/models/passing/ifa-drm-mg.R | 2 inst/models/passing/ifa-lmp.R | 2 inst/models/passing/jointFactorWls.R | 24 ++- inst/models/passing/nonlinearDefinitionTest.R | 7 inst/models/passing/startingValues.R | 3 man/mxDataWLS.Rd | 9 - src/AlgebraFunctions.h | 6 src/Compute.cpp | 4 src/EnableWarnings.h | 1 src/omxData.cpp | 43 +++++ src/omxData.h | 3 src/omxDefines.h | 6 src/omxExpectation.cpp | 1 src/omxFIMLFitFunction.h | 12 - src/omxImportFrontendState.cpp | 2 src/omxMatrix.h | 2 src/omxNormalExpectation.cpp | 2 src/omxState.cpp | 23 +- src/omxState.h | 6 40 files changed, 289 insertions(+), 124 deletions(-)
Title: Tools for Management of Survey Data and for the Presentation of
Analysis Results
Description: One of the aims of this package is to make life easier for
R users who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) 'SPSS' and
'Stata' files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to 'LaTeX' and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.99.14.1 dated 2017-09-07 and 0.99.14.2 dated 2017-09-08
DESCRIPTION | 8 +- MD5 | 14 ++-- R/mtable-format-html.R | 1 inst/ChangeLog | 10 ++- inst/doc/anes48.Rmd | 6 +- inst/doc/anes48.html | 4 - inst/doc/mtable-html.html | 138 ++++++++++++++++++++++++++++++++++++++++++++-- vignettes/anes48.Rmd | 6 +- 8 files changed, 159 insertions(+), 28 deletions(-)
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.16 dated 2017-01-14 and 0.0.17 dated 2017-09-08
DESCRIPTION | 10 MD5 | 64 NAMESPACE | 20 R/LPDMRSort.R | 10 R/LPDMRSortIdentifyIncompatibleAssignments.R | 10 R/LPDMRSortInferenceApprox.R |only R/LPDMRSortInferenceExact.R | 41 R/MRSortInferenceApprox.R | 1437 ++++------------ R/MRSortInferenceExact.R | 18 R/SRMP.R |only R/SRMPInference.R |only R/SRMPInferenceApprox.R |only R/SRMPInferenceApproxFixedLexicographicOrder.R |only R/SRMPInferenceApproxFixedProfilesNumber.R |only R/SRMPInferenceFixedLexicographicOrder.R |only R/SRMPInferenceFixedProfilesNumber.R |only R/SRMPInferenceNoInconsist.R |only R/SRMPInferenceNoInconsistFixedLexicographicOrder.R |only R/SRMPInferenceNoInconsistFixedProfilesNumber.R |only R/deprecatedMRSortInferenceApprox.R |only inst/extdata/SRMPMinInconsist.gmpl |only inst/extdata/SRMPMinInconsistIndif.gmpl |only inst/extdata/SRMPNoInconsist.gmpl |only inst/extdata/SRMPNoInconsistIndif.gmpl |only man/LPDMRSort.Rd | 6 man/LPDMRSortIdentifyIncompatibleAssignments.Rd | 6 man/LPDMRSortInferenceApprox.Rd |only man/LPDMRSortInferenceExact.Rd | 7 man/MRSortInferenceApprox.Rd | 114 - man/MRSortInferenceExact.Rd | 1 man/SRMP.Rd |only man/SRMPInference.Rd |only man/SRMPInferenceApprox.Rd |only man/SRMPInferenceApproxFixedLexicographicOrder.Rd |only man/SRMPInferenceApproxFixedProfilesNumber.Rd |only man/SRMPInferenceFixedLexicographicOrder.Rd |only man/SRMPInferenceFixedProfilesNumber.Rd |only man/SRMPInferenceNoInconsist.Rd |only man/SRMPInferenceNoInconsistFixedLexicographicOrder.Rd |only man/SRMPInferenceNoInconsistFixedProfilesNumber.Rd |only tests/LPDMRSortInferenceApprox.R |only tests/MRSortInferenceApprox.R | 4 tests/SRMP.R |only tests/SRMPInference.R |only tests/SRMPInferenceApprox.R |only tests/SRMPInferenceApproxFixedLexicographicOrder.R |only tests/SRMPInferenceApproxFixedProfilesNumber.R |only tests/SRMPInferenceFixedLexicographicOrder.R |only tests/SRMPInferenceFixedProfilesNumber.R |only tests/SRMPInferenceNoInconsist.R |only tests/SRMPInferenceNoInconsistFixedLexicographicOrder.R |only tests/SRMPInferenceNoInconsistFixedProfilesNumber.R |only 52 files changed, 552 insertions(+), 1196 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: A collection of functions to help build complex HTML or 'LaTeX'
tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'.
