Title: Stratification and Matching for Large Observational Data Sets
Description: A pilot matching design to automatically
stratify and match large datasets. The manual_stratify() function allows
users to manually stratify a dataset based on categorical variables of
interest, while the auto_stratify() function does automatically by
allocating a held-aside (pilot) data set, fitting a prognostic score
(see Hansen (2008) <doi:10.1093/biomet/asn004>) on the pilot set, and stratifying the data set based
on prognostic score quantiles. The strata_match() function then does optimal
matching of the data set in parallel within strata.
Author: Rachael C. Aikens [aut, cre],
Joseph Rigdon [aut],
Justin Lee [aut],
Michael Baiocchi [aut],
Jonathan Chen [aut]
Maintainer: Rachael C. Aikens <rockyaikens@gmail.com>
Diff between stratamatch versions 0.1.3 dated 2020-01-14 and 0.1.4 dated 2020-02-18
DESCRIPTION | 8 +- MD5 | 91 +++++++++++++++++---------------- NAMESPACE | 1 R/ICU_data_documentation.R | 2 R/S3_methods.R | 43 ++++++++++++--- R/auto_stratify.R | 46 +++++++++++++++- R/make_issue_table.R | 2 R/manual_stratify.R | 23 +++++++- R/match_functions.R | 2 R/split_pilot_set.R | 1 R/strata_object_constructors.R | 4 + inst/doc/Intro_to_stratamatch.R | 6 +- inst/doc/Intro_to_stratamatch.Rmd | 6 +- inst/doc/Intro_to_stratamatch.html | 22 ++++--- man/ICU_data.Rd | 2 man/auto_stratify.Rd | 35 ++++++++++++ man/build_autostrata.Rd | 1 man/check_base_inputs_auto_stratify.Rd | 1 man/check_inputs_manual_stratify.Rd | 1 man/check_inputs_matcher.Rd | 1 man/check_outcome.Rd | 1 man/check_pilot_set_options.Rd | 1 man/check_prognostic_formula.Rd | 1 man/check_prop_formula.Rd | 1 man/check_scores.Rd | 3 - man/estimate_scores.Rd | 1 man/fit_prognostic_model.Rd | 1 man/get_issues.Rd | 1 man/get_prop_scores.Rd | 1 man/is_binary.Rd | 1 man/make_SR_plot.Rd | 1 man/make_autostrata_table.Rd | 1 man/make_fm_plot.Rd | 1 man/make_hist_plot.Rd | 1 man/make_issue_table.Rd | 1 man/make_resid_plot.Rd | 1 man/manual_stratify.Rd | 21 +++++++ man/new_auto_strata.Rd | 1 man/new_manual_strata.Rd | 3 - man/strata_match_nstrat.Rd | 1 man/summary.strata.Rd |only man/warn_if_continuous.Rd | 1 tests/testthat/ref_astrat_print | 4 - tests/testthat/ref_astrat_summary |only tests/testthat/ref_mstrat_print | 4 - tests/testthat/ref_mstrat_summary |only tests/testthat/test-S3_functions.R | 17 ++++++ vignettes/Intro_to_stratamatch.Rmd | 6 +- 48 files changed, 288 insertions(+), 86 deletions(-)
Title: Distances and Routes on Geographical Grids
Description: Calculate distances and routes on geographic grids.
Author: Jacob van Etten [aut] (<https://orcid.org/0000-0001-7554-2558>),
Kaue de Sousa [cre, ctb] (<https://orcid.org/0000-0002-7571-7845>)
Maintainer: Kaue de Sousa <kaue.desousa@inn.no>
Diff between gdistance versions 1.2-2 dated 2018-05-06 and 1.3-0 dated 2020-02-18
gdistance-1.2-2/gdistance/ChangeLog |only gdistance-1.2-2/gdistance/R/adjacency.R |only gdistance-1.2-2/gdistance/inst/doc/gdistance1.R |only gdistance-1.2-2/gdistance/inst/doc/gdistance1.Rnw |only gdistance-1.2-2/gdistance/inst/doc/gdistance1.pdf |only gdistance-1.2-2/gdistance/man/Arith-methods.Rd |only gdistance-1.2-2/gdistance/man/Coords.Rd |only gdistance-1.2-2/gdistance/man/Transition-class.Rd |only gdistance-1.2-2/gdistance/man/adjacency.Rd |only gdistance-1.2-2/gdistance/man/commuteDistance.Rd |only gdistance-1.2-2/gdistance/man/costDistance.Rd |only gdistance-1.2-2/gdistance/man/gdistance-package.Rd |only gdistance-1.2-2/gdistance/man/probPassage.Rd |only gdistance-1.2-2/gdistance/man/rasterFromTransition.Rd |only gdistance-1.2-2/gdistance/man/sumT.Rd |only gdistance-1.2-2/gdistance/man/summary-methods.Rd |only gdistance-1.2-2/gdistance/vignettes/gdistance1.Rnw |only gdistance-1.2-2/gdistance/vignettes/jsslogo.jpg |only gdistance-1.3-0/gdistance/DESCRIPTION | 30 gdistance-1.3-0/gdistance/MD5 | 122 - gdistance-1.3-0/gdistance/NAMESPACE | 80 gdistance-1.3-0/gdistance/NEWS.md |only gdistance-1.3-0/gdistance/R/AAATransition-class.R | 198 +- gdistance-1.3-0/gdistance/R/Coords-class.R | 20 gdistance-1.3-0/gdistance/R/Summary-methods.R | 278 +-- gdistance-1.3-0/gdistance/R/Transition-extract-replace.R | 369 +--- gdistance-1.3-0/gdistance/R/Transition-methods.R | 338 ++- gdistance-1.3-0/gdistance/R/Transition-slots.R |only gdistance-1.3-0/gdistance/R/accCost.R | 137 + gdistance-1.3-0/gdistance/R/adjacencyFromTransition.R |only gdistance-1.3-0/gdistance/R/coerce.R | 88 gdistance-1.3-0/gdistance/R/commuteDistance.R | 226 +- gdistance-1.3-0/gdistance/R/costDistance.R | 257 +- gdistance-1.3-0/gdistance/R/gdistance.R |only gdistance-1.3-0/gdistance/R/genDist.R |only gdistance-1.3-0/gdistance/R/geoCorrection.R | 245 +- gdistance-1.3-0/gdistance/R/internal-functions.R | 381 ++-- gdistance-1.3-0/gdistance/R/normalize.R | 161 + gdistance-1.3-0/gdistance/R/pathInc.R | 1107 +++++++----- gdistance-1.3-0/gdistance/R/probPassage.R | 578 +++--- gdistance-1.3-0/gdistance/R/rSPdistance.R | 226 +- gdistance-1.3-0/gdistance/R/rasterFromTransition.R | 45 gdistance-1.3-0/gdistance/R/shortestPath.R | 227 +- gdistance-1.3-0/gdistance/R/show.R | 42 gdistance-1.3-0/gdistance/R/stack.R | 65 gdistance-1.3-0/gdistance/R/sumT.R | 84 gdistance-1.3-0/gdistance/R/summary.R | 59 gdistance-1.3-0/gdistance/R/transition.R | 519 +++-- gdistance-1.3-0/gdistance/build/vignette.rds |binary gdistance-1.3-0/gdistance/inst/CITATION |only gdistance-1.3-0/gdistance/inst/doc/Overview.R |only gdistance-1.3-0/gdistance/inst/doc/Overview.Rmd |only gdistance-1.3-0/gdistance/inst/doc/Overview.html |only gdistance-1.3-0/gdistance/inst/external/Europe.grd | 54 gdistance-1.3-0/gdistance/inst/external/maungawhau.grd | 56 gdistance-1.3-0/gdistance/inst/paper |only gdistance-1.3-0/gdistance/man/ArithMath-methods.Rd |only gdistance-1.3-0/gdistance/man/Coords-class.Rd |only gdistance-1.3-0/gdistance/man/Summary-methods.Rd |only gdistance-1.3-0/gdistance/man/Transition-classes.Rd |only gdistance-1.3-0/gdistance/man/Transition-extract-replace.Rd | 79 gdistance-1.3-0/gdistance/man/Transition-slots.Rd | 71 gdistance-1.3-0/gdistance/man/accCost.Rd | 122 - gdistance-1.3-0/gdistance/man/adjacencyFromTransition.Rd |only gdistance-1.3-0/gdistance/man/commuteDistance-methods.Rd |only gdistance-1.3-0/gdistance/man/costDistance-methods.Rd |only gdistance-1.3-0/gdistance/man/figures |only gdistance-1.3-0/gdistance/man/gdistance.Rd |only gdistance-1.3-0/gdistance/man/genDist.Rd | 51 gdistance-1.3-0/gdistance/man/geoCorrection.Rd | 131 - gdistance-1.3-0/gdistance/man/normalize.Rd | 101 - gdistance-1.3-0/gdistance/man/overlap.Rd | 60 gdistance-1.3-0/gdistance/man/passage.Rd |only gdistance-1.3-0/gdistance/man/pathInc.Rd | 224 +- gdistance-1.3-0/gdistance/man/rSPDistance.Rd | 119 - gdistance-1.3-0/gdistance/man/shortestPath.Rd | 127 - gdistance-1.3-0/gdistance/man/sumReciprocal.Rd |only gdistance-1.3-0/gdistance/man/transition.Rd | 220 +- gdistance-1.3-0/gdistance/vignettes/Overview.Rmd |only gdistance-1.3-0/gdistance/vignettes/gdistance1.bib | 14 gdistance-1.3-0/gdistance/vignettes/logo.png |only 81 files changed, 4411 insertions(+), 2900 deletions(-)
Title: Czekanowski's Diagrams
Description: Allows for production of Czekanowski's Diagrams. See A. Vasterlund (2019) Master thesis, Linkoping University.
Author: Albin Vasterlund [aut],
Krzysztof Bartoszek [cre, aut, ths]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between RMaCzek versions 1.3 dated 2020-01-29 and 1.3.1 dated 2020-02-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- data/skulls_distances.RData |binary man/RMaCzek.Rd | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Explain Interactions in 'XGBoost'
Description: Structure mining from 'XGBoost' and 'LightGBM' models.
Key functionalities of this package cover: visualisation of tree-based ensembles models,
identification of interactions, measuring of variable importance,
measuring of interaction importance, explanation of single prediction
with break down plots (based on 'xgboostExplainer' and 'iBreakDown' packages).
