Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance
measures for asset or portfolio returns using methods as described in
Chen and Martin (2018) <https://www.ssrn.com/abstract=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPESE versions 1.2.1 dated 2021-05-07 and 1.2.2 dated 2021-05-13
RPESE-1.2.1/RPESE/data |only RPESE-1.2.1/RPESE/man/edhec.Rd |only RPESE-1.2.2/RPESE/DESCRIPTION | 13 +-- RPESE-1.2.2/RPESE/MD5 | 74 ++++++++++----------- RPESE-1.2.2/RPESE/NEWS.md | 4 + RPESE-1.2.2/RPESE/R/DSR_SE.R | 2 RPESE-1.2.2/RPESE/R/ES_SE.R | 2 RPESE-1.2.2/RPESE/R/ESratio_SE.R | 2 RPESE-1.2.2/RPESE/R/EstimatorSE.R | 4 - RPESE-1.2.2/RPESE/R/LPM_SE.R | 2 RPESE-1.2.2/RPESE/R/Mean_SE.R | 4 - RPESE-1.2.2/RPESE/R/OmegaRatio_SE.R | 2 RPESE-1.2.2/RPESE/R/RachevRatio_SE.R | 2 RPESE-1.2.2/RPESE/R/SD_SE.R | 2 RPESE-1.2.2/RPESE/R/SR_SE.R | 2 RPESE-1.2.2/RPESE/R/SemiSD_SE.R | 2 RPESE-1.2.2/RPESE/R/SoR_SE.R | 2 RPESE-1.2.2/RPESE/R/VaR_SE.R | 2 RPESE-1.2.2/RPESE/R/VaRratio_SE.R | 2 RPESE-1.2.2/RPESE/R/printSE.R | 2 RPESE-1.2.2/RPESE/R/robMean_SE.R | 2 RPESE-1.2.2/RPESE/inst/doc/RPESEVignette.pdf |binary RPESE-1.2.2/RPESE/man/DSR.SE.Rd | 2 RPESE-1.2.2/RPESE/man/ES.SE.Rd | 2 RPESE-1.2.2/RPESE/man/ESratio.SE.Rd | 2 RPESE-1.2.2/RPESE/man/EstimatorSE.Rd | 2 RPESE-1.2.2/RPESE/man/LPM.SE.Rd | 2 RPESE-1.2.2/RPESE/man/Mean.SE.Rd | 2 RPESE-1.2.2/RPESE/man/OmegaRatio.SE.Rd | 2 RPESE-1.2.2/RPESE/man/RachevRatio.SE.Rd | 2 RPESE-1.2.2/RPESE/man/SD.SE.Rd | 2 RPESE-1.2.2/RPESE/man/SR.SE.Rd | 2 RPESE-1.2.2/RPESE/man/SemiSD.SE.Rd | 2 RPESE-1.2.2/RPESE/man/SoR.SE.Rd | 2 RPESE-1.2.2/RPESE/man/VaR.SE.Rd | 2 RPESE-1.2.2/RPESE/man/VaRratio.SE.Rd | 2 RPESE-1.2.2/RPESE/man/printSE.Rd | 2 RPESE-1.2.2/RPESE/man/robMean.SE.Rd | 2 RPESE-1.2.2/RPESE/tests/testthat/test_input_data.R | 2 39 files changed, 81 insertions(+), 80 deletions(-)
Title: Gamma and Exponential Generalized Linear Models with Elastic Net
Penalty
Description: Implements the fast iterative shrinkage-thresholding algorithm
(FISTA) algorithm to fit a Gamma distribution with an elastic net
penalty as described in Chen, Arakvin and Martin (2018)
<arxiv:1804.07780>. An implementation for the case of the
exponential distribution is also available, with details available
in Chen and Martin (2018) <https://papers.ssrn.com/abstract_id=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>,
Daniel Hanson <hansondj@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEGLMEN versions 1.1.0 dated 2020-10-25 and 1.1.1 dated 2021-05-13
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ NEWS.md | 5 ++++- R/glmGammaNet.R | 2 +- R/glmnet_exp.R | 2 +- man/fit.glmGammaNet.Rd | 2 +- man/glmnet_exp.Rd | 2 +- 7 files changed, 19 insertions(+), 17 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX <https://sdmx.org>) Web Services
(<https://ec.europa.eu/eurostat/web/sdmx-web-services/about-this-service>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Mátyás Mészáros [aut, cre]
Maintainer: Mátyás Mészáros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.10.3 dated 2021-04-16 and 0.10.6 dated 2021-05-13
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 25 ++++++++++++++++++++++--- R/clean_restatapi_cache.R | 10 ++++++---- R/create_filter_table.R | 6 +++++- R/extract_data.R | 1 + R/get_compressed_sdmx.R | 6 +++--- R/get_eurostat_bulk.R | 3 ++- R/get_eurostat_cache.R | 6 +++--- R/get_eurostat_data.R | 36 +++++++++++++++++++----------------- R/get_eurostat_raw.R | 6 +++--- R/get_eurostat_toc.R | 6 +++--- R/load_cfg.R | 2 +- inst/tinytest/test_restatapi.R | 12 +++++++++--- man/extract_data.Rd | 1 + man/get_eurostat_bulk.Rd | 1 + man/get_eurostat_data.Rd | 3 ++- 17 files changed, 101 insertions(+), 63 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for classification
and regression problems. 'mikropml' implements the ML pipeline described
by Topçuoğlu et al. (2020) <doi:10.1128/mBio.00434-20> with reasonable
default options for data preprocessing, hyperparameter tuning,
cross-validation, testing, model evaluation, and interpretation steps.
See the website <http://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Begüm Topçuoğlu [aut] (<https://orcid.org/0000-0003-3140-537X>),
Zena Lapp [aut] (<https://orcid.org/0000-0003-4674-2176>),
Kelly Sovacool [aut, cre] (<https://orcid.org/0000-0003-3283-829X>),
Evan Snitkin [aut] (<https://orcid.org/0000-0001-8409-278X>),
Jenna Wiens [aut] (<https://orcid.org/0000-0002-1057-7722>),
Patrick Schloss [aut] (<https://orcid.org/0000-0002-6935-4275>),
Nick Lesniak [ctb] (<https://orcid.org/0000-0001-9359-5194>),
Courtney Armour [ctb] (<https://orcid.org/0000-0002-5250-1224>)
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 0.0.2 dated 2020-12-03 and 1.0.0 dated 2021-05-13
DESCRIPTION | 20 LICENSE | 2 MD5 | 88 ++- NAMESPACE | 2 NEWS.md | 17 R/checks.R | 2 R/corr_feats.R | 17 R/data.R | 3 R/feature_importance.R | 104 +++- R/mikropml.R | 2 R/performance_metrics.R | 36 - R/plot.R | 8 R/preprocess_data.R | 145 ++++-- R/run_ml.R | 11 R/utils.R | 57 ++ README.md | 20 build/partial.rdb |only data/otu_mini_multi_group.rda |only data/otu_mini_multi_results_glmnet.rda |binary inst/CITATION | 6 inst/doc/introduction.Rmd | 255 ++++++---- inst/doc/introduction.html | 709 +++++++++++------------------- inst/doc/paper.Rmd | 6 inst/doc/paper.html | 361 +++------------ man/calc_perf_metrics.Rd | 2 man/combine_hp_performance.Rd | 2 man/figures |only man/get_feature_importance.Rd | 58 ++ man/get_performance_tbl.Rd | 3 man/mikropml.Rd | 2 man/otu_mini_multi_group.Rd |only man/plot_hp_performance.Rd | 2 man/plot_model_performance.Rd | 2 man/preprocess_data.Rd | 31 + man/remove_singleton_columns.Rd |only man/replace_spaces.Rd |only man/run_ml.Rd | 6 man/tidy_perf_data.Rd | 2 tests/testthat/test-corr_feats.R | 38 - tests/testthat/test-feature_importance.R | 57 ++ tests/testthat/test-performance_metrics.R | 15 tests/testthat/test-preprocess_data.R | 251 ++++++++-- tests/testthat/test-run_ml.R | 15 tests/testthat/test-train_model.R | 7 tests/testthat/test-utils.R | 19 vignettes/introduction.Rmd | 255 ++++++---- vignettes/mikropml-logo.png |only vignettes/paper.Rmd | 6 vignettes/review-responses.md |only 49 files changed, 1460 insertions(+), 1184 deletions(-)
Title: Multimodal and Multilevel Network Analysis
Description: A set of tools that extend common social network analysis packages
for analysing multimodal and multilevel networks.
It includes functions for one- and two-mode (and sometimes three-mode)
centrality, centralization, clustering, and constraint,
as well as for one- and two-mode network regression and block-modelling.
All functions operate with matrices, edge lists,
and 'igraph', 'network'/'sna', and 'tidygraph' objects.
The package is released as a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Author: James Hollway [cph, cre, aut, ctb] (IHEID,
<https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 0.6.5 dated 2021-05-10 and 0.6.6 dated 2021-05-13
DESCRIPTION | 8 ++-- MD5 | 19 ++++++----- NAMESPACE | 3 + NEWS.md | 16 +++++++++ R/coercion.R | 59 ++++++++++++++++++------------------ R/plot.R | 35 ++++++++++++++------- man/coercion.Rd | 26 ++++++++------- man/plot_releases.Rd | 2 + tests/testthat/Rplots.pdf |only tests/testthat/test-coercion.R | 11 ++---- tests/testthat/test-plot_releases.R | 8 +++- 11 files changed, 112 insertions(+), 75 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.3.15 dated 2021-02-18 and 1.4.0 dated 2021-05-13
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 9 +++++++++ R/evalbin.R | 2 +- R/logistic.R | 4 ++-- R/mnl.R | 3 +-- R/regress.R | 9 +++++---- README.md | 4 ++-- inst/app/tools/help/mnl.Rmd | 2 +- inst/app/tools/help/mnl.md | 2 +- man/auc.Rd | 4 ++-- 11 files changed, 38 insertions(+), 29 deletions(-)
Title: General Purpose 'Oai-PMH' Services Client
Description: A general purpose client to work with any 'OAI-PMH'
(Open Archives Initiative Protocol for 'Metadata' Harvesting) service.
The 'OAI-PMH' protocol is described at
<http://www.openarchives.org/OAI/openarchivesprotocol.html>.
Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord',
'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and
'ListSets'.
Author: Scott Chamberlain [aut, cre],
Michal Bojanowski [aut] (supported by NCN grant 2012/07/D/HS6/01971)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between oai versions 0.3.0 dated 2019-09-07 and 0.3.2 dated 2021-05-13
DESCRIPTION | 12 +- LICENSE | 4 MD5 | 32 +++--- NEWS.md | 8 + R/update_providers.R | 8 - README.md | 185 +++++++++++++++++------------------- build/vignette.rds |binary man/count_identifiers.Rd | 3 man/dumpers.Rd | 20 +++ man/get_records.Rd | 11 +- man/list_identifiers.Rd | 13 +- man/list_metadataformats.Rd | 7 - man/list_records.Rd | 13 +- man/list_sets.Rd | 8 + man/update_providers.Rd | 8 - tests/testthat/test-dumpers.R | 1 tests/testthat/test-handle_errors.R | 15 +- 17 files changed, 193 insertions(+), 155 deletions(-)
Title: Data Used to Illustrate 'Loon' Functionality
Description: Data used as examples in the 'loon' package.
Author: R. Wayne Oldford [aut, cre],
Adrian Waddell [aut]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between loon.data versions 0.1.1 dated 2020-08-26 and 0.1.3 dated 2021-05-13
DESCRIPTION | 8 ++-- MD5 | 83 ++++++++++++++++++++++++----------------------- NEWS.md | 11 ++++++ R/SAheart.R | 4 +- R/alaska_forest.R | 4 +- R/binaryalphadigits.R | 2 - R/bone.R | 4 +- R/bone_ext.R | 4 +- R/covidNZ.R | 7 +-- R/crabSpecies.R | 6 +-- R/diabetes.R | 5 -- R/digits.R | 2 - R/faces.R | 2 - R/frey.R | 2 - R/igg1.R | 5 -- R/lepto.R | 7 +-- R/lightspeeds.R | 2 - R/medicalRecords.R | 2 - R/michelson_1879.R | 4 -- R/minority.R | 2 - R/pandemic.R | 6 +++ R/trtPan.R |only data/covidNZ.rda |binary data/datalist | 1 data/trtPan.rda |only man/SAheart.Rd | 4 +- man/alaska_forest.Rd | 3 + man/binaryalphadigits.Rd | 2 - man/bone.Rd | 4 +- man/bone_ext.Rd | 4 +- man/covidNZ.Rd | 7 +-- man/crabSpecies.Rd | 7 +-- man/diabetes.Rd | 5 -- man/digits.Rd | 2 - man/faces.Rd | 2 - man/frey.Rd | 2 - man/igg1.Rd | 6 --- man/lepto.Rd | 7 +-- man/lightspeeds.Rd | 2 - man/medicalRecords.Rd | 2 - man/michelson_1879.Rd | 5 -- man/minority.Rd | 3 - man/pandemic.Rd | 6 +++ man/trtPan.Rd |only 44 files changed, 120 insertions(+), 126 deletions(-)
Title: Tidy Geospatial Networks
Description: Provides a tidy approach to spatial network
analysis, in the form of classes and functions that enable a seamless
interaction between the network analysis package 'tidygraph' and the
spatial analysis package 'sf'.