Function 'kable()' is a light weight table generator coming from 'knitr'.
This package simplifies the way to manipulate the HTML or 'LaTeX' codes
generated by 'kable()' and allows users to construct complex tables
and customize styles using a readable syntax.
Author: Hao Zhu [aut, cre],
Timothy Tsai [ctb],
Thomas Travison [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stéphane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 0.5.0 dated 2017-09-05 and 0.5.1 dated 2017-09-08
DESCRIPTION | 6 +-- MD5 | 27 +++++++++-------- NAMESPACE | 1 R/kable_styling.R | 15 ++++++++- R/util.R | 29 ++++++++++++++++++ inst/NEWS.md | 10 ++++++ inst/doc/awesome_table_in_html.R | 6 +-- inst/doc/awesome_table_in_html.Rmd | 6 +-- inst/doc/awesome_table_in_html.html | 56 ++++++++++++++++++------------------ inst/doc/awesome_table_in_pdf.R | 6 +-- inst/doc/awesome_table_in_pdf.Rmd | 6 +-- inst/doc/awesome_table_in_pdf.pdf |binary man/kableExtra_latex_packages.Rd |only vignettes/awesome_table_in_html.Rmd | 6 +-- vignettes/awesome_table_in_pdf.Rmd | 6 +-- 15 files changed, 116 insertions(+), 64 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs (BiDAG)
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data. The algorithms may provide the maximum a posteriori (MAP) graph or
a sample (a collection of DAGs) from the posterior distribution given the data.
References:
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
J. Kuipers and G. Moffa (2016) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.minkina@bsse.ethz.ch>
Diff between BiDAG versions 1.0.1 dated 2017-07-26 and 1.0.2 dated 2017-09-08
DESCRIPTION | 20 +++-- MD5 | 36 +++++----- R/WeightedCI.R | 142 ++++++++++++++++++++-------------------- R/corescore.R | 159 ++++++++++++++++++++++----------------------- R/genericmethods.R | 14 +-- R/graphhelpfns.R | 9 ++ R/initpar.R | 67 +++++++++++++----- R/iterativeMCMC.R | 48 ++++++------- R/main.R | 9 +- R/newbinaryscoring.R | 38 +++++++--- R/partitionMCMCmain.R | 30 +++++--- R/performanceassess.R | 28 +++++-- R/scoreagainstdag.R | 78 ++++++++++------------ R/scorefns.R | 5 - man/dag.threshold.Rd | 4 - man/edges.posterior.Rd | 8 +- man/iterativeMCMCsearch.Rd | 9 +- man/sample.check.Rd | 6 - man/scoreparameters.Rd | 5 + 19 files changed, 392 insertions(+), 323 deletions(-)
Title: Importing Data from Loligo Systems Software, Calculating
Metabolic Rates and Critical Tensions
Description: Analysis of oxygen consumption data generated by Loligo (R) Systems respirometry equipment. The package includes a function for loading data output by Loligo's 'AutoResp' software (get.witrox.data()), functions for calculating metabolic rates over user-specified time intervals, extracting critical points from data using broken stick regressions based on Yeager and Ultsch (<DOI:10.1086/physzool.62.4.30157935>), and easy functions for converting between different units of barometric pressure.
Author: Tyler L. Moulton
Maintainer: Tyler L. Moulton <tyler.moulton@cortland.edu>
Diff between rMR versions 1.0.4 dated 2017-01-20 and 1.0.5 dated 2017-09-08
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/rMR.R | 39 ++++++++++++++++++++++++++------------- build/partial.rdb |binary man/Eq.Ox.conc.Rd | 4 ++-- man/rMR-package.Rd | 6 +++--- 6 files changed, 41 insertions(+), 28 deletions(-)
Title: Simulation and Estimation of Multi-State Discrete-Time
Semi-Markov and Markov Models
Description: Performs parametric and non-parametric estimation and simulation for multi-state discrete-time semi-Markov processes.
For the parametric estimation, several discrete distributions are considered for the sojourn times: Uniform, Geometric, Poisson, Discrete Weibull and Negative Binomial. The non-parametric estimation concerns the sojourn time distributions, where no assumptions are done on the shape of distributions.