To download the 'LightGBM' use the following link: <https://github.com/Microsoft/LightGBM>.
'EIX' is a part of the 'DrWhy.AI' universe.
Author: Ewelina Karbowiak [aut, cre],
Przemyslaw Biecek [aut, ths]
Maintainer: Ewelina Karbowiak <ewelina.karbowiak12@gmail.com>
Diff between EIX versions 1.0 dated 2019-05-31 and 1.1 dated 2020-02-18
DESCRIPTION | 8 MD5 | 64 +- NAMESPACE | 48 - R/HR_data.R | 48 - R/calculateGain.R | 274 +++++----- R/importance.R | 444 ++++++++--------- R/interactions.R | 198 +++---- R/lollipop.R | 124 ++-- R/plot_importance.R | 286 +++++------ R/plot_interactions.R | 156 +++--- R/plot_lollipop.R | 170 +++--- R/titanic_data.R | 88 +-- R/waterfall.R | 880 +++++++++++++++++----------------- build/vignette.rds |binary inst/doc/EIX.R | 132 ++--- inst/doc/EIX.Rmd | 330 ++++++------ inst/doc/EIX.html | 1144 ++++++++++++++++++++++++++------------------- inst/doc/titanic_data.R | 88 +-- inst/doc/titanic_data.Rmd | 172 +++--- inst/doc/titanic_data.html | 740 +++++++++++++++++------------ man/HR_data.Rd | 58 +- man/calculateGain.Rd | 40 - man/importance.Rd | 170 +++--- man/interactions.Rd | 136 ++--- man/lollipop.Rd | 92 +-- man/plot.importance.Rd | 196 +++---- man/plot.interactions.Rd | 116 ++-- man/plot.lollipop.Rd | 106 ++-- man/tableOfTrees.Rd | 40 - man/titanic_data.Rd | 106 ++-- man/waterfall.Rd | 122 ++-- vignettes/EIX.Rmd | 330 ++++++------ vignettes/titanic_data.Rmd | 172 +++--- 33 files changed, 3702 insertions(+), 3376 deletions(-)
Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational
algebra, and on production experience using 'SQL' and 'dplyr' at big data
scale. The design represents an attempt to make 'SQL' more teachable by
denoting composition by a sequential pipeline notation instead of nested
queries or functions. The implementation delivers reliable high
performance data processing on large data systems such as 'Spark',
databases, and 'data.table'. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 1.4.3 dated 2020-02-01 and 1.4.4 dated 2020-02-18
DESCRIPTION | 8 +++--- MD5 | 32 ++++++++++++------------- NAMESPACE | 1 NEWS.md | 5 +++ R/ex_data_frame.R | 2 - R/lapply_bquote.R | 29 +++++++++++----------- README.md | 47 ++++++++++++++++++++++++++++--------- build/vignette.rds |binary inst/doc/AssigmentPartitioner.html | 12 +++------ inst/doc/Parameterized_rquery.html | 12 +++------ inst/doc/PipeableSQL.html | 12 +++------ inst/doc/QueryGeneration.html | 12 +++------ inst/doc/R_mapping.html | 12 +++------ inst/doc/rquery_intro.html | 12 +++------ inst/doc/rquery_many_columns.html | 12 +++------ inst/doc/rquery_substitution.html | 12 +++------ inst/doc/sql_quoting.html | 12 +++------ 17 files changed, 121 insertions(+), 111 deletions(-)
Title: An Easy to Use Multilayer Perceptron
Description: Trains neural networks (multilayer perceptrons with one hidden layer) for bi- or multi-class classification.
Author: David Dernoncourt [aut, cre] (LUNAM Universite, Universite Angers,
Laboratoire d'ergonomie et d'epidemiologie en sante au travail
(LEEST), w/ support from the French National Research Program for
Environmental and Occupational Health of Anses (2012/18))
Maintainer: David Dernoncourt <me@daviddernoncourt.com>
Diff between simpleNeural versions 0.1.1 dated 2015-04-28 and 0.1.3 dated 2020-02-18
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Easy Web Scraping
Description: The goal of 'ralger' is to facilitate web scraping in R.
The user has the ability to extract a vector with scrap(), a tidy dataframe using tidy_scrap(), a table with table_scrap() and web links with weblink_scrap().
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between ralger versions 1.0.0 dated 2019-12-22 and 1.1.0 dated 2020-02-18
DESCRIPTION | 15 +- MD5 | 31 +++-- NAMESPACE | 11 + NEWS.md |only R/scrap.R | 34 +++++- R/table_scrap.R |only R/tidy_scrap.R | 36 +++++- R/weblink_scrap.R |only README.md | 204 +++++++++++++++++++----------------- inst/doc/ralger.R | 40 ++++++- inst/doc/ralger.Rmd | 83 +++++++++++++- inst/doc/ralger.html | 76 +++++++++++++ man/figures/Thumbs.db |binary man/scrap.Rd | 64 +++++------ man/table_scrap.Rd |only man/tidy_scrap.Rd | 70 ++++++------ man/weblink_scrap.Rd |only tests/testthat/test-table_scrap.R |only tests/testthat/test-weblink_scrap.R |only vignettes/ralger.Rmd | 83 +++++++++++++- 20 files changed, 536 insertions(+), 211 deletions(-)
Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. The methods implemented include 'InterVA4' by Byass et al (2012) <doi:10.3402/gha.v5i0.19281>, 'InterVA5' by Byass at al (2019) <doi:10.1186/s12916-019-1333-6>, 'InSilicoVA' by McCormick et al (2016) <doi:10.1080/01621459.2016.1152191>, 'NBC' by Miasnikof et al (2015) <doi:10.1186/s12916-015-0521-2>, and a replication of 'Tariff' method by James et al (2011) <doi:10.1186/1478-7954-9-31> and Serina, et al. (2015) <doi:10.1186/s12916-015-0527-9>. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist in the implementation of the 'Tariff' method.
Author: Zehang Richard Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Richard Li <lizehang@gmail.com>
Diff between openVA versions 1.0.8 dated 2019-02-18 and 1.0.9 dated 2020-02-18
DESCRIPTION | 20 +- MD5 | 28 +-- NAMESPACE | 2 NEWS.md | 10 + R/CSMF.r | 49 ++--- R/ConvertData.r | 2 R/VAmain.r | 22 +- R/stackplot.r | 424 +++++++++++++++++++++++++---------------------- man/ConvertData.phmrc.Rd | 2 man/codeVA.Rd | 4 man/getCSMF.Rd | 4 man/getIndivProb.Rd | 6 man/getTopCOD.Rd | 2 man/stackplotVA.Rd | 30 +-- tests |only 15 files changed, 323 insertions(+), 282 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Richard Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Richard Li <lizehang@gmail.com>
Diff between InSilicoVA versions 1.2.6 dated 2020-02-18 and 1.2.7 dated 2020-02-18
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ R/insilico_core.r | 7 +++++++ inst/java/Insilico.jar |binary 5 files changed, 22 insertions(+), 10 deletions(-)
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.4.2 dated 2020-01-19 and 1.4.3 dated 2020-02-18
GWASinspector-1.4.2/GWASinspector/R/sample_inspector.R |only GWASinspector-1.4.3/GWASinspector/DESCRIPTION | 8 +- GWASinspector-1.4.3/GWASinspector/MD5 | 24 +++--- GWASinspector-1.4.3/GWASinspector/NAMESPACE | 1 GWASinspector-1.4.3/GWASinspector/R/aaa.R | 2 GWASinspector-1.4.3/GWASinspector/R/demo_inspector.R |only GWASinspector-1.4.3/GWASinspector/R/headerRelatedFunctions.R | 2 GWASinspector-1.4.3/GWASinspector/R/reportRelatedFunctions.R | 2 GWASinspector-1.4.3/GWASinspector/R/run_inspector.R | 5 - GWASinspector-1.4.3/GWASinspector/R/system_check.R | 15 ---- GWASinspector-1.4.3/GWASinspector/R/terminationFunctions.R | 35 ++++------ GWASinspector-1.4.3/GWASinspector/inst/doc/GWASinspector.html | 4 - GWASinspector-1.4.3/GWASinspector/inst/extdata/alt_headers.txt | 1 GWASinspector-1.4.3/GWASinspector/man/demo.inspector.Rd | 2 14 files changed, 43 insertions(+), 58 deletions(-)
Title: Modern Text Mining Framework for R
Description: Fast and memory-friendly tools for text vectorization, topic
modeling (LDA, LSA), word embeddings (GloVe), similarities. This package
provides a source-agnostic streaming API, which allows researchers to perform
analysis of collections of documents which are larger than available RAM. All
core functions are parallelized to benefit from multicore machines.
Author: Dmitriy Selivanov [aut, cre, cph],
Manuel Bickel [aut, cph] (Coherence measures for topic models),
Qing Wang [aut, cph] (Author of the WaprLDA C++ code)
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between text2vec versions 0.5.1 dated 2018-01-11 and 0.6 dated 2020-02-18
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Title: Single Trial Analysis (STA) of Field Trials
Description: Phenotypic analysis of field trials using mixed models with and
without spatial components. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments developed
by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<http://www.vsni.co.uk/software/asreml-r>).