Author: Lucas van der Meer [aut, cre] (<https://orcid.org/0000-0001-6336-8628>),
Lorena Abad [aut] (<https://orcid.org/0000-0003-0554-734X>),
Andrea Gilardi [aut] (<https://orcid.org/0000-0002-9424-7439>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Lucas van der Meer <luukvandermeer@live.nl>
Diff between sfnetworks versions 0.5.1 dated 2021-03-27 and 0.5.2 dated 2021-05-13
DESCRIPTION | 12 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 12 R/blend.R | 6 R/paths.R | 54 ++ R/s2.R |only R/sfnetwork.R | 12 R/zzz.R | 2 README.md | 4 build/vignette.rds |binary inst/doc/join_filter.html | 690 ++++++++++------------------- inst/doc/morphers.html | 742 +++++++++++--------------------- inst/doc/preprocess_and_clean.html | 788 ++++++++++++---------------------- inst/doc/routing.Rmd | 14 inst/doc/routing.html | 853 +++++++++++++------------------------ inst/doc/structure.R | 6 inst/doc/structure.Rmd | 8 inst/doc/structure.html | 805 ++++++++++++---------------------- man/s2.Rd |only man/st_network_cost.Rd | 33 + man/st_network_paths.Rd | 21 tests/testthat/test_edges_nodes.R | 2 tests/testthat/test_geometry.R | 1 vignettes/routing.Rmd | 14 vignettes/structure.Rmd | 8 26 files changed, 1551 insertions(+), 2585 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org'
archives (<http://vertnet.org/>). Functions allow searching by many
parameters, including 'taxonomic' names, places, and dates. In addition,
there is an interface for conducting spatially delimited searches, and
another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre] (0000-0003-1444-9135),
Chris Ray [ctb],
Vijay Barve [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.8.0 dated 2020-01-29 and 0.8.2 dated 2021-05-13
rvertnet-0.8.0/rvertnet/build |only rvertnet-0.8.0/rvertnet/inst/doc |only rvertnet-0.8.0/rvertnet/vignettes |only rvertnet-0.8.2/rvertnet/DESCRIPTION | 18 rvertnet-0.8.2/rvertnet/LICENSE | 2 rvertnet-0.8.2/rvertnet/MD5 | 32 rvertnet-0.8.2/rvertnet/NAMESPACE | 2 rvertnet-0.8.2/rvertnet/NEWS.md | 7 rvertnet-0.8.2/rvertnet/R/rvertnet-package.R | 3 rvertnet-0.8.2/rvertnet/R/traitsearch.R | 3 rvertnet-0.8.2/rvertnet/R/vert_id.R | 11 rvertnet-0.8.2/rvertnet/R/yyy.R | 8 rvertnet-0.8.2/rvertnet/R/zzz.R | 2 rvertnet-0.8.2/rvertnet/README.md | 16 rvertnet-0.8.2/rvertnet/man/traitsearch.Rd | 3 rvertnet-0.8.2/rvertnet/man/vert_id.Rd | 5 rvertnet-0.8.2/rvertnet/tests/fixtures/vertsummary_prep_vertsearch.yml | 1739 +++++++++- rvertnet-0.8.2/rvertnet/tests/testthat/test-vertsummary.R | 5 18 files changed, 1763 insertions(+), 93 deletions(-)
Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a
C API that can be used to write high-performance C and C++
geometry operations using R as an interface. Headers are provided
to make linking to and using these functions from C++ code as
easy and as safe as possible. This package contains an internal
copy of the 'GEOS' library to guarantee the best possible
consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
GEOS authors [aut],
Martin Davis [ctb, cph],
Benjamin Campbell [ctb, cph],
Tomasz Sowa [ctb, cph],
Christian Kaiser [ctb, cph],
David Skea [ctb, cph],
Daniel Baston [ctb, cph],
Sandro Santilli [ctb, cph],
Mateusz Loskot [ctb, cph],
Paul Ramsey [ctb, cph],
Olivier Devillers [ctb, cph],
Sean Gillies [ctb, cph],
Mika Heiskanen [ctb, cph],
Safe Software Inc. [cph],
Refractions Research Inc. [cph],
Vivid Solutions Inc. [cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between libgeos versions 3.8.1-4 dated 2021-03-22 and 3.9.1-1 dated 2021-05-13
libgeos-3.8.1-4/libgeos/inst/include/libgeos-rcpp.h |only libgeos-3.8.1-4/libgeos/src/geos/geomgraph/Position.cpp |only libgeos-3.8.1-4/libgeos/src/geos/geomgraph/Quadrant.cpp |only libgeos-3.8.1-4/libgeos/src/geos/index/quadtree/DoubleBits.cpp |only libgeos-3.8.1-4/libgeos/src/geos/noding/snapround/SimpleSnapRounder.cpp |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/algorithm/ttmath |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geom/BinaryOp.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geomUtil.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geomgraph.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geomgraph/Position.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geomgraph/Quadrant.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geomgraph/Quadrant.inl |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geomgraphindex.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/geosAlgorithm.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/index/quadtree/DoubleBits.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/indexBintree.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/indexChain.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/indexQuadtree.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/indexStrtree.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/indexSweepline.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/io.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/noding.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/noding/snapround/SimpleSnapRounder.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/nodingSnapround.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opBuffer.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opDistance.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opLinemerge.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opOverlay.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opPolygonize.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opPredicate.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opRelate.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/opValid.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/operation.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/planargraph.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/precision.h |only libgeos-3.8.1-4/libgeos/src/geos_include/geos/spatialIndex.h |only libgeos-3.8.1-4/libgeos/src/libgeos-version.c |only libgeos-3.8.1-4/libgeos/tests/testthat/helper-source-rcpp.R |only libgeos-3.8.1-4/libgeos/tests/testthat/test-rcpp-api.R |only libgeos-3.8.1-4/libgeos/tools |only libgeos-3.9.1-1/libgeos/DESCRIPTION | 9 libgeos-3.9.1-1/libgeos/MD5 | 839 - libgeos-3.9.1-1/libgeos/NEWS.md | 10 libgeos-3.9.1-1/libgeos/README.md | 88 libgeos-3.9.1-1/libgeos/inst/include/libgeos.c | 23 libgeos-3.9.1-1/libgeos/inst/include/libgeos.h | 32 libgeos-3.9.1-1/libgeos/src/Makevars | 70 libgeos-3.9.1-1/libgeos/src/geos/algorithm/Area.cpp | 10 libgeos-3.9.1-1/libgeos/src/geos/algorithm/CGAlgorithmsDD.cpp | 53 libgeos-3.9.1-1/libgeos/src/geos/algorithm/ConvexHull.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/algorithm/InteriorPointArea.cpp | 5 libgeos-3.9.1-1/libgeos/src/geos/algorithm/Intersection.cpp | 3 libgeos-3.9.1-1/libgeos/src/geos/algorithm/LineIntersector.cpp | 625 - libgeos-3.9.1-1/libgeos/src/geos/algorithm/MinimumBoundingCircle.cpp | 94 libgeos-3.9.1-1/libgeos/src/geos/algorithm/Orientation.cpp | 148 libgeos-3.9.1-1/libgeos/src/geos/algorithm/PointLocator.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/algorithm/construct |only libgeos-3.9.1-1/libgeos/src/geos/algorithm/distance/DiscreteHausdorffDistance.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/algorithm/locate/IndexedPointInAreaLocator.cpp | 9 libgeos-3.9.1-1/libgeos/src/geos/algorithm/locate/SimplePointInAreaLocator.cpp | 22 libgeos-3.9.1-1/libgeos/src/geos/edgegraph |only libgeos-3.9.1-1/libgeos/src/geos/geom/CoordinateArraySequence.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geom/CoordinateSequence.cpp | 13 libgeos-3.9.1-1/libgeos/src/geos/geom/Envelope.cpp | 37 libgeos-3.9.1-1/libgeos/src/geos/geom/Geometry.cpp | 58 libgeos-3.9.1-1/libgeos/src/geos/geom/GeometryCollection.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geom/GeometryFactory.cpp | 83 libgeos-3.9.1-1/libgeos/src/geos/geom/HeuristicOverlay.cpp |only libgeos-3.9.1-1/libgeos/src/geos/geom/IntersectionMatrix.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geom/LineSegment.cpp | 1 libgeos-3.9.1-1/libgeos/src/geos/geom/LineString.cpp | 35 libgeos-3.9.1-1/libgeos/src/geos/geom/Location.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geom/MultiLineString.cpp | 11 libgeos-3.9.1-1/libgeos/src/geos/geom/MultiPoint.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/geom/MultiPolygon.cpp | 14 libgeos-3.9.1-1/libgeos/src/geos/geom/Point.cpp | 9 libgeos-3.9.1-1/libgeos/src/geos/geom/Polygon.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/geom/Position.cpp |only libgeos-3.9.1-1/libgeos/src/geos/geom/PrecisionModel.cpp | 11 libgeos-3.9.1-1/libgeos/src/geos/geom/Quadrant.cpp |only libgeos-3.9.1-1/libgeos/src/geos/geom/prep/BasicPreparedGeometry.cpp | 16 libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedLineString.cpp | 31 libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedLineStringDistance.cpp |only libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedLineStringIntersects.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedLineStringNearestPoints.cpp |only libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedPolygon.cpp | 20 libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedPolygonContainsProperly.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedPolygonDistance.cpp |only libgeos-3.9.1-1/libgeos/src/geos/geom/prep/PreparedPolygonPredicate.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geom/util/CoordinateOperation.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geom/util/GeometryTransformer.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/geom/util/LinearComponentExtracter.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geom/util/PointExtracter.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/geom/util/ShortCircuitedGeometryVisitor.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geom/util/SineStarFactory.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/Depth.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/DirectedEdge.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/DirectedEdgeStar.cpp | 61 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/Edge.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/EdgeEnd.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/EdgeEndStar.cpp | 38 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/EdgeIntersectionList.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/EdgeList.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/EdgeRing.cpp | 42 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/GeometryGraph.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/Node.cpp | 10 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/NodeMap.cpp | 15 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/PlanarGraph.cpp | 31 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/TopologyLocation.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/index/MonotoneChainIndexer.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/index/SegmentIntersector.cpp | 5 libgeos-3.9.1-1/libgeos/src/geos/geomgraph/index/SimpleSweepLineIntersector.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/geos_ts_c.cpp | 5355 +--------- libgeos-3.9.1-1/libgeos/src/geos/index/bintree/Bintree.cpp | 12 libgeos-3.9.1-1/libgeos/src/geos/index/bintree/Key.cpp | 11 libgeos-3.9.1-1/libgeos/src/geos/index/bintree/Root.cpp | 14 libgeos-3.9.1-1/libgeos/src/geos/index/chain/MonotoneChain.cpp | 74 libgeos-3.9.1-1/libgeos/src/geos/index/chain/MonotoneChainBuilder.cpp | 3 libgeos-3.9.1-1/libgeos/src/geos/index/intervalrtree/SortedPackedIntervalRTree.cpp | 30 libgeos-3.9.1-1/libgeos/src/geos/index/kdtree |only libgeos-3.9.1-1/libgeos/src/geos/index/quadtree/IntervalSize.cpp | 5 libgeos-3.9.1-1/libgeos/src/geos/index/quadtree/Key.cpp | 7 libgeos-3.9.1-1/libgeos/src/geos/index/quadtree/Root.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/index/strtree/AbstractSTRtree.cpp | 37 libgeos-3.9.1-1/libgeos/src/geos/index/strtree/BoundablePair.cpp | 12 libgeos-3.9.1-1/libgeos/src/geos/index/strtree/SIRtree.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/index/strtree/STRtree.cpp | 195 libgeos-3.9.1-1/libgeos/src/geos/index/strtree/SimpleSTRdistance.cpp |only libgeos-3.9.1-1/libgeos/src/geos/index/strtree/SimpleSTRnode.cpp |only libgeos-3.9.1-1/libgeos/src/geos/index/strtree/SimpleSTRtree.cpp |only libgeos-3.9.1-1/libgeos/src/geos/index/sweepline/SweepLineIndex.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/inlines.cpp | 7 libgeos-3.9.1-1/libgeos/src/geos/io/WKBReader.cpp | 60 libgeos-3.9.1-1/libgeos/src/geos/io/WKBWriter.cpp | 26 libgeos-3.9.1-1/libgeos/src/geos/io/WKTReader.cpp | 38 libgeos-3.9.1-1/libgeos/src/geos/io/WKTWriter.cpp | 28 libgeos-3.9.1-1/libgeos/src/geos/linearref/ExtractLineByLocation.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/linearref/LengthIndexOfPoint.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/linearref/LengthLocationMap.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/linearref/LinearLocation.cpp | 15 libgeos-3.9.1-1/libgeos/src/geos/linearref/LocationIndexOfPoint.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/math |only libgeos-3.9.1-1/libgeos/src/geos/noding/GeometryNoder.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/noding/IntersectionAdder.cpp | 9 libgeos-3.9.1-1/libgeos/src/geos/noding/IntersectionFinderAdder.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/noding/IteratedNoder.cpp | 36 libgeos-3.9.1-1/libgeos/src/geos/noding/MCIndexNoder.cpp | 20 libgeos-3.9.1-1/libgeos/src/geos/noding/MCIndexSegmentSetMutualIntersector.cpp | 10 libgeos-3.9.1-1/libgeos/src/geos/noding/NodedSegmentString.cpp | 10 libgeos-3.9.1-1/libgeos/src/geos/noding/NodingIntersectionFinder.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/noding/SegmentNode.cpp | 9 libgeos-3.9.1-1/libgeos/src/geos/noding/SegmentNodeList.cpp | 152 libgeos-3.9.1-1/libgeos/src/geos/noding/SimpleNoder.cpp | 11 libgeos-3.9.1-1/libgeos/src/geos/noding/ValidatingNoder.cpp |only libgeos-3.9.1-1/libgeos/src/geos/noding/snap |only libgeos-3.9.1-1/libgeos/src/geos/noding/snapround/HotPixel.cpp | 263 libgeos-3.9.1-1/libgeos/src/geos/noding/snapround/HotPixelIndex.cpp |only libgeos-3.9.1-1/libgeos/src/geos/noding/snapround/MCIndexPointSnapper.cpp | 65 libgeos-3.9.1-1/libgeos/src/geos/noding/snapround/MCIndexSnapRounder.cpp | 13 libgeos-3.9.1-1/libgeos/src/geos/noding/snapround/SnapRoundingIntersectionAdder.cpp |only libgeos-3.9.1-1/libgeos/src/geos/noding/snapround/SnapRoundingNoder.cpp |only libgeos-3.9.1-1/libgeos/src/geos/operation/IsSimpleOp.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/BufferBuilder.cpp | 14 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/BufferInputLineSimplifier.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/BufferOp.cpp | 29 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/BufferParameters.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/BufferSubgraph.cpp | 22 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/OffsetCurveBuilder.cpp | 22 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/OffsetCurveSetBuilder.cpp | 65 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/OffsetSegmentGenerator.cpp | 64 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/RightmostEdgeFinder.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/operation/buffer/SubgraphDepthLocater.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/ConnectedElementLocationFilter.cpp | 5 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/ConnectedElementPointFilter.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/DistanceOp.cpp | 72 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/FacetSequence.cpp | 44 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/FacetSequenceTreeBuilder.cpp | 34 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/GeometryLocation.cpp | 28 libgeos-3.9.1-1/libgeos/src/geos/operation/distance/IndexedFacetDistance.cpp | 16 libgeos-3.9.1-1/libgeos/src/geos/operation/intersection/RectangleIntersection.cpp | 9 libgeos-3.9.1-1/libgeos/src/geos/operation/linemerge/EdgeString.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/linemerge/LineMergeEdge.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/linemerge/LineMerger.cpp | 19 libgeos-3.9.1-1/libgeos/src/geos/operation/linemerge/LineSequencer.cpp | 12 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/LineBuilder.cpp | 10 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/MaximalEdgeRing.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/OverlayOp.cpp | 16 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/PointBuilder.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/PolygonBuilder.cpp | 3 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/snap/GeometrySnapper.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/overlay/snap/LineStringSnapper.cpp | 7 libgeos-3.9.1-1/libgeos/src/geos/operation/overlayng |only libgeos-3.9.1-1/libgeos/src/geos/operation/polygonize/BuildArea.cpp | 60 libgeos-3.9.1-1/libgeos/src/geos/operation/polygonize/PolygonizeGraph.cpp | 27 libgeos-3.9.1-1/libgeos/src/geos/operation/polygonize/Polygonizer.cpp | 18 libgeos-3.9.1-1/libgeos/src/geos/operation/predicate/RectangleContains.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/operation/predicate/RectangleIntersects.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/operation/relate/EdgeEndBuilder.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/relate/EdgeEndBundle.cpp | 56 libgeos-3.9.1-1/libgeos/src/geos/operation/relate/RelateComputer.cpp | 54 libgeos-3.9.1-1/libgeos/src/geos/operation/relate/RelateNode.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/relate/RelateNodeGraph.cpp | 7 libgeos-3.9.1-1/libgeos/src/geos/operation/union/CascadedPolygonUnion.cpp | 81 libgeos-3.9.1-1/libgeos/src/geos/operation/union/CascadedUnion.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/operation/union/CoverageUnion.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/operation/union/OverlapUnion.cpp | 23 libgeos-3.9.1-1/libgeos/src/geos/operation/union/UnaryUnionOp.cpp | 11 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/ConnectedInteriorTester.cpp | 17 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/ConsistentAreaTester.cpp | 15 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/IndexedNestedRingTester.cpp | 41 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/IndexedNestedRingTester.h | 8 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/IndexedNestedShellTester.cpp |only libgeos-3.9.1-1/libgeos/src/geos/operation/valid/IsValidOp.cpp | 145 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/MakeValid.cpp | 40 libgeos-3.9.1-1/libgeos/src/geos/operation/valid/RepeatedPointTester.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/planargraph/DirectedEdge.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/planargraph/Edge.cpp | 12 libgeos-3.9.1-1/libgeos/src/geos/precision/GeometryPrecisionReducer.cpp | 95 libgeos-3.9.1-1/libgeos/src/geos/precision/MinimumClearance.cpp | 31 libgeos-3.9.1-1/libgeos/src/geos/precision/PrecisionReducerCoordinateOperation.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/precision/SimpleGeometryPrecisionReducer.cpp | 4 libgeos-3.9.1-1/libgeos/src/geos/shape |only libgeos-3.9.1-1/libgeos/src/geos/simplify/TaggedLineStringSimplifier.