Moreover, the estimation can be done on the basis of one or several sample paths, with or without censoring at the beginning or/and at the end of the sample paths. The implemented methods are described in Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>, Barbu, V.S., Limnios, N. (2008) <doi:10.1080/10485250701261913> and
Trevezas, S., Limnios, N. (2011) <doi:10.1080/10485252.2011.555543>.
Estimation and simulation of discrete-time k-th order Markov chains are also considered.
Author: Vlad Stefan Barbu, Caroline Berard, Dominique Cellier, Mathilde Sautreuil and Nicolas Vergne
Maintainer: Nicolas Vergne <nicolas.vergne@univ-rouen.fr>
Diff between SMM versions 1.0 dated 2017-07-22 and 1.0.1 dated 2017-09-08
SMM-1.0.1/SMM/DESCRIPTION | 8 +++--- SMM-1.0.1/SMM/MD5 | 19 ++++++--------- SMM-1.0.1/SMM/build/vignette.rds |binary SMM-1.0.1/SMM/inst/doc/SMM-manual.pdf |binary SMM-1.0.1/SMM/inst/doc/smm.Rnw |only SMM-1.0.1/SMM/inst/doc/smm.pdf |only SMM-1.0.1/SMM/vignettes/smm.Rnw |only SMM-1.0.1/SMM/vignettes/smm.bib |only SMM-1.0.1/SMM/vignettes/smm_packageBW.pdf |only SMM-1.0/SMM/inst/doc/SMM.Rnw |only SMM-1.0/SMM/inst/doc/SMM.pdf |only SMM-1.0/SMM/vignettes/Package.bib |only SMM-1.0/SMM/vignettes/SMM.Rnw |only SMM-1.0/SMM/vignettes/natbib.bst |only SMM-1.0/SMM/vignettes/natbib.sty |only SMM-1.0/SMM/vignettes/smm_packageBW-eps-converted-to.pdf |only SMM-1.0/SMM/vignettes/smm_packageBW.eps |only 17 files changed, 12 insertions(+), 15 deletions(-)
Title: Multi-Purpose Core Subset Selection
Description: Core Hunter is a tool to sample diverse, representative subsets from large germplasm
collections, with minimum redundancy. Such so-called core collections have applications in plant
breeding and genetic resource management in general. Core Hunter can construct cores based on
genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many
provided evaluation measures depending on the precise purpose of the core (e.g. high diversity,
representativeness, or allelic richness). In addition, multiple measures can be simultaneously
optimized as part of a weighted index to bring the different perspectives closer together.
The Core Hunter library is implemented in Java 8 as an open source project (see
<http://www.corehunter.org>).
Author: Herman De Beukelaer [aut, cre],
Guy Davenport [aut],
Veerle Fack [ths]
Maintainer: Herman De Beukelaer <herman.debeukelaer@gmail.com>
Diff between corehunter versions 3.1.0 dated 2017-02-20 and 3.2.0 dated 2017-09-08
corehunter-3.1.0/corehunter/inst/java/corehunter-3.1.0.jar |only corehunter-3.2.0/corehunter/DESCRIPTION | 10 corehunter-3.2.0/corehunter/MD5 | 63 +- corehunter-3.2.0/corehunter/NAMESPACE | 1 corehunter-3.2.0/corehunter/NEWS.md | 10 corehunter-3.2.0/corehunter/R/data.R | 138 ++++- corehunter-3.2.0/corehunter/R/execution.R | 246 +++++++--- corehunter-3.2.0/corehunter/R/java.R | 10 corehunter-3.2.0/corehunter/inst/java/corehunter-base-3.2.0.jar |only corehunter-3.2.0/corehunter/man/coreHunterData.Rd | 1 corehunter-3.2.0/corehunter/man/corehunter.Rd | 1 corehunter-3.2.0/corehunter/man/distances.Rd | 1 corehunter-3.2.0/corehunter/man/evaluateCore.Rd | 1 corehunter-3.2.0/corehunter/man/exampleData.Rd | 3 corehunter-3.2.0/corehunter/man/genotypes.Rd | 3 corehunter-3.2.0/corehunter/man/getAlleleFrequencies.Rd | 1 corehunter-3.2.0/corehunter/man/getNormalizationRanges.Rd | 81 ++- corehunter-3.2.0/corehunter/man/objective.Rd | 5 corehunter-3.2.0/corehunter/man/phenotypes.Rd | 7 corehunter-3.2.0/corehunter/man/read.autodelim.Rd | 30 - corehunter-3.2.0/corehunter/man/sampleCore.Rd | 99 ++-- corehunter-3.2.0/corehunter/man/setRange.Rd | 1 corehunter-3.2.0/corehunter/man/wrapData.Rd | 1 corehunter-3.2.0/corehunter/tests/testthat/data/distances-small.txt | 12 corehunter-3.2.0/corehunter/tests/testthat/data/genotypes-bi-small.csv | 12 corehunter-3.2.0/corehunter/tests/testthat/data/genotypes-freq-small.csv | 14 corehunter-3.2.0/corehunter/tests/testthat/data/genotypes-small.csv | 12 corehunter-3.2.0/corehunter/tests/testthat/data/phenotypes-no-types.csv | 4 corehunter-3.2.0/corehunter/tests/testthat/data/phenotypes-single.csv |only corehunter-3.2.0/corehunter/tests/testthat/data/phenotypes-small.csv | 4 corehunter-3.2.0/corehunter/tests/testthat/data/phenotypes-unknown-type.csv | 14 corehunter-3.2.0/corehunter/tests/testthat/testData.R | 44 + corehunter-3.2.0/corehunter/tests/testthat/testExecution.R | 111 ++++ corehunter-3.2.0/corehunter/tests/testthat/testUtils.R | 4 34 files changed, 685 insertions(+), 259 deletions(-)
Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, etc.