Author: Bart-Jan van Rossum [aut, cre],
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Willem Kruijer [ctb] (<https://orcid.org/0000-0001-7179-1733>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenSTA versions 1.0.2 dated 2020-01-14 and 1.0.3 dated 2020-02-18
statgenSTA-1.0.2/statgenSTA/tests/testthat/test-plots.R |only statgenSTA-1.0.3/statgenSTA/DESCRIPTION | 15 statgenSTA-1.0.3/statgenSTA/MD5 | 41 statgenSTA-1.0.3/statgenSTA/NAMESPACE | 2 statgenSTA-1.0.3/statgenSTA/NEWS.md | 7 statgenSTA-1.0.3/statgenSTA/R/createSTA.R | 65 - statgenSTA-1.0.3/statgenSTA/R/createTD.R | 288 +++++- statgenSTA-1.0.3/statgenSTA/R/statgenSTA.R | 5 statgenSTA-1.0.3/statgenSTA/R/utils.R | 17 statgenSTA-1.0.3/statgenSTA/README.md | 5 statgenSTA-1.0.3/statgenSTA/inst/doc/statgenSTA.R | 5 statgenSTA-1.0.3/statgenSTA/inst/doc/statgenSTA.Rmd | 12 statgenSTA-1.0.3/statgenSTA/inst/doc/statgenSTA.html | 480 +++++------ statgenSTA-1.0.3/statgenSTA/inst/reports/modelReport.Rnw | 57 - statgenSTA-1.0.3/statgenSTA/man/plot.TD.Rd | 345 ++++--- statgenSTA-1.0.3/statgenSTA/man/statgenSTA-package.Rd | 78 - statgenSTA-1.0.3/statgenSTA/tests/testthat/Rplots.pdf |binary statgenSTA-1.0.3/statgenSTA/tests/testthat/test-STA.R | 30 statgenSTA-1.0.3/statgenSTA/tests/testthat/test-STAplots.R |only statgenSTA-1.0.3/statgenSTA/tests/testthat/test-TDplots.R |only statgenSTA-1.0.3/statgenSTA/tests/testthat/test-fitTDLme4.R | 4 statgenSTA-1.0.3/statgenSTA/tests/testthat/test-fitTDSpATS.R | 4 statgenSTA-1.0.3/statgenSTA/vignettes/statgenSTA.Rmd | 12 23 files changed, 903 insertions(+), 569 deletions(-)
Title: Model Agnostic Instance Level Variable Attributions
Description: Model agnostic tool for decomposition of predictions from black boxes.
Supports additive attributions and attributions with interactions.
The Break Down Table shows contributions of every variable to a final prediction.
The Break Down Plot presents variable contributions in a concise graphical way.
This package works for classification and regression models.
It is an extension of the 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>,
with new and faster strategies for orderings.
It supports interactions in explanations and has interactive visuals (implemented with 'D3.js' library).
The methodology behind is described in the 'iBreakDown' article (Gosiewska and Biecek 2019) <arXiv:1903.11420>
This package is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre],
Alicja Gosiewska [aut],
Hubert Baniecki [aut],
Adam Izdebski [aut],
Dariusz Komosinski [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between iBreakDown versions 0.9.9 dated 2019-08-26 and 1.0 dated 2020-02-18
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Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides graphical modelling features
used by e.g. the packages 'gRain', 'gRim' and 'gRc'.
'gRbase' contains data sets relevant for use in connection with
graphical models (in particular all data sets used in the book Graphical
Models with R (2012)).
'gRbase' implements graph algorithms including
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data. These features, however, are not maintained anymore and
remains in 'gRbase' only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The 'gRbase' Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for
installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.8-5.1 dated 2020-01-10 and 1.8-6.4 dated 2020-02-18
gRbase-1.8-5.1/gRbase/R/t_array-operations-bristol.R |only gRbase-1.8-5.1/gRbase/R/t_array-parray.R |only gRbase-1.8-5.1/gRbase/R/t_array_api_cpp.R |only gRbase-1.8-5.1/gRbase/R/t_array_cell_cpp.R |only gRbase-1.8-5.1/gRbase/R/t_array_core_algebra_cpp.R |only gRbase-1.8-5.1/gRbase/R/t_array_core_operations_cpp.R |only gRbase-1.8-5.1/gRbase/R/t_array_create.R |only gRbase-1.8-5.1/gRbase/R/t_array_misc.R |only gRbase-1.8-5.1/gRbase/R/t_array_properties_cpp.R |only gRbase-1.8-5.1/gRbase/R/t_array_simulate.R |only gRbase-1.8-5.1/gRbase/R/t_array_slice.R |only gRbase-1.8-5.1/gRbase/inst/doc/grbase-arrays.R |only gRbase-1.8-5.1/gRbase/inst/doc/grbase-arrays.Rnw |only gRbase-1.8-5.1/gRbase/inst/doc/grbase-arrays.pdf |only gRbase-1.8-5.1/gRbase/inst/doc/grbase-graphs.R |only gRbase-1.8-5.1/gRbase/inst/doc/grbase-graphs.Rnw |only gRbase-1.8-5.1/gRbase/inst/doc/grbase-graphs.pdf |only gRbase-1.8-5.1/gRbase/man/array-algebra.Rd |only gRbase-1.8-5.1/gRbase/man/array-api.Rd |only gRbase-1.8-5.1/gRbase/man/array-cell.Rd |only gRbase-1.8-5.1/gRbase/man/array-create.Rd |only gRbase-1.8-5.1/gRbase/man/array-dimnames.Rd |only gRbase-1.8-5.1/gRbase/man/array-distribution.Rd |only gRbase-1.8-5.1/gRbase/man/array-normalize.Rd |only gRbase-1.8-5.1/gRbase/man/array-operations-07.Rd |only gRbase-1.8-5.1/gRbase/man/array-operations.Rd |only gRbase-1.8-5.1/gRbase/man/array-parray.Rd |only gRbase-1.8-5.1/gRbase/man/array-properties.Rd |only gRbase-1.8-5.1/gRbase/man/array-slice.Rd |only gRbase-1.8-5.1/gRbase/man/arraypack-internal.Rd |only gRbase-1.8-5.1/gRbase/man/df2xtabs.Rd |only gRbase-1.8-5.1/gRbase/man/gRbase_utilities.Rd |only gRbase-1.8-5.1/gRbase/man/gmwr-book.Rd |only gRbase-1.8-5.1/gRbase/man/graph-cliques.Rd |only gRbase-1.8-5.1/gRbase/man/graph-mintriang.Rd |only gRbase-1.8-5.1/gRbase/man/graph_coerce.Rd |only gRbase-1.8-5.1/gRbase/man/graph_coerce_api.Rd |only gRbase-1.8-5.1/gRbase/src/t_array_cell.cpp |only gRbase-1.8-5.1/gRbase/src/t_array_core.cpp |only gRbase-1.8-5.1/gRbase/vignettes/grbase-arrays.Rnw |only gRbase-1.8-5.1/gRbase/vignettes/grbase-graphs.Rnw |only gRbase-1.8-6.4/gRbase/ChangeLog | 6 gRbase-1.8-6.4/gRbase/DESCRIPTION | 12 gRbase-1.8-6.4/gRbase/MD5 | 185 ++-- gRbase-1.8-6.4/gRbase/NAMESPACE | 717 ++++++++++-------- gRbase-1.8-6.4/gRbase/NEWS |only gRbase-1.8-6.4/gRbase/R/RcppExports.R | 50 - gRbase-1.8-6.4/gRbase/R/api_array_cell.R |only gRbase-1.8-6.4/gRbase/R/api_array_parray.R |only gRbase-1.8-6.4/gRbase/R/api_array_pct.R |only gRbase-1.8-6.4/gRbase/R/api_array_properties.R |only gRbase-1.8-6.4/gRbase/R/api_array_simulate.R |only gRbase-1.8-6.4/gRbase/R/api_array_tab-create.R |only gRbase-1.8-6.4/gRbase/R/api_array_tabX.R |only gRbase-1.8-6.4/gRbase/R/api_array_tableX_bristol.R |only gRbase-1.8-6.4/gRbase/R/combnC-c.R | 1 gRbase-1.8-6.4/gRbase/R/cov2pcor.R | 1 gRbase-1.8-6.4/gRbase/R/data-description.R | 376 ++++----- gRbase-1.8-6.4/gRbase/R/generics.R | 4 gRbase-1.8-6.4/gRbase/R/graph-coerce-list.R | 115 +- gRbase-1.8-6.4/gRbase/R/graph-coerce-xxx2yyy.R | 166 ++-- gRbase-1.8-6.4/gRbase/R/graph-coerce.R | 52 - gRbase-1.8-6.4/gRbase/R/graph-create-ugdag.R | 75 - gRbase-1.8-6.4/gRbase/R/graph-iplot.R | 3 gRbase-1.8-6.4/gRbase/R/graph-is.R |only gRbase-1.8-6.4/gRbase/R/graph-mcs.R | 40 - gRbase-1.8-6.4/gRbase/R/graph-mintriang.R | 18 gRbase-1.8-6.4/gRbase/R/graph-moralize.R | 15 gRbase-1.8-6.4/gRbase/R/graph-mpd.R | 3 gRbase-1.8-6.4/gRbase/R/graph-properties.R | 364 +-------- gRbase-1.8-6.4/gRbase/R/graph-querygraph.R | 24 gRbase-1.8-6.4/gRbase/R/graph-rip.R | 85 +- gRbase-1.8-6.4/gRbase/R/graph-topoSort.R | 66 - 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Title: Generalized Polynomial Modelling
Description: Platform dedicated to the Global Modelling technique. Its aim
is to obtain ordinary differential equations of polynomial form directly
from time series. It can be applied to single or multiple time series under
various conditions of noise, time series lengths, sampling, etc. This platform
is developped at the Centre d'Etudes Spatiales de la Biosphere (CESBIO),
UMR 5126 UPS/CNRS/CNES/IRD, 18 av. Edouard Belin, 31401 TOULOUSE, FRANCE.
The developments were funded by the French program Les Enveloppes Fluides
et l'Environnement (LEFE, MANU, projets GloMo, SpatioGloMo and MoMu). The
French program Defi InFiNiTi (CNRS) and PNTS are also acknowledged (projects
Crops'IChaos and Musc & SlowFast).
