Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table,
actuarial tables (also multiple decrements tables). Moreover, functions to easily
perform demographic, financial and actuarial mathematics on life contingencies
insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J.
Owens [ctb], Christophe Dutang [ctb], Ernesto Schirmacher[ctb], Gian Paolo Clemente [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.3.2 dated 2017-12-09 and 1.3.5 dated 2018-09-18
lifecontingencies-1.3.2/lifecontingencies/man/exn_1.Rd |only lifecontingencies-1.3.2/lifecontingencies/man/rLife.Rd |only lifecontingencies-1.3.2/lifecontingencies/man/rLifeContingenciesXyz.Rd |only lifecontingencies-1.3.5/lifecontingencies/ChangeLog | 9 lifecontingencies-1.3.5/lifecontingencies/DESCRIPTION | 15 lifecontingencies-1.3.5/lifecontingencies/MD5 | 147 +- lifecontingencies-1.3.5/lifecontingencies/NAMESPACE | 111 +- lifecontingencies-1.3.5/lifecontingencies/NEWS | 6 lifecontingencies-1.3.5/lifecontingencies/R/0_lifetableAndActuarialtableClassesAndMethods.R | 28 lifecontingencies-1.3.5/lifecontingencies/R/1_mdtClassesAndMethods.R | 26 lifecontingencies-1.3.5/lifecontingencies/R/2_commonMethods.R | 26 lifecontingencies-1.3.5/lifecontingencies/R/3_demographicFunctions.R | 366 ++++++- lifecontingencies-1.3.5/lifecontingencies/R/4_financialFunctions.R | 155 ++ lifecontingencies-1.3.5/lifecontingencies/R/5_actuarialFunctions.R | 517 +++++++--- lifecontingencies-1.3.5/lifecontingencies/R/5b_BackupActuarialFunctions.R |only lifecontingencies-1.3.5/lifecontingencies/R/6_randomGenerationFunctions.R | 172 +++ lifecontingencies-1.3.5/lifecontingencies/R/7_tomarkovchain.R | 23 lifecontingencies-1.3.5/lifecontingencies/R/8_mdtFunctions.R | 26 lifecontingencies-1.3.5/lifecontingencies/R/data.R | 50 lifecontingencies-1.3.5/lifecontingencies/R/testfunc-demographic.R |only lifecontingencies-1.3.5/lifecontingencies/R/testfunc-financial.R |only lifecontingencies-1.3.5/lifecontingencies/R/util-testargument-func.R |only lifecontingencies-1.3.5/lifecontingencies/R/zzz.R | 41 lifecontingencies-1.3.5/lifecontingencies/build/vignette.rds |binary lifecontingencies-1.3.5/lifecontingencies/data/AF92Lt.rda |binary lifecontingencies-1.3.5/lifecontingencies/data/demoUk.rda |binary lifecontingencies-1.3.5/lifecontingencies/data/demoUsa.rda |binary lifecontingencies-1.3.5/lifecontingencies/data/soaLt.rda |binary lifecontingencies-1.3.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.R | 2 lifecontingencies-1.3.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.Rnw | 12 lifecontingencies-1.3.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary lifecontingencies-1.3.5/lifecontingencies/inst/doc/compute-detail.R |only lifecontingencies-1.3.5/lifecontingencies/inst/doc/compute-detail.Rmd |only lifecontingencies-1.3.5/lifecontingencies/inst/doc/compute-detail.pdf |only lifecontingencies-1.3.5/lifecontingencies/inst/doc/introToLifecontingencies.pdf |binary lifecontingencies-1.3.5/lifecontingencies/inst/doc/mortality_projection.R | 2 lifecontingencies-1.3.5/lifecontingencies/inst/doc/mortality_projection.Rnw | 10 lifecontingencies-1.3.5/lifecontingencies/inst/doc/mortality_projection.pdf |binary lifecontingencies-1.3.5/lifecontingencies/inst/doc/pensionfunding.R |only lifecontingencies-1.3.5/lifecontingencies/inst/doc/pensionfunding.Rmd |only lifecontingencies-1.3.5/lifecontingencies/inst/doc/pensionfunding.html |only lifecontingencies-1.3.5/lifecontingencies/man/AExn.Rd | 6 lifecontingencies-1.3.5/lifecontingencies/man/DAxn.Rd | 6 lifecontingencies-1.3.5/lifecontingencies/man/IAxn.Rd | 6 lifecontingencies-1.3.5/lifecontingencies/man/Multiple-life-insurances.Rd | 16 lifecontingencies-1.3.5/lifecontingencies/man/accumulatedValue.Rd | 7 lifecontingencies-1.3.5/lifecontingencies/man/annuity.Rd | 7 lifecontingencies-1.3.5/lifecontingencies/man/axn.Rd | 25 lifecontingencies-1.3.5/lifecontingencies/man/axn_1.Rd | 20 lifecontingencies-1.3.5/lifecontingencies/man/axyn.Rd | 18 lifecontingencies-1.3.5/lifecontingencies/man/de_angelis_di_falco.Rd | 3 lifecontingencies-1.3.5/lifecontingencies/man/decreasingAnnuity.Rd | 8 lifecontingencies-1.3.5/lifecontingencies/man/demoUk.Rd | 73 - lifecontingencies-1.3.5/lifecontingencies/man/demoUsa.Rd | 40 lifecontingencies-1.3.5/lifecontingencies/man/exn.Rd | 65 - lifecontingencies-1.3.5/lifecontingencies/man/getLifeContingencies.Rd | 10 lifecontingencies-1.3.5/lifecontingencies/man/increasingAnnuity.Rd | 5 lifecontingencies-1.3.5/lifecontingencies/man/intensity-interest.Rd | 48 lifecontingencies-1.3.5/lifecontingencies/man/lifecontingencies-package.Rd | 4 lifecontingencies-1.3.5/lifecontingencies/man/multiple-life-probabilities.Rd | 35 lifecontingencies-1.3.5/lifecontingencies/man/nominal-real-convertible.Rd | 60 - lifecontingencies-1.3.5/lifecontingencies/man/pureendowment.Rd |only lifecontingencies-1.3.5/lifecontingencies/man/pxt.Rd | 21 lifecontingencies-1.3.5/lifecontingencies/man/pxyt.Rd | 6 lifecontingencies-1.3.5/lifecontingencies/man/rLifeContingencies.Rd | 94 + lifecontingencies-1.3.5/lifecontingencies/man/rLifes.Rd |only lifecontingencies-1.3.5/lifecontingencies/man/rmdt.Rd | 3 lifecontingencies-1.3.5/lifecontingencies/man/soaLt.Rd | 38 lifecontingencies-1.3.5/lifecontingencies/src/Makevars |only lifecontingencies-1.3.5/lifecontingencies/src/Makevars.win |only lifecontingencies-1.3.5/lifecontingencies/tests/test-comput-mult-table-annuity.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-computation-time-act-annuity.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-computation-time-act-capital.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-computation-time-demog-multlife.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-computation-time-demog.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-defensive-prog-act.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-defensive-prog-demog.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-defensive-prog-fin.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-defensive-prog-rng.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-file-US7981-annuity.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-file-US7981-livingprob.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-pxt-allclass.R |only lifecontingencies-1.3.5/lifecontingencies/tests/test-strg-ex.R |only lifecontingencies-1.3.5/lifecontingencies/tests/testthat.R | 1 lifecontingencies-1.3.5/lifecontingencies/tests/testthat/testFinancialMathematics.R | 9 lifecontingencies-1.3.5/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package.Rnw | 12 lifecontingencies-1.3.5/lifecontingencies/vignettes/compute-detail.Rmd |only lifecontingencies-1.3.5/lifecontingencies/vignettes/lifecontingenciesBiblio.bib | 14 lifecontingencies-1.3.5/lifecontingencies/vignettes/mortality_projection.Rnw | 10 lifecontingencies-1.3.5/lifecontingencies/vignettes/pensionfunding.Rmd | 8 90 files changed, 1758 insertions(+), 664 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Utilities for Delaying Function Execution
Description: Executes arbitrary R or C functions some time after the current
time, after the R execution stack has emptied.
Author: Joe Cheng [aut, cre],
RStudio [cph],
Marcus Geelnard [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/),
Evan Nemerson [ctb, cph] (TinyCThread library,
https://tinycthread.github.io/)
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between later versions 0.7.4 dated 2018-08-31 and 0.7.5 dated 2018-09-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/RcppExports.R | 4 ++++ inst/doc/later-cpp.html | 6 ++++-- src/RcppExports.cpp | 9 +++++++++ src/callback_registry.cpp | 37 +++++++++++++++++++++++++++++++++++++ src/callback_registry.h | 15 ++++++++------- src/init.c | 12 +++++++----- tests/testthat/test-run_now.R | 28 ++++++++++++++++++++++++++++ 10 files changed, 114 insertions(+), 27 deletions(-)
Title: R Bindings for 'ZeroMQ'
Description: Interface to the 'ZeroMQ' lightweight messaging kernel (see <http://www.zeromq.org/> for more information).
Author: Whit Armstrong [aut],
Michael Schubert [ctb],
Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between rzmq versions 0.9.3 dated 2017-10-02 and 0.9.4 dated 2018-09-18
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NEWS | 3 + README.md | 8 ++- configure | 6 +- src/interface.cpp | 127 ++++++++++++++++++++++++++++++++---------------------- 6 files changed, 100 insertions(+), 64 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Jianxiao Yang [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] (provided the TinyThread library),
Rutgers University [cph, ctb] (provided the HParSearch routine),
R Development Core Team [cph, ctb] (provided the ZeroIn routine)
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 1.3.4 dated 2018-06-15 and 2.0.0 dated 2018-09-18
DESCRIPTION | 12 MD5 | 140 NAMESPACE | 2 NEWS | 8 R/DataManagement.R | 27 R/ModelFit.R | 71 R/NewDataConversion.R | 33 R/RcppExports.R | 38 R/SpecialPriors.R | 2 man/convertToCyclopsData.Rd | 10 man/createControl.Rd | 6 man/createCyclopsData.Rd | 5 man/fitCyclopsModel.Rd | 4 man/getFloatingPointSize.Rd |only man/printMatrixMarket.Rd | 1 src/Makevars.win | 21 src/RcppCyclopsInterface.cpp | 69 src/RcppCyclopsInterface.h | 21 src/RcppExports.cpp | 73 src/RcppModelData.cpp | 399 +- src/RcppModelData.h | 358 + src/cyclops/CcdInterface.cpp | 43 src/cyclops/CcdInterface.h | 37 src/cyclops/CompressedDataMatrix.cpp | 134 src/cyclops/CompressedDataMatrix.h | 107 src/cyclops/CyclicCoordinateDescent.cpp | 642 ++- src/cyclops/CyclicCoordinateDescent.h | 48 src/cyclops/Iterators.h | 66 src/cyclops/ModelData.cpp | 245 + src/cyclops/ModelData.h | 573 ++- src/cyclops/Types.h | 49 src/cyclops/drivers/AbstractCrossValidationDriver.cpp | 6 src/cyclops/drivers/AbstractCrossValidationDriver.h | 4 src/cyclops/drivers/AbstractSelector.h | 4 src/cyclops/drivers/AutoSearchCrossValidationDriver.cpp | 4 src/cyclops/drivers/AutoSearchCrossValidationDriver.h | 8 src/cyclops/drivers/BootstrapDriver.cpp | 28 src/cyclops/drivers/BootstrapDriver.h | 4 src/cyclops/drivers/BootstrapSelector.cpp | 4 src/cyclops/drivers/BootstrapSelector.h | 4 src/cyclops/drivers/CrossValidationSelector.cpp | 36 src/cyclops/drivers/CrossValidationSelector.h | 14 src/cyclops/drivers/GridSearchCrossValidationDriver.cpp | 6 src/cyclops/drivers/GridSearchCrossValidationDriver.h | 4 src/cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.cpp | 6 src/cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.h | 6 src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.cpp | 10 src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.h | 2 src/cyclops/drivers/ProportionSelector.cpp | 8 src/cyclops/drivers/ProportionSelector.h | 4 src/cyclops/engine/AbstractModelSpecifics.cpp | 488 +- src/cyclops/engine/AbstractModelSpecifics.h | 168 src/cyclops/engine/ModelSpecifics.h | 1677 +++------ src/cyclops/engine/ModelSpecifics.hpp | 1859 ++++++---- src/cyclops/engine/ParallelLoops.h | 22 src/cyclops/engine/Ranges.h | 164 src/cyclops/engine/Recursions.hpp | 233 - src/cyclops/imputation/ImputationPolicy.h | 2 src/cyclops/io/BaseInputReader.h | 147 src/cyclops/io/InputReader.cpp | 2 src/cyclops/io/InputReader.h | 6 src/cyclops/io/NewGenericInputReader.h | 32 src/cyclops/io/OutputWriter.h | 16 src/cyclops/io/SparseIndexer.h | 23 tests/testthat/test-cv.R | 4 tests/testthat/test-dataConversionStratified.R | 3 tests/testthat/test-floatingPoint.R |only tests/testthat/test-smallCox.R | 198 - tests/testthat/test-smallExactCLR.R | 82 tests/testthat/test-smallPoisson.R | 50 tests/testthat/test-weighted_cv.R |only tests/testthat/test-weighting.R |only tests/testthat/test-xyConstructor.R | 4 73 files changed, 5176 insertions(+), 3410 deletions(-)
Title: An Integrated Framework for Textual Sentiment Time Series
Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2017) <doi:10.2139/ssrn.3067734>.