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/simplify/TopologyPreservingSimplifier.cpp | 10 libgeos-3.9.1-1/libgeos/src/geos/triangulate/IncrementalDelaunayTriangulator.cpp | 6 libgeos-3.9.1-1/libgeos/src/geos/triangulate/quadedge/LastFoundQuadEdgeLocator.cpp | 2 libgeos-3.9.1-1/libgeos/src/geos/triangulate/quadedge/LocateFailureException.cpp | 7 libgeos-3.9.1-1/libgeos/src/geos/triangulate/quadedge/QuadEdge.cpp | 80 libgeos-3.9.1-1/libgeos/src/geos/triangulate/quadedge/QuadEdgeSubdivision.cpp | 88 libgeos-3.9.1-1/libgeos/src/geos/triangulate/quadedge/Vertex.cpp | 8 libgeos-3.9.1-1/libgeos/src/geos/util/GeometricShapeFactory.cpp | 12 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/Angle.h | 18 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/CGAlgorithmsDD.h | 39 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/Centroid.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/ConvexHull.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/Distance.h | 28 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/InteriorPointPoint.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/Intersection.h | 43 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/Length.h | 21 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/LineIntersector.h | 89 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/MinimumBoundingCircle.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/NotRepresentableException.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/Orientation.h | 61 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/PointLocation.h | 22 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/PointLocator.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/RayCrossingCounterDD.h | 1 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/construct |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/locate/IndexedPointInAreaLocator.h | 9 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/locate/PointOnGeometryLocator.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/algorithm/locate/SimplePointInAreaLocator.h | 10 libgeos-3.9.1-1/libgeos/src/geos_include/geos/constants.h | 5 libgeos-3.9.1-1/libgeos/src/geos_include/geos/edgegraph |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/CoordinateSequence.h | 17 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Dimension.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Envelope.h | 44 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Envelope.inl | 62 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/FixedSizeCoordinateSequence.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Geometry.h | 19 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/GeometryCollection.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/GeometryFactory.h | 31 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/HeuristicOverlay.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/LineSegment.h | 8 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/LineSegment.inl | 13 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/LineString.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Location.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/MultiLineString.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/MultiPoint.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/MultiPolygon.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Point.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Polygon.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Position.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/PrecisionModel.h | 23 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/PrecisionModel.inl | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Quadrant.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/Quadrant.inl |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/BasicPreparedGeometry.h | 10 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedGeometry.h | 74 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedGeometryFactory.h | 28 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedLineString.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedLineStringDistance.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedLineStringNearestPoints.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygon.h | 5 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygonContains.h | 12 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygonContainsProperly.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygonCovers.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygonDistance.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygonIntersects.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geom/prep/PreparedPolygonPredicate.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/Depth.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/Depth.inl | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/DirectedEdge.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/EdgeEndStar.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/EdgeIntersection.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/EdgeIntersectionList.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/EdgeList.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/EdgeRing.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/GeometryGraph.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/Label.h | 37 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/Label.inl | 72 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/Node.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/PlanarGraph.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/TopologyLocation.h | 10 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/TopologyLocation.inl | 15 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/index/EdgeSetIntersector.h | 10 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/index/MonotoneChainEdge.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/index/MonotoneChainIndexer.h | 23 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/index/SegmentIntersector.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/geomgraph/index/SimpleEdgeSetIntersector.h | 5 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/bintree/Bintree.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/bintree/NodeBase.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/chain/MonotoneChain.h | 23 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/intervalrtree/SortedPackedIntervalRTree.h | 9 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/kdtree |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/quadtree/IntervalSize.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/quadtree/Root.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/AbstractSTRtree.h | 15 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/Boundable.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/SIRtree.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/STRtree.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/SimpleSTRdistance.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/SimpleSTRnode.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/index/strtree/SimpleSTRtree.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/ByteOrderDataInStream.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/ByteOrderValues.h | 8 libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/ParseException.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/WKBReader.h | 15 libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/WKBWriter.h | 20 libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/WKTReader.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/io/WKTWriter.h | 9 libgeos-3.9.1-1/libgeos/src/geos_include/geos/linearref/LengthLocationMap.h | 7 libgeos-3.9.1-1/libgeos/src/geos_include/geos/math |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/namespaces.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/IntersectionAdder.h | 11 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/IteratedNoder.h | 3 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/MCIndexNoder.h | 11 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/NodedSegmentString.h | 11 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/Noder.h | 5 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/NodingIntersectionFinder.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/NodingValidator.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/OrientedCoordinateArray.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/SegmentNode.h | 4 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/SegmentNodeList.h | 51 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/SegmentPointComparator.h | 5 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/SegmentString.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/ValidatingNoder.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snap |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snapround/HotPixel.h | 153 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snapround/HotPixel.inl | 20 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snapround/HotPixelIndex.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snapround/MCIndexPointSnapper.h | 7 libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snapround/SnapRoundingIntersectionAdder.h |only libgeos-3.9.1-1/libgeos/src/geos_include/geos/noding/snapround/SnapRoundingNoder.h |only 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libgeos-3.9.1-1/libgeos/src/geos_include/geos/util/GeometricShapeFactory.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos/util/IllegalArgumentException.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/util/IllegalStateException.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/util/Interrupt.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/util/TopologyException.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/util/UnsupportedOperationException.h | 2 libgeos-3.9.1-1/libgeos/src/geos_include/geos/version.h | 6 libgeos-3.9.1-1/libgeos/src/geos_include/geos_c.h | 95 libgeos-3.9.1-1/libgeos/src/geos_include/libgeos-cpp-compat.h | 9 libgeos-3.9.1-1/libgeos/src/libgeos-cpp-compat.cpp | 103 libgeos-3.9.1-1/libgeos/src/libgeos-init.c | 41 libgeos-3.9.1-1/libgeos/tests/testthat/test-version.R | 43 421 files changed, 5477 insertions(+), 7918 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.0.1 dated 2020-09-14 and 2.0.2 dated 2021-05-13
Rfast-2.0.1/Rfast/R/allttests.R |only Rfast-2.0.1/Rfast/R/ancova1.R |only Rfast-2.0.1/Rfast/R/ancovas.R |only Rfast-2.0.1/Rfast/R/anova1.R |only Rfast-2.0.1/Rfast/R/anova_propreg.R |only Rfast-2.0.1/Rfast/R/anova_qpois.reg.R |only Rfast-2.0.1/Rfast/R/anova_quasipois.reg.R |only Rfast-2.0.1/Rfast/R/anovas.R |only Rfast-2.0.1/Rfast/R/bcdcor.R |only Rfast-2.0.1/Rfast/R/block.anova.R |only Rfast-2.0.1/Rfast/R/block.anovas.R |only Rfast-2.0.1/Rfast/R/boot.ttest2.R |only Rfast-2.0.1/Rfast/R/chi2Test_univariate.R |only Rfast-2.0.1/Rfast/R/chi2tests.R |only Rfast-2.0.1/Rfast/R/col_mle.R |only Rfast-2.0.1/Rfast/R/colexpmle.R |only Rfast-2.0.1/Rfast/R/colgammamle.R |only Rfast-2.0.1/Rfast/R/colpoisson.anovas.R |only Rfast-2.0.1/Rfast/R/colquasipoisson.anovas.R |only Rfast-2.0.1/Rfast/R/dcor.R |only Rfast-2.0.1/Rfast/R/dcor.ttest.R |only Rfast-2.0.1/Rfast/R/dcov.R |only Rfast-2.0.1/Rfast/R/dvar.R |only Rfast-2.0.1/Rfast/R/eel.test1.R |only Rfast-2.0.1/Rfast/R/eel.test2.R |only Rfast-2.0.1/Rfast/R/el.test1.R |only Rfast-2.0.1/Rfast/R/el.test2.R |only Rfast-2.0.1/Rfast/R/expmle.R |only Rfast-2.0.1/Rfast/R/geom.anova.R |only Rfast-2.0.1/Rfast/R/geom.anovas.R |only Rfast-2.0.1/Rfast/R/matrnorm.R |only Rfast-2.0.1/Rfast/R/multinomnb.pred.R |only Rfast-2.0.1/Rfast/R/percent.ttest.R |only Rfast-2.0.1/Rfast/R/percent.ttests.R |only Rfast-2.0.1/Rfast/R/poisson.anova.R |only Rfast-2.0.1/Rfast/R/poisson.anovas.R |only Rfast-2.0.1/Rfast/R/poisson.nb.R |only Rfast-2.0.1/Rfast/R/poissonnb.pred.R |only Rfast-2.0.1/Rfast/R/qpois.reg.R |only Rfast-2.0.1/Rfast/R/quasi.poisson_only.R |only Rfast-2.0.1/Rfast/R/quasipoisson.anova.R |only Rfast-2.0.1/Rfast/R/quasipoisson.anovas.R |only Rfast-2.0.1/Rfast/R/tmle.R |only Rfast-2.0.1/Rfast/R/ttest.R |only Rfast-2.0.1/Rfast/R/ttest1.R |only Rfast-2.0.1/Rfast/R/ttest2.R |only Rfast-2.0.1/Rfast/R/ttests.R |only Rfast-2.0.1/Rfast/R/ttests.pairs.R |only Rfast-2.0.1/Rfast/R/var2test.R |only Rfast-2.0.1/Rfast/R/var2tests.R |only Rfast-2.0.1/Rfast/R/vartest.R |only Rfast-2.0.1/Rfast/R/vartests.R |only Rfast-2.0.2/Rfast/DESCRIPTION | 9 Rfast-2.0.2/Rfast/MD5 | 372 ++++++-------- Rfast-2.0.2/Rfast/NAMESPACE | 2 Rfast-2.0.2/Rfast/R/anova_related.R |only Rfast-2.0.2/Rfast/R/chi2Test.R | 12 Rfast-2.0.2/Rfast/R/column-wise_mle.R |only Rfast-2.0.2/Rfast/R/data.frame.to_matrix.R | 24 Rfast-2.0.2/Rfast/R/directional_mle.R | 4 Rfast-2.0.2/Rfast/R/distance_cov_cor.R |only Rfast-2.0.2/Rfast/R/empirical_likelihood_tests.R |only Rfast-2.0.2/Rfast/R/group.R | 3 Rfast-2.0.2/Rfast/R/many_regression_models_correlations.R | 6 Rfast-2.0.2/Rfast/R/random_values_simulation.R | 26 Rfast-2.0.2/Rfast/R/regression_models.R | 47 + Rfast-2.0.2/Rfast/R/ttest_related_functions.R |only Rfast-2.0.2/Rfast/R/variance_tests.R |only Rfast-2.0.2/Rfast/README.md | 6 Rfast-2.0.2/Rfast/inst/include/Rfast/templates.h | 4 Rfast-2.0.2/Rfast/man/Lchoose.Rd | 2 Rfast-2.0.2/Rfast/man/Outer.Rd | 2 Rfast-2.0.2/Rfast/man/Rfast-package.Rd | 6 Rfast-2.0.2/Rfast/man/Rnorm.Rd | 7 Rfast-2.0.2/Rfast/man/Var.Rd | 2 Rfast-2.0.2/Rfast/man/acg.mle.Rd | 2 Rfast-2.0.2/Rfast/man/allbetas.Rd | 2 Rfast-2.0.2/Rfast/man/allttests.Rd | 2 Rfast-2.0.2/Rfast/man/ancova1.Rd | 2 Rfast-2.0.2/Rfast/man/ancovas.Rd | 2 Rfast-2.0.2/Rfast/man/anova_propreg.Rd | 2 Rfast-2.0.2/Rfast/man/anova_quasipois.reg.Rd | 2 Rfast-2.0.2/Rfast/man/apply.condition.Rd | 2 Rfast-2.0.2/Rfast/man/ar1.Rd | 2 Rfast-2.0.2/Rfast/man/as.Rfast.function.Rd | 2 Rfast-2.0.2/Rfast/man/bc.Rd | 2 Rfast-2.0.2/Rfast/man/beta.mle.Rd | 2 Rfast-2.0.2/Rfast/man/bic.corfsreg.Rd | 2 Rfast-2.0.2/Rfast/man/boot.ttest2.Rd | 4 Rfast-2.0.2/Rfast/man/btmprobs.Rd | 2 Rfast-2.0.2/Rfast/man/cat.goftests.Rd | 2 Rfast-2.0.2/Rfast/man/check_data.Rd | 2 Rfast-2.0.2/Rfast/man/cholesky.Rd | 2 Rfast-2.0.2/Rfast/man/circlin.cor.Rd | 2 Rfast-2.0.2/Rfast/man/col.yule.Rd | 2 Rfast-2.0.2/Rfast/man/colCumMaxs.Rd | 2 Rfast-2.0.2/Rfast/man/colMads.Rd | 2 Rfast-2.0.2/Rfast/man/colVars.Rd | 2 Rfast-2.0.2/Rfast/man/colanovas.Rd | 2 Rfast-2.0.2/Rfast/man/colaucs.Rd | 2 Rfast-2.0.2/Rfast/man/colcvs.Rd | 2 Rfast-2.0.2/Rfast/man/colkurtosis.Rd | 2 Rfast-2.0.2/Rfast/man/colnormal.mle.Rd | 2 Rfast-2.0.2/Rfast/man/colnth.Rd | 2 Rfast-2.0.2/Rfast/man/colpoisdisp.tests.Rd | 2 Rfast-2.0.2/Rfast/man/colpoisson.anovas.Rd | 2 Rfast-2.0.2/Rfast/man/colrint.regbx.Rd | 2 Rfast-2.0.2/Rfast/man/colvarcomps.mom.Rd | 2 Rfast-2.0.2/Rfast/man/colwatsons.Rd | 2 Rfast-2.0.2/Rfast/man/cor.fbed.Rd | 5 Rfast-2.0.2/Rfast/man/cor.fsreg.Rd | 2 Rfast-2.0.2/Rfast/man/corpairs.Rd | 2 Rfast-2.0.2/Rfast/man/correls.Rd | 2 Rfast-2.0.2/Rfast/man/cova.Rd | 2 Rfast-2.0.2/Rfast/man/cox.poisrat.Rd | 2 Rfast-2.0.2/Rfast/man/dcor.Rd | 2 Rfast-2.0.2/Rfast/man/dcor.ttest.Rd | 2 Rfast-2.0.2/Rfast/man/dcov.Rd | 18 Rfast-2.0.2/Rfast/man/diri.nr2.Rd | 2 Rfast-2.0.2/Rfast/man/dirknn.cv.Rd | 2 Rfast-2.0.2/Rfast/man/dista.Rd | 2 Rfast-2.0.2/Rfast/man/dmvnorm.Rd | 2 Rfast-2.0.2/Rfast/man/edist.Rd | 3 Rfast-2.0.2/Rfast/man/eel.test1.Rd | 2 Rfast-2.0.2/Rfast/man/eel.test2.Rd | 2 Rfast-2.0.2/Rfast/man/exact.ttest2.Rd | 2 Rfast-2.0.2/Rfast/man/expregs.Rd | 2 Rfast-2.0.2/Rfast/man/fish.kent.Rd | 2 Rfast-2.0.2/Rfast/man/freq.min.Rd | 2 Rfast-2.0.2/Rfast/man/ftest.Rd | 2 Rfast-2.0.2/Rfast/man/ftests.Rd | 2 Rfast-2.0.2/Rfast/man/gammamle.Rd | 2 Rfast-2.0.2/Rfast/man/gammareg.Rd | 2 Rfast-2.0.2/Rfast/man/gaussian.nb.Rd | 2 Rfast-2.0.2/Rfast/man/gaussiannb.pred.Rd | 2 Rfast-2.0.2/Rfast/man/gchi2Test.Rd | 2 Rfast-2.0.2/Rfast/man/ginis.Rd | 2 Rfast-2.0.2/Rfast/man/glm_logistic.Rd | 2 Rfast-2.0.2/Rfast/man/group.Rd | 2 Rfast-2.0.2/Rfast/man/hd.eigen.Rd | 2 Rfast-2.0.2/Rfast/man/invdir.mle.Rd | 2 Rfast-2.0.2/Rfast/man/invgauss.reg.Rd | 2 Rfast-2.0.2/Rfast/man/james.Rd | 2 Rfast-2.0.2/Rfast/man/kruskaltests.Rd | 2 Rfast-2.0.2/Rfast/man/kuiper.Rd | 2 Rfast-2.0.2/Rfast/man/list.ftests.Rd | 2 Rfast-2.0.2/Rfast/man/lmfit.Rd | 2 Rfast-2.0.2/Rfast/man/logistic.cat1.Rd | 2 Rfast-2.0.2/Rfast/man/logistic_only.Rd | 2 Rfast-2.0.2/Rfast/man/mad2.Rd | 2 Rfast-2.0.2/Rfast/man/mat.mat.Rd | 2 Rfast-2.0.2/Rfast/man/match.coefs.Rd | 2 Rfast-2.0.2/Rfast/man/matrnorm.Rd | 7 Rfast-2.0.2/Rfast/man/med.Rd | 2 Rfast-2.0.2/Rfast/man/mediandir.Rd | 2 Rfast-2.0.2/Rfast/man/min_max.Rd | 2 Rfast-2.0.2/Rfast/man/multinom.mle.Rd | 2 Rfast-2.0.2/Rfast/man/multinom.reg.Rd | 2 Rfast-2.0.2/Rfast/man/mv.eeltest1.Rd | 2 Rfast-2.0.2/Rfast/man/mv.eeltest2.Rd | 2 Rfast-2.0.2/Rfast/man/mvbetas.Rd | 2 Rfast-2.0.2/Rfast/man/mvkurtosis.Rd | 2 Rfast-2.0.2/Rfast/man/mvnorm.mle.Rd | 2 Rfast-2.0.2/Rfast/man/mvt.mle.Rd | 2 Rfast-2.0.2/Rfast/man/normal.mle.Rd | 2 Rfast-2.0.2/Rfast/man/normlog.regs.Rd | 2 Rfast-2.0.2/Rfast/man/odds.Rd | 2 Rfast-2.0.2/Rfast/man/odds.ratio.Rd | 2 Rfast-2.0.2/Rfast/man/ompr.Rd | 12 Rfast-2.0.2/Rfast/man/pc.skel.Rd | 6 Rfast-2.0.2/Rfast/man/percent.ttest.Rd | 2 Rfast-2.0.2/Rfast/man/percent.ttests.Rd | 2 Rfast-2.0.2/Rfast/man/poisdisp.test.Rd | 2 Rfast-2.0.2/Rfast/man/poisson.anova.Rd | 2 Rfast-2.0.2/Rfast/man/poisson.anovas.Rd | 2 Rfast-2.0.2/Rfast/man/poly.cor.Rd | 2 Rfast-2.0.2/Rfast/man/pooled.cov.Rd | 2 Rfast-2.0.2/Rfast/man/prop.reg.Rd | 2 Rfast-2.0.2/Rfast/man/proptests.Rd | 2 Rfast-2.0.2/Rfast/man/quasi.poisson_only.Rd | 2 Rfast-2.0.2/Rfast/man/racg.Rd | 15 Rfast-2.0.2/Rfast/man/rbing.Rd | 2 Rfast-2.0.2/Rfast/man/rbingham.Rd | 2 Rfast-2.0.2/Rfast/man/regression.Rd | 2 Rfast-2.0.2/Rfast/man/rint.regbx.Rd | 2 Rfast-2.0.2/Rfast/man/rm.anova.Rd | 2 Rfast-2.0.2/Rfast/man/rm.lines.Rd | 2 Rfast-2.0.2/Rfast/man/rmdp.Rd | 4 Rfast-2.0.2/Rfast/man/rmvlaplace.Rd | 7 Rfast-2.0.2/Rfast/man/rmvnorm.Rd | 25 Rfast-2.0.2/Rfast/man/rvmf.Rd | 2 Rfast-2.0.2/Rfast/man/rvonmises.Rd | 2 Rfast-2.0.2/Rfast/man/score.glms.Rd | 13 Rfast-2.0.2/Rfast/man/sftests.Rd | 2 Rfast-2.0.2/Rfast/man/skew.test2.Rd | 6 Rfast-2.0.2/Rfast/man/spat.med.Rd | 2 Rfast-2.0.2/Rfast/man/spatmed.reg.Rd | 2 Rfast-2.0.2/Rfast/man/spdinv.Rd | 2 Rfast-2.0.2/Rfast/man/spml.reg.Rd | 2 Rfast-2.0.2/Rfast/man/spml.regs.Rd | 2 Rfast-2.0.2/Rfast/man/sscov.Rd | 2 Rfast-2.0.2/Rfast/man/standardise.Rd | 2 Rfast-2.0.2/Rfast/man/tobit.mle.Rd | 2 Rfast-2.0.2/Rfast/man/topological_sort.Rd | 2 Rfast-2.0.2/Rfast/man/ttest.Rd | 2 Rfast-2.0.2/Rfast/man/ttest1.Rd | 2 Rfast-2.0.2/Rfast/man/ttests.Rd | 2 Rfast-2.0.2/Rfast/man/twoway.anovas.Rd | 2 Rfast-2.0.2/Rfast/man/univglms.Rd | 2 Rfast-2.0.2/Rfast/man/varcomps.mom.Rd | 2 Rfast-2.0.2/Rfast/man/vm.mle.Rd | 2 Rfast-2.0.2/Rfast/man/yule.Rd | 2 Rfast-2.0.2/Rfast/man/zip.mle.Rd | 2 Rfast-2.0.2/Rfast/src/group.cpp | 26 Rfast-2.0.2/Rfast/src/init.c | 4 Rfast-2.0.2/Rfast/src/utilities.cpp | 6 216 files changed, 494 insertions(+), 451 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Description: GEE solver for correlated nominal or ordinal multinomial responses
using a local odds ratios parameterization.