Author: Sylvain Mangiarotti [aut],
Mireille Huc [cre, aut],
Flavie Le Jean [ctb],
Malika Chassan [ctb],
Laurent Drapeau [ctb],
Institut de Recherche pour le Développement [fnd],
Centre National de la Recherche Scientifique [fnd]
Maintainer: Mireille Huc <mireille.huc@cesbio.cnes.fr>
Diff between GPoM versions 1.2 dated 2018-07-26 and 1.3 dated 2020-02-18
DESCRIPTION | 52 ++-- MD5 | 152 +++++++------ NAMESPACE | 9 R/GPoM-package.R | 8 R/P1FxCh-data.R |only R/P1FxChP2-data.R |only R/TS-data.R |only R/allToTest-data.R | 2 R/autoGPoMoSearch.R | 7 R/autoGPoMoTest.R | 428 ++++++++++++++++++++++++++++++-------- R/cano2M.R | 2 R/combiEq.R |only R/compDeriv.R | 2 R/concatMulTS.R |only R/data_vignetteIII-data.R | 2 R/data_vignetteVII-data.R | 2 R/derivODE2.R | 2 R/derivODEwMultiX.R |only R/detectP1limCycl.R | 3 R/extractEq.R |only R/findAllSets.R | 2 R/gPoMo.R | 108 ++++++++- R/gloMoId.R | 2 R/numiMultiX.R |only R/numicano.R | 11 R/numinoisy.R | 20 - R/pTimEv.R |only R/predictab.R | 6 R/subSysD.R |only R/testP.R |only R/visuEq.R | 96 ++++---- R/visuOutGP.R | 338 +++++++++++++++++++----------- build/vignette.rds |binary data/P1FxCh.rda |only data/P1FxChP2.rda |only data/TS.rda |only data/datalist | 3 inst/doc/a_GeneralIntro.pdf |binary inst/doc/b1_Conventions.R | 44 +-- inst/doc/b1_Conventions.Rmd | 8 inst/doc/b1_Conventions.pdf |binary inst/doc/b2_PreProcessing.R | 14 - inst/doc/b2_PreProcessing.pdf |binary inst/doc/b3_Modelling.R | 110 ++++----- inst/doc/b3_Modelling.Rmd | 22 - inst/doc/b3_Modelling.pdf |binary inst/doc/b4_VisualizeOutputs.R | 30 +- inst/doc/b4_VisualizeOutputs.Rmd | 6 inst/doc/b4_VisualizeOutputs.pdf |binary inst/doc/b5_Predictability.R | 26 +- inst/doc/b5_Predictability.Rmd | 4 inst/doc/b5_Predictability.pdf |binary inst/doc/b6_Sensitivity.R | 90 +++---- inst/doc/b6_Sensitivity.Rmd | 22 - inst/doc/b6_Sensitivity.pdf |binary inst/doc/b7_Retro-modelling.R | 364 ++++++++++++++++---------------- inst/doc/b7_Retro-modelling.Rmd | 126 +++++------ inst/doc/b7_Retro-modelling.pdf |binary man/GPoM-package.Rd | 19 - man/P1FxCh.Rd |only man/P1FxChP2.Rd |only man/TS.Rd |only man/allToTest.Rd | 2 man/autoGPoMoSearch.Rd | 12 - man/autoGPoMoTest.Rd | 31 ++ man/cano2M.Rd | 2 man/combiEq.Rd |only man/concatMulTS.Rd |only man/derivODEwMultiX.Rd |only man/drvSucc.Rd | 3 man/gPoMo.Rd | 62 ++++- man/gloMoId.Rd | 15 + man/numiMultiX.Rd |only man/numicano.Rd | 16 + man/numinoisy.Rd | 21 + man/odeBruitMult2.Rd | 11 man/pTimEv.Rd |only man/poLabs.Rd | 4 man/predictab.Rd | 14 + man/subSysD.Rd |only man/testP.Rd |only man/visuEq.Rd | 36 ++- man/visuOutGP.Rd | 19 + vignettes/b1_Conventions.Rmd | 8 vignettes/b3_Modelling.Rmd | 22 - vignettes/b4_VisualizeOutputs.Rmd | 6 vignettes/b5_Predictability.Rmd | 4 vignettes/b6_Sensitivity.Rmd | 22 - vignettes/b7_Retro-modelling.Rmd | 126 +++++------ 89 files changed, 1607 insertions(+), 971 deletions(-)
Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics. This package is based on the Stan platform (Carpenter et el. 2017 <doi:10.18637/jss.v076.i01>).
Author: Jure Demšar [cre, aut],
Grega Repovš [aut],
Erik Štrumbelj [aut],
Trustees of Columbia University [cph],
John Kruschke [cph] (R/shared_functions.R - mcmc_hdi,
src/stan_files/ttest.stan),
Rasmus Baath [cph] (R/b_bootstrap.R)
Maintainer: Jure Demšar <jure.demsar@fri.uni-lj.si>
Diff between bayes4psy versions 1.2.0 dated 2019-12-13 and 1.2.2 dated 2020-02-18
DESCRIPTION | 12 MD5 | 234 ++--- NAMESPACE | 2 NEWS.md | 13 inst/doc/adaptation_level.R | 7 inst/doc/adaptation_level.Rmd | 9 inst/doc/adaptation_level.html | 271 ++++-- inst/doc/afterimages.R | 15 inst/doc/afterimages.Rmd | 17 inst/doc/afterimages.html | 585 +++++++++----- inst/doc/flanker.R | 11 inst/doc/flanker.Rmd | 13 inst/doc/flanker.html | 427 ++++++---- inst/doc/stroop.R | 11 inst/doc/stroop.Rmd | 13 inst/doc/stroop.html | 277 +++++- man/b_bootstrap.Rd | 111 +- man/b_color.Rd | 219 ++--- man/b_linear.Rd | 144 +-- man/b_prior-class.Rd | 34 man/b_prior-get_prior_id.Rd | 35 man/b_reaction_time.Rd | 131 +-- man/b_results-class.Rd | 16 man/b_results-compare_distributions.Rd | 32 man/b_results-compare_means.Rd | 32 man/b_results-get_parameters.Rd | 26 man/b_results-get_subject_parameters.Rd | 26 man/b_results-plot_distributions.Rd | 32 man/b_results-plot_distributions_difference.Rd | 32 man/b_results-plot_fit.Rd | 32 man/b_results-plot_means.Rd | 30 man/b_results-plot_means_difference.Rd | 32 man/b_results-plot_trace.Rd | 26 man/b_success_rate.Rd | 121 +-- man/b_ttest.Rd | 118 +- man/bayes4psy-datasets.Rd | 356 ++++---- man/bayes4psy-package.Rd | 30 man/color_class-class.Rd | 602 +++++++-------- man/color_class-compare_distributions.Rd | 55 - man/color_class-compare_means.Rd | 55 - man/color_class-get_parameters.Rd | 51 - man/color_class-plot_distributions.Rd | 55 - man/color_class-plot_distributions_difference.Rd | 55 - man/color_class-plot_distributions_hsv.Rd | 61 - man/color_class-plot_fit.Rd | 55 - man/color_class-plot_fit_hsv.Rd | 57 - man/color_class-plot_hsv.Rd | 57 - man/color_class-plot_means.Rd | 55 - man/color_class-plot_means_difference.Rd | 55 - man/color_class-plot_means_hsv.Rd | 61 - man/color_class-plot_trace.Rd | 51 - man/linear_class-class.Rd | 326 ++++---- man/linear_class-compare_distributions.Rd | 55 - man/linear_class-compare_means.Rd | 55 - man/linear_class-get_parameters.Rd | 51 - man/linear_class-get_subject_parameters.Rd | 51 - man/linear_class-plot_distributions.Rd | 55 - man/linear_class-plot_distributions_difference.Rd | 55 - man/linear_class-plot_fit.Rd | 55 - man/linear_class-plot_means.Rd | 55 - man/linear_class-plot_means_difference.Rd | 55 - man/linear_class-plot_trace.Rd | 51 - man/mcmc_hdi.Rd | 42 - man/plot-color_class-missing-method.Rd | 51 - man/plot-linear_class-missing-method.Rd | 51 - man/plot-reaction_time_class-missing-method.Rd | 51 - man/plot-success_rate_class-missing-method.Rd | 51 - man/plot-ttest_class-missing-method.Rd | 43 - man/reaction_time_class-class.Rd | 378 ++++----- man/reaction_time_class-compare_distributions.Rd | 55 - man/reaction_time_class-compare_means.Rd | 55 - man/reaction_time_class-get_parameters.Rd | 51 - man/reaction_time_class-get_subject_parameters.Rd | 51 - man/reaction_time_class-plot_distributions.Rd | 55 - man/reaction_time_class-plot_distributions_difference.Rd | 55 - man/reaction_time_class-plot_fit.Rd | 55 - man/reaction_time_class-plot_means.Rd | 55 - man/reaction_time_class-plot_means_difference.Rd | 55 - man/reaction_time_class-plot_trace.Rd | 51 - man/show-color_class-method.Rd | 43 - man/show-linear_class-method.Rd | 43 - man/show-reaction_time_class-method.Rd | 43 - man/show-success_rate_class-method.Rd | 43 - man/show-ttest_class-method.Rd | 43 - man/success_rate_class-class.Rd | 346 ++++---- man/success_rate_class-compare_distributions.Rd | 55 - man/success_rate_class-compare_means.Rd | 55 - man/success_rate_class-get_parameters.Rd | 51 - man/success_rate_class-get_subject_parameters.Rd | 51 - man/success_rate_class-plot_distributions.Rd | 55 - man/success_rate_class-plot_distributions_difference.Rd | 55 - man/success_rate_class-plot_fit.Rd | 55 - man/success_rate_class-plot_means.Rd | 55 - man/success_rate_class-plot_means_difference.Rd | 55 - man/success_rate_class-plot_trace.Rd | 51 - man/summary-color_class-method.Rd | 43 - man/summary-linear_class-method.Rd | 43 - man/summary-reaction_time_class-method.Rd | 43 - man/summary-success_rate_class-method.Rd | 43 - man/summary-ttest_class-method.Rd | 43 - man/ttest_class-class.Rd | 426 +++++----- man/ttest_class-compare_distributions.Rd | 55 - man/ttest_class-compare_means.Rd | 55 - man/ttest_class-get_parameters.Rd | 51 - man/ttest_class-plot_distributions.Rd | 55 - man/ttest_class-plot_distributions_difference.Rd | 55 - man/ttest_class-plot_fit.Rd | 51 - man/ttest_class-plot_means.Rd | 55 - man/ttest_class-plot_means_difference.Rd | 55 - man/ttest_class-plot_trace.Rd | 51 - tests/testthat/test_color.R | 14 tests/testthat/test_linear.R | 22 tests/testthat/test_reaction_time.R | 24 tests/testthat/test_success_rate.R | 16 vignettes/adaptation_level.Rmd | 9 vignettes/afterimages.Rmd | 17 vignettes/flanker.Rmd | 13 vignettes/stroop.Rmd | 13 118 files changed, 4842 insertions(+), 4435 deletions(-)
Title: R Interface to the ClassyFire RESTful API
Description: Access to the ClassyFire RESTful API <http://classyfire.wishartlab.com>. Retrieve existing entity classifications and submit new entities for classification.