Author: David Ardia [aut],
Keven Bluteau [aut],
Samuel Borms [aut, cre],
Kris Boudt [aut]
Maintainer: Samuel Borms <samuel.borms@unine.ch>
Diff between sentometrics versions 0.4 dated 2018-05-28 and 0.5 dated 2018-09-18
sentometrics-0.4/sentometrics/R/sentomeasures.R |only sentometrics-0.4/sentometrics/man/almons.Rd |only sentometrics-0.4/sentometrics/man/ctr_merge.Rd |only sentometrics-0.4/sentometrics/man/exponentials.Rd |only sentometrics-0.4/sentometrics/man/nobs.Rd |only sentometrics-0.4/sentometrics/man/perform_MCS.Rd |only sentometrics-0.4/sentometrics/man/perform_agg.Rd |only sentometrics-0.4/sentometrics/man/plot_attributions.Rd |only sentometrics-0.4/sentometrics/man/retrieve_attributions.Rd |only sentometrics-0.4/sentometrics/man/setup_lexicons.Rd |only sentometrics-0.4/sentometrics/man/to_global.Rd |only sentometrics-0.5/sentometrics/DESCRIPTION | 21 sentometrics-0.5/sentometrics/MD5 | 142 +- sentometrics-0.5/sentometrics/NAMESPACE | 20 sentometrics-0.5/sentometrics/NEWS.md | 43 sentometrics-0.5/sentometrics/R/RcppExports.R | 8 sentometrics-0.5/sentometrics/R/attribution.R | 318 ++-- sentometrics-0.5/sentometrics/R/deprecated.R | 222 ++- sentometrics-0.5/sentometrics/R/sentiment_engines.R | 290 +--- sentometrics-0.5/sentometrics/R/sentocorpus.R | 105 - sentometrics-0.5/sentometrics/R/sentolexicons.R |only sentometrics-0.5/sentometrics/R/sentomeasures_main.R |only sentometrics-0.5/sentometrics/R/sentomeasures_measures_xyz.R |only sentometrics-0.5/sentometrics/R/sentomeasures_methods.R |only sentometrics-0.5/sentometrics/R/sentometrics.R | 104 - sentometrics-0.5/sentometrics/R/sentomodel.R | 679 ++++------ sentometrics-0.5/sentometrics/R/utils.R | 459 ++++-- sentometrics-0.5/sentometrics/R/zzz.R | 2 sentometrics-0.5/sentometrics/README.md | 13 sentometrics-0.5/sentometrics/data/epu.rda |binary sentometrics-0.5/sentometrics/data/list_lexicons.rda |binary sentometrics-0.5/sentometrics/data/list_valence_shifters.rda |binary sentometrics-0.5/sentometrics/data/usnews.rda |binary sentometrics-0.5/sentometrics/inst/CITATION | 2 sentometrics-0.5/sentometrics/man/add_features.Rd | 35 sentometrics-0.5/sentometrics/man/aggregate.Rd |only sentometrics-0.5/sentometrics/man/attributions.Rd |only sentometrics-0.5/sentometrics/man/compute_sentiment.Rd | 96 - sentometrics-0.5/sentometrics/man/ctr_agg.Rd | 50 sentometrics-0.5/sentometrics/man/ctr_model.Rd | 57 sentometrics-0.5/sentometrics/man/data-defunct.Rd | 1 sentometrics-0.5/sentometrics/man/diff.sentomeasures.Rd | 4 sentometrics-0.5/sentometrics/man/epu.Rd | 14 sentometrics-0.5/sentometrics/man/get_dates.Rd |only sentometrics-0.5/sentometrics/man/get_dimensions.Rd |only sentometrics-0.5/sentometrics/man/get_hows.Rd | 10 sentometrics-0.5/sentometrics/man/get_loss_data.Rd |only sentometrics-0.5/sentometrics/man/get_measures.Rd |only sentometrics-0.5/sentometrics/man/list_lexicons.Rd | 33 sentometrics-0.5/sentometrics/man/list_valence_shifters.Rd | 22 sentometrics-0.5/sentometrics/man/measures_delete.Rd | 17 sentometrics-0.5/sentometrics/man/measures_fill.Rd | 31 sentometrics-0.5/sentometrics/man/measures_global.Rd |only sentometrics-0.5/sentometrics/man/measures_merge.Rd | 47 sentometrics-0.5/sentometrics/man/measures_select.Rd | 17 sentometrics-0.5/sentometrics/man/measures_subset.Rd | 4 sentometrics-0.5/sentometrics/man/nmeasures.Rd | 2 sentometrics-0.5/sentometrics/man/nobs.sentomeasures.Rd |only sentometrics-0.5/sentometrics/man/peakdocs.Rd | 4 sentometrics-0.5/sentometrics/man/plot.attributions.Rd |only sentometrics-0.5/sentometrics/man/plot.sentomeasures.Rd | 13 sentometrics-0.5/sentometrics/man/plot.sentomodeliter.Rd | 37 sentometrics-0.5/sentometrics/man/predict.sentomodel.Rd | 8 sentometrics-0.5/sentometrics/man/scale.sentomeasures.Rd | 31 sentometrics-0.5/sentometrics/man/sento_corpus.Rd | 49 sentometrics-0.5/sentometrics/man/sento_lexicons.Rd |only sentometrics-0.5/sentometrics/man/sento_measures.Rd | 16 sentometrics-0.5/sentometrics/man/sento_model.Rd | 70 - sentometrics-0.5/sentometrics/man/sentometrics-defunct.Rd |only sentometrics-0.5/sentometrics/man/sentometrics-deprecated.Rd | 116 + sentometrics-0.5/sentometrics/man/sentometrics-package.Rd | 37 sentometrics-0.5/sentometrics/man/usnews.Rd | 3 sentometrics-0.5/sentometrics/man/weights_almon.Rd |only sentometrics-0.5/sentometrics/man/weights_beta.Rd |only sentometrics-0.5/sentometrics/man/weights_exponential.Rd |only sentometrics-0.5/sentometrics/src/Makevars | 2 sentometrics-0.5/sentometrics/src/Makevars.win | 4 sentometrics-0.5/sentometrics/src/RcppExports.cpp | 29 sentometrics-0.5/sentometrics/src/SentimentScorerBigrams.h |only sentometrics-0.5/sentometrics/src/SentimentScorerClusters.h |only sentometrics-0.5/sentometrics/src/SentimentScorerOnegrams.h |only sentometrics-0.5/sentometrics/src/compute_df.cpp | 36 sentometrics-0.5/sentometrics/src/compute_sentiment_onegrams.cpp |only sentometrics-0.5/sentometrics/src/compute_sentiment_valence.cpp |only sentometrics-0.5/sentometrics/src/utils.h |only sentometrics-0.5/sentometrics/tests/testthat/test_aggregation.R | 52 sentometrics-0.5/sentometrics/tests/testthat/test_attribution.R | 59 sentometrics-0.5/sentometrics/tests/testthat/test_corpus_building.R |only sentometrics-0.5/sentometrics/tests/testthat/test_measures_manipulation.R |only sentometrics-0.5/sentometrics/tests/testthat/test_methods_sentomeasures.R |only sentometrics-0.5/sentometrics/tests/testthat/test_model_specification.R |only sentometrics-0.5/sentometrics/tests/testthat/test_sentiment_computation.R |only 92 files changed, 2033 insertions(+), 1401 deletions(-)
Title: Extract Data Tables and Comments from 'Microsoft' 'Word'
Documents
Description: 'Microsoft Word' 'docx' files provide an 'XML' structure that is fairly
straightforward to navigate, especially when it applies to 'Word' tables and
comments. Tools are provided to determine table count/structure, comment count
and also to extract/clean tables and comments from 'Microsoft Word' 'docx' documents.
There is also nascent support for '.doc' files.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>),
Mark Dulhunty [ctb],
Karlo Guidoni-Martins [ctb],
Chris Muir [aut, ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between docxtractr versions 0.2.0 dated 2016-07-20 and 0.5.0 dated 2018-09-18
DESCRIPTION | 44 ++++++++---- MD5 | 54 ++++++++------- NAMESPACE | 13 +++ NEWS.md | 20 +++++ R/aaa.r | 2 R/assign_colnames.r | 9 ++ R/comments.R |only R/describe.r | 11 +-- R/docx-extract-tbl.r |only R/docx_find_tbls.r | 54 --------------- R/docxtractr-package.r | 20 +++-- R/extract_all.r | 45 ++----------- R/mcga.r |only R/read_docs.r | 68 ++++++++++++++++--- R/utils.r | 135 +++++++++++++++++++++++++++++++++++++-- inst/examples/preserve.docx |only man/assign_colnames.Rd | 5 - man/docx_cmnt_count.Rd | 1 man/docx_describe_cmnts.Rd | 1 man/docx_describe_tbls.Rd | 1 man/docx_extract_all.Rd | 7 +- man/docx_extract_all_cmnts.Rd | 8 +- man/docx_extract_all_tbls.Rd | 8 +- man/docx_extract_tbl.Rd | 14 ++-- man/docx_tbl_count.Rd | 1 man/docxtractr.Rd | 11 +-- man/mcga.Rd |only man/print.docx.Rd | 1 man/read_docx.Rd | 7 -- man/set_libreoffice_path.Rd |only tests/testthat/test-docxtractr.R | 39 +++++++++-- 31 files changed, 379 insertions(+), 200 deletions(-)
Title: Query 'Team Cymru' 'IP' Address, Autonomous System Number
('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware'
Hash Data Services
Description: A toolkit for querying 'Team Cymru' <http://team-cymru.org> 'IP'
address, Autonomous System Number ('ASN'), Border Gateway Protocol ('BGP'), Bogon
and 'Malware' Hash Data Services.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: Bob Rudis <bob@rud.is>
Diff between cymruservices versions 0.2.0 dated 2016-03-01 and 0.5.0 dated 2018-09-18
cymruservices-0.2.0/cymruservices/NEWS |only cymruservices-0.2.0/cymruservices/README.md |only cymruservices-0.5.0/cymruservices/DESCRIPTION | 20 cymruservices-0.5.0/cymruservices/MD5 | 37 - cymruservices-0.5.0/cymruservices/NAMESPACE | 7 cymruservices-0.5.0/cymruservices/R/aaa.R |only cymruservices-0.5.0/cymruservices/R/asn.R | 336 +++++----- cymruservices-0.5.0/cymruservices/R/bogons.R | 139 ++-- cymruservices-0.5.0/cymruservices/R/cymruservices-package.r | 8 cymruservices-0.5.0/cymruservices/R/malwarehash.R | 104 +-- cymruservices-0.5.0/cymruservices/R/utils-safely.R |only cymruservices-0.5.0/cymruservices/R/utils.R | 6 cymruservices-0.5.0/cymruservices/R/zflush.r |only cymruservices-0.5.0/cymruservices/man/bulk_origin.Rd | 1 cymruservices-0.5.0/cymruservices/man/bulk_origin_asn.Rd | 1 cymruservices-0.5.0/cymruservices/man/bulk_peer.Rd | 1 cymruservices-0.5.0/cymruservices/man/cymru_active.Rd |only cymruservices-0.5.0/cymruservices/man/cymruservices.Rd | 3 cymruservices-0.5.0/cymruservices/man/flush.Rd |only cymruservices-0.5.0/cymruservices/man/ipv4_bogons.Rd | 1 cymruservices-0.5.0/cymruservices/man/ipv6_bogons.Rd | 1 cymruservices-0.5.0/cymruservices/man/malware_hash.Rd | 1 cymruservices-0.5.0/cymruservices/tests/testthat/test-cymruservices.R | 24 23 files changed, 392 insertions(+), 298 deletions(-)
Title: Conditional Akaike Information Criterion for 'lme4'
Description: Provides functions for the estimation of the conditional Akaike
information in generalized mixed-effect models fitted with (g)lmer()
from 'lme4'.