Author: Anestis Touloumis [aut, cre] (<https://orcid.org/0000-0002-5965-1639>)
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between multgee versions 1.7.0 dated 2020-04-20 and 1.8.0 dated 2021-05-13
DESCRIPTION | 19 - MD5 | 67 ++-- NAMESPACE | 2 R/LORgee.control.R | 82 ++--- R/RcppExports.R |only R/fitLORgee.R | 658 ++++++++++++++++++++--------------------- R/matrixLOR.R | 116 +++---- R/multgee-package.R | 10 R/multgee_data.R | 98 +++--- R/multgee_internals_derivs.R | 172 +++++----- R/multgee_internals_utils.R | 158 ++++----- R/print.LORgee.R | 7 R/print.summary.LORgee.R | 5 R/print.waldts.R | 7 R/waldts.R | 5 build/vignette.rds |binary inst/CITATION | 8 inst/NEWS.Rd | 344 +++++++++++---------- inst/doc/multgee_vignette.Rmd | 9 inst/doc/multgee_vignette.pdf |binary man/LORgee.control.Rd | 86 ++--- man/arthritis.Rd | 68 ++-- man/confint.LORgee.Rd | 88 ++--- man/housing.Rd | 64 +-- man/intrinsic.pars.Rd | 150 ++++----- man/ipfp.control.Rd | 58 +-- man/matrixLOR.Rd | 108 +++--- man/multgee-package.Rd | 155 ++++----- man/nomLORgee.Rd | 350 ++++++++++----------- man/ordLORgee.Rd | 370 +++++++++++------------ man/vcov.LORgee.Rd | 78 ++-- man/waldts.Rd | 66 ++-- src |only vignettes/multgee_vignette.Rmd | 9 34 files changed, 1726 insertions(+), 1691 deletions(-)
Title: Multiple Imputation by Chained Equations with Random Forests
Description: Multiple Imputation has been shown to
be a flexible method to impute missing values by
Van Buuren (2007) <doi:10.1177/0962280206074463>.
Expanding on this, random forests have been shown
to be an accurate model by Stekhoven and Buhlmann
<arXiv:1105.0828> to impute missing values in datasets.
They have the added benefits of returning out of bag
error and variable importance estimates, as well as
being simple to run in parallel.
Author: Sam Wilson [aut, cre]
Maintainer: Sam Wilson <samwilson303@gmail.com>
Diff between miceRanger versions 1.3.5 dated 2020-04-03 and 1.4.0 dated 2021-05-13
DESCRIPTION | 8 +-- MD5 | 16 +++---- NEWS.md | 5 ++ R/imputeFromPred.R | 3 + R/runIterations.R | 20 +++++++-- build/vignette.rds |binary inst/doc/diagnosticPlotting.html | 80 +++++++++++++++----------------------- inst/doc/miceAlgorithm.html | 68 ++++++++++++-------------------- inst/doc/usingMiceRanger.html | 82 ++++++++++++++++----------------------- 9 files changed, 129 insertions(+), 153 deletions(-)
Title: Combinatorial Efficient Global Optimization
Description: Model building, surrogate model
based optimization and Efficient Global Optimization in combinatorial
or mixed search spaces.
Author: Martin Zaefferer <mzaefferer@gmail.com>
Maintainer: Martin Zaefferer <mzaefferer@gmail.com>
Diff between CEGO versions 2.4.0 dated 2019-12-08 and 2.4.2 dated 2021-05-13
DESCRIPTION | 11 +++--- MD5 | 69 +++++++++++++++++++------------------- NAMESPACE | 3 + NEWS | 6 +++ R/cegoPackage.R | 6 +-- R/modelKriging.R | 2 - R/modelKrigingLikelihood.R | 2 - R/modelLm.R | 2 - R/optim2opt.R | 2 - R/optimCEGO.R | 4 +- R/optimMIES.R | 2 - R/permutationBenchmarkFunctions.R | 9 ---- R/permutationDistances.r | 36 +++++++++++++++++++ inst/CITATION | 40 +++++++++++----------- man/CEGO-package.Rd | 6 +-- man/benchmarkGeneratorFSP.Rd | 2 - man/distancePermutationInsert.Rd | 2 - man/distancePermutationSwap.Rd | 4 ++ man/distancePermutationSwapInv.Rd |only man/distanceRealEuclidean.Rd | 48 +++++++++++++------------- man/distanceStringHamming.Rd | 44 ++++++++++++------------ man/fcorrCubic.Rd | 44 ++++++++++++------------ man/fcorrGauss.Rd | 44 ++++++++++++------------ man/fcorrLinear.Rd | 44 ++++++++++++------------ man/fcorrSphere.Rd | 44 ++++++++++++------------ man/modelKriging.Rd | 2 - man/modelKrigingLikelihood.Rd | 2 - man/modelLinear.Rd | 2 - man/optim2Opt.Rd | 2 - man/optimCEGO.Rd | 2 - man/optimMIES.Rd | 2 - man/print.Rd | 32 ++++++++--------- man/removeDuplicates.Rd | 38 ++++++++++---------- man/step2Opt.Rd | 42 +++++++++++------------ src/init.c | 2 + src/permutationDistance.c | 41 +++++++++++++++++++++- 36 files changed, 361 insertions(+), 282 deletions(-)
Title: Utilities for Sampling
Description: Interactive tools for generating random samples. Users select an
.xlsx, .csv, or delimited .txt file with population data and are walked through selecting the
sample type (Simple Random Sample or Stratified), the number of backups
desired, and a "stratify_on" value (if desired). The sample size is determined
using a normal approximation to the hypergeometric distribution based on
Nicholson (1956) <doi:10.1214/aoms/1177728270>. An .xlsx file is created
with the sample and key metadata for reference. It is menu-driven and lets
users pick an output directory. See vignettes for a detailed walk-through.
Author: Paul West [aut, cre]
Maintainer: Paul West <fp8049@gmail.com>
Diff between whSample versions 0.9.4 dated 2021-01-14 and 0.9.6.2 dated 2021-05-13
DESCRIPTION | 7 - MD5 | 18 +- R/sampler.R | 4 README.md | 94 ++++++------- build/vignette.rds |binary inst/doc/Using_sampler.R | 2 inst/doc/Using_sampler.Rmd | 8 - inst/doc/Using_sampler.html | 307 ++++---------------------------------------- inst/doc/Using_ssize.html | 297 +++--------------------------------------- vignettes/Using_sampler.Rmd | 8 - 10 files changed, 122 insertions(+), 623 deletions(-)
Title: Building and Estimating Structural Equation Models
Description: A powerful, easy to syntax for specifying and estimating complex
Structural Equation Models. Models can be estimated using Partial
Least Squares Path Modeling or Covariance-Based Structural Equation
Modeling or covariance based Confirmatory Factor Analysis.
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre],
André Calero Valdez [aut],
Juan Manuel Velasquez Estrada [ctb],
James Uanhoro [ctb],
Johannes Nakayama [ctb],
Lilian Koyan [ctb],
Laura Burbach [ctb],
Arturo Heynar Cano Bejar [ctb],
Susanne Adler [ctb]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminr versions 2.0.2 dated 2021-04-25 and 2.1.0 dated 2021-05-13
seminr-2.0.2/seminr/man/confidence_interval.Rd |only seminr-2.1.0/seminr/DESCRIPTION | 12 - seminr-2.1.0/seminr/MD5 | 80 ++++---- seminr-2.1.0/seminr/NAMESPACE | 4 seminr-2.1.0/seminr/R/data.R | 44 ++++ seminr-2.1.0/seminr/R/estimate_bootstrap.R | 27 ++- seminr-2.1.0/seminr/R/estimate_pls.R | 38 +++- seminr-2.1.0/seminr/R/evaluate_effects.R | 9 - seminr-2.1.0/seminr/R/evaluate_reliability.R | 2 seminr-2.1.0/seminr/R/evaluate_warnings.R | 33 +-- seminr-2.1.0/seminr/R/feature_higher_order.R | 6 seminr-2.1.0/seminr/R/feature_plspredict.R | 16 + seminr-2.1.0/seminr/R/library.R | 12 - seminr-2.1.0/seminr/R/plot_dot.R | 66 ++++++- seminr-2.1.0/seminr/R/plot_results.R | 2 seminr-2.1.0/seminr/R/report_descriptives.R | 2 seminr-2.1.0/seminr/R/report_paths_and_intervals.R | 47 ++--- seminr-2.1.0/seminr/R/specify_constructs.R | 38 +++- seminr-2.1.0/seminr/README.md | 90 +++++----- seminr-2.1.0/seminr/data/influencer_data.rda |only seminr-2.1.0/seminr/demo/00Index | 1 seminr-2.1.0/seminr/demo/seminr-pls-influencer.R |only seminr-2.1.0/seminr/demo/seminr-primer-chap3.R | 12 - seminr-2.1.0/seminr/demo/seminr-primer-chap4.R | 4 seminr-2.1.0/seminr/demo/seminr-primer-chap5.R | 11 - seminr-2.1.0/seminr/demo/seminr-primer-chap6.R | 30 +-- seminr-2.1.0/seminr/demo/seminr-primer-chap7.R | 10 - seminr-2.1.0/seminr/demo/seminr-primer-chap8.R | 2 seminr-2.1.0/seminr/inst/doc/SEMinR.R | 18 +- seminr-2.1.0/seminr/inst/doc/SEMinR.Rmd | 20 +- seminr-2.1.0/seminr/inst/doc/SEMinR.html | 48 ++--- seminr-2.1.0/seminr/man/estimate_pls.Rd | 10 + seminr-2.1.0/seminr/man/figures/model.png |binary seminr-2.1.0/seminr/man/figures/model2.png |binary seminr-2.1.0/seminr/man/figures/model_pls.png |binary seminr-2.1.0/seminr/man/get_mm_edge_style.Rd | 4 seminr-2.1.0/seminr/man/higher_composite.Rd | 10 - seminr-2.1.0/seminr/man/higher_reflective.Rd |only seminr-2.1.0/seminr/man/influencer_data.Rd |only seminr-2.1.0/seminr/man/is_sink.Rd |only seminr-2.1.0/seminr/man/specific_effect_significance.Rd |only seminr-2.1.0/seminr/tests/fixtures/V_3_6_0/missing_cases_item_descriptives.csv |only seminr-2.1.0/seminr/tests/fixtures/V_3_6_0/missing_cases_paths.csv |only seminr-2.1.0/seminr/tests/testthat/test-bootstrap.R | 88 +++++++++ seminr-2.1.0/seminr/tests/testthat/test-cbsem-higher-order.R |only seminr-2.1.0/seminr/vignettes/SEMinR.Rmd | 20 +- 46 files changed, 556 insertions(+), 260 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] (<https://orcid.org/0000-0002-6608-0619>),
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.3.0 dated 2020-12-04 and 1.3.1 dated 2021-05-13
RNifti-1.3.0/RNifti/inst/doxygen |only RNifti-1.3.1/RNifti/DESCRIPTION | 8 RNifti-1.3.1/RNifti/MD5 | 251 -------------- RNifti-1.3.1/RNifti/NEWS | 14 RNifti-1.3.1/RNifti/R/nifti.R | 11 RNifti-1.3.1/RNifti/R/xform.R | 2 RNifti-1.3.1/RNifti/README.md | 2 RNifti-1.3.1/RNifti/inst/include/RNifti.h | 2 RNifti-1.3.1/RNifti/inst/include/RNifti/NiftiImage_impl.h | 3 RNifti-1.3.1/RNifti/man/niftiHeader.Rd | 2 RNifti-1.3.1/RNifti/man/readNifti.Rd | 2 RNifti-1.3.1/RNifti/man/writeNifti.Rd | 2 RNifti-1.3.1/RNifti/man/xform.Rd | 2 RNifti-1.3.1/RNifti/src/main.cpp | 54 ++- RNifti-1.3.1/RNifti/src/niftilib/nifti2_io.c | 5 RNifti-1.3.1/RNifti/tests/testthat/test-05-nifti.R | 11 16 files changed, 107 insertions(+), 264 deletions(-)
Title: Analyze Bacterial Pangenomes in R with 'Pagoo'
Description: Provides an encapsulated, object-oriented class system for
analyzing bacterial pangenomes. For a definition of this concept, see
Tettelin, et al. (2005) <doi:10.1073/pnas.0506758102>. It uses the R6
package as backend. It was designed in order to facilitate and speed-up
the comparative analysis of multiple bacterial genomes, standardizing and
optimizing routine tasks performed everyday. There are a handful of things
done everyday when working with bacterial pangenomes: subset, summarize,
extract, visualize and store data. So, 'pagoo' is intended to facilitate these
tasks as much as possible. For a description of the implemented data structure
and methods, see Ferres & Iraola (2020), <doi:10.1101/2020.07.29.226951>.