Author: Tom Wilson [aut, cre] (<https://orcid.org/0000-0003-3112-4682>),
Jasen Finch [aut]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>
Diff between classyfireR versions 0.3.0 dated 2019-11-18 and 0.3.3 dated 2020-02-18
DESCRIPTION | 10 +++---- MD5 | 14 +++++----- NAMESPACE | 2 + NEWS.md | 14 ++++++++++ R/get_classification.R | 57 ++++++++++++++++++++++++++++++-------------- R/internals.R | 28 ++++++++++----------- R/show-method.R | 5 +++ inst/classyfireR-manual.pdf |binary 8 files changed, 87 insertions(+), 43 deletions(-)
Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model.
The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots.
This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre] (<https://orcid.org/0000-0001-6563-5742>),
Przemyslaw Biecek [aut, ths] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Tomasz Mikołajczyk [aut],
Michal Burdukiewicz [ctb],
Szymon Maksymiuk [ctb]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>
Diff between auditor versions 1.1.0 dated 2019-09-24 and 1.2.0 dated 2020-02-18
auditor-1.1.0/auditor/R/plot_support_function.R |only auditor-1.1.0/auditor/R/scores_support_functions.R |only auditor-1.2.0/auditor/DESCRIPTION | 13 auditor-1.2.0/auditor/MD5 | 167 ++-- auditor-1.2.0/auditor/NAMESPACE | 3 auditor-1.2.0/auditor/NEWS.md | 12 auditor-1.2.0/auditor/R/model_evaluation.R | 68 - auditor-1.2.0/auditor/R/model_performance.R | 65 + auditor-1.2.0/auditor/R/plotD3_lift.R | 22 auditor-1.2.0/auditor/R/plotD3_rec.R | 8 auditor-1.2.0/auditor/R/plotD3_roc.R | 21 auditor-1.2.0/auditor/R/plotD3_rroc.R | 2 auditor-1.2.0/auditor/R/plot_lift.R | 48 + auditor-1.2.0/auditor/R/plot_rec.R | 4 auditor-1.2.0/auditor/R/plot_roc.R | 7 auditor-1.2.0/auditor/R/plot_rroc.R | 4 auditor-1.2.0/auditor/R/print.R | 14 auditor-1.2.0/auditor/R/score.R | 84 +- auditor-1.2.0/auditor/R/score_F1.R | 34 auditor-1.2.0/auditor/R/score_acc.R | 34 auditor-1.2.0/auditor/R/score_auc.R | 25 auditor-1.2.0/auditor/R/score_cooksdistance.R | 22 auditor-1.2.0/auditor/R/score_dw.R | 13 auditor-1.2.0/auditor/R/score_gini.R |only auditor-1.2.0/auditor/R/score_halfnormal.R | 12 auditor-1.2.0/auditor/R/score_mae.R | 13 auditor-1.2.0/auditor/R/score_mse.R | 13 auditor-1.2.0/auditor/R/score_peak.R | 12 auditor-1.2.0/auditor/R/score_precision.R | 32 auditor-1.2.0/auditor/R/score_r2.R |only auditor-1.2.0/auditor/R/score_rec.R | 11 auditor-1.2.0/auditor/R/score_recall.R | 28 auditor-1.2.0/auditor/R/score_rmse.R | 11 auditor-1.2.0/auditor/R/score_rroc.R | 11 auditor-1.2.0/auditor/R/score_runs.R | 12 auditor-1.2.0/auditor/R/score_specificity.R | 28 auditor-1.2.0/auditor/R/support_function_plot.R |only auditor-1.2.0/auditor/R/support_function_score.R |only auditor-1.2.0/auditor/inst/d3js/plotAutocorrelationSingle.js | 356 +++++----- auditor-1.2.0/auditor/inst/d3js/plotCooksDistanceSingle.js | 309 ++++---- auditor-1.2.0/auditor/inst/d3js/plotLIFT.js | 187 ++--- auditor-1.2.0/auditor/inst/d3js/plotREC.js | 188 ++--- auditor-1.2.0/auditor/inst/d3js/plotROC.js | 207 +++-- auditor-1.2.0/auditor/inst/d3js/plotRROC.js | 207 +++-- auditor-1.2.0/auditor/inst/d3js/plotScatterSingle.js | 352 +++++---- auditor-1.2.0/auditor/inst/doc/model_evaluation_audit.html | 2 auditor-1.2.0/auditor/inst/doc/model_performance_audit.html | 19 auditor-1.2.0/auditor/inst/doc/model_residuals_audit.html | 4 auditor-1.2.0/auditor/man/figures/logo.png |binary auditor-1.2.0/auditor/man/model_evaluation.Rd | 2 auditor-1.2.0/auditor/man/model_performance.Rd | 31 auditor-1.2.0/auditor/man/plotD3_lift.Rd | 4 auditor-1.2.0/auditor/man/plot_lift.Rd | 4 auditor-1.2.0/auditor/man/plot_rec.Rd | 4 auditor-1.2.0/auditor/man/plot_rroc.Rd | 4 auditor-1.2.0/auditor/man/print.auditor_model_cooksdistance.Rd | 2 auditor-1.2.0/auditor/man/print.auditor_model_evaluation.Rd | 2 auditor-1.2.0/auditor/man/print.auditor_model_halfnormal.Rd | 2 auditor-1.2.0/auditor/man/print.auditor_model_performance.Rd | 2 auditor-1.2.0/auditor/man/print.auditor_model_residual.Rd | 2 auditor-1.2.0/auditor/man/print.auditor_score.Rd | 4 auditor-1.2.0/auditor/man/score.Rd | 29 auditor-1.2.0/auditor/man/score_acc.Rd | 12 auditor-1.2.0/auditor/man/score_auc.Rd | 10 auditor-1.2.0/auditor/man/score_cooksdistance.Rd | 8 auditor-1.2.0/auditor/man/score_dw.Rd | 10 auditor-1.2.0/auditor/man/score_f1.Rd | 12 auditor-1.2.0/auditor/man/score_gini.Rd |only auditor-1.2.0/auditor/man/score_halfnormal.Rd | 5 auditor-1.2.0/auditor/man/score_mae.Rd | 10 auditor-1.2.0/auditor/man/score_mse.Rd | 10 auditor-1.2.0/auditor/man/score_one_minus_acc.Rd | 12 auditor-1.2.0/auditor/man/score_one_minus_auc.Rd | 10 auditor-1.2.0/auditor/man/score_one_minus_f1.Rd | 12 auditor-1.2.0/auditor/man/score_one_minus_gini.Rd |only auditor-1.2.0/auditor/man/score_one_minus_precision.Rd | 12 auditor-1.2.0/auditor/man/score_one_minus_recall.Rd | 12 auditor-1.2.0/auditor/man/score_one_minus_specificity.Rd | 12 auditor-1.2.0/auditor/man/score_peak.Rd | 10 auditor-1.2.0/auditor/man/score_precision.Rd | 12 auditor-1.2.0/auditor/man/score_r2.Rd |only auditor-1.2.0/auditor/man/score_rec.Rd | 10 auditor-1.2.0/auditor/man/score_recall.Rd | 12 auditor-1.2.0/auditor/man/score_rmse.Rd | 10 auditor-1.2.0/auditor/man/score_rroc.Rd | 10 auditor-1.2.0/auditor/man/score_runs.Rd | 10 auditor-1.2.0/auditor/man/score_specificity.Rd | 12 auditor-1.2.0/auditor/tests/testthat/test_plotsR.R | 2 auditor-1.2.0/auditor/tests/testthat/test_scores.R | 28 89 files changed, 1783 insertions(+), 1256 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-07 0.1.4
2019-03-18 0.1.3
2019-03-14 0.1.2
2019-01-19 0.1.1
2018-12-09 0.1.0
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc.html> for more information).
Choose files with 'selectDWD()', download and process data sets with 'dataDWD()' and 'readDWD()'.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 1.2.0 dated 2019-10-28 and 1.3.1 dated 2020-02-18
rdwd-1.2.0/rdwd/data/DEU.rda |only rdwd-1.2.0/rdwd/data/EUR.rda |only rdwd-1.3.1/rdwd/DESCRIPTION | 15 - rdwd-1.3.1/rdwd/MD5 | 108 ++++----- rdwd-1.3.1/rdwd/NAMESPACE | 7 rdwd-1.3.1/rdwd/NEWS | 7 rdwd-1.3.1/rdwd/R/addBorders.R |only rdwd-1.3.1/rdwd/R/dataDWD.R | 9 rdwd-1.3.1/rdwd/R/indexFTP.R | 11 rdwd-1.3.1/rdwd/R/metaInfo.R |only rdwd-1.3.1/rdwd/R/plotRadar.R |only rdwd-1.3.1/rdwd/R/projectRasterDWD.R | 76 +++--- rdwd-1.3.1/rdwd/R/rdwd-package.R | 149 ------------ rdwd-1.3.1/rdwd/R/readDWD.R | 23 + rdwd-1.3.1/rdwd/R/runLocalTests.R | 25 +- rdwd-1.3.1/rdwd/R/updateRdwd.R |only rdwd-1.3.1/rdwd/README.md | 3 rdwd-1.3.1/rdwd/data/datalist | 2 rdwd-1.3.1/rdwd/inst/doc/rdwd.html | 11 rdwd-1.3.1/rdwd/inst/extdata |only rdwd-1.3.1/rdwd/man/DEU.Rd | 52 ++-- rdwd-1.3.1/rdwd/man/EUR.Rd | 50 ++-- rdwd-1.3.1/rdwd/man/addBorders.Rd | 76 +++--- rdwd-1.3.1/rdwd/man/checkIndex.Rd | 90 ++++--- rdwd-1.3.1/rdwd/man/checkSuggestedPackage.Rd | 54 ++-- rdwd-1.3.1/rdwd/man/createIndex.Rd | 176 ++++++++------- rdwd-1.3.1/rdwd/man/dataDWD.Rd | 271 ++++++++++++----------- rdwd-1.3.1/rdwd/man/dirDWD.Rd | 62 ++--- rdwd-1.3.1/rdwd/man/dwdbase.Rd | 38 +-- rdwd-1.3.1/rdwd/man/dwdparams.Rd | 60 ++--- rdwd-1.3.1/rdwd/man/findID.Rd | 107 ++++----- rdwd-1.3.1/rdwd/man/index.Rd | 124 +++++----- rdwd-1.3.1/rdwd/man/indexFTP.Rd | 193 ++++++++-------- rdwd-1.3.1/rdwd/man/lldist.Rd | 92 +++---- rdwd-1.3.1/rdwd/man/localtestdir.Rd | 68 ++--- rdwd-1.3.1/rdwd/man/metaInfo.Rd | 60 ++--- rdwd-1.3.1/rdwd/man/nearbyStations.Rd | 124 +++++----- rdwd-1.3.1/rdwd/man/newColumnNames.Rd | 76 +++--- rdwd-1.3.1/rdwd/man/plotRadar.Rd |only rdwd-1.3.1/rdwd/man/projectRasterDWD.Rd | 127 +++++----- rdwd-1.3.1/rdwd/man/rdwd.Rd | 72 +++--- rdwd-1.3.1/rdwd/man/readDWD.Rd | 247 +++++++++++---------- rdwd-1.3.1/rdwd/man/readDWD.asc.Rd | 178 +++++++-------- rdwd-1.3.1/rdwd/man/readDWD.binary.Rd | 190 ++++++++-------- rdwd-1.3.1/rdwd/man/readDWD.data.Rd | 113 +++++---- rdwd-1.3.1/rdwd/man/readDWD.meta.Rd | 98 ++++---- rdwd-1.3.1/rdwd/man/readDWD.multia.Rd | 157 ++++++------- rdwd-1.3.1/rdwd/man/readDWD.nc.Rd | 153 ++++++------- rdwd-1.3.1/rdwd/man/readDWD.radar.Rd | 128 +++++------ rdwd-1.3.1/rdwd/man/readDWD.raster.Rd | 130 +++++------ rdwd-1.3.1/rdwd/man/readDWD.stand.Rd | 163 +++++++------- rdwd-1.3.1/rdwd/man/readMeta.Rd | 70 +++--- rdwd-1.3.1/rdwd/man/readVars.Rd | 76 +++--- rdwd-1.3.1/rdwd/man/release_questions.Rd | 22 - rdwd-1.3.1/rdwd/man/rowDisplay.Rd | 52 ++-- rdwd-1.3.1/rdwd/man/runLocalTests.Rd | 91 ++++--- rdwd-1.3.1/rdwd/man/selectDWD.Rd | 313 +++++++++++++-------------- rdwd-1.3.1/rdwd/man/updateIndexes.Rd | 110 ++++----- rdwd-1.3.1/rdwd/man/updateRdwd.Rd |only 59 files changed, 2373 insertions(+), 2336 deletions(-)
Title: Effects and Importances of Model Ingredients
Description: Collection of tools for assessment of feature importance and feature effects.
