Title: RNA Secondary Structure Module Mining, Comparison and Plotting
Description: Provides function for RNA secondary structure plotting, comparison and module mining. Given a RNA secondary structure, you can obtain stem regions, hairpin loops, internal loops, bulge loops and multibranch loops of this RNA structure using this program. They are the basic modules of RNA secondary structure. For each module you get, you can use this program to label the RNA structure with a specific color. You can also use this program to compare two RNA secondary structures to get a score that represents similarity. Reference: Reuter JS, Mathews DH (2010) <doi:10.1186/1471-2105-11-129>.
Author: Zheng HeWei
Maintainer: Zheng HeWei<zhenghw@hrbmu.edu.cn>
Diff between RNAsmc versions 0.5.0 dated 2020-03-24 and 0.6.0 dated 2020-03-28
DESCRIPTION | 6 - MD5 | 12 +- NAMESPACE | 9 + R/getScore.R |only R/strCompare.R | 273 +++++------------------------------------------------ R/strComparePlot.R | 36 +++--- man/getScore.rd |only man/strCompare.rd | 5 8 files changed, 66 insertions(+), 275 deletions(-)
Title: Preprocessing and Multivariate Analysis of Bidimensional Gas
Chromatography Data
Description: Toolbox for chemometrics analysis of bidimensional gas
chromatography data. This package import data for common scientific data
format (NetCDF) and fold it to 2D chromatogram. Then, it can perform
preprocessing and multivariate analysis. In the preprocessing algorithms,
baseline correction, smoothing, and peak alignment are available.
While in multivariate analysis, multiway principal component analysis is
incorporated.
Author: Cristian Quiroz-Moreno [aut, cre]
(<https://orcid.org/0000-0002-9069-9147>),
Guilherme L. Alexandrino [aut]
(<https://orcid.org/0000-0002-2007-378X>),
Noroska G.S. Mogollón [aut] (<https://orcid.org/0000-0002-0756-6184>)
Maintainer: Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>
Diff between RGCxGC versions 1.1-1 dated 2020-03-25 and 1.1-2 dated 2020-03-28
DESCRIPTION | 31 ++- MD5 | 71 +++++---- R/Myrothecium.R | 11 - R/baseline_corr.R | 4 R/batchTwoDCOW.R | 12 - R/get_metadata.R | 2 R/import_mixOmics.R | 4 R/m_prcomp.R | 8 - R/plot.R | 2 R/plot_loading.R | 6 R/read_chrom.R | 2 R/set_metadata.R | 2 R/twod_cow.R | 8 - R/wsmooth.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 60 ++++--- inst/doc/Explanation.Rmd | 38 ++-- inst/doc/Explanation.html | 272 ++++++++++++++++++----------------- inst/doc/plotting_chromatograms.R |only inst/doc/plotting_chromatograms.Rmd |only inst/doc/plotting_chromatograms.html |only inst/extdata/mylbd5.CDF |only man/Myrothecium.Rd | 10 - man/baseline_corr.Rd | 4 man/batch_2DCOW.Rd | 12 - man/get_metadata-methods.Rd | 2 man/import_mixOmics-methods.Rd | 4 man/m_prcomp.Rd | 8 - man/plot-methods.Rd | 2 man/plot_loading-methods.Rd | 6 man/read_chrom.Rd | 2 man/set_metadata-methods.Rd | 2 man/twod_cow.Rd | 8 - man/wsmooth.Rd | 6 vignettes/Explanation.Rmd | 38 ++-- vignettes/REFERENCES.bib | 132 +++++++++------- vignettes/images/RGCxGC.png |only vignettes/images/may_chrom.jpg |only vignettes/plotting_chromatograms.Rmd |only 40 files changed, 417 insertions(+), 358 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 1.1.1 dated 2019-10-30 and 1.1.2 dated 2020-03-28