Author: Ignacio Ferres [aut, cre] (<https://orcid.org/0000-0003-0910-6568>),
Gregorio Iraola [aut] (<https://orcid.org/0000-0002-6516-3404>),
Institut Pasteur de Montevideo [fnd]
Maintainer: Ignacio Ferres <iferres@pasteur.edu.uy>
Diff between pagoo versions 0.3.8 dated 2021-02-12 and 0.3.9 dated 2021-05-13
DESCRIPTION | 9 MD5 | 48 +-- NAMESPACE | 1 NEWS.md | 6 R/PgR6.R | 67 ++-- R/panaroo_2_pagoo.R |only R/roary_2_pagoo.R | 2 README.md | 8 build/vignette.rds |binary inst/doc/Input.Rmd | 6 inst/doc/Input.html | 187 ++++++++---- inst/doc/Methods_Plots.Rmd | 2 inst/doc/Methods_Plots.html | 161 +++++++---- inst/doc/Querying_Data.html | 243 ++++++++-------- inst/doc/Recipes.R | 47 ++- inst/doc/Recipes.Rmd | 66 +++- inst/doc/Recipes.html | 640 ++++++++++++++++++++++++-------------------- inst/doc/Subseting.html | 361 ++++++++++++------------ inst/doc/pagoo.html | 123 +++++--- man/PgR6.Rd | 4 man/panaroo_2_pagoo.Rd |only man/roary_2_pagoo.Rd | 2 tests/testthat/test_input.R | 50 +++ vignettes/Input.Rmd | 6 vignettes/Methods_Plots.Rmd | 2 vignettes/Recipes.Rmd | 66 +++- 26 files changed, 1246 insertions(+), 861 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for descriptive statistics (e.g., frequency table, cross tabulation, multilevel descriptive statistics, coefficient alpha and omega, and various effect size measures), missing data (e.g., descriptive statistics for missing data, missing data pattern and auxiliary variable analysis), data management (e.g., grand-mean and group-mean centering, recode variables and reverse code items, scale and group scores, reading and writing SPSS and Excel files), and statistical analysis (e.g., confidence intervals, collinearity diagnostics, Levene's test, t-test, Welch's test, z-test, and sample size determination).
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.3.2 dated 2020-06-08 and 0.4.0 dated 2021-05-13
misty-0.3.2/misty/R/alpha.coef.R |only misty-0.3.2/misty/R/cont.coef.R |only misty-0.3.2/misty/R/cramers.v.R |only misty-0.3.2/misty/R/levenes.test.R |only misty-0.3.2/misty/R/mgsub.R |only misty-0.3.2/misty/R/omega.coef.R |only misty-0.3.2/misty/R/phi.coef.R |only misty-0.3.2/misty/R/poly.cor.R |only misty-0.3.2/misty/R/reverse.item.R |only misty-0.3.2/misty/R/scores.R |only misty-0.3.2/misty/R/stromit.R |only misty-0.3.2/misty/R/trim.R |only misty-0.3.2/misty/R/z.test.R |only misty-0.3.2/misty/build |only misty-0.3.2/misty/inst |only misty-0.3.2/misty/man/alpha.coef.Rd |only misty-0.3.2/misty/man/cont.coef.Rd |only misty-0.3.2/misty/man/cramers.v.Rd |only misty-0.3.2/misty/man/levenes.test.Rd |only misty-0.3.2/misty/man/mgsub.Rd |only misty-0.3.2/misty/man/omega.coef.Rd |only misty-0.3.2/misty/man/phi.coef.Rd |only misty-0.3.2/misty/man/poly.cor.Rd |only misty-0.3.2/misty/man/reverse.item.Rd |only misty-0.3.2/misty/man/scores.Rd |only misty-0.3.2/misty/man/stromit.Rd |only misty-0.3.2/misty/man/trim.Rd |only misty-0.3.2/misty/man/z.test.Rd |only misty-0.3.2/misty/vignettes |only misty-0.4.0/misty/DESCRIPTION | 13 misty-0.4.0/misty/MD5 | 243 +- misty-0.4.0/misty/NAMESPACE | 55 misty-0.4.0/misty/NEWS.md | 64 misty-0.4.0/misty/R/as.na.R | 94 misty-0.4.0/misty/R/center.R | 53 misty-0.4.0/misty/R/chr.gsub.R |only misty-0.4.0/misty/R/chr.omit.R |only misty-0.4.0/misty/R/chr.trim.R |only misty-0.4.0/misty/R/ci.mean.R | 110 - misty-0.4.0/misty/R/ci.mean.diff.R | 372 +-- misty-0.4.0/misty/R/ci.median.R | 98 misty-0.4.0/misty/R/ci.prop.R | 108 - misty-0.4.0/misty/R/ci.prop.diff.R | 337 +-- misty-0.4.0/misty/R/ci.sd.R | 108 - misty-0.4.0/misty/R/ci.var.R | 110 - misty-0.4.0/misty/R/cohens.d.R | 1534 +++++++++++---- misty-0.4.0/misty/R/collin.diag.R | 57 misty-0.4.0/misty/R/cor.cont.R |only misty-0.4.0/misty/R/cor.cramer.R |only misty-0.4.0/misty/R/cor.matrix.R | 396 ++-- misty-0.4.0/misty/R/cor.phi.R |only misty-0.4.0/misty/R/cor.poly.R |only misty-0.4.0/misty/R/crosstab.R | 44 misty-0.4.0/misty/R/descript.R | 195 + misty-0.4.0/misty/R/df.duplicated.R | 38 misty-0.4.0/misty/R/df.merge.R | 18 misty-0.4.0/misty/R/df.rbind.R | 38 misty-0.4.0/misty/R/df.rename.R | 24 misty-0.4.0/misty/R/df.sort.R | 16 misty-0.4.0/misty/R/dummy.c.R | 42 misty-0.4.0/misty/R/eta.sq.R | 46 misty-0.4.0/misty/R/freq.R | 107 - misty-0.4.0/misty/R/group.scores.R | 30 misty-0.4.0/misty/R/item.alpha.R |only misty-0.4.0/misty/R/item.omega.R |only misty-0.4.0/misty/R/item.reverse.R |only misty-0.4.0/misty/R/item.scores.R |only misty-0.4.0/misty/R/kurtosis.R | 26 misty-0.4.0/misty/R/multilevel.descript.R | 72 misty-0.4.0/misty/R/multilevel.icc.R | 123 - misty-0.4.0/misty/R/na.as.R | 30 misty-0.4.0/misty/R/na.auxiliary.R | 38 misty-0.4.0/misty/R/na.coverage.R | 18 misty-0.4.0/misty/R/na.descript.R | 18 misty-0.4.0/misty/R/na.indicator.R | 12 misty-0.4.0/misty/R/na.pattern.R | 20 misty-0.4.0/misty/R/na.prop.R | 14 misty-0.4.0/misty/R/print.misty.object.R | 2661 ++++++++++++++++++--------- misty-0.4.0/misty/R/read.mplus.R | 63 misty-0.4.0/misty/R/read.sav.R | 149 + misty-0.4.0/misty/R/read.xlsx.R | 14 misty-0.4.0/misty/R/rec.R | 48 misty-0.4.0/misty/R/run.mplus.R | 94 misty-0.4.0/misty/R/rwg.lindell.R | 36 misty-0.4.0/misty/R/size.cor.R | 26 misty-0.4.0/misty/R/size.mean.R | 16 misty-0.4.0/misty/R/size.prop.R | 40 misty-0.4.0/misty/R/skewness.R | 24 misty-0.4.0/misty/R/std.coef.R | 34 misty-0.4.0/misty/R/test.levene.R |only misty-0.4.0/misty/R/test.t.R |only misty-0.4.0/misty/R/test.welch.R |only misty-0.4.0/misty/R/test.z.R |only misty-0.4.0/misty/R/write.mplus.R | 16 misty-0.4.0/misty/R/write.sav.R | 78 misty-0.4.0/misty/man/as.na.Rd | 28 misty-0.4.0/misty/man/center.Rd | 6 misty-0.4.0/misty/man/chr.gsub.Rd |only misty-0.4.0/misty/man/chr.omit.Rd |only misty-0.4.0/misty/man/chr.trim.Rd |only misty-0.4.0/misty/man/ci.mean.Rd | 4 misty-0.4.0/misty/man/ci.mean.diff.Rd | 163 - 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misty-0.4.0/misty/man/na.auxiliary.Rd | 15 misty-0.4.0/misty/man/na.coverage.Rd | 6 misty-0.4.0/misty/man/na.descript.Rd | 6 misty-0.4.0/misty/man/na.pattern.Rd | 8 misty-0.4.0/misty/man/print.misty.object.Rd | 42 misty-0.4.0/misty/man/read.mplus.Rd | 2 misty-0.4.0/misty/man/read.sav.Rd | 22 misty-0.4.0/misty/man/read.xlsx.Rd | 204 +- misty-0.4.0/misty/man/rec.Rd | 4 misty-0.4.0/misty/man/size.cor.Rd | 130 - misty-0.4.0/misty/man/size.mean.Rd | 176 - misty-0.4.0/misty/man/size.prop.Rd | 191 - misty-0.4.0/misty/man/std.coef.Rd | 4 misty-0.4.0/misty/man/test.levene.Rd |only misty-0.4.0/misty/man/test.t.Rd |only misty-0.4.0/misty/man/test.welch.Rd |only misty-0.4.0/misty/man/test.z.Rd |only misty-0.4.0/misty/man/write.mplus.Rd | 2 misty-0.4.0/misty/man/write.sav.Rd | 10 151 files changed, 6659 insertions(+), 4422 deletions(-)
Title: Framework for the Visualization of Distributional Regression
Models
Description: Functions for visualizing distributional regression models fitted using the 'gamlss', 'bamlss' or 'betareg' R package. The core of the package consists of a 'shiny' application, where the model results can be interactively explored and visualized.
Author: Stanislaus Stadlmann [cre, aut]
(<https://orcid.org/0000-0001-6542-6342>)
Maintainer: Stanislaus Stadlmann <stadlmann@uni-goettingen.de>
Diff between distreg.vis versions 1.7.1 dated 2021-02-18 and 1.7.2 dated 2021-05-13
distreg.vis-1.7.1/distreg.vis/man/expl_vars.Rd |only distreg.vis-1.7.2/distreg.vis/DESCRIPTION | 8 distreg.vis-1.7.2/distreg.vis/MD5 | 17 - distreg.vis-1.7.2/distreg.vis/R/moments.R | 2 distreg.vis-1.7.2/distreg.vis/R/object_specific.R | 34 -- distreg.vis-1.7.2/distreg.vis/R/preds.R | 3 distreg.vis-1.7.2/distreg.vis/R/vis.R | 14 distreg.vis-1.7.2/distreg.vis/data/dists.rda |binary distreg.vis-1.7.2/distreg.vis/inst/extdata/dist_df.csv | 252 ++++++++--------- distreg.vis-1.7.2/distreg.vis/man/moments.Rd | 2 10 files changed, 158 insertions(+), 174 deletions(-)
Title: Adaptive Gauss Hermite Quadrature for Bayesian Inference
Description: Adaptive Gauss Hermite Quadrature for Bayesian inference.
The AGHQ method for normalizing posterior distributions
and making Bayesian inferences based on them. Functions are provided for doing
quadrature and marginal Laplace approximations, and summary methods are provided
for making inferences based on the results.
See Stringer (2021). "Implementing Adaptive Quadrature for Bayesian Inference:
the aghq Package" <arXiv:2101.04468>.
Author: Alex Stringer
Maintainer: Alex Stringer <alex.stringer@mail.utoronto.ca>
Diff between aghq versions 0.2.0 dated 2021-05-10 and 0.2.1 dated 2021-05-13
DESCRIPTION | 6 +++--- MD5 | 17 ++++++++++------- NEWS.md | 3 +++ R/00-misc-support-functions.R | 3 ++- R/01-optimization.R | 1 + README.md | 2 +- inst/extsrc |only tests/testthat/setup-01-optimization.R | 4 ++++ tests/testthat/test-04-aghq.R | 5 +++++ 9 files changed, 29 insertions(+), 12 deletions(-)
Title: Using KEEL in R Code
Description: 'KEEL' is a popular Java software for a large number of different knowledge data discovery tasks.
This package takes the advantages of 'KEEL' and R, allowing to use 'KEEL' algorithms in simple R code.
The implemented R code layer between R and 'KEEL' makes easy both using 'KEEL' algorithms in R as implementing new algorithms for 'RKEEL' in a very simple way.
It includes more than 100 algorithms for classification, regression, preprocess, association rules and imbalance learning, which allows a more complete experimentation process.
For more information about KEEL, see <http://www.keel.es/>.
Author: Jose M. Moyano [aut, cre],
Luciano Sanchez [aut],
Oliver Sanchez [ctb],
Jesus Alcala-Fernandez [ctb]
Maintainer: Jose M. Moyano <jmoyano@uco.es>
Diff between RKEEL versions 1.3.2 dated 2020-03-19 and 1.3.3 dated 2021-05-13
CHANGELOG |only DESCRIPTION | 8 MD5 | 11 R/KeelUtils.R | 1240 +++++++++++++++++++++++------------------------ man/CART-R.Rd | 10 man/FPgrowth-A.Rd | 10 man/Nominal2Binary-TR.Rd | 4 7 files changed, 642 insertions(+), 641 deletions(-)
Title: Relative Importance of Regressors in Linear Models
Description: Provides several metrics for assessing relative importance in linear models. These can be printed, plotted and bootstrapped. The recommended metric is lmg, which provides a decomposition of the model explained variance into non-negative contributions. There is a version of this package available that additionally provides a new and also recommended metric called pmvd. If you are a non-US user, you can download this extended version from Ulrike Groempings web site.