Key functions are:
feature_importance() for assessment of global level feature importance,
ceteris_paribus() for calculation of the what-if plots,
partial_dependence() for partial dependence plots,
conditional_dependence() for conditional dependence plots,
accumulated_dependence() for accumulated local effects plots,
aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,
generic print() and plot() for better usability of selected explainers,
generic plotD3() for interactive, D3 based explanations, and
generic describe() for explanations in natural language.
The package 'ingredients' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Adam Izdebski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ingredients versions 0.5.0 dated 2019-12-20 and 1.0 dated 2020-02-18
ingredients-0.5.0/ingredients/R/accumulated_dependency.R |only ingredients-0.5.0/ingredients/R/conditional_dependency.R |only ingredients-0.5.0/ingredients/R/partial_dependency.R |only ingredients-0.5.0/ingredients/man/accumulated_dependency.Rd |only ingredients-0.5.0/ingredients/man/conditional_dependency.Rd |only ingredients-0.5.0/ingredients/man/partial_dependency.Rd |only ingredients-1.0/ingredients/DESCRIPTION | 16 - ingredients-1.0/ingredients/MD5 | 123 +++++----- ingredients-1.0/ingredients/NAMESPACE | 23 + ingredients-1.0/ingredients/NEWS.md | 14 + ingredients-1.0/ingredients/R/accumulated_dependence.R |only ingredients-1.0/ingredients/R/aggregate_profiles.R | 29 +- ingredients-1.0/ingredients/R/bind_plots.R |only ingredients-1.0/ingredients/R/calculate_oscillations.R | 4 ingredients-1.0/ingredients/R/calculate_variable_profile.R | 2 ingredients-1.0/ingredients/R/ceteris_paribus.R | 4 ingredients-1.0/ingredients/R/cluster_profiles.R | 4 ingredients-1.0/ingredients/R/conditional_dependence.R |only ingredients-1.0/ingredients/R/describe_aggregated_profiles.R | 5 ingredients-1.0/ingredients/R/describe_feature_importance.R | 2 ingredients-1.0/ingredients/R/feature_importance.R | 4 ingredients-1.0/ingredients/R/partial_dependence.R |only ingredients-1.0/ingredients/R/plotD3_aggregated_profiles.R | 6 ingredients-1.0/ingredients/R/plotD3_ceteris_paribus.R | 5 ingredients-1.0/ingredients/R/plot_aggregated_profiles.R | 10 ingredients-1.0/ingredients/R/plot_ceteris_paribus.R | 48 +-- ingredients-1.0/ingredients/R/plot_ceteris_paribus_2d.R | 2 ingredients-1.0/ingredients/R/plot_ceteris_paribus_oscillations.R | 2 ingredients-1.0/ingredients/R/plot_feature_importance.R | 13 - ingredients-1.0/ingredients/R/print_feature_importance.R | 2 ingredients-1.0/ingredients/R/show_aggregated_profiles.R | 1 ingredients-1.0/ingredients/R/show_observations.R | 9 ingredients-1.0/ingredients/R/show_profiles.R | 54 ++-- ingredients-1.0/ingredients/R/show_residuals.R | 10 ingredients-1.0/ingredients/inst/doc/vignette_describe.Rmd | 4 ingredients-1.0/ingredients/inst/doc/vignette_describe.html | 80 +++--- ingredients-1.0/ingredients/inst/doc/vignette_simulated.R | 24 - ingredients-1.0/ingredients/inst/doc/vignette_simulated.Rmd | 30 +- ingredients-1.0/ingredients/inst/doc/vignette_simulated.html | 64 ++--- ingredients-1.0/ingredients/inst/doc/vignette_titanic.R | 6 ingredients-1.0/ingredients/inst/doc/vignette_titanic.Rmd | 12 ingredients-1.0/ingredients/inst/doc/vignette_titanic.html | 48 +-- ingredients-1.0/ingredients/man/accumulated_dependence.Rd |only ingredients-1.0/ingredients/man/aggregate_profiles.Rd | 13 - ingredients-1.0/ingredients/man/bind_plots.Rd |only ingredients-1.0/ingredients/man/calculate_oscillations.Rd | 4 ingredients-1.0/ingredients/man/calculate_variable_profile.Rd | 2 ingredients-1.0/ingredients/man/ceteris_paribus.Rd | 4 ingredients-1.0/ingredients/man/cluster_profiles.Rd | 4 ingredients-1.0/ingredients/man/conditional_dependence.Rd |only ingredients-1.0/ingredients/man/describe.Rd | 6 ingredients-1.0/ingredients/man/feature_importance.Rd | 4 ingredients-1.0/ingredients/man/figures/logo.png |binary ingredients-1.0/ingredients/man/partial_dependence.Rd |only ingredients-1.0/ingredients/man/plot.aggregated_profiles_explainer.Rd | 10 ingredients-1.0/ingredients/man/plot.ceteris_paribus_2d_explainer.Rd | 2 ingredients-1.0/ingredients/man/plot.ceteris_paribus_explainer.Rd | 4 ingredients-1.0/ingredients/man/plot.ceteris_paribus_oscillations.Rd | 2 ingredients-1.0/ingredients/man/plot.feature_importance_explainer.Rd | 15 - ingredients-1.0/ingredients/man/plotD3_aggregated_profiles.Rd | 4 ingredients-1.0/ingredients/man/plotD3_ceteris_paribus.Rd | 2 ingredients-1.0/ingredients/man/print.feature_importance_explainer.Rd | 2 ingredients-1.0/ingredients/man/show_residuals.Rd | 2 ingredients-1.0/ingredients/tests/testthat/helper-objects.R | 4 ingredients-1.0/ingredients/tests/testthat/test_aggregated_profiles.R | 10 ingredients-1.0/ingredients/tests/testthat/test_bind_plots.R |only ingredients-1.0/ingredients/tests/testthat/test_variable_dropout.R | 5 ingredients-1.0/ingredients/vignettes/vignette_describe.Rmd | 4 ingredients-1.0/ingredients/vignettes/vignette_simulated.Rmd | 30 +- ingredients-1.0/ingredients/vignettes/vignette_titanic.Rmd | 12 70 files changed, 444 insertions(+), 361 deletions(-)
Title: Pedigree and Genetic Groups
Description: Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between ggroups versions 1.3.0 dated 2020-02-09 and 2.0.1 dated 2020-02-18
DESCRIPTION | 8 ++-- MD5 | 42 +++++++++++++------------ NAMESPACE | 2 + NEWS.md | 6 +++ R/buildA.R | 42 ++++++++++++------------- R/buildD.R |only R/mat2tab.R | 40 +++++++++++++++++------- R/offspring.R | 2 - R/peddown.R | 7 +--- R/pedup.R | 8 +--- R/qmat.R |only R/qmatL.R | 4 +- R/qmatXL.R | 2 - R/renum.R | 2 - R/rg.R | 6 +-- R/tab2mat.R | 6 +-- R/tabA.R | 2 - R/tabAinv.R | 89 ++++++++++++++++++++++++++--------------------------- R/tabD.R | 95 ++++++++++++++++++++++++++++++++++++++++----------------- R/tabDinv.R | 28 ++++++---------- man/buildD.Rd |only man/qmat.Rd |only man/tabD.Rd | 8 +++- man/tabDinv.Rd | 6 ++- 24 files changed, 234 insertions(+), 171 deletions(-)
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre],
Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.6.0.1 dated 2020-01-31 and 1.6.0.2 dated 2020-02-18
DESCRIPTION | 13 +++++-------- MD5 | 4 ++-- tests/testthat/Rplots.pdf |binary 3 files changed, 7 insertions(+), 10 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 0.6.2 dated 2019-12-10 and 0.6.9 dated 2020-02-18
DESCRIPTION | 10 +-- MD5 | 36 +++++------ R/get_eurostat_data.R | 73 +++++++++++----------- R/get_eurostat_toc.R | 46 +++++--------- R/load_cfg.R | 4 - R/search_eurostat_dsd.R | 16 ++--- README.md | 11 +++ inst/extdata/rest_api_config.json | 121 ++++++++++++++++++++++++++++++++++++++ man/extract_data.Rd | 8 +- man/extract_dsd.Rd | 4 - man/get_eurostat_bulk.Rd | 19 ++++- man/get_eurostat_data.Rd | 43 ++++++++++--- man/get_eurostat_dsd.Rd | 11 ++- man/get_eurostat_raw.Rd | 17 ++++- man/get_eurostat_toc.Rd | 13 +++- man/load_cfg.Rd | 9 ++ man/put_eurostat_cache.Rd | 9 ++ man/search_eurostat_dsd.Rd | 5 - tests/testthat/test-all.R | 26 +++++--- 19 files changed, 342 insertions(+), 139 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut] (<https://orcid.org/0000-0001-8301-0471>),