Author: Christian Roever [aut, cre], Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 1.5 dated 2017-07-08 and 1.6 dated 2017-09-08
bayesmeta-1.5/bayesmeta/data/GoralczykEtAl2011.rda |only bayesmeta-1.5/bayesmeta/data/RoweEtAl2000.rda |only bayesmeta-1.5/bayesmeta/man/GoralczykEtAl2011.Rd |only bayesmeta-1.5/bayesmeta/man/RoweEtAl2000.Rd |only bayesmeta-1.6/bayesmeta/DESCRIPTION | 8 bayesmeta-1.6/bayesmeta/MD5 | 33 bayesmeta-1.6/bayesmeta/NAMESPACE | 5 bayesmeta-1.6/bayesmeta/R/bayesmeta.R | 819 +++++++++++++++++--- bayesmeta-1.6/bayesmeta/inst/doc/bayesmeta.html | 48 - bayesmeta-1.6/bayesmeta/man/CrinsEtAl2014.Rd | 5 bayesmeta-1.6/bayesmeta/man/HinksEtAl2010.Rd | 6 bayesmeta-1.6/bayesmeta/man/Peto1980.Rd | 4 bayesmeta-1.6/bayesmeta/man/TurnerEtAlPrior.Rd | 8 bayesmeta-1.6/bayesmeta/man/bayesmeta-package.Rd | 7 bayesmeta-1.6/bayesmeta/man/bayesmeta.Rd | 66 + bayesmeta-1.6/bayesmeta/man/forest.bayesmeta.Rd | 10 bayesmeta-1.6/bayesmeta/man/forestplot.bayesmeta.Rd | 8 bayesmeta-1.6/bayesmeta/man/normalmixture.Rd | 14 bayesmeta-1.6/bayesmeta/man/plot.bayesmeta.Rd | 14 bayesmeta-1.6/bayesmeta/man/pppvalue.Rd |only 20 files changed, 846 insertions(+), 209 deletions(-)
Title: Graph Kernels
Description: A fast C++ implementation for computing various graph kernels including (1) simple kernels between vertex and/or edge label histograms, (2) graphlet kernels, (3) random walk kernels (popular baselines), and (4) the Weisfeiler-Lehman graph kernel (state-of-the-art).
Author: Mahito Sugiyama
Maintainer: Mahito Sugiyama <mahito@nii.ac.jp>
Diff between graphkernels versions 1.3 dated 2017-09-06 and 1.4 dated 2017-09-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/graphKernels.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Compute Sun Position, Sunlight Phases, Moon Position and Lunar
Phase
Description: R interface to 'suncalc.js' library, part of the 'SunCalc.net' project <http://suncalc.net>,
for calculating sun position, sunlight phases (times for sunrise, sunset, dusk, etc.),
moon position and lunar phase for the given location and time.
Author: Vladimir Agafonkin [aut, cph] (suncalc.js library/lib,
https://github.com/mourner),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between suncalc versions 0.1 dated 2017-05-15 and 0.2 dated 2017-09-08
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md |only R/getMoonPosition.R | 2 +- R/getMoonTimes.R | 2 +- R/getSunlightPosition.R | 2 +- R/getSunlightTimes.R | 2 +- README.md | 4 +++- 8 files changed, 18 insertions(+), 15 deletions(-)