Author: Ulrike Groemping [aut, cre],
Lehrkamp Matthias [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between relaimpo versions 2.2-3 dated 2018-03-10 and 2.2-4 dated 2021-05-13
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- R/calc.relimp.default.intern.R | 6 ++++-- inst/NEWS | 6 ++++++ man/booteval.relimp.Rd | 8 ++++---- man/calc.relimp.Rd | 6 +++--- man/mianalyze.relimp.Rd | 10 +++++----- man/relaimpo-package.Rd | 6 +++--- 8 files changed, 37 insertions(+), 28 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Eamon B. O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 3.3 dated 2021-03-18 and 3.4 dated 2021-05-13
pomp-3.3/pomp/R/deprecated.R |only pomp-3.3/pomp/R/pomp-package.R |only pomp-3.3/pomp/R/profileDesign.R |only pomp-3.3/pomp/R/runifDesign.R |only pomp-3.3/pomp/R/sliceDesign.R |only pomp-3.3/pomp/R/sobolDesign.R |only pomp-3.3/pomp/man/deprecated.Rd |only pomp-3.4/pomp/DESCRIPTION | 32 +-- pomp-3.4/pomp/MD5 | 284 ++++++++++++++--------------- pomp-3.4/pomp/NAMESPACE | 5 pomp-3.4/pomp/R/aaa.R | 2 pomp-3.4/pomp/R/abc.R | 12 - pomp-3.4/pomp/R/as_data_frame.R | 75 ++----- pomp-3.4/pomp/R/as_pomp.R | 5 pomp-3.4/pomp/R/blowflies.R | 1 pomp-3.4/pomp/R/bsflu.R | 1 pomp-3.4/pomp/R/bsmc2.R | 10 - pomp-3.4/pomp/R/coef.R | 20 -- pomp-3.4/pomp/R/concat.R | 1 pomp-3.4/pomp/R/cond_logLik.R | 21 -- pomp-3.4/pomp/R/continue.R | 2 pomp-3.4/pomp/R/covariate_table.R | 11 - pomp-3.4/pomp/R/covmat.R | 18 - pomp-3.4/pomp/R/csnippet.R | 6 pomp-3.4/pomp/R/dmeasure_spec.R | 2 pomp-3.4/pomp/R/ebola.R | 3 pomp-3.4/pomp/R/eff_sample_size.R | 8 pomp-3.4/pomp/R/elementary_algorithms.R | 2 pomp-3.4/pomp/R/estimation_algorithms.R | 6 pomp-3.4/pomp/R/extract.R | 6 pomp-3.4/pomp/R/filter_mean.R | 8 pomp-3.4/pomp/R/filter_traj.R | 11 - pomp-3.4/pomp/R/flow.R | 4 pomp-3.4/pomp/R/forecast.R | 6 pomp-3.4/pomp/R/kalman.R | 12 - pomp-3.4/pomp/R/listie.R | 11 - pomp-3.4/pomp/R/load.R | 16 - pomp-3.4/pomp/R/loglik.R | 55 +---- pomp-3.4/pomp/R/logmeanexp.R | 5 pomp-3.4/pomp/R/lookup.R | 2 pomp-3.4/pomp/R/melt.R | 15 + pomp-3.4/pomp/R/mif2.R | 16 - pomp-3.4/pomp/R/nlf.R | 14 - pomp-3.4/pomp/R/objfun.R | 20 -- pomp-3.4/pomp/R/obs.R | 3 pomp-3.4/pomp/R/package.R |only pomp-3.4/pomp/R/parameter_trans.R | 23 -- pomp-3.4/pomp/R/parmat.R | 5 pomp-3.4/pomp/R/pfilter.R | 13 - pomp-3.4/pomp/R/plot.R | 57 +---- pomp-3.4/pomp/R/pmcmc.R | 14 - pomp-3.4/pomp/R/pomp_fun.R | 4 pomp-3.4/pomp/R/pred_mean.R | 6 pomp-3.4/pomp/R/pred_var.R | 6 pomp-3.4/pomp/R/print.R | 18 + pomp-3.4/pomp/R/probe.R | 16 - pomp-3.4/pomp/R/probe_match.R | 23 -- pomp-3.4/pomp/R/sannbox.R | 2 pomp-3.4/pomp/R/saved_states.R | 7 pomp-3.4/pomp/R/show.R | 26 +- pomp-3.4/pomp/R/simulate.R | 22 -- pomp-3.4/pomp/R/skeleton_spec.R | 12 - pomp-3.4/pomp/R/spect.R | 12 - pomp-3.4/pomp/R/spect_match.R | 23 -- pomp-3.4/pomp/R/spy.R | 1 pomp-3.4/pomp/R/states.R | 3 pomp-3.4/pomp/R/summary.R | 9 pomp-3.4/pomp/R/time.R | 15 - pomp-3.4/pomp/R/timezero.R | 11 - pomp-3.4/pomp/R/traces.R | 21 -- pomp-3.4/pomp/R/traj_match.R | 14 - pomp-3.4/pomp/R/trajectory.R | 4 pomp-3.4/pomp/R/userdata.R | 2 pomp-3.4/pomp/R/window.R | 9 pomp-3.4/pomp/R/workhorses.R | 27 -- pomp-3.4/pomp/R/wpfilter.R | 12 - pomp-3.4/pomp/build/partial.rdb |binary pomp-3.4/pomp/inst/NEWS | 14 + pomp-3.4/pomp/inst/NEWS.Rd | 11 + pomp-3.4/pomp/man/abc.Rd | 13 - pomp-3.4/pomp/man/as_data_frame.Rd | 20 -- pomp-3.4/pomp/man/as_pomp.Rd | 5 pomp-3.4/pomp/man/basic_probes.Rd | 2 pomp-3.4/pomp/man/bsflu.Rd | 1 pomp-3.4/pomp/man/bsmc2.Rd | 8 pomp-3.4/pomp/man/coef.Rd | 7 pomp-3.4/pomp/man/concat.Rd | 1 pomp-3.4/pomp/man/cond_logLik.Rd | 4 pomp-3.4/pomp/man/continue.Rd | 3 pomp-3.4/pomp/man/covariate_table.Rd | 4 pomp-3.4/pomp/man/covmat.Rd | 5 pomp-3.4/pomp/man/csnippet.Rd | 4 pomp-3.4/pomp/man/dmeasure.Rd | 3 pomp-3.4/pomp/man/dmeasure_spec.Rd | 2 pomp-3.4/pomp/man/dprior.Rd | 3 pomp-3.4/pomp/man/dprocess.Rd | 3 pomp-3.4/pomp/man/eff_sample_size.Rd | 3 pomp-3.4/pomp/man/elementary_algorithms.Rd | 2 pomp-3.4/pomp/man/estimation_algorithms.Rd | 12 - pomp-3.4/pomp/man/filter_mean.Rd | 4 pomp-3.4/pomp/man/filter_traj.Rd | 4 pomp-3.4/pomp/man/flow.Rd | 1 pomp-3.4/pomp/man/forecast.Rd | 1 pomp-3.4/pomp/man/kalman.Rd | 14 - pomp-3.4/pomp/man/listie.Rd | 12 - pomp-3.4/pomp/man/load.Rd | 10 - pomp-3.4/pomp/man/loglik.Rd | 27 +- pomp-3.4/pomp/man/lookup.Rd | 2 pomp-3.4/pomp/man/melt.Rd | 3 pomp-3.4/pomp/man/mif2.Rd | 10 - pomp-3.4/pomp/man/nlf.Rd | 13 - pomp-3.4/pomp/man/obs.Rd | 1 pomp-3.4/pomp/man/parameter_trans.Rd | 14 - pomp-3.4/pomp/man/partrans.Rd | 3 pomp-3.4/pomp/man/pfilter.Rd | 8 pomp-3.4/pomp/man/plot.Rd | 26 -- pomp-3.4/pomp/man/pmcmc.Rd | 10 - pomp-3.4/pomp/man/pomp-package.Rd | 18 - pomp-3.4/pomp/man/pred_mean.Rd | 2 pomp-3.4/pomp/man/pred_var.Rd | 1 pomp-3.4/pomp/man/print.Rd | 15 + pomp-3.4/pomp/man/probe.Rd | 14 - pomp-3.4/pomp/man/probe_match.Rd | 22 +- pomp-3.4/pomp/man/rinit.Rd | 3 pomp-3.4/pomp/man/rmeasure.Rd | 3 pomp-3.4/pomp/man/rprior.Rd | 3 pomp-3.4/pomp/man/rprocess.Rd | 3 pomp-3.4/pomp/man/sannbox.Rd | 2 pomp-3.4/pomp/man/saved_states.Rd | 2 pomp-3.4/pomp/man/show.Rd | 56 +++-- pomp-3.4/pomp/man/simulate.Rd | 4 pomp-3.4/pomp/man/sir.Rd | 3 pomp-3.4/pomp/man/skeleton.Rd | 3 pomp-3.4/pomp/man/skeleton_spec.Rd | 2 pomp-3.4/pomp/man/spect.Rd | 11 - pomp-3.4/pomp/man/spect_match.Rd | 14 - pomp-3.4/pomp/man/states.Rd | 1 pomp-3.4/pomp/man/summary.Rd | 9 pomp-3.4/pomp/man/time.Rd | 2 pomp-3.4/pomp/man/timezero.Rd | 2 pomp-3.4/pomp/man/traces.Rd | 17 - pomp-3.4/pomp/man/traj_match.Rd | 11 - pomp-3.4/pomp/man/trajectory.Rd | 2 pomp-3.4/pomp/man/userdata.Rd | 2 pomp-3.4/pomp/man/window.Rd | 1 pomp-3.4/pomp/man/wpfilter.Rd | 5 pomp-3.4/pomp/src/distributions.c | 5 147 files changed, 560 insertions(+), 1119 deletions(-)
Title: Joint Frailty-Copula Models for Tumour Progression and Death in
Meta-Analysis
Description: Fit survival data and perform dynamic prediction under joint frailty-copula models for tumour progression and death.
Likelihood-based methods are employed for estimating model parameters, where the baseline hazard functions are modeled by the cubic M-spline or the Weibull model.
The methods are applicable for meta-analytic data containing individual-patient information from several studies.
Survival outcomes need information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
Methodologies were published in
Emura et al. (2017) <doi:10.1177/0962280215604510>, Emura et al. (2018) <doi:10.1177/0962280216688032>,
Emura et al. (2020) <doi:10.1177/0962280219892295>, Shinohara et al. (2020) <doi:10.1080/03610918.2020.1855449>
and Wu et al. (2020) <doi:10.1007/s00180-020-00977-1>.
See also the book of Emura et al. (2019) <doi:10.1007/978-981-13-3516-7>.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 3.11 dated 2021-04-24 and 3.12 dated 2021-05-13
DESCRIPTION | 8 +++---- MD5 | 10 ++++---- NAMESPACE | 2 - R/Weibull.simu.R | 53 +++++++++++++++++++++++++++++++++-------------- man/Weibull.simu.Rd | 8 +++++-- man/joint.Cox-package.Rd | 4 +-- 6 files changed, 56 insertions(+), 29 deletions(-)
Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Description: A disk-based data manipulation tool for working with
large-than-RAM datasets. Aims to lower the barrier-to-entry for
manipulating large datasets by adhering closely to popular and
familiar data manipulation paradigms like 'dplyr' verbs and
'data.table' syntax.
Author: Dai ZJ [aut, cre],
Jacky Poon [ctb]
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>
Diff between disk.frame versions 0.4.1 dated 2021-03-14 and 0.5.0 dated 2021-05-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 -- NEWS.md | 3 +++ R/dplyr_verbs.r | 8 ++++---- README.md | 30 +++++++++++++++--------------- man/dplyr_verbs.Rd | 3 --- 7 files changed, 32 insertions(+), 34 deletions(-)
Title: Efficient Bayesian Inference for Time-Varying Parameter Models
with Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of time-varying parameter models with shrinkage priors. Details on the algorithms used are provided in Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and
Cadonna et al. (2020) <doi:10.3390/econometrics8020020>.
Author: Peter Knaus [aut, cre] (<https://orcid.org/0000-0001-6498-7084>),
Angela Bitto-Nemling [aut],
Annalisa Cadonna [aut] (<https://orcid.org/0000-0003-0360-7628>),
Sylvia Frühwirth-Schnatter [aut]
(<https://orcid.org/0000-0003-0516-5552>),
Daniel Winkler [ctb],
Kemal Dingic [ctb]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkTVP versions 2.0.1 dated 2020-11-09 and 2.0.2 dated 2021-05-13
DESCRIPTION | 9 ++---- MD5 | 22 ++++++++-------- NEWS.md | 8 +++++ build/vignette.rds |binary inst/doc/shrinkTVP.pdf |binary inst/include/shrinkTVP.h | 10 ++----- src/Makevars | 2 - src/Makevars.win | 2 - src/cpp_utilities.cpp | 29 ++++++++++++--------- src/cpp_utilities.h | 3 +- src/do_rgig1.cpp | 7 ++--- src/shrinkTVP.cpp | 64 +++++++++++++++++------------------------------ 12 files changed, 74 insertions(+), 82 deletions(-)
Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google
Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>
Diff between ngramr versions 1.7.2 dated 2020-08-24 and 1.7.4 dated 2021-05-13
DESCRIPTION | 12 ++++++------ MD5 | 19 ++++++++++--------- NEWS | 8 ++++++++ R/ggram.R | 3 ++- R/ngram.R | 30 ++++++++++++++++-------------- R/ngramr-package.R | 4 ++-- man/chunk.Rd | 8 ++++---- man/ggram.Rd | 4 ++-- man/ngram.Rd | 30 +++++++++++++++++------------- man/ngramr.Rd | 5 +++-- tests/results.txt |only 11 files changed, 70 insertions(+), 53 deletions(-)
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Title: High-Dimensional Inference
Description: Implementation of multiple approaches to perform inference in high-dimensional models.
Author: Lukas Meier [aut, cre], Ruben Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann [aut]
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>
Diff between hdi versions 0.1-7 dated 2019-03-29 and 0.1-8 dated 2021-05-13
DESCRIPTION | 13 +++++-------- MD5 | 28 ++++++++++++++-------------- build/partial.rdb |binary data/riboflavin.RData |binary man/boot.lasso.proj.Rd | 2 +- man/fdr.adjust.Rd | 2 +- man/groupBound.rd | 2 +- man/hdi.Rd | 2 +- man/lasso.cv.Rd | 2 +- man/lasso.firstq.Rd | 2 +- man/lasso.proj.Rd | 2 +- man/lm.ci.Rd | 2 +- man/lm.pval.Rd | 2 +- man/multi.split.Rd | 2 +- man/stability.Rd | 2 +- 15 files changed, 30 insertions(+), 33 deletions(-)
Title: Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Description: Bayesian nonparametric density estimation modeling mixtures by a Ferguson-Klass type algorithm for posterior normalized random measures.
Author: Julyan Arbel [ctb],
Ernesto Barrios [aut],
Guillaume Kon Kam King [aut, cre],
Antonio Lijoi [aut],
Luis E. Nieto-Barajas [aut],
Igor Prünster [aut]
Maintainer: Guillaume Kon Kam King <guillaume.konkamking.work@gmail.com>
Diff between BNPdensity versions 2020.3.4 dated 2020-03-08 and 2021.5.4 dated 2021-05-13
BNPdensity-2020.3.4/BNPdensity/data/datalist |only BNPdensity-2021.5.4/BNPdensity/DESCRIPTION | 12 BNPdensity-2021.5.4/BNPdensity/MD5 | 83 ++++-- BNPdensity-2021.5.4/BNPdensity/NAMESPACE | 8 BNPdensity-2021.5.4/BNPdensity/R/BNPdensity-package.R | 6 BNPdensity-2021.5.4/BNPdensity/R/MixNRMI1.R | 49 +++- BNPdensity-2021.5.4/BNPdensity/R/MixNRMI1cens.R | 48 +++ BNPdensity-2021.5.4/BNPdensity/R/MixNRMI2.R | 61 +++-- BNPdensity-2021.5.4/BNPdensity/R/MixNRMI2cens.R | 47 ++- BNPdensity-2021.5.4/BNPdensity/R/MixPY1.R |only BNPdensity-2021.5.4/BNPdensity/R/MixPY2.R |only BNPdensity-2021.5.4/BNPdensity/R/MvInv.R | 23 + BNPdensity-2021.5.4/BNPdensity/R/convert_fit_to_MCMC_chain.R | 2 BNPdensity-2021.5.4/BNPdensity/R/dt_.R | 6 BNPdensity-2021.5.4/BNPdensity/R/gs3.R | 121 +++++++++- BNPdensity-2021.5.4/BNPdensity/R/multMixNRMI.R | 23 - BNPdensity-2021.5.4/BNPdensity/R/summarytext.R | 8 BNPdensity-2021.5.4/BNPdensity/R/thresholdGG.R | 19 + BNPdensity-2021.5.4/BNPdensity/man/BNPdensity-package.Rd | 6 BNPdensity-2021.5.4/BNPdensity/man/MixNRMI1.Rd | 11 BNPdensity-2021.5.4/BNPdensity/man/MixNRMI1cens.Rd | 11 BNPdensity-2021.5.4/BNPdensity/man/MixNRMI2.Rd | 23 + BNPdensity-2021.5.4/BNPdensity/man/MixNRMI2cens.Rd | 16 - BNPdensity-2021.5.4/BNPdensity/man/MixPY1.Rd |only BNPdensity-2021.5.4/BNPdensity/man/MixPY2.Rd |only BNPdensity-2021.5.4/BNPdensity/man/MvInv.Rd | 34 +- BNPdensity-2021.5.4/BNPdensity/man/acidity.Rd | 4 BNPdensity-2021.5.4/BNPdensity/man/dt_.Rd | 22 + BNPdensity-2021.5.4/BNPdensity/man/enzyme.Rd | 6 BNPdensity-2021.5.4/BNPdensity/man/galaxy.Rd | 6 BNPdensity-2021.5.4/BNPdensity/man/gs3.Rd | 8 BNPdensity-2021.5.4/BNPdensity/man/gs3_adaptive3.Rd |only BNPdensity-2021.5.4/BNPdensity/man/gs3_log.Rd |only BNPdensity-2021.5.4/BNPdensity/man/logacceptance_ratio_logu.Rd |only BNPdensity-2021.5.4/BNPdensity/man/logdprop_logu.Rd |only BNPdensity-2021.5.4/BNPdensity/man/logf_logu_cond_y.Rd |only BNPdensity-2021.5.4/BNPdensity/man/logf_u_cond_y.Rd |only BNPdensity-2021.5.4/BNPdensity/man/multMixNRMI1.Rd | 3 BNPdensity-2021.5.4/BNPdensity/man/multMixNRMI1cens.Rd | 3 BNPdensity-2021.5.4/BNPdensity/man/multMixNRMI2.Rd | 7 BNPdensity-2021.5.4/BNPdensity/man/multMixNRMI2cens.Rd | 5 BNPdensity-2021.5.4/BNPdensity/man/plot.PY1.Rd |only BNPdensity-2021.5.4/BNPdensity/man/plot.PY2.Rd |only BNPdensity-2021.5.4/BNPdensity/man/plot.multNRMI.Rd | 1 BNPdensity-2021.5.4/BNPdensity/man/print.PY1.Rd |only BNPdensity-2021.5.4/BNPdensity/man/print.PY2.Rd |only BNPdensity-2021.5.4/BNPdensity/man/rprop_logu.Rd |only BNPdensity-2021.5.4/BNPdensity/man/salinity.Rd | 6 BNPdensity-2021.5.4/BNPdensity/man/summary.PY1.Rd |only BNPdensity-2021.5.4/BNPdensity/man/summary.PY2.Rd |only BNPdensity-2021.5.4/BNPdensity/man/summarytext.Rd | 11 BNPdensity-2021.5.4/BNPdensity/man/thresholdGG.Rd |only 52 files changed, 510 insertions(+), 189 deletions(-)
More information about zoomGroupStats at CRAN
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Title: Tools to Read and Manipulate Fisheries Data
Description: Set of tools to read and manipulate various data formats for fisheries. Mainly
catered towards scientific trawl survey sampling ('biotic') data, acoustic
trawl data, and commercial fishing catch ('landings') data. Among the
supported data formats are the data products from the Norwegian Institute
Marine Research ('IMR') and the International Council for the Exploration of
the Sea (ICES).