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut, cre] (<https://orcid.org/0000-0003-2810-3186>),
Fabian Sobotka [ctb],
Fabian Scheipl [ctb],
Andreas Mayr [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between mboost versions 2.9-1 dated 2018-08-22 and 2.9-2 dated 2020-02-18
mboost-2.9-1/mboost/cleanup |only mboost-2.9-2/mboost/DESCRIPTION | 8 mboost-2.9-2/mboost/MD5 | 155 mboost-2.9-2/mboost/NAMESPACE | 210 mboost-2.9-2/mboost/R/AAA.R | 56 mboost-2.9-2/mboost/R/bkernel.R | 228 mboost-2.9-2/mboost/R/bkronecker.R | 550 - mboost-2.9-2/mboost/R/bl.R | 17 mboost-2.9-2/mboost/R/bmono.R | 784 - mboost-2.9-2/mboost/R/bmrf.R | 210 mboost-2.9-2/mboost/R/bolscw.R | 248 mboost-2.9-2/mboost/R/brad.R | 326 mboost-2.9-2/mboost/R/btree.R | 254 mboost-2.9-2/mboost/R/buser.R | 194 mboost-2.9-2/mboost/R/confint.R | 652 - mboost-2.9-2/mboost/R/control.R | 28 mboost-2.9-2/mboost/R/crossvalidation.R | 326 mboost-2.9-2/mboost/R/family.R | 2458 ++--- mboost-2.9-2/mboost/R/helpers.R | 592 - mboost-2.9-2/mboost/R/mboost.R | 1778 +-- mboost-2.9-2/mboost/R/mboost_intern.R | 20 mboost-2.9-2/mboost/R/methods.R | 1330 +- mboost-2.9-2/mboost/R/stabsel.R | 212 mboost-2.9-2/mboost/R/survival.R | 202 mboost-2.9-2/mboost/R/varimp.R | 494 - mboost-2.9-2/mboost/README.md | 104 mboost-2.9-2/mboost/build/partial.rdb |binary mboost-2.9-2/mboost/build/vignette.rds |binary mboost-2.9-2/mboost/inst/CITATION | 188 mboost-2.9-2/mboost/inst/India_quantiles.R | 88 mboost-2.9-2/mboost/inst/NEWS.Rd | 20 mboost-2.9-2/mboost/inst/birds_Biometrics.R | 196 mboost-2.9-2/mboost/inst/cache/mboost_illustrations_benchmarks.R | 298 mboost-2.9-2/mboost/inst/doc/SurvivalEnsembles.R | 582 - mboost-2.9-2/mboost/inst/doc/SurvivalEnsembles.Rnw | 830 - mboost-2.9-2/mboost/inst/doc/SurvivalEnsembles.pdf |binary mboost-2.9-2/mboost/inst/doc/mboost.R | 348 mboost-2.9-2/mboost/inst/doc/mboost.Rnw | 902 +- mboost-2.9-2/mboost/inst/doc/mboost.pdf |binary mboost-2.9-2/mboost/inst/doc/mboost_illustrations.R | 672 - mboost-2.9-2/mboost/inst/doc/mboost_illustrations.Rnw | 1388 +-- mboost-2.9-2/mboost/inst/doc/mboost_illustrations.pdf |binary mboost-2.9-2/mboost/inst/doc/mboost_tutorial.R | 1198 +- mboost-2.9-2/mboost/inst/doc/mboost_tutorial.Rnw | 4208 ++++----- mboost-2.9-2/mboost/inst/doc/mboost_tutorial.pdf |binary mboost-2.9-2/mboost/inst/india_additive.R | 144 mboost-2.9-2/mboost/inst/india_analysis.R | 298 mboost-2.9-2/mboost/inst/india_blackboost.R | 104 mboost-2.9-2/mboost/inst/india_helpfunc.R | 378 mboost-2.9-2/mboost/inst/india_plots.R | 1212 +- mboost-2.9-2/mboost/inst/india_preproc.R | 550 - mboost-2.9-2/mboost/inst/india_stumps.R | 104 mboost-2.9-2/mboost/inst/india_summary.R | 424 mboost-2.9-2/mboost/inst/india_vcm.R | 178 mboost-2.9-2/mboost/inst/mboost_Bioinf.R | 202 mboost-2.9-2/mboost/inst/readAML_Bullinger.R | 298 mboost-2.9-2/mboost/man/FP.Rd | 136 mboost-2.9-2/mboost/man/Family.Rd | 900 +- mboost-2.9-2/mboost/man/IPCweights.Rd | 84 mboost-2.9-2/mboost/man/blackboost.Rd | 284 mboost-2.9-2/mboost/man/boost_family-class.Rd | 76 mboost-2.9-2/mboost/man/confint.Rd | 352 mboost-2.9-2/mboost/man/control.Rd | 106 mboost-2.9-2/mboost/man/gamboost.Rd | 308 mboost-2.9-2/mboost/man/glmboost.Rd | 328 mboost-2.9-2/mboost/man/mboost_fit.Rd | 251 mboost-2.9-2/mboost/man/mboost_intern.Rd | 46 mboost-2.9-2/mboost/man/mboost_package.Rd | 4 mboost-2.9-2/mboost/man/plot.Rd | 412 mboost-2.9-2/mboost/man/stabsel.Rd | 280 mboost-2.9-2/mboost/man/varimp.Rd | 288 mboost-2.9-2/mboost/vignettes/SurvivalEnsembles.Rnw | 830 - mboost-2.9-2/mboost/vignettes/boost.bib | 4478 +++++----- mboost-2.9-2/mboost/vignettes/jmlr2e.sty | 642 - mboost-2.9-2/mboost/vignettes/mboost.Rnw | 902 +- mboost-2.9-2/mboost/vignettes/mboost_illustrations.Rnw | 1388 +-- mboost-2.9-2/mboost/vignettes/mboost_tutorial.Rnw | 4208 ++++----- mboost-2.9-2/mboost/vignettes/mboost_tutorial.bib | 822 - mboost-2.9-2/mboost/vignettes/setup.R | 66 79 files changed, 21730 insertions(+), 21707 deletions(-)
Title: Bayes Factors, Model Choice and Variable Selection in Linear
Models
Description: Conceived to calculate Bayes factors in Linear models and then to provide a formal Bayesian answer to testing and variable selection problems. From a theoretical side, the emphasis in this package is placed on the prior distributions and it allows a wide range of them: Jeffreys (1961); Zellner and Siow(1980)<DOI:10.1007/bf02888369>; Zellner and Siow(1984); Zellner (1986)<DOI:10.2307/2233941>; Fernandez et al. (2001)<DOI:10.1016/s0304-4076(00)00076-2>; Liang et al. (2008)<DOI:10.1198/016214507000001337> and Bayarri et al. (2012)<DOI:10.1214/12-aos1013>. The interaction with the package is through a friendly interface that syntactically mimics the well-known lm() command of R. The resulting objects can be easily explored providing the user very valuable information (like marginal, joint and conditional inclusion probabilities of potential variables; the highest posterior probability model, HPM; the median probability model, MPM) about the structure of the true -data generating- model. Additionally, this package incorporates abilities to handle problems with a large number of potential explanatory variables through parallel and heuristic versions of the main commands, Garcia-Donato and Martinez-Beneito (2013)<DOI:10.1080/01621459.2012.742443>. It also allows problems with p>n and p>>n and also incorporates routines to handle problems with variable selection with factors.
Author: Gonzalo Garcia-Donato [aut],
Anabel Forte [aut, cre],
Carlos Vergara-Hernández [ctb]
Maintainer: Anabel Forte <anabel.forte@uv.es>
Diff between BayesVarSel versions 1.8.0 dated 2017-12-04 and 2.0.1 dated 2020-02-18
DESCRIPTION | 27 - MD5 | 83 ++- NAMESPACE | 5 NEWS.md | 25 + R/BMAcoeff.R | 2 R/Bvs.R | 115 +++-- R/GibbsBvs.R | 194 +++++++- R/GibbsBvsF.R |only R/auxfuncs4BvsF.R |only R/package.R | 4 R/plotBvs.R | 2 R/pltltn.R |only R/predictBvs.R | 103 ++++ README.md | 16 build |only demo/BayesVarSel.Hald.R | 1 inst |only man/BMAcoeff.Rd | 2 man/BayesVarSel-package.Rd | 2 man/Btest.Rd | 10 man/Bvs.Rd | 41 + man/GibbsBvs.Rd | 41 + man/GibbsBvsF.Rd |only man/histBMA.Rd | 10 man/plot.Bvs.Rd | 2 man/pltltn.Rd |only man/print.Bvs.Rd | 3 src/BayesVarSel_init.c | 19 src/Gibbsauxiliaryfuncs.c | 100 +++- src/Gibbsauxiliaryfuncs.h | 6 src/allBF.c | 51 +- src/allBF.h | 2 src/auxiliaryfuncs.c | 1 src/auxiliaryfuncs.h | 1 src/main.c | 15 src/mainGibbs.c | 1014 +++++++++++++++++++++++++++++++++++++++++++++ src/mainGibbsF.c |only src/priorprob.c | 147 ++++++ src/priorprob.h | 6 vignettes |only 40 files changed, 1870 insertions(+), 180 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the function inventory to create a structure of directories and template scripts.