Author: Benjamin Saefken and David Ruegamer, with contributions from Sonja
Greven and Thomas Kneib
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between cAIC4 versions 0.4 dated 2018-05-22 and 0.5 dated 2018-09-18
DESCRIPTION | 10 +- MD5 | 33 +++--- NAMESPACE | 1 R/biasCorrectionBernoulli.R | 23 +++- R/biasCorrectionPoisson.R | 18 +++ R/cAIC.R | 36 ++++--- R/calculateGaussianBc.R | 14 ++ R/datasets.R | 14 ++ R/deleteZeroComponents.R | 23 ++-- R/getModelComponents.R | 2 R/helperfuns_stepcAIC.R | 199 +++++++++++++++++++++++++++++++++-------- R/methods.R |only R/stepcAIC.R | 213 +++++++++++++++++++++++++++++++------------- build/partial.rdb |binary data/Zambia.RData |only man/Zambia.Rd |only man/anocAIC.Rd |only man/cAIC.Rd | 9 + man/print.cAIC.Rd |only man/stepcAIC.Rd | 63 ++++++++----- 20 files changed, 476 insertions(+), 182 deletions(-)
Title: Improved Standard Evaluation Interfaces for Common Data
Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved
standard evaluation adapter methods for important common 'dplyr' data manipulation tasks.
In addition the 'seplyr' package supplies several new "key operations
bound together" methods. These include 'group_summarize()' (which
combines grouping, arranging and calculation in an atomic unit),
'add_group_summaries()' (which joins grouped summaries into a 'data.frame'
in a well documented manner), 'add_group_indices()' (which adds
per-group identifiers to a 'data.frame' without depending on row-order),
'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()'
(which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between seplyr versions 0.8.0 dated 2018-09-10 and 0.8.1 dated 2018-09-18
DESCRIPTION | 12 +++++------ MD5 | 42 ++++++++++++++++++++-------------------- NEWS.md | 5 ++++ R/add_group_summaries.R | 9 ++++---- R/add_rank_indices.R | 9 ++++---- R/arrange_se.R | 4 +-- R/filter_se.R | 5 ++-- R/group_summarize.R | 9 ++++---- R/in_group_indices.R | 9 ++++---- R/mutate_nse.R | 3 -- R/mutate_se.R | 7 ++---- R/select_se.R | 5 ++-- R/summarize_se.R | 11 +++++----- R/transmute_se.R | 5 ++-- inst/doc/MutatePartitioner.html | 4 +-- inst/doc/named_map_builder.html | 4 +-- inst/doc/rename_se.html | 4 +-- inst/doc/seplyr.html | 4 +-- inst/doc/using_seplyr.html | 4 +-- man/mutate_nse.Rd | 3 -- man/mutate_se.Rd | 3 -- man/summarize_se.Rd | 2 - 22 files changed, 86 insertions(+), 77 deletions(-)
Title: Heteroskedastic Gaussian Process Modeling and Design under
Replication
Description: Performs Gaussian process regression with heteroskedastic noise following Binois, M., Gramacy, R., Ludkovski, M. (2016) <arXiv:1611.05902>. The input dependent noise is modeled as another Gaussian process. Replicated observations are encouraged as they yield computational savings. Sequential design procedures based on the integrated mean square prediction error and lookahead heuristics are provided, and notably fast update functions when adding new observations.
Author: Mickael Binois, Robert B. Gramacy
Maintainer: Mickael Binois <mbinois@mcs.anl.gov>
Diff between hetGP versions 1.0.2 dated 2018-02-06 and 1.1.0 dated 2018-09-18
DESCRIPTION | 10 - MD5 | 54 ++++---- NAMESPACE | 11 + NEWS | 11 + R/IMSE.R | 42 ++++-- R/TestFunctions.R | 2 R/contour.R |only R/hetGP.R | 304 ++++++++++++++++++++++++++++++----------------- R/hetTP.R | 290 +++++++++++++++++++++++++++++--------------- R/optim.R |only R/update_hetGP.R | 118 +++++++++++++----- man/IMSE.search.Rd | 5 man/IMSE_nsteps_ahead.Rd | 4 man/IMSPE.Rd | 4 man/LOO_preds.Rd |only man/SIR.Rd | 4 man/allocate_mult.Rd | 18 ++ man/crit_EI.Rd |only man/crit_ICU.Rd |only man/crit_IMSE.Rd | 6 man/crit_MCU.Rd |only man/crit_cSUR.Rd |only man/crit_tMSE.Rd |only man/find_reps.Rd | 4 man/mleHetGP.Rd | 23 +-- man/mleHetTP.Rd | 24 +-- man/mleHomGP.Rd | 16 +- man/mleHomTP.Rd | 8 - man/update.hetGP.Rd | 4 man/update.hetTP.Rd | 4 man/update.homGP.Rd | 3 man/update.homTP.Rd | 3 32 files changed, 635 insertions(+), 337 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of a categorical
variable; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on the same endpoint
for many variables (univariate or adjusted for standard covariates);
freqlist(), a powerful frequency table across many categorical variables;
compare.data.frame(), the S3 method for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 1.3.0 dated 2018-07-20 and 1.4.0 dated 2018-09-18
DESCRIPTION | 8 MD5 | 114 ++++++------- NAMESPACE | 6 NEWS.md | 79 +++++++++ R/as.data.frame.modelsum.R | 11 - R/as.data.frame.tableby.R | 36 ++-- R/compare.data.frame.R | 37 ++-- R/compare.internal.R | 25 ++ R/modelsum.R | 137 +++++++++------ R/modelsum.control.R | 89 +++++++--- R/modelsum.families.R |only R/modelsum.internal.R | 5 R/paired.R | 36 ++-- R/paired.internal.R | 1 R/summary.compare.R | 40 +++- R/summary.freqlist.R | 2 R/summary.modelsum.R | 28 +-- R/summary.tableby.R | 46 +++-- R/tableby.R | 30 ++- R/tableby.control.R | 16 + R/tableby.internal.R | 9 - R/tableby.stat.tests.R | 2 R/tableby.stats.R | 4 README.md | 3 inst/doc/compare.Rmd | 4 inst/doc/compare.html | 285 ++++++++++++++++++++++++++++++++ inst/doc/freqlist.html | 2 inst/doc/labels.Rmd | 3 inst/doc/labels.html | 4 inst/doc/modelsum.Rmd | 38 ++-- inst/doc/modelsum.html | 358 +++++++++++++++++++++-------------------- inst/doc/paired.R | 6 inst/doc/paired.Rmd | 20 ++ inst/doc/paired.html | 28 +++ inst/doc/tableby.R | 13 + inst/doc/tableby.Rmd | 38 +++- inst/doc/tableby.html | 225 ++++++++++++++++++++++--- inst/doc/write2.Rmd | 12 + inst/doc/write2.html | 8 man/compare.data.frame.Rd | 2 man/diffs.Rd | 11 + man/modelsum.Rd | 6 man/modelsum.control.Rd | 12 - man/modelsum.family.Rd |only man/summary.compare.Rd | 10 - man/summary.modelsum.Rd | 19 +- man/summary.tableby.Rd | 21 +- man/tableby.control.Rd | 37 ++-- man/tableby.stats.Rd | 6 tests/testthat/test_compare.R | 121 ++++++++++++- tests/testthat/test_modelsum.R | 105 ++++++++++++ tests/testthat/test_paired.R | 17 + tests/testthat/test_tableby.R | 68 +++++++ vignettes/compare.Rmd | 4 vignettes/labels.Rmd | 3 vignettes/modelsum.Rmd | 38 ++-- vignettes/paired.Rmd | 20 ++ vignettes/tableby.Rmd | 38 +++- vignettes/write2.Rmd | 12 + 59 files changed, 1783 insertions(+), 575 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers
needed to build R packages on various platforms and ensures the PATH is
configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
RStudio [cph]
Maintainer: Jim Hester <james.hester@rstudio.com>
Diff between pkgbuild versions 1.0.0 dated 2018-06-27 and 1.0.1 dated 2018-09-18
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS.md | 11 ++++++++++- R/build-tools.R | 14 +++++++++++++- R/compile-dll.R | 16 ++++++++++++++-- R/compiler-flags.R | 12 ++++++------ R/utils.R | 29 +++++++++++++++++++++++++++++ README.md | 2 +- man/build.Rd | 6 +++--- man/compiler_flags.Rd | 3 ++- man/has_build_tools.Rd | 8 +++++++- man/with_debug.Rd | 3 ++- 13 files changed, 106 insertions(+), 35 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 4.3 dated 2017-09-20 and 4.4 dated 2018-09-18
DESCRIPTION | 14 ++++++------- MD5 | 56 ++++++++++++++++++++++++++--------------------------- R/Check2D.R | 4 +++ R/DNE.R | 4 +++ R/DNE3d.R | 4 +++ R/OPC.R | 6 ++++- R/OPC3d.R | 4 +++ R/OPCr.R | 1 R/RFI.R | 6 ++++- R/RFI3d.R | 5 +++- R/Slope.R | 6 ++++- R/Slope3d.R | 6 ++++- R/Slope_Legend.R | 2 - R/molaR_Clean.R | 3 ++ R/plyClip.R | 3 +- R/read.AVIZO.ply.R | 1 build/vignette.rds |binary man/Check2D.Rd | 4 +++ man/DNE.Rd | 4 +++ man/DNE3d.Rd | 10 ++++++--- man/OPC.Rd | 4 +++ man/OPC3d.Rd | 8 +++++-- man/RFI.Rd | 4 +++ man/RFI3d.Rd | 4 +++ man/Slope.Rd | 4 +++ man/Slope3d.Rd | 8 +++++-- man/molaR_Batch.Rd | 13 ++++++------ man/molaR_Clean.Rd | 3 ++ man/patches_per.Rd | 3 +- 29 files changed, 137 insertions(+), 57 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.5-2 dated 2018-07-09 and 1.5-3 dated 2018-09-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/ci.p.r | 19 ++++++++++++------- inst/doc/ranef.cov.pdf |binary inst/doc/simpson.pdf |binary man/ci.p.rd | 34 +++++++++++++++++++++++----------- man/heart.rd | 2 +- man/refinery.rd | 3 --- 8 files changed, 47 insertions(+), 33 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>
Diff between psychmeta versions 2.1.9 dated 2018-08-23 and 2.2.0 dated 2018-09-18
DESCRIPTION | 8 MD5 | 66 +-- NAMESPACE | 2 NEWS | 28 + R/control_intercor.R | 35 + R/create_ad.R | 6 R/create_ad_list.R | 52 ++ R/estimate_mixture.R | 11 R/filters.R | 28 - R/impute_artifacts_wrapper.R | 8 R/itemize_scales.R | 1 R/ma_d.R | 17 R/ma_generic.R | 16 R/ma_r.R | 213 ++++++++++ R/ma_r_ad.R | 28 + R/methods_print.R | 9 R/methods_summary.R | 8 R/output.R | 835 +++++++++++++++++++++---------------------- R/remove_dependency.R | 6 R/simulate_r.R | 7 R/wrangle_ads.R | 13 R/wrangle_data.R | 147 +++++-- R/zzz.R | 4 inst/CITATION | 8 man/control_intercor.Rd | 11 man/create_ad_tibble.Rd | 48 +- man/ma_d.Rd | 10 man/ma_r.Rd | 32 - man/metabulate.Rd | 5 man/metabulate_rmd_helper.Rd | 2 man/mix_dist.Rd | 6 man/organize_database.Rd | 9 man/screen_ad_int.Rd | 4 man/screen_ad_tsa.Rd | 4 34 files changed, 1073 insertions(+), 614 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear models
(see, e.g., Piironen and Vehtari, 2017, <doi:10.1007/s11222-016-9649-y>).