ParallelLogger-1.1.1/ParallelLogger/man/ParallelLogger.Rd |only ParallelLogger-1.1.2/ParallelLogger/DESCRIPTION | 10 - ParallelLogger-1.1.2/ParallelLogger/MD5 | 80 +++++----- ParallelLogger-1.1.2/ParallelLogger/NEWS.md | 7 ParallelLogger-1.1.2/ParallelLogger/R/Appenders.R | 2 ParallelLogger-1.1.2/ParallelLogger/R/Args.R | 4 ParallelLogger-1.1.2/ParallelLogger/R/Cluster.R | 2 ParallelLogger-1.1.2/ParallelLogger/R/Layouts.R | 6 ParallelLogger-1.1.2/ParallelLogger/R/Loggers.R | 2 ParallelLogger-1.1.2/ParallelLogger/R/Logging.R | 30 ++- ParallelLogger-1.1.2/ParallelLogger/R/ParallelLogger.R | 9 - ParallelLogger-1.1.2/ParallelLogger/R/ShinyApps.R | 2 ParallelLogger-1.1.2/ParallelLogger/build/vignette.rds |binary ParallelLogger-1.1.2/ParallelLogger/inst/doc/Logging.R | 40 ++--- ParallelLogger-1.1.2/ParallelLogger/inst/doc/Logging.pdf |binary ParallelLogger-1.1.2/ParallelLogger/inst/doc/Parallel.R | 14 - ParallelLogger-1.1.2/ParallelLogger/inst/doc/Parallel.pdf |binary ParallelLogger-1.1.2/ParallelLogger/man/ParallelLogger-package.Rd |only ParallelLogger-1.1.2/ParallelLogger/man/addDefaultConsoleLogger.Rd | 44 ++--- ParallelLogger-1.1.2/ParallelLogger/man/addDefaultEmailLogger.Rd | 7 ParallelLogger-1.1.2/ParallelLogger/man/addDefaultFileLogger.Rd | 38 ++-- ParallelLogger-1.1.2/ParallelLogger/man/clusterApply.Rd | 3 ParallelLogger-1.1.2/ParallelLogger/man/convertJsonToSettings.Rd | 2 ParallelLogger-1.1.2/ParallelLogger/man/convertSettingsToJson.Rd | 42 ++--- ParallelLogger-1.1.2/ParallelLogger/man/createArgFunction.Rd | 10 + ParallelLogger-1.1.2/ParallelLogger/man/createConsoleAppender.Rd | 56 +++---- ParallelLogger-1.1.2/ParallelLogger/man/createEmailAppender.Rd | 8 - ParallelLogger-1.1.2/ParallelLogger/man/createLogger.Rd | 7 ParallelLogger-1.1.2/ParallelLogger/man/launchLogViewer.Rd | 66 ++++---- ParallelLogger-1.1.2/ParallelLogger/man/layoutEmail.Rd | 2 ParallelLogger-1.1.2/ParallelLogger/man/layoutStackTrace.Rd | 2 ParallelLogger-1.1.2/ParallelLogger/man/layoutTimestamp.Rd | 54 +++--- ParallelLogger-1.1.2/ParallelLogger/man/logFatal.Rd | 40 ++--- ParallelLogger-1.1.2/ParallelLogger/man/logInfo.Rd | 58 +++---- ParallelLogger-1.1.2/ParallelLogger/man/logTrace.Rd | 58 +++---- ParallelLogger-1.1.2/ParallelLogger/man/logWarn.Rd | 40 ++--- ParallelLogger-1.1.2/ParallelLogger/man/makeCluster.Rd | 8 - ParallelLogger-1.1.2/ParallelLogger/man/matchInList.Rd | 74 ++++----- ParallelLogger-1.1.2/ParallelLogger/man/registerLogger.Rd | 58 +++---- ParallelLogger-1.1.2/ParallelLogger/man/saveSettingsToJson.Rd | 40 ++--- ParallelLogger-1.1.2/ParallelLogger/man/selectFromList.Rd | 76 ++++----- ParallelLogger-1.1.2/ParallelLogger/man/unregisterLogger.Rd | 64 ++++---- 42 files changed, 547 insertions(+), 518 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: Probabilistic Composition of Correlated Preference
Description: Individual classification method based on multivariate normal distribution, taking into account the correlation between the characteristics observed in the individuals. Entering a data set whose individuals are previously classified, this method will seek to understand how these individuals were grouped into their classes. This package will help you identify the class of new individuals without prior knowledge of your class. The way out is a set of measures that identify these new individuals. An interesting measure is accuracy, which measures how well the method correctly identified an individual for his or her class. The reference of this method was the result of the thesis of Marcelo Carlos Ribeiro, also author of the 'cppcor' package, and is still in the phase of corrections for publication. In the next updates of the package, we will add the reference of this method.