Author: Ibrahim Umar [cre, aut],
Sindre Vatnehol [aut],
Arne Johannes Holmin [aut],
Edvin Fuglebakk [aut],
Espen Johnsen [aut],
Norwegian Institute of Marine Research [cph, fnd]
Maintainer: Ibrahim Umar <ibrahim.umar@hi.no>
Diff between RstoxData versions 1.1.1 dated 2021-03-05 and 1.1.8 dated 2021-05-13
RstoxData-1.1.1/RstoxData/man/ReportICESAcoustic.Rd |only RstoxData-1.1.1/RstoxData/man/ReportICESAcousticData.Rd |only RstoxData-1.1.1/RstoxData/man/ReportICESBiotic.Rd |only RstoxData-1.1.1/RstoxData/man/ReportICESBioticData.Rd |only RstoxData-1.1.1/RstoxData/man/ReportICESDatras.Rd |only RstoxData-1.1.1/RstoxData/man/ReportICESDatrasData.Rd |only RstoxData-1.1.8/RstoxData/DESCRIPTION | 11 RstoxData-1.1.8/RstoxData/MD5 | 78 RstoxData-1.1.8/RstoxData/NAMESPACE | 14 RstoxData-1.1.8/RstoxData/NEWS.md | 33 RstoxData-1.1.8/RstoxData/R/DefineAndUpdateVariables.R | 1016 ++++++----- RstoxData-1.1.8/RstoxData/R/Definitions.R | 32 RstoxData-1.1.8/RstoxData/R/Filter.R | 22 RstoxData-1.1.8/RstoxData/R/Read.R | 98 - RstoxData-1.1.8/RstoxData/R/RstoxData-package.R | 49 RstoxData-1.1.8/RstoxData/R/StoxAcoustic.R | 61 RstoxData-1.1.8/RstoxData/R/StoxBiotic.R | 74 RstoxData-1.1.8/RstoxData/R/StoxExport.R | 218 +- RstoxData-1.1.8/RstoxData/R/Utilities.R | 107 - RstoxData-1.1.8/RstoxData/R/backwardCompatibility.R | 19 RstoxData-1.1.8/RstoxData/R/data.R | 133 + RstoxData-1.1.8/RstoxData/R/readXmlFile.R | 18 RstoxData-1.1.8/RstoxData/R/stoxFunctionAttributes.R | 69 RstoxData-1.1.8/RstoxData/R/stoxLanding.R | 4 RstoxData-1.1.8/RstoxData/R/writeXmlFile.R |only RstoxData-1.1.8/RstoxData/R/xsdUtils.R | 33 RstoxData-1.1.8/RstoxData/data/stoxBioticObject.rda |binary RstoxData-1.1.8/RstoxData/inst/extdata/functionArguments.rds |binary RstoxData-1.1.8/RstoxData/inst/extdata/stripns.xsl |only RstoxData-1.1.8/RstoxData/man/DefineTranslation.Rd | 7 RstoxData-1.1.8/RstoxData/man/ICESAcoustic.Rd | 8 RstoxData-1.1.8/RstoxData/man/ICESBiotic.Rd | 12 RstoxData-1.1.8/RstoxData/man/ICESDatras.Rd | 8 RstoxData-1.1.8/RstoxData/man/ModelData.Rd | 6 RstoxData-1.1.8/RstoxData/man/StoxBiotic.Rd | 3 RstoxData-1.1.8/RstoxData/man/StoxBioticFormat.Rd |only RstoxData-1.1.8/RstoxData/man/TranslateICESAcoustic.Rd |only RstoxData-1.1.8/RstoxData/man/TranslateICESBiotic.Rd |only RstoxData-1.1.8/RstoxData/man/WriteICESAcoustic.Rd |only RstoxData-1.1.8/RstoxData/man/WriteICESAcousticData.Rd |only RstoxData-1.1.8/RstoxData/man/WriteICESBiotic.Rd |only RstoxData-1.1.8/RstoxData/man/WriteICESBioticData.Rd |only RstoxData-1.1.8/RstoxData/man/WriteICESDatras.Rd |only RstoxData-1.1.8/RstoxData/man/WriteICESDatrasData.Rd |only RstoxData-1.1.8/RstoxData/man/generalSamplingHierarhcy.Rd |only RstoxData-1.1.8/RstoxData/man/getNumberOfCores.Rd |only RstoxData-1.1.8/RstoxData/man/mapplyOnCores.Rd | 8 RstoxData-1.1.8/RstoxData/man/stoxFunctionAttributes.Rd | 2 RstoxData-1.1.8/RstoxData/tests/testthat/test-StoxExport.R | 14 RstoxData-1.1.8/RstoxData/tests/testthat/test-writeXmlFile.R |only 50 files changed, 1365 insertions(+), 792 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>).
As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses. Since version 0.70, 'chillR' contains a function for interpolating
hourly temperature records.
Author: Eike Luedeling [aut, cre] (<https://orcid.org/0000-0002-7316-3631>)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.72.2 dated 2021-01-06 and 0.72.4 dated 2021-05-13
chillR-0.72.2/chillR/R/handle_chile_agromet.R |only chillR-0.72.2/chillR/R/handle_wunderground.R |only chillR-0.72.2/chillR/man/handle_chile_agromet.Rd |only chillR-0.72.2/chillR/man/handle_wunderground.Rd |only chillR-0.72.4/chillR/DESCRIPTION | 10 chillR-0.72.4/chillR/MD5 | 36 - chillR-0.72.4/chillR/NAMESPACE | 4 chillR-0.72.4/chillR/R/get_weather.R | 14 chillR-0.72.4/chillR/R/handle_cimis.R | 3 chillR-0.72.4/chillR/R/handle_gsod.R | 4 chillR-0.72.4/chillR/R/make_daily_chill_plot.R | 4 chillR-0.72.4/chillR/R/patch_daily_temperatures.R | 2 chillR-0.72.4/chillR/R/patch_daily_temps.R |only chillR-0.72.4/chillR/R/temperature_generation.R | 1 chillR-0.72.4/chillR/R/weather2chillR.R | 10 chillR-0.72.4/chillR/build/vignette.rds |binary chillR-0.72.4/chillR/inst/doc/PhenoFlex.html | 357 ++---------- chillR-0.72.4/chillR/inst/doc/hourly_temperatures.html | 502 +++++------------ chillR-0.72.4/chillR/man/get_weather.Rd | 10 chillR-0.72.4/chillR/man/patch_daily_temperatures.Rd | 3 chillR-0.72.4/chillR/man/patch_daily_temps.Rd |only chillR-0.72.4/chillR/man/weather2chillR.Rd | 3 22 files changed, 294 insertions(+), 669 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to where the current file is,
print strings with rich formats and colors);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of regression models and other results
(to R Console and MS Word);
(7) mediation and moderation analyses;
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.6.2 dated 2021-04-11 and 0.6.4 dated 2021-05-13
DESCRIPTION | 15 +- MD5 | 51 ++++---- NAMESPACE | 1 NEWS.md | 23 +++ R/bruceR.R | 2 R/bruceR_basic.R | 199 ++++++++++++++++++++++++++++--- R/bruceR_stats_01_basic.R | 231 +++++++++++++++++++++++------------- R/bruceR_stats_03_manova.R | 134 +++++++++++++++------ R/bruceR_stats_04_regress.R | 175 ++++++++++++++++----------- R/bruceR_stats_05_advance.R | 276 ++++++++++++++++++++++++++++++++++++++++---- R/bruceR_stats_06_plot.R | 3 README.md | 43 ++++++ build/partial.rdb |binary inst/CITATION | 2 man/Corr.Rd | 29 ++-- man/Describe.Rd | 23 ++- man/Freq.Rd | 10 - man/HLM_ICC_rWG.Rd | 16 +- man/HLM_summary.Rd | 2 man/MANOVA.Rd | 12 - man/bruceR-package.Rd | 2 man/granger_causality.Rd |only man/granger_test.Rd | 13 -- man/med_summary.Rd | 6 man/model_summary.Rd | 34 +++-- man/print_table.Rd | 53 +++++++- man/set.wd.Rd | 4 27 files changed, 1016 insertions(+), 343 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with raster and vector data. Raster methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' can do more, is simpler to use, and it is faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Karl Forner [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.2-5 dated 2021-04-30 and 1.2-10 dated 2021-05-13
terra-1.2-10/terra/DESCRIPTION | 10 terra-1.2-10/terra/MD5 | 166 ++++----- terra-1.2-10/terra/NAMESPACE | 4 terra-1.2-10/terra/NEWS.md | 66 +++ terra-1.2-10/terra/R/Agenerics.R | 21 - terra-1.2-10/terra/R/SpatRasterDataset.R | 2 terra-1.2-10/terra/R/Zdeprecated.R |only terra-1.2-10/terra/R/autocor.R | 55 ++- terra-1.2-10/terra/R/coerce.R | 78 ++++ terra-1.2-10/terra/R/dimensions.R | 6 terra-1.2-10/terra/R/expand.R | 6 terra-1.2-10/terra/R/extent.R | 9 terra-1.2-10/terra/R/extract.R | 86 +++- terra-1.2-10/terra/R/generics.R | 63 ++- terra-1.2-10/terra/R/geom.R | 54 ++- terra-1.2-10/terra/R/lines.R | 6 terra-1.2-10/terra/R/plotRGB.R | 110 ++++++ terra-1.2-10/terra/R/plot_raster.R | 10 terra-1.2-10/terra/R/plot_vector.R | 8 terra-1.2-10/terra/R/rasterize.R | 4 terra-1.2-10/terra/R/sample.R | 2 terra-1.2-10/terra/R/show.R | 2 terra-1.2-10/terra/R/spatvec.R | 24 - terra-1.2-10/terra/R/tiles.R | 2 terra-1.2-10/terra/R/vect.R | 6 terra-1.2-10/terra/R/zoom.R | 19 - terra-1.2-10/terra/inst/ex/meuse.tif |only terra-1.2-10/terra/inst/tinytest/test_vector-subset.R | 2 terra-1.2-10/terra/man/RGB.Rd | 16 terra-1.2-10/terra/man/area.Rd | 65 +-- terra-1.2-10/terra/man/as.spatvector.Rd | 13 terra-1.2-10/terra/man/autocor.Rd | 27 + terra-1.2-10/terra/man/barplot.Rd | 6 terra-1.2-10/terra/man/cellSize.Rd |only terra-1.2-10/terra/man/convhull.Rd |only terra-1.2-10/terra/man/coords.Rd | 16 terra-1.2-10/terra/man/copy.Rd | 8 terra-1.2-10/terra/man/crs.Rd | 4 terra-1.2-10/terra/man/dimensions.Rd | 18 - terra-1.2-10/terra/man/ext.Rd | 1 terra-1.2-10/terra/man/extend.Rd |only terra-1.2-10/terra/man/extract.Rd | 22 - terra-1.2-10/terra/man/interpolate.Rd | 16 terra-1.2-10/terra/man/intersect.Rd | 2 terra-1.2-10/terra/man/makeTiles.Rd |only terra-1.2-10/terra/man/nearby.Rd |only terra-1.2-10/terra/man/perim.Rd |only terra-1.2-10/terra/man/plot.Rd | 11 terra-1.2-10/terra/man/plotRGB.Rd | 9 terra-1.2-10/terra/man/relate.Rd | 2 terra-1.2-10/terra/man/sbar.Rd | 2 terra-1.2-10/terra/man/segregate.Rd |only terra-1.2-10/terra/man/setValues.Rd | 3 terra-1.2-10/terra/man/sources.Rd | 3 terra-1.2-10/terra/man/split.Rd |only terra-1.2-10/terra/man/summarize-generics.Rd | 2 terra-1.2-10/terra/man/summary.Rd | 2 terra-1.2-10/terra/man/terra-package.Rd | 23 - terra-1.2-10/terra/man/topology.Rd |only terra-1.2-10/terra/man/union.Rd | 2 terra-1.2-10/terra/man/values.Rd | 17 terra-1.2-10/terra/man/vrt.Rd | 2 terra-1.2-10/terra/man/window.Rd | 4 terra-1.2-10/terra/man/wrap.Rd |only terra-1.2-10/terra/src/RcppModule.cpp | 12 terra-1.2-10/terra/src/arith.cpp | 14 terra-1.2-10/terra/src/distRaster.cpp | 219 +++++++++--- terra-1.2-10/terra/src/extract.cpp | 54 ++- terra-1.2-10/terra/src/gdal_algs.cpp | 6 terra-1.2-10/terra/src/gdalio.cpp | 16 terra-1.2-10/terra/src/geos_methods.cpp | 312 +++++++++++++++++- terra-1.2-10/terra/src/geos_spat.h | 98 ++++- terra-1.2-10/terra/src/raster_stats.cpp | 33 + terra-1.2-10/terra/src/rasterize.cpp | 135 ++++--- terra-1.2-10/terra/src/read_ogr.cpp | 19 - terra-1.2-10/terra/src/sample.cpp | 8 terra-1.2-10/terra/src/spatBase.h | 15 terra-1.2-10/terra/src/spatRaster.cpp | 84 ++++ terra-1.2-10/terra/src/spatRaster.h | 26 - terra-1.2-10/terra/src/spatSources.cpp | 234 +++++++++---- terra-1.2-10/terra/src/spatVector.cpp | 100 +++-- terra-1.2-10/terra/src/spatVector.h | 18 - terra-1.2-10/terra/src/vector_methods.cpp | 30 + terra-1.2-10/terra/src/write.cpp | 1 terra-1.2-10/terra/src/write_gdal.cpp | 75 ++++ terra-1.2-10/terra/src/write_ogr.cpp | 31 + terra-1.2-5/terra/R/Zdepracated.R |only terra-1.2-5/terra/inst/ex/test.tif |only terra-1.2-5/terra/man/chull.Rd |only terra-1.2-5/terra/man/expand.Rd |only terra-1.2-5/terra/man/near.Rd |only terra-1.2-5/terra/man/pack.Rd |only terra-1.2-5/terra/man/separate.Rd |only terra-1.2-5/terra/man/tiles.Rd |only 94 files changed, 1977 insertions(+), 680 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2021) <arXiv:2105.04451>.
Author: David B. Dahl [aut, cre] (<https://orcid.org/0000-0002-8173-1547>),
Devin J. Johnson [aut] (<https://orcid.org/0000-0003-2619-6649>),
Peter Müller [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.2.20 dated 2021-03-27 and 0.2.22 dated 2021-05-13
salso-0.2.20/salso/R/confidence.R |only salso-0.2.22/salso/DESCRIPTION | 12 +++--- salso-0.2.22/salso/MD5 | 33 ++++++++--------- salso-0.2.22/salso/NAMESPACE | 2 + salso-0.2.22/salso/NEWS | 9 ++++ salso-0.2.22/salso/R/partition.loss.R | 3 - salso-0.2.22/salso/R/plot.salso.summary.R | 15 ++++--- salso-0.2.22/salso/R/salso.R | 2 - salso-0.2.22/salso/R/summary.salso.estimate.R | 12 +++++- salso-0.2.22/salso/man/partition.loss.Rd | 2 - salso-0.2.22/salso/man/plot.salso.summary.Rd | 7 ++- salso-0.2.22/salso/man/salso.Rd | 2 - salso-0.2.22/salso/man/summary.salso.estimate.Rd | 6 ++- salso-0.2.22/salso/src/Makevars | 2 - salso-0.2.22/salso/src/Makevars.win | 2 - salso-0.2.22/salso/src/rustlib/Cargo.lock | 44 +++++++++++------------ salso-0.2.22/salso/src/rustlib/Cargo.toml | 4 +- salso-0.2.22/salso/tools/staticlib.R | 37 ------------------- 18 files changed, 92 insertions(+), 102 deletions(-)
Title: Computation and Plots of Influence Functions for Risk and
Performance Measures
Description: Computes the influence functions time series of the returns for the risk and
performance measures as mentioned in Chen and Martin (2018)
<https://www.ssrn.com/abstract=3085672>, as well as in Zhang et al. (2019)
<https://www.ssrn.com/abstract=3415903>. Also evaluates estimators influence
functions at a set of parameter values and plots them to display the shapes of
the influence functions.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Shengyu Zhang <syzhang@uw.edu>,
Douglas Martin <doug@amath.washington.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEIF versions 1.2.1 dated 2021-05-06 and 1.2.2 dated 2021-05-13
RPEIF-1.2.1/RPEIF/R/IF_mean.R |only RPEIF-1.2.1/RPEIF/R/IF_robLoc.R |only RPEIF-1.2.1/RPEIF/data |only RPEIF-1.2.1/RPEIF/man/IF.mean.Rd |only RPEIF-1.2.1/RPEIF/man/edhec.Rd |only RPEIF-1.2.2/RPEIF/DESCRIPTION | 13 +- RPEIF-1.2.2/RPEIF/MD5 | 74 ++++++++--------- RPEIF-1.2.2/RPEIF/NAMESPACE | 2 RPEIF-1.2.2/RPEIF/NEWS.md | 4 RPEIF-1.2.2/RPEIF/R/IF_DSR.R | 2 RPEIF-1.2.2/RPEIF/R/IF_ES.R | 2 RPEIF-1.2.2/RPEIF/R/IF_ESRatio.R | 2 RPEIF-1.2.2/RPEIF/R/IF_LPM.R | 2 RPEIF-1.2.2/RPEIF/R/IF_Mean.R |only RPEIF-1.2.2/RPEIF/R/IF_OmegaRatio.R | 2 RPEIF-1.2.2/RPEIF/R/IF_RachevRatio.R | 2 RPEIF-1.2.2/RPEIF/R/IF_SD.R | 2 RPEIF-1.2.2/RPEIF/R/IF_SR.R | 2 RPEIF-1.2.2/RPEIF/R/IF_SemiSD.R | 2 RPEIF-1.2.2/RPEIF/R/IF_SoR.R | 2 RPEIF-1.2.2/RPEIF/R/IF_VaR.R | 2 RPEIF-1.2.2/RPEIF/R/IF_VaRratio.R | 2 RPEIF-1.2.2/RPEIF/R/IF_robMean.R |only RPEIF-1.2.2/RPEIF/R/InfluenceFunctions.R | 12 +- RPEIF-1.2.2/RPEIF/R/RiskPerformanceMeasure_Functions.R | 10 +- RPEIF-1.2.2/RPEIF/R/RobustFilter.R | 6 - RPEIF-1.2.2/RPEIF/inst/doc/RPEIFVignette.pdf |binary RPEIF-1.2.2/RPEIF/man/IF.DSR.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.ES.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.ESratio.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.LPM.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.Mean.Rd |only RPEIF-1.2.2/RPEIF/man/IF.OmegaRatio.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.RachevRatio.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.Rd | 8 - RPEIF-1.2.2/RPEIF/man/IF.SD.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.SR.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.SemiSD.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.SoR.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.VaR.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.VaRratio.Rd | 2 RPEIF-1.2.2/RPEIF/man/IF.robMean.Rd | 4 42 files changed, 91 insertions(+), 90 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included.