The package is compatible with 'rstanarm' package, but other reference models
can also be used. See the package vignette for more information and examples.
Author: Juho Piironen [cre, aut],
Markus Paasiniemi [aut],
Aki Vehtari [aut],
Jonah Gabry [ctb]
Maintainer: Juho Piironen <juho.piironen@aalto.fi>
Diff between projpred versions 0.8.0 dated 2018-04-16 and 1.0.0 dated 2018-09-18
projpred-0.8.0/projpred/man/cvind.Rd |only projpred-0.8.0/projpred/vignettes/quickstart_cache |only projpred-1.0.0/projpred/DESCRIPTION | 30 projpred-1.0.0/projpred/MD5 | 106 +- projpred-1.0.0/projpred/NAMESPACE | 9 projpred-1.0.0/projpred/NEWS.md |only projpred-1.0.0/projpred/R/RcppExports.R | 8 projpred-1.0.0/projpred/R/cv_varsel.R | 358 +++--- projpred-1.0.0/projpred/R/glmfun.R | 223 ++-- projpred-1.0.0/projpred/R/kl_helpers.R | 85 - projpred-1.0.0/projpred/R/methods.R | 440 +++----- projpred-1.0.0/projpred/R/misc.R | 221 +--- projpred-1.0.0/projpred/R/project.R | 95 + projpred-1.0.0/projpred/R/projfun.R | 105 +- projpred-1.0.0/projpred/R/projpred-package.R | 9 projpred-1.0.0/projpred/R/refmodel.R |only projpred-1.0.0/projpred/R/search.R | 61 - projpred-1.0.0/projpred/R/summary_funs.R | 386 +++---- projpred-1.0.0/projpred/R/varsel.R | 216 ++-- projpred-1.0.0/projpred/inst/doc/quickstart.R | 104 + projpred-1.0.0/projpred/inst/doc/quickstart.Rmd | 159 ++- projpred-1.0.0/projpred/inst/doc/quickstart.html | 626 ++++++++---- projpred-1.0.0/projpred/man/cv-indices.Rd |only projpred-1.0.0/projpred/man/cv_varsel.Rd | 43 projpred-1.0.0/projpred/man/get-refmodel.Rd |only projpred-1.0.0/projpred/man/init_refmodel.Rd | 96 + projpred-1.0.0/projpred/man/predict.refmodel.Rd |only projpred-1.0.0/projpred/man/proj-pred.Rd | 30 projpred-1.0.0/projpred/man/project.Rd | 36 projpred-1.0.0/projpred/man/projpred.Rd | 7 projpred-1.0.0/projpred/man/suggest_size.Rd | 44 projpred-1.0.0/projpred/man/varsel-statistics.Rd | 27 projpred-1.0.0/projpred/man/varsel.Rd | 48 projpred-1.0.0/projpred/src/RcppExports.cpp | 18 projpred-1.0.0/projpred/src/glmfun.cpp | 101 + projpred-1.0.0/projpred/tests/testthat.R | 1 projpred-1.0.0/projpred/tests/testthat/test_as_matrix.R | 9 projpred-1.0.0/projpred/tests/testthat/test_datafit.R |only projpred-1.0.0/projpred/tests/testthat/test_glm_elnet.R | 329 ++---- projpred-1.0.0/projpred/tests/testthat/test_glm_ridge.R | 10 projpred-1.0.0/projpred/tests/testthat/test_init_refmodel.R | 177 --- projpred-1.0.0/projpred/tests/testthat/test_misc.R | 5 projpred-1.0.0/projpred/tests/testthat/test_proj_pred.R | 6 projpred-1.0.0/projpred/tests/testthat/test_project.R | 71 - projpred-1.0.0/projpred/tests/testthat/test_varsel.R | 251 ++-- projpred-1.0.0/projpred/vignettes/quickstart.Rmd | 159 ++- projpred-1.0.0/projpred/vignettes/quickstart_files |only 47 files changed, 2706 insertions(+), 2003 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. MacOS users can download the most up-to-date
package binaries from <http://openmx.ssri.psu.edu>.
See Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
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],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.10.0 dated 2018-08-03 and 2.11.3 dated 2018-09-18
OpenMx-2.10.0/OpenMx/man/mxComputeBenchmark.Rd |only OpenMx-2.11.3/OpenMx/DESCRIPTION | 30 OpenMx-2.11.3/OpenMx/MD5 | 1241 +++++----- OpenMx-2.11.3/OpenMx/NAMESPACE | 5 OpenMx-2.11.3/OpenMx/NEWS | 28 OpenMx-2.11.3/OpenMx/R/0ClassUnion.R | 2 OpenMx-2.11.3/OpenMx/R/DefinitionVars.R | 2 OpenMx-2.11.3/OpenMx/R/DiagMatrix.R | 2 OpenMx-2.11.3/OpenMx/R/FullMatrix.R | 2 OpenMx-2.11.3/OpenMx/R/IdenMatrix.R | 2 OpenMx-2.11.3/OpenMx/R/LowerMatrix.R | 2 OpenMx-2.11.3/OpenMx/R/MxAlgebra.R | 2 OpenMx-2.11.3/OpenMx/R/MxAlgebraConvert.R | 2 OpenMx-2.11.3/OpenMx/R/MxAlgebraFunctions.R | 37 OpenMx-2.11.3/OpenMx/R/MxAlgebraObjective.R | 2 OpenMx-2.11.3/OpenMx/R/MxAlgebraTransform.R | 2 OpenMx-2.11.3/OpenMx/R/MxApply.R | 2 OpenMx-2.11.3/OpenMx/R/MxAutoStart.R | 30 OpenMx-2.11.3/OpenMx/R/MxBaseNamed.R | 2 OpenMx-2.11.3/OpenMx/R/MxBounds.R | 2 OpenMx-2.11.3/OpenMx/R/MxCommunication.R | 2 OpenMx-2.11.3/OpenMx/R/MxCompare.R | 97 OpenMx-2.11.3/OpenMx/R/MxCompute.R | 352 ++ OpenMx-2.11.3/OpenMx/R/MxConstraint.R | 2 OpenMx-2.11.3/OpenMx/R/MxCycleDetection.R | 2 OpenMx-2.11.3/OpenMx/R/MxData.R | 13 OpenMx-2.11.3/OpenMx/R/MxDataWLS.R | 5 OpenMx-2.11.3/OpenMx/R/MxDeparse.R | 2 OpenMx-2.11.3/OpenMx/R/MxDependencies.R | 2 OpenMx-2.11.3/OpenMx/R/MxDetectCores.R | 2 OpenMx-2.11.3/OpenMx/R/MxDiff.R | 2 OpenMx-2.11.3/OpenMx/R/MxErrorHandling.R | 2 OpenMx-2.11.3/OpenMx/R/MxEval.R | 4 OpenMx-2.11.3/OpenMx/R/MxExpectation.R | 26 OpenMx-2.11.3/OpenMx/R/MxExpectationBA81.R | 2 OpenMx-2.11.3/OpenMx/R/MxExpectationGREML.R | 2 OpenMx-2.11.3/OpenMx/R/MxExpectationHiddenMarkov.R | 2 OpenMx-2.11.3/OpenMx/R/MxExpectationLISREL.R | 6 OpenMx-2.11.3/OpenMx/R/MxExpectationMixture.R | 25 OpenMx-2.11.3/OpenMx/R/MxExpectationNormal.R | 137 - OpenMx-2.11.3/OpenMx/R/MxExpectationRAM.R | 6 OpenMx-2.11.3/OpenMx/R/MxExpectationStateSpace.R | 40 OpenMx-2.11.3/OpenMx/R/MxFIMLObjective.R | 2 OpenMx-2.11.3/OpenMx/R/MxFactorScores.R | 2 OpenMx-2.11.3/OpenMx/R/MxFitFunction.R | 2 OpenMx-2.11.3/OpenMx/R/MxFitFunctionAlgebra.R | 2 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OpenMx-2.11.3/OpenMx/inst/models/passing/IntroSEM-UnivariateRaw.R | 19 OpenMx-2.11.3/OpenMx/inst/models/passing/IntroSEM-UnivariateStd.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/InvalidCovarianceMLObjective.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/JointFIMLRegressionTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/JointFIMLTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LAD--CheckCode6.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LCAlazarsfeld-rewrite.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LCAlazarsfeld.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LGC_MatrixCov.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LGC_PathCov.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LISRELExoEndoOnly.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LISRELFactorRegressionWithMeansFIMLOrder_MatrixRaw.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LISRELFactorRegressionWithMeans_Matrix.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LISRELFactorRegressionWithMeans_MatrixRaw.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LISRELFactorRegression_Matrix.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/LisrelTypeCheck.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MLErrorConditions.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MatrixCreation.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MatrixErrorDetection.R | 7 OpenMx-2.11.3/OpenMx/inst/models/passing/ModelIndexErrorChecking.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/ModelRemovePaths.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/ModelTransformTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MultiRegStdTestSE.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MultilevelUniRandomSlopeInt.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MultipleGroupML.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MultipleGroupRAM.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MultipleGroupRAMconstraint.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/MultipleGroupWLS.R | 2 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OpenMx-2.11.3/OpenMx/inst/models/passing/OneFactorModel_PathCovReverse.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/OrdinalPathTest.R | 6 OpenMx-2.11.3/OpenMx/inst/models/passing/OrdinalTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/OrdinalTestAlgebra.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/PearsonSelection.R |only OpenMx-2.11.3/OpenMx/inst/models/passing/RAM-FIML-defvars.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/RAMInverseTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/RAMObjectiveErrors.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/RemoveEntriesTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/RenameAndSummary.R | 12 OpenMx-2.11.3/OpenMx/inst/models/passing/SanityTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SaturatedWLSTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/Simple--CheckCode6.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SimpleAlgebraCIs.R | 5 OpenMx-2.11.3/OpenMx/inst/models/passing/SimpleConfidenceIntervals.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SimpleConstraint.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SimpleCovariance.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SimpleMLAlgebraCIs.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SimpleRObjective.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/StandardErrorsSimple.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/StateSpaceAlg.R | 14 OpenMx-2.11.3/OpenMx/inst/models/passing/StateSpaceErrorCheck.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/StateSpaceInputs.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/StateSpaceMissingData.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/StateSpaceOsc.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SubStateSpaceOsc.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/Substitutions.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SummaryCheck.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/SummaryFitStatistics.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/TestRowObjective.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/TestRowObjectiveExistenceVector.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/TestUseOptimizer.R | 5 OpenMx-2.11.3/OpenMx/inst/models/passing/Tiny_GREML_model_for_full_debug_logging.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/TwinAnalysisLikelihoodVector.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/TwinAnalysis_Multivariate_Matrix_Raw.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/UnivHetModTwinAnalysis_MatrixRawOrdNIQmfFv3.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/UnivariateRandomInterceptWide.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/UselessConstraint.R | 12 OpenMx-2.11.3/OpenMx/inst/models/passing/WarmStartTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/ZeroWeightSkip.R | 4 OpenMx-2.11.3/OpenMx/inst/models/passing/automaticStarts.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/bivCorM.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/bivLognormDemo.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/checkStandardizedLoadingsEtcetera.R | 72 OpenMx-2.11.3/OpenMx/inst/models/passing/check_models_can_be_rerun.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/cycle.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/defvaralgebra.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/derivFilter.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/dmvnorm.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/jointFactorWls.R | 12 OpenMx-2.11.3/OpenMx/inst/models/passing/loadData.R |only OpenMx-2.11.3/OpenMx/inst/models/passing/loadMatrix.R |only OpenMx-2.11.3/OpenMx/inst/models/passing/mxLog.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/mxSE_test.R | 6 OpenMx-2.11.3/OpenMx/inst/models/passing/mxSave.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/mxVersion.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/mxmanual31-a.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/mxmanual61-a.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/mxmanual61-b.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/nonlinearDefinitionTest.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/omxMnor.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/oneLocusLikelihood.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/rfitfunc.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/rowAlgTest140708.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/simplestCI.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/startingValues.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/startingValues2.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/stdizedRAMpaths--UserProvidedCov.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/testAllint.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/testNumericDerivWithConstraintWarning.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/test_mxBootstrapStdizeRAMpaths.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/test_thresh_kept_in_order.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/twoLocusLikelihood.R | 2 OpenMx-2.11.3/OpenMx/inst/models/passing/univACEP.R | 2 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OpenMx-2.11.3/OpenMx/man/mxRObjective.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxRename.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxRestore.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxRowObjective.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxRun.Rd | 41 OpenMx-2.11.3/OpenMx/man/mxSE.Rd | 24 OpenMx-2.11.3/OpenMx/man/mxSave.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxStandardizeRAMpaths.Rd | 18 OpenMx-2.11.3/OpenMx/man/mxThreshold.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxTryHard.Rd | 12 OpenMx-2.11.3/OpenMx/man/mxTypes.Rd | 2 OpenMx-2.11.3/OpenMx/man/mxVersion.Rd | 2 OpenMx-2.11.3/OpenMx/man/myFADataRaw.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxAllInt.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxApply.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxAssignFirstParameters.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxBrownie.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxCheckEquals.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxCheckIdentical.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxCheckSetEquals.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxCheckTrue.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxCheckWithinPercentError.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxGetParameters.Rd | 30 OpenMx-2.11.3/OpenMx/man/omxGraphviz.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxLapply.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxLocateParameters.Rd | 24 OpenMx-2.11.3/OpenMx/man/omxLogical.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxMatrixOperations.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxMnor.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxModelDeleteData.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxParallelCI.Rd | 44 OpenMx-2.11.3/OpenMx/man/omxRMSEA.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxSapply.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxSaturatedModel.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxSelectRowsAndCols.Rd | 2 OpenMx-2.11.3/OpenMx/man/omxSetParameters.Rd | 2 OpenMx-2.11.3/OpenMx/man/rvectorize.Rd | 2 OpenMx-2.11.3/OpenMx/man/summary.MxModel.Rd | 2 OpenMx-2.11.3/OpenMx/man/tr.Rd | 2 OpenMx-2.11.3/OpenMx/man/twinData.Rd | 2 OpenMx-2.11.3/OpenMx/man/vec2diag.Rd | 2 OpenMx-2.11.3/OpenMx/man/vech.Rd | 2 OpenMx-2.11.3/OpenMx/man/vech2full.Rd | 2 OpenMx-2.11.3/OpenMx/man/vechs.Rd | 2 OpenMx-2.11.3/OpenMx/man/vechs2full.Rd | 2 OpenMx-2.11.3/OpenMx/src/AlgebraFunctions.h | 175 + OpenMx-2.11.3/OpenMx/src/Compute.cpp | 695 +++++ OpenMx-2.11.3/OpenMx/src/Compute.h | 11 OpenMx-2.11.3/OpenMx/src/ComputeGD.cpp | 628 ++++- OpenMx-2.11.3/OpenMx/src/ComputeGD.h | 6 OpenMx-2.11.3/OpenMx/src/ComputeNM.cpp | 28 OpenMx-2.11.3/OpenMx/src/ComputeNM.h | 2 OpenMx-2.11.3/OpenMx/src/ComputeNR.cpp | 9 OpenMx-2.11.3/OpenMx/src/ComputeSD.cpp | 2 OpenMx-2.11.3/OpenMx/src/Connectedness.h | 2 OpenMx-2.11.3/OpenMx/src/EnableWarnings.h | 5 OpenMx-2.11.3/OpenMx/src/FellnerFitFunction.cpp | 2 OpenMx-2.11.3/OpenMx/src/Makevars.in | 2 OpenMx-2.11.3/OpenMx/src/Makevars.win | 5 OpenMx-2.11.3/OpenMx/src/MarkovExpectation.cpp | 16 OpenMx-2.11.3/OpenMx/src/MarkovFF.cpp | 2 OpenMx-2.11.3/OpenMx/src/asa.c |only OpenMx-2.11.3/OpenMx/src/asa.h |only OpenMx-2.11.3/OpenMx/src/asa_usr_asa.h |only OpenMx-2.11.3/OpenMx/src/ba81quad.cpp | 2 OpenMx-2.11.3/OpenMx/src/finiteDifferences.h | 27 OpenMx-2.11.3/OpenMx/src/glue.cpp | 14 OpenMx-2.11.3/OpenMx/src/glue.h | 2 OpenMx-2.11.3/OpenMx/src/jsoncons |only OpenMx-2.11.3/OpenMx/src/jsoncons_ext |only OpenMx-2.11.3/OpenMx/src/minicsv.h |only OpenMx-2.11.3/OpenMx/src/nloptcpp.cpp | 30 OpenMx-2.11.3/OpenMx/src/omxAlgebra.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxAlgebra.h | 2 OpenMx-2.11.3/OpenMx/src/omxAlgebraFitFunction.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxCsolnp.h | 2 OpenMx-2.11.3/OpenMx/src/omxData.cpp | 247 + OpenMx-2.11.3/OpenMx/src/omxData.h | 11 OpenMx-2.11.3/OpenMx/src/omxDefines.h | 4 OpenMx-2.11.3/OpenMx/src/omxExpectation.cpp | 82 OpenMx-2.11.3/OpenMx/src/omxExpectation.h | 7 OpenMx-2.11.3/OpenMx/src/omxExportBackendState.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxFIMLFitFunction.cpp | 50 OpenMx-2.11.3/OpenMx/src/omxFIMLFitFunction.h | 12 OpenMx-2.11.3/OpenMx/src/omxFitFunction.cpp | 3 OpenMx-2.11.3/OpenMx/src/omxFitFunction.h | 3 OpenMx-2.11.3/OpenMx/src/omxFitFunctionBA81.cpp | 5 OpenMx-2.11.3/OpenMx/src/omxGREMLExpectation.cpp | 19 OpenMx-2.11.3/OpenMx/src/omxGREMLExpectation.h | 2 OpenMx-2.11.3/OpenMx/src/omxGREMLfitfunction.cpp | 76 OpenMx-2.11.3/OpenMx/src/omxHessianCalculation.cpp | 6 OpenMx-2.11.3/OpenMx/src/omxImportFrontendState.cpp | 5 OpenMx-2.11.3/OpenMx/src/omxLISRELExpectation.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxLISRELExpectation.h | 2 OpenMx-2.11.3/OpenMx/src/omxMLFitFunction.cpp | 20 OpenMx-2.11.3/OpenMx/src/omxMatrix.cpp | 79 OpenMx-2.11.3/OpenMx/src/omxMatrix.h | 14 OpenMx-2.11.3/OpenMx/src/omxNPSOLSpecific.cpp | 4 OpenMx-2.11.3/OpenMx/src/omxNPSOLSpecific.h | 2 OpenMx-2.11.3/OpenMx/src/omxNormalExpectation.cpp | 7 OpenMx-2.11.3/OpenMx/src/omxRAMExpectation.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxRFitFunction.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxRFitFunction.h | 2 OpenMx-2.11.3/OpenMx/src/omxRowFitFunction.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxRowFitFunction.h | 2 OpenMx-2.11.3/OpenMx/src/omxSadmvnWrapper.h | 2 OpenMx-2.11.3/OpenMx/src/omxState.cpp | 24 OpenMx-2.11.3/OpenMx/src/omxState.h | 8 OpenMx-2.11.3/OpenMx/src/omxStateSpaceExpectation.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxSymbolTable.cpp | 2 OpenMx-2.11.3/OpenMx/src/omxSymbolTable.h | 2 OpenMx-2.11.3/OpenMx/src/omxWLSFitFunction.cpp | 2 OpenMx-2.11.3/OpenMx/src/sadmvn.f | 1 OpenMx-2.11.3/OpenMx/src/slsqp.c | 2 OpenMx-2.11.3/OpenMx/src/ssMLFit.cpp | 20 OpenMx-2.11.3/OpenMx/src/subnp.cpp | 17 613 files changed, 5258 insertions(+), 2305 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding in Observational
Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding for either an observational study or a meta-analysis of observational studies. For a single observational study, the package reports E-values, defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would need to have with both the treatment and the outcome to fully explain away a specific treatment-outcome association, conditional on the measured covariates. You can use one of the evalues.XX() functions to compute E-values for the relevant outcome types. Outcome types include risk ratios, odds ratio with common or rare outcomes, hazard ratios with common or rare outcomes, and standardized differences in outcomes. Optionally, you can use the bias_plot() function to plot the bias factor as a function of two sensitivity parameters. (See VanderWeele & Ding, 2017 [<http://annals.org/aim/article/2643434>] for details.) For a meta-analysis, use the function confounded_meta to compute point estimates and inference for: (1) the proportion of studies with true causal effect sizes more extreme than a specified threshold of scientific importance; and (2) the minimum bias factor and confounding strength required to reduce to less than a specified threshold the proportion of studies with true effect sizes of scientifically significant size. The functions sens_plot() and sens_table() create plots and tables for visualizing these meta-analysis metrics across a range of bias values, and scrape_meta helps scrape study-level data from a published forest plot or summary table to obtain the needed estimates when these are not reported. (See Mathur & VanderWeele [<https://osf.io/jkhfg/>] for details.) Most of the analyses available in this package can also be conducted using web-based graphical interfaces (for a single observational study: [<https://evalue.hmdc.harvard.edu/app/>]; for a meta-analysis: [<https://mmathur.shinyapps.io/meta_gui_2/>]).
Author: Maya B. Mathur, Peng Ding, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between EValue versions 1.1.4 dated 2018-05-18 and 1.1.5 dated 2018-09-18
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative signal is expected to be
localized, a series of filters determine which peak signals are characterized by
an implausible spatial distribution. The filters reduce the dataset dimensionality
and increase its information vs noise ratio, improving the quality of the
unsupervised analysis results, reducing data dimensionality and simplifying
the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>
Diff between SPUTNIK versions 1.0.3.3 dated 2018-08-22 and 1.0.3.4 dated 2018-09-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/graph_funcs.R | 45 +++++++++++++++++++++++++++++++++++++++------ 3 files changed, 44 insertions(+), 11 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows various cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features enhancing the graphic presentation of maps like cartographic palettes, layout elements (scale, north arrow, title...), labels, legends or access to some cartographic APIs. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut],
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.1.1 dated 2018-06-25 and 2.1.2 dated 2018-09-18
DESCRIPTION | 8 +- MD5 | 64 ++++++++++--------- NEWS | 18 +++++ R/Package.R | 16 ++-- R/getGridLayer.R | 4 - R/getPencilLayer.R | 8 +- README.md | 23 +------ build/vignette.rds |binary inst/doc/cartography.R | 4 - inst/doc/cartography.Rmd | 8 +- inst/doc/cartography.html | 138 +++++++++++++++++++++---------------------- inst/doc/cheatsheet.Rmd |only inst/doc/cheatsheet.html |only man/cartography.Rd | 18 ++--- man/choroLayer.Rd | 13 ++-- man/discLayer.Rd | 4 - man/dotDensityLayer.Rd | 9 +- man/getBreaks.Rd | 3 man/gradLinkLayer.Rd | 13 ++-- man/gradLinkTypoLayer.Rd | 13 ++-- man/labelLayer.Rd | 6 - man/layoutLayer.Rd | 7 +- man/legendCirclesSymbols.Rd | 8 +- man/legendPropLines.Rd | 4 - man/legendSquaresSymbols.Rd | 8 +- man/legendTypo.Rd | 6 - man/propLinkLayer.Rd | 6 - man/propSymbolsChoroLayer.Rd | 19 +++-- man/propSymbolsLayer.Rd | 6 - man/propSymbolsTypoLayer.Rd | 17 ++--- man/propTrianglesLayer.Rd | 5 - man/smoothLayer.Rd | 11 +-- vignettes/cartography.Rmd | 8 +- vignettes/cheatsheet |only vignettes/cheatsheet.Rmd |only 35 files changed, 246 insertions(+), 229 deletions(-)
Title: Functions from "Reinsurance: Actuarial and Statistical Aspects"
Description: Functions from the book "Reinsurance: Actuarial and Statistical Aspects" (2017) by Hansjoerg Albrecher, Jan Beirlant and Jef Teugels <http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470772689.html>.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Roel Verbelen [aut] (R code for Mixed Erlang distribution,
<https://orcid.org/0000-0002-2347-9240>),
Anastasios Bardoutsos [ctb] (Original R code for cEPD estimator),
Dries Cornilly [ctb] (Original R code for EVT estimators for truncated
data),
Yuri Goegebeur [ctb] (Original S-Plus code for basic EVT estimators),
Klaus Herrmann [ctb] (Original R code for GPD estimator)
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between ReIns versions 1.0.7 dated 2018-04-24 and 1.0.8 dated 2018-09-18
DESCRIPTION | 8 MD5 | 14 build/vignette.rds |binary inst/NEWS.Rd | 15 + inst/doc/ReIns.html | 742 +++++++++++++++++++++++++++++++++------------------- man/soa.Rd | 2 src/Makevars | 3 src/SpliceEM_aux.h | 1 8 files changed, 507 insertions(+), 278 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.2-2 dated 2018-06-22 and 0.2-3 dated 2018-09-18
DESCRIPTION | 14 +++++++------- MD5 | 43 ++++++++++++++++++++++--------------------- NAMESPACE | 4 +++- R/internal.R | 5 +++-- R/methods.R | 3 +++ R/models.R | 33 +++++++++++++++++++++++++++++---- R/tram.R | 5 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 14 ++++++++++++++ inst/doc/tram.R | 20 ++++++++++++++++---- inst/doc/tram.Rnw | 29 ++++++++++++++++++++++++----- inst/doc/tram.pdf |binary man/BoxCox.Rd | 5 +++++ man/Colr.Rd | 8 ++++++++ man/Coxph.Rd | 3 +++ man/Lehmann.Rd |only man/Lm.Rd | 4 ++++ man/Polr.Rd | 10 +++++++++- man/Survreg.Rd | 7 +++++++ man/tram.Rd | 9 ++++++++- tests/Coxph-Ex.Rout.save | 14 +++----------- vignettes/tram.Rnw | 29 ++++++++++++++++++++++++----- 23 files changed, 195 insertions(+), 64 deletions(-)
Title: Toolkit for Corpus Analysis
Description: Library for corpus analysis using the Corpus Workbench as an
efficient back end for indexing and querying large corpora. The package offers
functionality to flexibly create partitions and to carry out basic statistical
operations (count, co-occurrences etc.). The original full text of documents
can be reconstructed and inspected at any time. Beyond that, the package is
intended to serve as an interface to packages implementing advanced statistical
procedures. Respective data structures (document term matrices, term co-
occurrence matrices etc.) can be created based on the indexed corpora.