Author: Sergio Ibarra-Espinosa [aut, cre]
(<https://orcid.org/0000-0002-3162-1905>),
Daniel Schuch [ctb] (<https://orcid.org/0000-0001-5977-4519>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between vein versions 0.8.5 dated 2020-01-17 and 0.8.7 dated 2020-02-18
vein-0.8.5/vein/R/st_explode.R |only vein-0.8.5/vein/man/emis_wrf.Rd |only vein-0.8.5/vein/man/matvect.Rd |only vein-0.8.5/vein/man/st_explode.Rd |only vein-0.8.7/vein/DESCRIPTION | 14 vein-0.8.7/vein/MD5 | 187 +-- vein-0.8.7/vein/NAMESPACE | 6 vein-0.8.7/vein/NEWS.md | 24 vein-0.8.7/vein/R/adt.R | 79 - vein-0.8.7/vein/R/age_hdv.R | 23 vein-0.8.7/vein/R/age_ldv.R | 14 vein-0.8.7/vein/R/age_moto.R | 15 vein-0.8.7/vein/R/aw.R |only vein-0.8.7/vein/R/ef_cetesb.R | 246 ++-- vein-0.8.7/vein/R/ef_china.R | 1 vein-0.8.7/vein/R/emis_grid.R | 210 ++- vein-0.8.7/vein/R/emis_hot_td.R | 26 vein-0.8.7/vein/R/emis_merge.R | 47 vein-0.8.7/vein/R/emis_order.R | 1 vein-0.8.7/vein/R/emis_paved.R | 65 - vein-0.8.7/vein/R/emis_post.R | 75 + vein-0.8.7/vein/R/emis_source.R | 16 vein-0.8.7/vein/R/emis_wrf.R | 15 vein-0.8.7/vein/R/grid_emis.R | 13 vein-0.8.7/vein/R/invcop.R | 240 ++-- vein-0.8.7/vein/R/make_grid.R | 17 vein-0.8.7/vein/R/matvect.R | 37 vein-0.8.7/vein/R/my_age.R | 12 vein-0.8.7/vein/R/net.R | 10 vein-0.8.7/vein/R/speciate.R | 45 vein-0.8.7/vein/R/sysdata.rda |binary vein-0.8.7/vein/R/wide_to_long.R | 4 vein-0.8.7/vein/data/net.rda |binary vein-0.8.7/vein/data/pollutants.rda |binary vein-0.8.7/vein/inst/README.Rmd | 167 +- vein-0.8.7/vein/inst/README.html | 1299 ++++++++++++----------- vein-0.8.7/vein/man/GriddedEmissionsArray.Rd | 3 vein-0.8.7/vein/man/adt.Rd | 51 vein-0.8.7/vein/man/age.Rd | 3 vein-0.8.7/vein/man/age_hdv.Rd | 15 vein-0.8.7/vein/man/age_ldv.Rd | 15 vein-0.8.7/vein/man/age_moto.Rd | 16 vein-0.8.7/vein/man/aw.Rd |only vein-0.8.7/vein/man/ef_cetesb.Rd | 83 + vein-0.8.7/vein/man/ef_china.Rd | 21 vein-0.8.7/vein/man/ef_evap.Rd | 15 vein-0.8.7/vein/man/ef_fun.Rd | 10 vein-0.8.7/vein/man/ef_hdv_scaled.Rd | 3 vein-0.8.7/vein/man/ef_hdv_speed.Rd | 16 vein-0.8.7/vein/man/ef_ive.Rd | 15 vein-0.8.7/vein/man/ef_ldv_cold.Rd | 14 vein-0.8.7/vein/man/ef_ldv_speed.Rd | 15 vein-0.8.7/vein/man/ef_nitro.Rd | 17 vein-0.8.7/vein/man/emis.Rd | 16 vein-0.8.7/vein/man/emis_cold.Rd | 20 vein-0.8.7/vein/man/emis_cold_td.Rd | 13 vein-0.8.7/vein/man/emis_det.Rd | 11 vein-0.8.7/vein/man/emis_evap.Rd | 15 vein-0.8.7/vein/man/emis_evap2.Rd | 26 vein-0.8.7/vein/man/emis_grid.Rd | 44 vein-0.8.7/vein/man/emis_hot_td.Rd | 3 vein-0.8.7/vein/man/emis_merge.Rd | 21 vein-0.8.7/vein/man/emis_paved.Rd | 45 vein-0.8.7/vein/man/emis_post.Rd | 18 vein-0.8.7/vein/man/emis_source.Rd | 14 vein-0.8.7/vein/man/emis_wear.Rd | 13 vein-0.8.7/vein/man/figures |only vein-0.8.7/vein/man/fuel_corr.Rd | 7 vein-0.8.7/vein/man/grid_emis.Rd | 7 vein-0.8.7/vein/man/invcop.Rd | 15 vein-0.8.7/vein/man/inventory.Rd | 15 vein-0.8.7/vein/man/long_to_wide.Rd | 9 vein-0.8.7/vein/man/make_grid.Rd | 8 vein-0.8.7/vein/man/my_age.Rd | 13 vein-0.8.7/vein/man/net.Rd | 9 vein-0.8.7/vein/man/netspeed.Rd | 3 vein-0.8.7/vein/man/running_losses-deprecated.Rd | 6 vein-0.8.7/vein/man/speciate.Rd | 3 vein-0.8.7/vein/man/vein-deprecated.Rd | 57 - vein-0.8.7/vein/man/vein-package.Rd | 6 vein-0.8.7/vein/man/vein_notes.Rd | 11 vein-0.8.7/vein/man/vkm.Rd | 11 vein-0.8.7/vein/man/wide_to_long.Rd | 2 vein-0.8.7/vein/src/e2d.f95 | 4 vein-0.8.7/vein/src/e3d.f95 | 4 vein-0.8.7/vein/src/e4d.f95 | 4 vein-0.8.7/vein/src/etd1.f95 | 4 vein-0.8.7/vein/src/etd2.f95 | 4 vein-0.8.7/vein/src/etd2cold.f95 | 4 vein-0.8.7/vein/src/etd3.f95 | 4 vein-0.8.7/vein/src/etd3cold.f95 | 4 vein-0.8.7/vein/src/etd4.f95 | 4 vein-0.8.7/vein/src/etd4cold.f95 | 4 vein-0.8.7/vein/src/etd5.f95 | 4 vein-0.8.7/vein/src/etd5cold.f95 | 4 vein-0.8.7/vein/src/etd6.f95 | 4 vein-0.8.7/vein/src/etd6cold.f95 | 4 vein-0.8.7/vein/src/etd7.f95 | 4 98 files changed, 2223 insertions(+), 1498 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@gmail.com>
Diff between InSilicoVA versions 1.2.5 dated 2018-10-29 and 1.2.6 dated 2020-02-18
DESCRIPTION | 12 ++- MD5 | 39 ++++++----- NAMESPACE | 1 NEWS.md | 9 ++ R/diag.r | 18 ++--- R/get_indiv.r | 2 R/groupplot.r | 4 - R/indivplot.r | 8 +- R/insilico_core.r | 84 ++++++++++++++++-------- R/insilico_standard.r | 8 +- R/insilico_train.r | 5 + R/plot.r | 6 - R/print_insilico_summary.r | 2 R/report.r | 2 inst/java/Insilico.jar |binary java/Insilico/src/sampler/InsilicoSampler2.java | 4 - man/insilico.Rd | 5 + man/insilico.fit.Rd | 4 - tests |only 19 files changed, 137 insertions(+), 76 deletions(-)
Title: Statistical Analysis of Circular Data using Nonnegative
Trigonometric Sums (NNTS) Models
Description: Includes functions for the analysis of circular data using distributions based on Nonnegative Trigonometric Sums (NNTS). The package includes functions for calculation of densities and distributions, for the estimation of parameters, for plotting and more.
Author: Juan Jose Fernandez-Duran and Maria Mercedes Gregorio-Dominguez
Maintainer: Maria Mercedes Gregorio-Dominguez <mercedes@itam.mx>
Diff between CircNNTSR versions 2.2 dated 2016-05-10 and 2.2-1 dated 2020-02-18
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/mnntsmanifoldnewtonestimation.R | 6 +++--- R/nntsmanifoldnewtonestimation.R | 4 ++-- man/CircNNTSR-package.Rd | 34 ++++++---------------------------- man/Datab6fisher_ready.rd | 6 +++--- man/mnntsdensity.Rd | 5 +++-- man/mnntsmanifoldnewtonestimation.Rd | 5 +++-- man/mnntsmarginal.Rd | 5 +++-- man/mnntsplot.Rd | 5 +++-- man/mnntsplotmarginal.Rd | 5 +++-- man/mnntsplotwithmarginals.Rd | 5 +++-- man/nntsmanifoldnewtonestimation.Rd | 10 ++++++---- man/nntsplot.Rd | 5 +++-- man/snntsdensityplot.Rd | 6 +++--- man/snntsmanifoldnewtonestimation.Rd | 10 ++++++---- man/snntsmarginallatitude.Rd | 5 +++-- man/snntsmarginallongitude.Rd | 5 +++-- 18 files changed, 77 insertions(+), 86 deletions(-)
Title: Biclustering with Missing Data
Description: Biclustering is a statistical learning technique that simultaneously
partitions and clusters rows and columns of a data matrix. Since the solution
space of biclustering is in infeasible to completely search with current
computational mechanisms, this package uses a greedy heuristic. The algorithm
featured in this package is, to the best our knowledge, the first biclustering
algorithm to work on data with missing values. Li, J., Reisner, J., Pham, H.,
Olafsson, S., and Vardeman, S. (2020) Biclustering with Missing Data. Information
Sciences, 510, 304–316.
Author: John Reisner [cre, aut, cph],
Hieu Pham [ctb, cph],
Jing Li [ctb, cph]
Maintainer: John Reisner <johntreisner@gmail.com>
Diff between biclustermd versions 0.2.0 dated 2019-12-07 and 0.2.1 dated 2020-02-18
DESCRIPTION | 12 +- MD5 | 18 +-- NAMESPACE | 3 R/biclustermd.R | 31 ++++- R/compare_biclusters.R | 37 +++++- R/rep_biclustermd.R | 2 inst/doc/Airports.html | 155 ++++++++++++++++------------- man/biclustermd.Rd | 2 man/rep_biclustermd.Rd | 2 tests/testthat/test-autoplot_biclustermd.R | 4 10 files changed, 165 insertions(+), 101 deletions(-)