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis.
b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534.
c) Tsagris M. (2015). A novel, divergence based, regression for compositional data. Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444.
d) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Statistics, 6(2):47--57.
e) Tsagris M., Preston S. and Wood A.T.A. (2016). Improved supervised classification for compositional data using the alpha-transformation. Journal of Classification, 33(2):243--261. <doi:10.1007/s00357-016-9207-5>.
f) Tsagris M., Preston S. and Wood A.T.A. (2017). Nonparametric hypothesis testing for equality of means on the simplex. Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>.
g) Tsagris M. and Stewart C. (2018). A Dirichlet regression model for compositional data with zeros. Lobachevskii Journal of Mathematics,39(3): 398--412. <doi:10.1134/S1995080218030198>.
h) Alenazi A. (2019). Regression for compositional data with compositional data as predictor variables with or without zero values. Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>.
i) Tsagris M. and Stewart C. (2020). A folded model for compositional data analysis. Australian and New Zealand Journal of Statistics, 62(2):249--277. <doi:10.1111/anzs.12289>.
j) Tsagris M., Alenazi A. and Stewart C. (2021). The alpha-k-NN regression for compositional data. <arXiv:2002.05137>.
We further include functions for percentages (or proportions).
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 4.6 dated 2021-04-27 and 4.7 dated 2021-05-13
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++++--------- R/akern.reg.R |only R/akernreg.tune.R |only R/frechet.R | 4 ++-- R/unitweibull.est.R |only man/Compositional-package.Rd | 10 +++++++--- man/akern.reg.Rd |only man/akernreg.tune.Rd |only man/aknn.reg.Rd | 8 ++++---- man/aknnreg.tune.Rd | 15 ++++++++------- man/alfa.knn.reg.Rd | 2 +- man/alfann.Rd | 4 ++-- man/beta.est.Rd | 17 ++++++++++++----- man/ols.compcomp.Rd | 4 ++-- 15 files changed, 57 insertions(+), 40 deletions(-)
Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Indirect methods for estimating bilateral migration flows in the presence of partial or missing data, including the estimation of bilateral migration flows from changes in bilateral migrant stock tables (e.g. Abel (2013) <doi:10.4054/DemRes.2013.28.18>).
Author: Guy J. Abel [aut, cre] (<https://orcid.org/0000-0002-4893-5687>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between migest versions 1.8.3 dated 2021-01-24 and 1.8.4 dated 2021-05-13
migest-1.8.3/migest/R/net_param.R |only migest-1.8.3/migest/R/net_scale.R |only migest-1.8.3/migest/R/sum_total.R |only migest-1.8.3/migest/man/net_param.Rd |only migest-1.8.3/migest/man/net_scale.Rd |only migest-1.8.3/migest/man/sum_total.Rd |only migest-1.8.4/migest/DESCRIPTION | 8 +- migest-1.8.4/migest/MD5 | 20 ++----- migest-1.8.4/migest/NAMESPACE | 3 - migest-1.8.4/migest/R/cm_net.R | 89 +++++++++++++++----------------- migest-1.8.4/migest/R/global.R | 2 migest-1.8.4/migest/R/sum_turnover.R | 83 ++++++++++++++++++++++++----- migest-1.8.4/migest/man/cm_net.Rd | 18 ++++-- migest-1.8.4/migest/man/sum_turnover.Rd | 51 ++++++++++++++++-- 14 files changed, 182 insertions(+), 92 deletions(-)
Title: Analysis of Data with Measurement Error Using a Validation
Subsample
Description: Analyze data with measurement error when there is a validation subsample randomly selected from the full sample. The method assumes surrogate variables measured with error are available for the full sample, and reference variables measured with little or no error are available for this randomly selected subsample of the full sample. Measurement errors may be differential or non differential, in any or all predictors (simultaneously) as well as outcome. The "augmented" estimates derived are based upon the multivariate correlation between regression model parameter estimates for the reference variables and for the surrogate variables in the validation subset. Because the validation subsample is chosen at random whatever biases are imposed by measurement error, non-differential or differential, are reflected in this correlation and can be used to derive estimates for the reference variables using data from the whole sample. The main functions in the package are meerva.fit which calculates estimates for a dataset, and meerva.sim.block which simulates multiple datasets as described by the user, and analyzes these datasets, storing the regression coefficient estimates for inspection. This work derives from Chen Y-H, Chen H. (2000) <doi:10.1111/1467-9868.00243>, Chen Y-H. (2002) <doi:10.1111/1467-9868.00324>, Wang X, Wang Q (2015) <doi:10.1016/j.jmva.2015.05.017> and Tong J, Huang J, Chubak J, et al. (2020) <doi:10.1093/jamia/ocz180>.
Author: Walter K Kremers [aut, cre] (<https://orcid.org/0000-0001-5714-3473>)
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between meerva versions 0.1-2 dated 2021-04-27 and 0.2-1 dated 2021-05-13
meerva-0.1-2/meerva/R/meerva.sim.brn_210424.R |only meerva-0.1-2/meerva/R/meerva.sim.cox_210424.R |only meerva-0.1-2/meerva/R/meerva.sim.nrm_210424.R |only meerva-0.1-2/meerva/R/meerva.sim.tools_210424.R |only meerva-0.1-2/meerva/R/meerva_210424.R |only meerva-0.2-1/meerva/DESCRIPTION | 12 ++--- meerva-0.2-1/meerva/MD5 | 50 +++++++++++----------- meerva-0.2-1/meerva/R/meerva.sim.brn_210503.R |only meerva-0.2-1/meerva/R/meerva.sim.cox_210503.R |only meerva-0.2-1/meerva/R/meerva.sim.nrm_210503.R |only meerva-0.2-1/meerva/R/meerva.sim.tools_210503.R |only meerva-0.2-1/meerva/R/meerva_210503.R |only meerva-0.2-1/meerva/inst/doc/COPYRIGHTS | 3 - meerva-0.2-1/meerva/man/compmse.Rd | 2 meerva-0.2-1/meerva/man/coverage.Rd | 2 meerva-0.2-1/meerva/man/coverage2.Rd | 6 +- meerva-0.2-1/meerva/man/dfbetac.Rd | 2 meerva-0.2-1/meerva/man/meerva.Rd | 4 - meerva-0.2-1/meerva/man/meerva.fit.Rd | 22 +++++++-- meerva-0.2-1/meerva/man/meerva.sim.block.Rd | 54 +++++++++++++++++------- meerva-0.2-1/meerva/man/meerva.sim.brn.Rd | 50 ++++++++++++++++------ meerva-0.2-1/meerva/man/meerva.sim.cox.Rd | 43 ++++++++++++++----- meerva-0.2-1/meerva/man/meerva.sim.nrm.Rd | 41 +++++++++++++----- meerva-0.2-1/meerva/man/myttest.Rd | 2 meerva-0.2-1/meerva/man/plot.meerva.sim.Rd | 2 meerva-0.2-1/meerva/man/print.meerva.Rd | 8 ++- meerva-0.2-1/meerva/man/reldif.Rd | 2 meerva-0.2-1/meerva/man/subvec.Rd | 2 meerva-0.2-1/meerva/man/summary.meerva.Rd | 8 ++- meerva-0.2-1/meerva/man/summary.meerva.sim.Rd | 2 meerva-0.2-1/meerva/man/ztest.Rd | 2 31 files changed, 212 insertions(+), 107 deletions(-)
Title: Comprehensive Statistical Analysis of Plant Breeding Experiments
Description: Performs statistical data analysis of various Plant Breeding experiments. Contains functions for Line by Tester analysis as per Arunachalam, V.(1974) <http://repository.ias.ac.in/89299/>.
Author: Nandan Patil [cre, aut] (<https://orcid.org/0000-0003-0100-9931>),
Lakshmi R. Gangavati [aut, ctb]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between gpbStat versions 0.3.0 dated 2020-11-18 and 0.3.1 dated 2021-05-13
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++--------- R/ltc.R | 35 +++------------------------------ R/ltcchk.R | 36 +++------------------------------- R/on-attach.R | 2 - README.md | 14 +++---------- inst/doc/ltc.html | 54 +++++++++++++++++++++------------------------------ inst/doc/ltcchk.html | 52 ++++++++++++++++++++----------------------------- man/ltc.Rd | 6 +---- man/ltcchk.Rd | 6 +---- 10 files changed, 75 insertions(+), 156 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kiên Kiêu [aut],
Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 2.0.4.1 dated 2020-07-06 and 2.0.4.2 dated 2021-05-13
DESCRIPTION | 12 MD5 | 23 - NEWS.md | 12 README.md | 9 build/vignette.rds |binary inst/doc/cubature.html | 654 +++++++++++++++++------------------ inst/doc/version2.html | 108 ++--- src/Cuba-4.2-win/src/common/Random.c | 8 src/Cuba-4.2/config.h |only src/Cuba-4.2/config.log |only src/Cuba-4.2/config.status |only src/Cuba-4.2/cuba.ts |only src/Cuba-4.2/makefile |only src/Makevars | 6 src/Makevars.win | 6 15 files changed, 438 insertions(+), 400 deletions(-)
Title: Bayesian Structural Equation Modeling in Multiple Omics Data
Integration
Description: Provides Markov Chain Monte Carlo (MCMC) routine for the
structural equation modelling described in
Maity et. al. (2020) <doi:10.1093/bioinformatics/btaa286>. This MCMC sampler is
useful when one attempts to perform an integrative survival analysis for multiple
platforms of the Omics data where the response is time to event and the
predictors are different omics expressions for different platforms.
Author: Arnab Maity [aut, cre],
Sang Chan Lee [aut],
Bani K. Mallick [aut],
Samsiddhi Bhattacharjee [aut],
Nidhan K. Biswas [aut]
Maintainer: Arnab Maity <arnab.maity@pfizer.com>
Diff between semmcmc versions 0.0.4 dated 2021-04-26 and 0.0.6 dated 2021-05-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/CITATION | 26 +++++++++++++------------- 3 files changed, 19 insertions(+), 19 deletions(-)
Title: Interface to the 'Biodiversity' 'Heritage' Library
Description: Interface to 'Biodiversity' 'Heritage' Library ('BHL')
(<https://www.biodiversitylibrary.org/>) API
(<https://www.biodiversitylibrary.org/docs/api3.html>). 'BHL' is a
repository of 'digitized' literature on 'biodiversity'
studies, including 'floras', research papers, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rbhl versions 0.9.0 dated 2020-01-29 and 0.9.2 dated 2021-05-13
rbhl-0.9.0/rbhl/build |only rbhl-0.9.0/rbhl/inst |only rbhl-0.9.0/rbhl/vignettes |only rbhl-0.9.2/rbhl/DESCRIPTION | 13 rbhl-0.9.2/rbhl/LICENSE | 4 rbhl-0.9.2/rbhl/MD5 | 40 - rbhl-0.9.2/rbhl/NEWS.md | 8 rbhl-0.9.2/rbhl/R/rbhl-package.R | 5 rbhl-0.9.2/rbhl/README.md | 23 rbhl-0.9.2/rbhl/man/rbhl-package.Rd | 7 rbhl-0.9.2/rbhl/tests/fixtures/bhl_authorsearch.yml | 66 -- rbhl-0.9.2/rbhl/tests/fixtures/bhl_bioherlib.yml | 118 +--- rbhl-0.9.2/rbhl/tests/fixtures/bhl_getcollections.yml | 342 +----------- rbhl-0.9.2/rbhl/tests/fixtures/bhl_getitemmetadata.yml | 98 +-- rbhl-0.9.2/rbhl/tests/fixtures/bhl_getlanguages.yml | 179 +----- rbhl-0.9.2/rbhl/tests/fixtures/bhl_getpagemetadata.yml | 118 +--- rbhl-0.9.2/rbhl/tests/fixtures/bhl_gettitlemetadata.yml | 105 +-- rbhl-0.9.2/rbhl/tests/fixtures/bhl_namesearch.yml | 210 +++---- rbhl-0.9.2/rbhl/tests/fixtures/bhl_openurl.yml | 80 -- rbhl-0.9.2/rbhl/tests/fixtures/bhl_publicationsearch.yml | 80 +- rbhl-0.9.2/rbhl/tests/fixtures/bhl_publicationsearchadv.yml | 15 rbhl-0.9.2/rbhl/tests/fixtures/bhl_subjectsearch.yml | 111 +-- 22 files changed, 528 insertions(+), 1094 deletions(-)
Title: Fitting the Multinomial Probit Model
Description: Fits the Bayesian multinomial probit model via Markov chain
Monte Carlo. The multinomial probit model is often used to analyze
the discrete choices made by individuals recorded in survey data.
Examples where the multinomial probit model may be useful include the
analysis of product choice by consumers in market research and the
analysis of candidate or party choice by voters in electoral studies.
The MNP package can also fit the model with different choice sets for
each individual, and complete or partial individual choice orderings
of the available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm that is
developed by Imai and van Dyk (2005). "A Bayesian Analysis of the
Multinomial Probit Model Using the Data Augmentation." Journal of
Econometrics, Vol. 124, No. 2 (February), pp. 311-334.
<doi:10.1016/j.jeconom.2004.02.002> Detailed examples are given in
Imai and van Dyk (2005). "MNP: R Package for Fitting the Multinomial
Probit Model." Journal of Statistical Software, Vol. 14, No. 3 (May),
pp. 1-32. <doi:10.18637/jss.v014.i03>.
Author: Kosuke Imai [aut, cre],
David van Dyk [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@harvard.edu>
Diff between MNP versions 3.1-1 dated 2020-10-22 and 3.1-2 dated 2021-05-13
ChangeLog | 6 ++++-- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/MNP.Rnw | 26 +++++++++++++------------- inst/doc/MNP.pdf |binary vignettes/MNP.Rnw | 26 +++++++++++++------------- 7 files changed, 40 insertions(+), 38 deletions(-)
Title: A Code Converter from the Matlab/Octave Language to R
Description: Transferring over a code base from Matlab to R is often a repetitive
and inefficient use of time. This package provides a translator for Matlab /
Octave code into R code. It does some syntax changes, but most of the heavy
lifting is in the function changes since the languages are so similar.
Options for different data structures and the functions that can be changed
are given. The Matlab code should be mostly in adherence to the standard
style guide but some effort has been made to accommodate different number of
spaces and other small syntax issues. This will not make the code more R
friendly and may not even run afterwards. However, the rudimentary syntax,
base function and data structure conversion is done quickly so that the
maintainer can focus on changes to the design structure.
Author: Siddarta Jairam [aut, cre],
David Hiebeler [ctb]
Maintainer: Siddarta Jairam <sidjsb@gmail.com>
Diff between matconv versions 0.4.0 dated 2019-01-07 and 0.4.2 dated 2021-05-13
DESCRIPTION | 10 +- MD5 | 24 +++--- build/vignette.rds |binary inst/doc/basicSyntax.R | 8 +- inst/doc/basicSyntax.html | 79 ++++++++++++++-------- inst/doc/functionCalls.R | 10 +- inst/doc/functionCalls.html | 81 +++++++++++++---------- inst/doc/overallUse.R | 10 +- inst/doc/overallUse.html | 154 +++++++++++++++++++++++++++++--------------- inst/doc/overallUse.rmd | 2 man/mat2r.Rd | 13 ++- man/matconv.Rd | 1 vignettes/overallUse.rmd | 2 13 files changed, 242 insertions(+), 152 deletions(-)