Author: Andreas Blaette [aut, cre] (<https://orcid.org/0000-0001-8970-8010>)
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between polmineR versions 0.7.9 dated 2018-07-09 and 0.7.10 dated 2018-09-18
polmineR-0.7.10/polmineR/DESCRIPTION | 18 polmineR-0.7.10/polmineR/MD5 | 179 polmineR-0.7.10/polmineR/NAMESPACE | 9 polmineR-0.7.10/polmineR/NEWS.md | 232 polmineR-0.7.10/polmineR/R/S4classes.R | 258 polmineR-0.7.10/polmineR/R/TermDocumentMatrix.R | 10 polmineR-0.7.10/polmineR/R/as.VCorpus.R | 2 polmineR-0.7.10/polmineR/R/as.markdown.R | 4 polmineR-0.7.10/polmineR/R/browse.R | 2 polmineR-0.7.10/polmineR/R/bundle.R | 10 polmineR-0.7.10/polmineR/R/chisquare.R | 1 polmineR-0.7.10/polmineR/R/context.R | 214 polmineR-0.7.10/polmineR/R/cooccurrences.R | 59 polmineR-0.7.10/polmineR/R/corpus.R | 30 polmineR-0.7.10/polmineR/R/count.R | 15 polmineR-0.7.10/polmineR/R/cqpserver.R | 4 polmineR-0.7.10/polmineR/R/decode.R | 2 polmineR-0.7.10/polmineR/R/enrich.R | 19 polmineR-0.7.10/polmineR/R/features.R | 39 polmineR-0.7.10/polmineR/R/highlight.R | 60 polmineR-0.7.10/polmineR/R/hits.R | 26 polmineR-0.7.10/polmineR/R/html.R | 26 polmineR-0.7.10/polmineR/R/kwic.R | 234 polmineR-0.7.10/polmineR/R/ll.R | 14 polmineR-0.7.10/polmineR/R/mail.R | 138 polmineR-0.7.10/polmineR/R/ngrams.R | 1 polmineR-0.7.10/polmineR/R/partition.R | 173 polmineR-0.7.10/polmineR/R/partition_bundle.R | 94 polmineR-0.7.10/polmineR/R/polmineR.R | 24 polmineR-0.7.10/polmineR/R/read.R | 21 polmineR-0.7.10/polmineR/R/regions.R | 48 polmineR-0.7.10/polmineR/R/registry.R | 8 polmineR-0.7.10/polmineR/R/s_attributes.R | 12 polmineR-0.7.10/polmineR/R/size.R | 2 polmineR-0.7.10/polmineR/R/store.R |only polmineR-0.7.10/polmineR/R/tempcorpus.R | 2 polmineR-0.7.10/polmineR/R/textstat.R | 48 polmineR-0.7.10/polmineR/R/tooltips.R | 72 polmineR-0.7.10/polmineR/R/trim.R | 2 polmineR-0.7.10/polmineR/R/use.R | 102 polmineR-0.7.10/polmineR/R/utils.R | 31 polmineR-0.7.10/polmineR/R/view.R | 2 polmineR-0.7.10/polmineR/R/weigh.R | 78 polmineR-0.7.10/polmineR/R/zzz.R | 14 polmineR-0.7.10/polmineR/README.md | 20 polmineR-0.7.10/polmineR/inst/doc/vignette.R | 40 polmineR-0.7.10/polmineR/inst/doc/vignette.Rmd | 90 polmineR-0.7.10/polmineR/inst/doc/vignette.html | 2742 +++++++++- polmineR-0.7.10/polmineR/inst/extdata/cwb/registry/germaparlmini | 4 polmineR-0.7.10/polmineR/inst/extdata/cwb/registry/reuters | 4 polmineR-0.7.10/polmineR/inst/shiny/modules/count.R | 2 polmineR-0.7.10/polmineR/inst/sticker |only polmineR-0.7.10/polmineR/man/as.DocumentTermMatrix.Rd | 3 polmineR-0.7.10/polmineR/man/as.VCorpus.Rd | 3 polmineR-0.7.10/polmineR/man/bundle.Rd | 7 polmineR-0.7.10/polmineR/man/chisquare-method.Rd | 1 polmineR-0.7.10/polmineR/man/context-class.Rd | 47 polmineR-0.7.10/polmineR/man/context-method.Rd | 37 polmineR-0.7.10/polmineR/man/cooccurrences-class.Rd | 5 polmineR-0.7.10/polmineR/man/cooccurrences.Rd | 12 polmineR-0.7.10/polmineR/man/corpus-method.Rd | 31 polmineR-0.7.10/polmineR/man/features.Rd | 10 polmineR-0.7.10/polmineR/man/highlight.Rd | 51 polmineR-0.7.10/polmineR/man/hits.Rd | 28 polmineR-0.7.10/polmineR/man/hits_class.Rd |only polmineR-0.7.10/polmineR/man/html-method.Rd | 12 polmineR-0.7.10/polmineR/man/kwic-class.Rd | 89 polmineR-0.7.10/polmineR/man/kwic.Rd | 98 polmineR-0.7.10/polmineR/man/mail-method.Rd | 43 polmineR-0.7.10/polmineR/man/ngrams.Rd | 7 polmineR-0.7.10/polmineR/man/ngrams_class.Rd |only polmineR-0.7.10/polmineR/man/partition.Rd | 83 polmineR-0.7.10/polmineR/man/partition_bundle-class.Rd | 13 polmineR-0.7.10/polmineR/man/partition_bundle-method.Rd | 6 polmineR-0.7.10/polmineR/man/partition_class.Rd | 30 polmineR-0.7.10/polmineR/man/polmineR.Rd |only polmineR-0.7.10/polmineR/man/read-method.Rd | 3 polmineR-0.7.10/polmineR/man/regions_class.Rd | 7 polmineR-0.7.10/polmineR/man/registry.Rd | 32 polmineR-0.7.10/polmineR/man/registry_reset.Rd |only polmineR-0.7.10/polmineR/man/s_attributes-method.Rd | 12 polmineR-0.7.10/polmineR/man/size-method.Rd | 3 polmineR-0.7.10/polmineR/man/store.Rd |only polmineR-0.7.10/polmineR/man/tempcorpus.Rd | 22 polmineR-0.7.10/polmineR/man/tempcorpus_class.Rd |only polmineR-0.7.10/polmineR/man/textstat-class.Rd | 112 polmineR-0.7.10/polmineR/man/tooltips.Rd | 31 polmineR-0.7.10/polmineR/man/use.Rd | 50 polmineR-0.7.10/polmineR/man/weigh-method.Rd | 70 polmineR-0.7.10/polmineR/vignettes/vignette.Rmd | 90 polmineR-0.7.9/polmineR/configure.win |only polmineR-0.7.9/polmineR/man/TermDocumentMatrix.Rd |only polmineR-0.7.9/polmineR/man/cooccurrences_reshaped.Rd |only polmineR-0.7.9/polmineR/man/cqpserver.Rd |only polmineR-0.7.9/polmineR/man/flatten.Rd |only polmineR-0.7.9/polmineR/man/getSlot.Rd |only polmineR-0.7.9/polmineR/man/polmineR-generics.Rd |only polmineR-0.7.9/polmineR/man/polmineR-package.Rd |only polmineR-0.7.9/polmineR/man/split-partition-method.Rd |only 99 files changed, 4748 insertions(+), 1541 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains some auxiliary functions for multiple
imputation which complements existing functionality
in R.
In addition to some utility functions, main features
include plausible value imputation, multilevel
imputation functions (arbitrary number of levels,
hierarchical and non-hierarchical datasets),
imputation using partial least squares (PLS) for
high dimensional predictors, and nested multiple
imputation.