Author: Marcelo Ribeiro [aut],
Ben Deivide [aut, cre],
Tiago Martins [aut],
Fernando Oliveira [aut]
Maintainer: Ben Deivide <ben.deivide@ufsj.edu.br>
Diff between cppcor versions 1.1 dated 2020-03-28 and 1.2 dated 2020-03-28
DESCRIPTION | 12 +++++------- MD5 | 2 +- 2 files changed, 6 insertions(+), 8 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut, cre],
Adam Banker [aut],
Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>
Diff between paws.common versions 0.2.6 dated 2020-02-23 and 0.3.0 dated 2020-03-28
DESCRIPTION | 6 - MD5 | 50 ++++++------- NAMESPACE | 2 NEWS.md | 9 ++ R/custom_s3.R | 30 ++++++- R/error.R | 60 +++++++++++++-- R/handlers.R | 6 - R/handlers_ec2query.R | 8 +- R/handlers_jsonrpc.R | 4 - R/handlers_query.R | 9 +- R/handlers_restjson.R | 4 - R/request.R | 8 +- R/service.R | 2 R/xmlutil.R | 9 +- man/aws_error.Rd |only man/handlers.Rd | 6 - man/new_request.Rd | 2 man/new_service.Rd | 2 man/send_request.Rd | 2 man/tags.Rd | 122 ++++++++++++++++---------------- tests/testthat/test_aws_error.R |only tests/testthat/test_custom_s3.R | 42 +++++++++++ tests/testthat/test_handlers_ec2query.R | 16 ++++ tests/testthat/test_handlers_jsonrpc.R | 6 + tests/testthat/test_handlers_query.R | 10 ++ tests/testthat/test_handlers_restjson.R | 4 + tests/testthat/test_handlers_restxml.R | 18 ++++ 27 files changed, 309 insertions(+), 128 deletions(-)
Title: Tidy Interface to 'data.table'
Description: Tidy interface to 'data.table'. 'rlang' compatible, which allows the user to build custom functions much like they would in the tidyverse.
Author: Mark Fairbanks [aut, cre],
Tyson Barrett [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.3.2 dated 2020-03-08 and 0.4.0 dated 2020-03-28
tidytable-0.3.2/tidytable/R/purrr.R |only tidytable-0.3.2/tidytable/man/dt_arrange.Rd |only tidytable-0.3.2/tidytable/man/dt_bind_rows.Rd |only tidytable-0.3.2/tidytable/man/dt_case.Rd |only tidytable-0.3.2/tidytable/man/dt_count.Rd |only tidytable-0.3.2/tidytable/man/dt_distinct.Rd |only tidytable-0.3.2/tidytable/man/dt_drop_na.Rd |only tidytable-0.3.2/tidytable/man/dt_fill.Rd |only tidytable-0.3.2/tidytable/man/dt_filter.Rd |only tidytable-0.3.2/tidytable/man/dt_get_dummies.Rd |only tidytable-0.3.2/tidytable/man/dt_group_nest.Rd |only tidytable-0.3.2/tidytable/man/dt_group_split.Rd |only tidytable-0.3.2/tidytable/man/dt_left_join.Rd |only tidytable-0.3.2/tidytable/man/dt_map.Rd |only tidytable-0.3.2/tidytable/man/dt_mutate.Rd |only tidytable-0.3.2/tidytable/man/dt_mutate_if.Rd |only tidytable-0.3.2/tidytable/man/dt_pivot_longer.Rd |only tidytable-0.3.2/tidytable/man/dt_pivot_wider.Rd |only tidytable-0.3.2/tidytable/man/dt_pull.Rd |only tidytable-0.3.2/tidytable/man/dt_relocate.Rd |only tidytable-0.3.2/tidytable/man/dt_rename.Rd |only tidytable-0.3.2/tidytable/man/dt_rename_all.Rd |only