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 2.13-63 dated 2018-07-05 and 2.14-26 dated 2018-09-18
miceadds-2.13-63/miceadds/R/norm.draw2.R |only miceadds-2.13-63/miceadds/R/norm.draw3.R |only miceadds-2.13-63/miceadds/R/remove.lindep_miceadds.R |only miceadds-2.14-26/miceadds/DESCRIPTION | 9 miceadds-2.14-26/miceadds/MD5 | 104 ++-- miceadds-2.14-26/miceadds/NAMESPACE | 2 miceadds-2.14-26/miceadds/R/RcppExports.R | 2 miceadds-2.14-26/miceadds/R/ma_rmvnorm.R | 9 miceadds-2.14-26/miceadds/R/mice.impute.2l.contextual.norm.R | 44 - miceadds-2.14-26/miceadds/R/mice.impute.2l.contextual.pmm.R | 11 miceadds-2.14-26/miceadds/R/mice.impute.2l.pls2.R | 250 ++++------ miceadds-2.14-26/miceadds/R/mice.impute.bygroup.R | 6 miceadds-2.14-26/miceadds/R/mice.impute.norm3.R | 4 miceadds-2.14-26/miceadds/R/mice.impute.plausible.values.R | 7 miceadds-2.14-26/miceadds/R/mice.impute.pls.R | 54 +- miceadds-2.14-26/miceadds/R/mice.impute.pmm3.R | 11 miceadds-2.14-26/miceadds/R/mice.impute.pmm4.R | 9 miceadds-2.14-26/miceadds/R/mice.impute.pmm5.R | 30 - miceadds-2.14-26/miceadds/R/mice.impute.tricube.pmm.R | 36 - miceadds-2.14-26/miceadds/R/mice.impute.tricube.pmm2.R | 61 +- miceadds-2.14-26/miceadds/R/mice.impute.weighted.pmm.R | 6 miceadds-2.14-26/miceadds/R/mice_imputation_multilevel_include_2l_predictors.R | 44 - miceadds-2.14-26/miceadds/R/mice_imputation_pls_do_impute.R | 23 miceadds-2.14-26/miceadds/R/mice_imputation_pls_estimate_pls_regression.R | 21 miceadds-2.14-26/miceadds/R/mice_imputation_pls_helper.R | 10 miceadds-2.14-26/miceadds/R/mice_imputation_prepare_2l_functions.R | 76 ++- miceadds-2.14-26/miceadds/R/mice_imputation_weighted_norm_draw.R | 3 miceadds-2.14-26/miceadds/R/mice_imputation_weighted_norm_prepare.R | 4 miceadds-2.14-26/miceadds/R/miceadds_call_internal.R |only miceadds-2.14-26/miceadds/R/miceadds_create_contextual_variables.R |only miceadds-2.14-26/miceadds/R/miceadds_norm_draw.R |only miceadds-2.14-26/miceadds/R/ml_mcmc.R | 2 miceadds-2.14-26/miceadds/R/ml_mcmc_proc_data.R | 3 miceadds-2.14-26/miceadds/R/pca.covridge.R | 10 miceadds-2.14-26/miceadds/R/pool.mi.R | 20 miceadds-2.14-26/miceadds/R/predict.kernelfit.pls2.R | 10 miceadds-2.14-26/miceadds/R/sumpreserving.rounding.R | 45 - miceadds-2.14-26/miceadds/R/write.datlist.R | 131 ++--- miceadds-2.14-26/miceadds/R/write_fwf2_format2.R | 3 miceadds-2.14-26/miceadds/inst/NEWS | 22 miceadds-2.14-26/miceadds/inst/include/miceadds_RcppExports.h | 68 ++ miceadds-2.14-26/miceadds/man/lmer_vcov.Rd | 4 miceadds-2.14-26/miceadds/man/mice.impute.2l.contextual.pmm.Rd | 28 - miceadds-2.14-26/miceadds/man/mice.impute.2l.latentgroupmean.ml.Rd | 18 miceadds-2.14-26/miceadds/man/mice.impute.2lonly.function.Rd | 10 miceadds-2.14-26/miceadds/man/mice.impute.bygroup.Rd | 38 + miceadds-2.14-26/miceadds/man/mice.impute.eap.Rd | 4 miceadds-2.14-26/miceadds/man/mice.impute.hotDeck.Rd | 5 miceadds-2.14-26/miceadds/man/mice.impute.ml.lmer.Rd | 11 miceadds-2.14-26/miceadds/man/mice.impute.pls.Rd | 5 miceadds-2.14-26/miceadds/man/mice_inits.Rd | 10 miceadds-2.14-26/miceadds/man/micombine.cor.Rd | 6 miceadds-2.14-26/miceadds/man/ml_mcmc.Rd | 12 miceadds-2.14-26/miceadds/man/visitSequence.determine.Rd | 6 miceadds-2.14-26/miceadds/src/RcppExports.cpp | 138 +++++ miceadds-2.14-26/miceadds/src/miceadds_rcpp_kernelpls_1dim.cpp | 10 56 files changed, 843 insertions(+), 612 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Thomas Nagler [aut, cre],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthias Killiches [ctb],
Harry Joe [ctb],
Thibault Vatter [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between VineCopula versions 2.1.7 dated 2018-08-31 and 2.1.8 dated 2018-09-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/BiCopHfuncDeriv.R | 2 +- R/BiCopHfuncDeriv2.R | 2 +- build/partial.rdb |binary 6 files changed, 18 insertions(+), 10 deletions(-)
Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with
corresponding random forest for conditional transformation models
as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>)
and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between trtf versions 0.3-2 dated 2018-06-23 and 0.3-3 dated 2018-09-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/methods.R | 4 ++-- R/trees_forests.R | 26 +++++++++++++++++--------- inst/NEWS.Rd | 9 +++++++++ man/traforest.Rd | 8 ++++++-- man/trafotree.Rd | 25 ++++++++++++++++++++++++- tests/GBSG2-Ex.Rout.save | 14 +++----------- tests/regtest-traforest.Rout.save | 14 +++----------- tests/regtest-trafotree.Rout.save | 14 +++----------- 10 files changed, 80 insertions(+), 60 deletions(-)
Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of
the server side file system in shiny apps. In case the app is running
locally this gives the user direct access to the file system without the
need to "download" files to a temporary location. Both file and folder
selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut],
Vincent Nijs [aut],
Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between shinyFiles versions 0.7.0 dated 2018-07-05 and 0.7.1 dated 2018-09-18
shinyFiles-0.7.0/shinyFiles/man/dropEmpty.Rd |only shinyFiles-0.7.1/shinyFiles/DESCRIPTION | 13 +- shinyFiles-0.7.1/shinyFiles/MD5 | 38 +++-- shinyFiles-0.7.1/shinyFiles/NAMESPACE | 11 + shinyFiles-0.7.1/shinyFiles/NEWS.md |only shinyFiles-0.7.1/shinyFiles/R/aaa.R | 15 -- shinyFiles-0.7.1/shinyFiles/R/dirchoose.R | 48 ++++--- shinyFiles-0.7.1/shinyFiles/R/filechoose.R | 64 +++++----- shinyFiles-0.7.1/shinyFiles/R/filesave.R | 25 ++- shinyFiles-0.7.1/shinyFiles/README.md | 5 shinyFiles-0.7.1/shinyFiles/inst/example/server.R | 61 ++++++--- shinyFiles-0.7.1/shinyFiles/inst/example/ui.R | 26 ++-- shinyFiles-0.7.1/shinyFiles/inst/www/fileIcons.css | 60 +++++++-- shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons16x16/file_extension_Rmd.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons16x16/file_extension_md.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons16x16/file_extension_r.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons16x16/file_extension_rproj.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons16x16/r-data-formats.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons32x32/file_extension_Rmd.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons32x32/file_extension_md.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons32x32/file_extension_r.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons32x32/file_extension_rproj.png |only shinyFiles-0.7.1/shinyFiles/inst/www/icons/Icons32x32/r-data-formats.png |only shinyFiles-0.7.1/shinyFiles/inst/www/shinyFiles.js | 51 +++++-- shinyFiles-0.7.1/shinyFiles/man/shinyFiles-buttons.Rd | 16 +- shinyFiles-0.7.1/shinyFiles/man/shinyFiles-package.Rd | 8 - 26 files changed, 274 insertions(+), 167 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of subgroup
identification and personalized medicine models under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre],
Aaron Potvien [ctb],
Alexandros Karatzoglou [cph],
Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.1.5 dated 2018-04-11 and 0.2.0 dated 2018-09-18
DESCRIPTION | 16 MD5 | 76 +-- NAMESPACE | 8 R/calculate_treatment_effects.R |only R/check_overlap.R | 15 R/est_subgroup_effects.R | 5 R/fit_losses.R | 239 ++++++--- R/fit_subgroup.R | 518 +++++++++++++++++++- R/plot_compare.R | 57 +- R/plot_subgroup_fitted.R | 39 - R/plot_subgroup_validated.R | 215 ++++---- R/predict_subgroup.R | 4 R/print_subgroup.R | 176 ++++++ R/summarize_subgroups.R | 1 R/summary_subgroup.R | 19 R/validate_subgroup.R | 62 ++ R/weighted_svm.R | 408 +++++++++++++++- README.md | 77 ++- build/vignette.rds |binary inst/doc/usage_of_the_personalized_package.Rmd | 23 inst/doc/usage_of_the_personalized_package.html | 586 ++++++++++++++--------- man/check.overlap.Rd | 4 man/figures/sticker.png |binary man/fit.subgroup.Rd | 331 ++++++++++++- man/plotCompare.Rd | 4 man/predict.Rd | 8 man/print.Rd | 8 man/print.individual_treatment_effects.Rd |only man/summarize.subgroups.Rd | 3 man/summary.Rd | 7 man/treatment.effects.Rd |only man/validate.subgroup.Rd | 58 ++ man/weighted.ksvm.Rd | 5 tests/testthat/test-fitsubgroup.R | 606 ++++++++++++++++++++++-- tests/testthat/test-plotandplotcompare.R | 85 +++ tests/testthat/test-treatmenteffects.R |only tests/testthat/test-validatesubgroup.R | 123 ++++ tests/testthat/test-wksvm.R | 23 vignettes/usage_of_the_personalized_package.Rmd | 23 vignettes/usage_overview-1.png |binary vignettes/vis_val-1.png |binary 41 files changed, 3155 insertions(+), 677 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre],
Julian Müller [ctb]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between netrankr versions 0.2.0 dated 2018-01-08 and 0.2.1 dated 2018-09-18
DESCRIPTION | 10 +- MD5 | 81 +++++++++---------- NEWS.md | 12 ++ R/aggregate.index.R | 2 R/index.builder.R | 22 ++--- R/indirect.relations.R | 131 +++++++++++++++++-------------- R/neighborhood.inclusion.R | 3 R/plot.rank.intervals.R | 12 +- R/positional.dominance.R | 28 ++++-- R/rank.analysis.R | 30 +++---- README.md | 10 +- inst/doc/benchmarks.html | 12 +- inst/doc/centrality_indices.R | 4 inst/doc/centrality_indices.Rmd | 11 +- inst/doc/centrality_indices.html | 11 +- inst/doc/indirect_relations.R | 2 inst/doc/indirect_relations.Rmd | 4 inst/doc/indirect_relations.html | 7 - inst/doc/neighborhood_inclusion.html | 31 +++---- inst/doc/partial_centrality.R | 8 - inst/doc/partial_centrality.Rmd | 13 --- inst/doc/partial_centrality.html | 37 +++----- inst/doc/positional_dominance.Rmd | 2 inst/doc/positional_dominance.html | 14 +-- inst/doc/probabilistic_cent.html | 71 +++++++++------- inst/doc/use_case.R | 10 +- inst/doc/use_case.Rmd | 20 ++-- inst/doc/use_case.html | 26 +++--- man/aggregate_positions.Rd | 2 man/exact_rank_prob.Rd | 4 man/indirect_relations.Rd | 7 + man/plot_rank_intervals.Rd | 4 src/Makevars |only src/Makevars.win | 6 - src/transreduct.cpp | 2 tests/testthat/test_exact_rank_prob.R | 2 tests/testthat/test_indirect_relations.R | 4 vignettes/centrality_indices.Rmd | 11 +- vignettes/indirect_relations.Rmd | 4 vignettes/partial_centrality.Rmd | 13 --- vignettes/positional_dominance.Rmd | 2 vignettes/use_case.Rmd | 20 ++-- 42 files changed, 367 insertions(+), 338 deletions(-)
Title: Wicked-Fast Streaming 'JSON' ('ndjson') Reader
Description: Streaming 'JSON' ('ndjson') has one 'JSON' record per-line and
many modern 'ndjson' files contain large numbers of records. These constructs
may not be columnar in nature, but it is often useful to read in these files
and "flatten" the structure out to enable working with the data in an R
'data.frame'-like context. Functions are provided that make it possible to read
in plain 'ndjson' files or compressed ('gz') 'ndjson' files and either validate
the format of the records or create "flat" 'data.table' structures from them.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>),
Niels Lohmann [aut] (C++ json parser),
Deepak Bandyopadhyay [aut] (C++ gzstream),
Lutz Kettner [aut] (C++ gzstream))
Maintainer: Bob Rudis <bob@rud.is>
Diff between ndjson versions 0.6.0 dated 2018-03-05 and 0.7.0 dated 2018-09-18
DESCRIPTION | 23 MD5 | 8 NEWS.md | 5 src/Makevars | 6 src/json.h | 4070 +++++++++++++++++++++++++++++++++++++++++------------------ 5 files changed, 2924 insertions(+), 1188 deletions(-)
Title: Vocabulary and Corpus Preprocessing for Natural Language
Pipelines
Description: Utilities for preprocessing of text corpora into data structures
suitable for natural language models: integer sequences or matrices,
vocabulary embedding matrices, term-doc, doc-term, term co-occurrence matrices
etc. All functions allow for full or partial hashing of the terms in the
vocabulary.
Author: Vitalie Spinu [aut, cre]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between mlvocab versions 0.0.1 dated 2018-04-13 and 0.1 dated 2018-09-18
mlvocab-0.0.1/mlvocab/src/vocab.cpp |only mlvocab-0.0.1/mlvocab/tests/testthat/test_index.R |only mlvocab-0.1/mlvocab/DESCRIPTION | 17 mlvocab-0.1/mlvocab/MD5 | 55 + mlvocab-0.1/mlvocab/NAMESPACE | 13 mlvocab-0.1/mlvocab/NEWS.md |only mlvocab-0.1/mlvocab/R/RcppExports.R | 40 - mlvocab-0.1/mlvocab/R/embed.R |only mlvocab-0.1/mlvocab/R/package.R | 9 mlvocab-0.1/mlvocab/R/term_indices.R | 90 ++- mlvocab-0.1/mlvocab/R/term_matrices.R | 92 +-- mlvocab-0.1/mlvocab/R/tfidf.R | 43 - mlvocab-0.1/mlvocab/R/vocab.R | 130 +--- mlvocab-0.1/mlvocab/README.md | 6 mlvocab-0.1/mlvocab/man/mlvocab-package.Rd | 7 mlvocab-0.1/mlvocab/man/prune_embeddings.Rd |only mlvocab-0.1/mlvocab/man/term_indices.Rd | 65 +- mlvocab-0.1/mlvocab/man/term_matrices.Rd | 70 +- mlvocab-0.1/mlvocab/man/tfidf.Rd | 4 mlvocab-0.1/mlvocab/man/vocab.Rd | 106 +-- mlvocab-0.1/mlvocab/src/Makevars |only mlvocab-0.1/mlvocab/src/PriSecMatrix.h |only mlvocab-0.1/mlvocab/src/RcppExports.cpp | 104 ++- mlvocab-0.1/mlvocab/src/TripletMatrix.h | 59 - mlvocab-0.1/mlvocab/src/common.h | 105 +++ mlvocab-0.1/mlvocab/src/corpus.h |only mlvocab-0.1/mlvocab/src/mlvocab.cpp |only mlvocab-0.1/mlvocab/src/vocab.h | 477 ++++++++++------ mlvocab-0.1/mlvocab/tests/testthat/test_embeddings.R | 20 mlvocab-0.1/mlvocab/tests/testthat/test_indices.R |only mlvocab-0.1/mlvocab/tests/testthat/test_term_matrices.R | 99 ++- mlvocab-0.1/mlvocab/tests/testthat/test_tfidf.R | 177 +++-- mlvocab-0.1/mlvocab/tests/testthat/test_tokenizer.R |only mlvocab-0.1/mlvocab/tests/testthat/test_vocab.R | 145 ++-- 34 files changed, 1174 insertions(+), 759 deletions(-)
Title: Generalized Autoregressive Score Models
Description: Simulate, estimate and forecast using univariate and multivariate GAS models
as described in Ardia et al. (2016) <https://ssrn.com/abstract=2825380>.
Author: Leopoldo Catania [aut,cre], Kris Boudt [ctb], David Ardia [ctb]
Maintainer: Leopoldo Catania <leopoldo.catania@econ.au.dk>
Diff between GAS versions 0.2.8 dated 2018-08-30 and 0.2.9 dated 2018-09-18
ChangeLog | 3 +++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 18 +++++++++--------- build/partial.rdb |binary src/snorm.cpp | 12 ++++++------ 6 files changed, 26 insertions(+), 23 deletions(-)
Title: Bivariate Probability Distributions
Description: Contains convenience functions for constructing and plotting bivariate probability distributions (probability mass functions, probability density functions and cumulative distribution functions). Currently supports uniform (discrete and continuous), binomial, Poisson, normal, bimodal and kernel distributions.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between bivariate versions 0.1.6 dated 2018-09-11 and 0.2.2 dated 2018-09-18
bivariate-0.1.6/bivariate/R/bivariate.r |only bivariate-0.1.6/bivariate/man/bivariate.Rd |only bivariate-0.2.2/bivariate/DESCRIPTION | 12 bivariate-0.2.2/bivariate/MD5 | 38 +- bivariate-0.2.2/bivariate/NAMESPACE | 37 +- bivariate-0.2.2/bivariate/R/bimodal.r |only bivariate-0.2.2/bivariate/R/binomial.r |only bivariate-0.2.2/bivariate/R/cu.r |only bivariate-0.2.2/bivariate/R/du.r |only bivariate-0.2.2/bivariate/R/generate.r |only bivariate-0.2.2/bivariate/R/kernel.r |only bivariate-0.2.2/bivariate/R/normal.r |only bivariate-0.2.2/bivariate/R/plot3d.r | 54 +-- bivariate-0.2.2/bivariate/R/poisson.r |only bivariate-0.2.2/bivariate/R/returned.functions.r |only bivariate-0.2.2/bivariate/inst/doc/bivariate.R | 211 ++++++++---- bivariate-0.2.2/bivariate/inst/doc/bivariate.Rnw | 341 ++++++++++++++------ bivariate-0.2.2/bivariate/inst/doc/bivariate.pdf |binary bivariate-0.2.2/bivariate/man/bimodal.Rd |only bivariate-0.2.2/bivariate/man/binomial.Rd |only bivariate-0.2.2/bivariate/man/generate.Rd |only bivariate-0.2.2/bivariate/man/kernel.Rd |only bivariate-0.2.2/bivariate/man/methods.Rd | 79 +++- bivariate-0.2.2/bivariate/man/normal.Rd |only bivariate-0.2.2/bivariate/man/plot3d.Rd | 19 - bivariate-0.2.2/bivariate/man/poisson.Rd |only bivariate-0.2.2/bivariate/man/returned.functions.Rd | 37 +- bivariate-0.2.2/bivariate/man/uniform.Rd |only bivariate-0.2.2/bivariate/vignettes/bivariate.Rnw | 341 ++++++++++++++------ 29 files changed, 832 insertions(+), 337 deletions(-)
Title: Circle Packing
Description: Simple algorithms for circle packing.
Author: Michael Bedward [aut, cre],
David Eppstein [aut] (Author of Python code for graph-based circle
packing ported to C++ for this package),
Peter Menzel [aut] (Author of C code for progressive circle packing
ported to C++ for this package)
Maintainer: Michael Bedward <michael.bedward@gmail.com>
Diff between packcircles versions 0.3.2 dated 2018-04-28 and 0.3.3 dated 2018-09-18
DESCRIPTION | 10 MD5 | 20 NEWS.md | 5 build/vignette.rds |binary inst/doc/graph_packing.html | 358 ++++++- inst/doc/intro.html | 516 +++++++---- inst/doc/progressive_packing.html | 1729 ++++++++++++++++++++++++++++++++++---- src/packcircles.cpp | 1 src/pads_circle_pack.cpp | 1 src/pmenzel_circle_pack.cpp | 2 src/select_non_overlapping.cpp | 4 11 files changed, 2250 insertions(+), 396 deletions(-)
Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence and 'd2b'
Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kevin Warne [aut, cph] (d2b sunburst library in htmlwidgets/lib,
https://github.com/d2bjs/d2b),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface),
CJ Yetman [ctb] (R interface, <https://orcid.org/0000-0001-5099-9500>)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 2.0.0 dated 2018-03-12 and 2.1.0 dated 2018-09-18
DESCRIPTION | 19 MD5 | 15 NEWS.md | 8 build |only inst/doc |only inst/htmlwidgets/lib/d2b/d2b.js |12428 ++++++++++++++++++------------------ inst/htmlwidgets/lib/d2b/d2b.min.js | 8 tests/testthat/test-basic.R | 2 vignettes |only 9 files changed, 6256 insertions(+), 6224 deletions(-)
Title: Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized
spatial polygons data frames. Utility scripts use these data sets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Ruby Fore [aut],
Will Leahy [aut],
Helen Miller [aut],
Henry Nguyen [aut],
Robin Winstanley [aut],
Alice Yang [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialUtils versions 0.5.2 dated 2017-12-07 and 0.5.4 dated 2018-09-18
DESCRIPTION | 21 +++++++------ MD5 | 64 +++++++++++++++++++++--------------------- NAMESPACE | 1 R/convertGADM.R | 2 - R/convertUSCensusCBSA.R |only R/getCountry.R | 2 - R/getCountryCode.R | 4 +- R/getCountryName.R | 2 - R/getHUC.R | 2 - R/getHUCName.R | 2 - R/getState.R | 2 - R/getStateCode.R | 5 +-- R/getStateName.R | 2 - R/getTimezone.R | 2 - R/getUSCounty.R | 2 - R/getVariable.R | 2 - README.md | 3 - build/vignette.rds |binary data/SimpleCountries.RData |binary data/SimpleCountriesEEZ.RData |binary data/SimpleTimezones.RData |binary inst/doc/introduction.R | 2 - inst/doc/introduction.Rmd | 22 ++++++-------- inst/doc/introduction.html | 24 ++++++--------- man/codeToState.Rd | 3 + man/convertGADM.Rd | 2 - man/convertUSCensusCBSA.Rd |only man/getCountry.Rd | 4 +- man/getHUCName.Rd | 3 + man/getStateCode.Rd | 6 +-- man/getStateName.Rd | 4 +- man/stateToCode.Rd | 3 + man/summarizeByPolygon.Rd | 4 +- vignettes/introduction.Rmd | 22 ++++++-------- 34 files changed, 106 insertions(+), 111 deletions(-)
More information about MazamaSpatialUtils at CRAN
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Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 0.9.2.0 dated 2018-08-12 and 0.9.4 dated 2018-09-18
jmv-0.9.2.0/jmv/data/bugs.csv |only jmv-0.9.4/jmv/DESCRIPTION | 12 jmv-0.9.4/jmv/MD5 | 44 - jmv-0.9.4/jmv/NAMESPACE | 1 jmv-0.9.4/jmv/R/ancova.b.R | 845 ++++++++++++++------------- jmv-0.9.4/jmv/R/ancova.h.R | 275 ++++---- jmv-0.9.4/jmv/R/anova.h.R | 243 ++++--- jmv-0.9.4/jmv/R/anovaonew.b.R |only jmv-0.9.4/jmv/R/anovaonew.h.R |only jmv-0.9.4/jmv/R/anovarm.b.R | 95 +-- jmv-0.9.4/jmv/R/anovarm.h.R | 59 + jmv-0.9.4/jmv/R/cfa.b.R | 4 jmv-0.9.4/jmv/R/conttablespaired.b.R | 2 jmv-0.9.4/jmv/R/conttablespaired.h.R | 2 jmv-0.9.4/jmv/R/ttestones.b.R | 4 jmv-0.9.4/jmv/R/ttestones.h.R | 2 jmv-0.9.4/jmv/data/bugs.csv.gz |only jmv-0.9.4/jmv/man/ancova.Rd | 51 - jmv-0.9.4/jmv/man/anova.Rd | 51 - jmv-0.9.4/jmv/man/anovaOneW.Rd |only jmv-0.9.4/jmv/man/anovaRM.Rd | 24 jmv-0.9.4/jmv/man/contTablesPaired.Rd | 2 jmv-0.9.4/jmv/man/ttestOneS.Rd | 2 jmv-0.9.4/jmv/tests/testthat/testancova.R | 8 jmv-0.9.4/jmv/tests/testthat/testanova.R | 8 jmv-0.9.4/jmv/tests/testthat/testanovaonew.R |only 26 files changed, 957 insertions(+), 777 deletions(-)
Title: Messages, Warnings, Strings with Ascii Animals
Description: Allows printing of character strings as messages/warnings/etc.
with ASCII animals, including cats, cows, frogs, chickens, ghosts,
and more.
Author: Scott Chamberlain [aut, cre],
Amanda Dobbyn [aut],
Tyler Rinker [ctb],
Thomas Leeper [ctb],
Noam Ross [ctb],
Rich FitzJohn [ctb],
Carson Sievert [ctb],
Kiyoko Gotanda [ctb],
Andy Teucher [ctb],
Karl Broman [ctb],
Franz-Sebastian Krah [ctb],
Lucy D'Agostino McGowan [ctb],
Guangchuang Yu [ctb],
Philipp Boersch-Supan [ctb],
Andreas Brandmaier [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between cowsay versions 0.6.0 dated 2018-05-15 and 0.7.0 dated 2018-09-18
DESCRIPTION | 18 ++-- MD5 | 35 ++++----- NEWS.md | 8 ++ R/cowsay-package.r | 20 ++--- R/endless_horse.R | 53 +++++++++++++ R/rms.r | 2 R/say.r | 109 +++++++++++++++++++++++++--- R/utils.R |only R/zzz.R | 8 +- README.md | 161 ++++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/cowsay_tutorial.R | 40 ++++++++++ inst/doc/cowsay_tutorial.Rmd | 61 +++++++++++++++ inst/doc/cowsay_tutorial.html | 159 ++++++++++++++++++++++++++++++++++++++++- man/cowsay.Rd | 20 ++--- man/endless_horse.Rd | 13 +++ man/say.Rd | 33 +++++++- tests/testthat/test-say.R | 49 ++++++++++++ vignettes/cowsay_tutorial.Rmd | 61 +++++++++++++++ 19 files changed, 748 insertions(+), 102 deletions(-)