tidytable-0.3.2/tidytable/man/dt_replace_na.Rd |only tidytable-0.3.2/tidytable/man/dt_select.Rd |only tidytable-0.3.2/tidytable/man/dt_separate.Rd |only tidytable-0.3.2/tidytable/man/dt_slice.Rd |only tidytable-0.3.2/tidytable/man/dt_starts_with.Rd |only tidytable-0.3.2/tidytable/man/dt_summarize.Rd |only tidytable-0.3.2/tidytable/man/dt_top_n.Rd |only tidytable-0.3.2/tidytable/man/dt_unnest_legacy.Rd |only tidytable-0.4.0/tidytable/DESCRIPTION | 6 tidytable-0.4.0/tidytable/MD5 | 208 ++++--- tidytable-0.4.0/tidytable/NAMESPACE | 211 +++++-- tidytable-0.4.0/tidytable/NEWS.md | 25 tidytable-0.4.0/tidytable/R/arrange.R | 22 tidytable-0.4.0/tidytable/R/bind.R | 34 - tidytable-0.4.0/tidytable/R/case.R | 6 tidytable-0.4.0/tidytable/R/count.R | 39 - tidytable-0.4.0/tidytable/R/distinct.R | 24 tidytable-0.4.0/tidytable/R/drop_na.R | 24 tidytable-0.4.0/tidytable/R/dt.R | 2 tidytable-0.4.0/tidytable/R/fill.R | 95 +-- tidytable-0.4.0/tidytable/R/filter.R | 46 + tidytable-0.4.0/tidytable/R/get_dummies.R | 50 + tidytable-0.4.0/tidytable/R/group_split.R | 23 tidytable-0.4.0/tidytable/R/ifelse.R |only tidytable-0.4.0/tidytable/R/inv_gc.R | 18 tidytable-0.4.0/tidytable/R/is_tidytable.R | 4 tidytable-0.4.0/tidytable/R/join.R | 77 +- tidytable-0.4.0/tidytable/R/map.R |only tidytable-0.4.0/tidytable/R/map2.R |only tidytable-0.4.0/tidytable/R/mutate.R | 66 +- tidytable-0.4.0/tidytable/R/mutate_across.R |only tidytable-0.4.0/tidytable/R/mutate_variants.R | 108 +-- tidytable-0.4.0/tidytable/R/n.R |only tidytable-0.4.0/tidytable/R/nest.R | 37 - tidytable-0.4.0/tidytable/R/pivot_longer.R | 57 +- tidytable-0.4.0/tidytable/R/pivot_wider.R | 99 +-- tidytable-0.4.0/tidytable/R/pull.R | 26 tidytable-0.4.0/tidytable/R/relocate.R | 22 tidytable-0.4.0/tidytable/R/rename.R | 19 tidytable-0.4.0/tidytable/R/rename_variants.R | 92 +-- tidytable-0.4.0/tidytable/R/rename_with.R |only tidytable-0.4.0/tidytable/R/replace_na.R | 12 tidytable-0.4.0/tidytable/R/row_number.R |only tidytable-0.4.0/tidytable/R/select.R | 33 - tidytable-0.4.0/tidytable/R/select_helpers.R | 72 +- tidytable-0.4.0/tidytable/R/separate.R | 34 - tidytable-0.4.0/tidytable/R/slice.R | 115 ++-- tidytable-0.4.0/tidytable/R/summarize.R | 53 + tidytable-0.4.0/tidytable/R/tidytable_package.R | 6 tidytable-0.4.0/tidytable/R/top_n.R | 29 - tidytable-0.4.0/tidytable/R/transmute.R |only tidytable-0.4.0/tidytable/R/unnest.R | 29 - tidytable-0.4.0/tidytable/R/utils-general.R | 10 tidytable-0.4.0/tidytable/R/utils-selectors.R | 102 ++- tidytable-0.4.0/tidytable/README.md | 275 +++++----- tidytable-0.4.0/tidytable/man/arrange..Rd |only tidytable-0.4.0/tidytable/man/bind_rows..Rd |only tidytable-0.4.0/tidytable/man/case..Rd |only tidytable-0.4.0/tidytable/man/count..Rd |only tidytable-0.4.0/tidytable/man/distinct..Rd |only tidytable-0.4.0/tidytable/man/drop_na..Rd |only tidytable-0.4.0/tidytable/man/figures/logo.png |binary tidytable-0.4.0/tidytable/man/fill..Rd |only tidytable-0.4.0/tidytable/man/filter..Rd |only tidytable-0.4.0/tidytable/man/get_dummies..Rd |only tidytable-0.4.0/tidytable/man/group_split..Rd |only tidytable-0.4.0/tidytable/man/ifelse..Rd |only tidytable-0.4.0/tidytable/man/inv_gc.Rd | 12 tidytable-0.4.0/tidytable/man/is_tidytable.Rd | 4 tidytable-0.4.0/tidytable/man/left_join..Rd |only tidytable-0.4.0/tidytable/man/map..Rd |only tidytable-0.4.0/tidytable/man/mutate..Rd |only tidytable-0.4.0/tidytable/man/mutate_across..Rd |only tidytable-0.4.0/tidytable/man/mutate_if..Rd |only tidytable-0.4.0/tidytable/man/n..Rd |only tidytable-0.4.0/tidytable/man/nest_by..Rd |only tidytable-0.4.0/tidytable/man/pivot_longer..Rd |only tidytable-0.4.0/tidytable/man/pivot_wider..Rd |only tidytable-0.4.0/tidytable/man/pull..Rd |only tidytable-0.4.0/tidytable/man/relocate..Rd |only tidytable-0.4.0/tidytable/man/rename..Rd |only tidytable-0.4.0/tidytable/man/rename_all..Rd |only tidytable-0.4.0/tidytable/man/rename_with..Rd |only tidytable-0.4.0/tidytable/man/replace_na..Rd |only tidytable-0.4.0/tidytable/man/row_number..Rd |only tidytable-0.4.0/tidytable/man/select..Rd |only tidytable-0.4.0/tidytable/man/separate..Rd |only tidytable-0.4.0/tidytable/man/slice..Rd |only tidytable-0.4.0/tidytable/man/starts_with..Rd |only tidytable-0.4.0/tidytable/man/summarize..Rd |only tidytable-0.4.0/tidytable/man/top_n..Rd |only tidytable-0.4.0/tidytable/man/transmute..Rd |only tidytable-0.4.0/tidytable/man/unnest..Rd |only tidytable-0.4.0/tidytable/tests/testthat/test-arrange.R | 14 tidytable-0.4.0/tidytable/tests/testthat/test-bind.R | 52 + tidytable-0.4.0/tidytable/tests/testthat/test-case_when.R | 26 tidytable-0.4.0/tidytable/tests/testthat/test-count.R | 19 tidytable-0.4.0/tidytable/tests/testthat/test-distinct.R | 21 tidytable-0.4.0/tidytable/tests/testthat/test-drop_na.R | 30 - tidytable-0.4.0/tidytable/tests/testthat/test-dt.R | 12 tidytable-0.4.0/tidytable/tests/testthat/test-fill.R | 74 ++ tidytable-0.4.0/tidytable/tests/testthat/test-filter.R | 29 - tidytable-0.4.0/tidytable/tests/testthat/test-get_dummies.R | 84 ++- tidytable-0.4.0/tidytable/tests/testthat/test-ifelse.R |only tidytable-0.4.0/tidytable/tests/testthat/test-join.R | 31 - tidytable-0.4.0/tidytable/tests/testthat/test-mutate.R | 95 +++ tidytable-0.4.0/tidytable/tests/testthat/test-mutate_variants.R | 76 +- tidytable-0.4.0/tidytable/tests/testthat/test-pivot_longer.R | 41 - tidytable-0.4.0/tidytable/tests/testthat/test-pivot_wider.R | 43 + tidytable-0.4.0/tidytable/tests/testthat/test-pull.R | 14 tidytable-0.4.0/tidytable/tests/testthat/test-purrr.R | 34 + tidytable-0.4.0/tidytable/tests/testthat/test-relocate.R | 30 - tidytable-0.4.0/tidytable/tests/testthat/test-rename.R | 78 +- tidytable-0.4.0/tidytable/tests/testthat/test-replace_na.R | 14 tidytable-0.4.0/tidytable/tests/testthat/test-select.R | 18 tidytable-0.4.0/tidytable/tests/testthat/test-separate.R | 21 tidytable-0.4.0/tidytable/tests/testthat/test-slice.R | 109 +++ tidytable-0.4.0/tidytable/tests/testthat/test-summarize.R | 72 ++ tidytable-0.4.0/tidytable/tests/testthat/test-top_n.R | 38 + tidytable-0.4.0/tidytable/tests/testthat/test-unnest.R | 25 142 files changed, 2156 insertions(+), 1170 deletions(-)
Title: Mapas de las Divisiones Politicas y Administrativas de Chile
(Maps of the Political and Administrative Divisions of Chile)
Description: Mapas terrestres con topologias simplificadas. Estos mapas no
tienen precision geodesica, por lo que aplica el DFL-83 de 1979 de la Republica
de Chile y se consideran referenciales sin validez legal.
No se incluyen los territorios antarticos y bajo ningun evento estos mapas
significan que exista una cesion u ocupacion de territorios soberanos en
contra del Derecho Internacional por parte de Chile. Esta paquete esta
documentado intencionalmente en castellano asciificado para que funcione sin
problema en diferentes plataformas.
(Terrestrial maps with simplified toplogies. These maps lack geodesic
precision, therefore DFL-83 1979 of the Republic of Chile applies and are
considered to have no legal validity.
Antartic territories are excluded and under no event these maps mean
there is a cession or occupation of sovereign territories against International
Laws from Chile. This package was intentionally documented in asciified
spanish to make it work without problem on different platforms.)
Author: Mauricio Vargas [aut, cre],
Roberto Salas [ctb],
Joshua Kunst [ctb],
Juan Correa [dtc],
Ricardo Aravena [ths],
Pontificia Universidad Catolica de Chile [cph],
Instituto Nacional de Estadisticas (INE) [dtc],
Subsecretaria de Desarrollo Regional (SUBDERE) [dtc],
Biblioteca del Congreso Nacional de Chile (BCN) [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between chilemapas versions 0.1.4 dated 2020-01-24 and 0.2 dated 2020-03-28
DESCRIPTION | 12 MD5 | 54 +- NAMESPACE | 37 - R/administrative-maps.R | 126 +++-- R/political-maps.R | 126 ++--- build/vignette.rds |binary data/datalist | 14 data/mapa_comunas.rda |binary data/mapa_zonas.rda |binary inst/doc/basic-usage.R | 216 ++++---- inst/doc/basic-usage.Rmd | 296 ++++++------ inst/doc/basic-usage.html | 915 ++++++++++++++++++-------------------- man/censo_2017_comunas.Rd | 52 +- man/censo_2017_zonas.Rd | 50 +- man/codigos_territoriales.Rd | 60 +- man/divisiones_electorales.Rd | 60 +- man/divisiones_salud.Rd | 54 +- man/generar_circunscripciones.Rd | 3 man/generar_distritos.Rd | 3 man/generar_provincias.Rd | 3 man/generar_regiones.Rd | 3 man/generar_servicios_salud.Rd | 3 man/mapa_comunas.Rd | 54 +- man/mapa_zonas.Rd | 56 +- tests/testthat.R | 8 tests/testthat/test-aggregation.R | 40 - tests/testthat/test-data.R | 10 vignettes/basic-usage.Rmd | 296 ++++++------ 28 files changed, 1298 insertions(+), 1253 deletions(-)
Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre],
Juliane Schmachtenberg [ctb],
Swenja Wagner [ctb],
Patricia Scheil [ctb],
Tom Waschischek [ctb],
Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 1.0.2 dated 2020-02-11 and 1.0.4 dated 2020-03-28
DESCRIPTION | 10 - MD5 | 262 ++++++++++++++-------------- NAMESPACE | 2 NEWS | 9 R/FilenameMapper.R | 5 R/MzTabReader.R | 68 ++++--- R/createReport.R | 8 R/fcn_MQ.R | 12 - R/fcn_QCHeat.R | 2 R/fcn_miscGGplot.R | 6 R/fcn_plots.R | 27 +- R/qcMetric_EVD.R | 20 +- R/qcMetric_PAR.R | 36 ++- README.md | 7 build/vignette.rds |binary inst/doc/PTXQC-Basic_Guide_for_R_users.R | 8 inst/doc/PTXQC-Basic_Guide_for_R_users.html | 4 inst/doc/PTXQC-CustomizeReport.html | 4 inst/doc/PTXQC-DragNDrop.html | 4 inst/doc/PTXQC-FAQ.html | 4 inst/doc/PTXQC-Input_And_Output_Data.R | 2 inst/doc/PTXQC-Input_And_Output_Data.html | 4 inst/doc/PTXQC-ListOfMetrics.R | 4 inst/doc/PTXQC-ListOfMetrics.html | 9 man/CV.Rd | 32 +-- man/FilenameMapper-class.Rd | 80 ++++---- man/LCS.Rd | 38 ++-- man/LCSn.Rd | 70 +++---- man/MQDataReader-class.Rd | 245 +++++++++++++------------- man/MzTabReader-class.Rd | 80 ++++---- man/PTXQC.Rd | 75 +++----- man/RSD.Rd | 32 +-- man/RTalignmentTree.Rd | 54 ++--- man/ScoreInAlignWindow.Rd | 42 ++-- man/YAMLClass-class.Rd | 74 +++---- man/addGGtitle.Rd | 44 ++-- man/alignmentCheck.Rd | 70 +++---- man/appendEnv.Rd | 48 ++--- man/assignBlocks.Rd | 56 ++--- man/boxplotCompare.Rd | 88 +++++---- man/brewer.pal.Safe.Rd | 40 ++-- man/byX.Rd | 72 +++---- man/byXflex.Rd | 70 +++---- man/computeMatchRTFractions.Rd | 40 ++-- man/correctSetSize.Rd | 86 ++++----- man/createReport.Rd | 92 +++++---- man/darken.Rd | 38 ++-- man/del0.Rd | 32 +-- man/delLCP.Rd | 104 +++++------ man/delLCS.Rd | 46 ++-- man/findAlignReference.Rd | 56 ++--- man/fixCalibration.Rd | 58 +++--- man/flattenList.Rd | 38 ++-- man/getAbundanceClass.Rd | 50 ++--- man/getECDF.Rd | 46 ++-- man/getFragmentErrors.Rd | 66 +++---- man/getHTMLTable.Rd | 58 +++--- man/getMQPARValue.Rd | 58 +++--- man/getMaxima.Rd | 54 ++--- man/getMetaData.Rd | 36 +-- man/getMetricsObjects.Rd | 32 +-- man/getPCA.Rd | 54 ++--- man/getPeptideCounts.Rd | 46 ++-- man/getProteinCounts.Rd | 46 ++-- man/getQCHeatMap.Rd | 66 +++---- man/getReportFilenames.Rd | 71 +++---- man/ggAxisLabels.Rd | 62 +++--- man/ggText.Rd | 40 ++-- man/grapes-plus-grapes.Rd | 36 +-- man/grepv.Rd | 54 ++--- man/idTransferCheck.Rd | 62 +++--- man/inMatchWindow.Rd | 48 ++--- man/lcpCount.Rd | 32 +-- man/lcsCount.Rd | 32 +-- man/longestCommonPrefix.Rd | 50 ++--- man/longestCommonSuffix.Rd | 50 ++--- man/mosaicize.Rd | 68 +++---- man/pasten.Rd | 42 ++-- man/pastet.Rd | 42 ++-- man/peakSegmentation.Rd | 76 ++++---- man/peakWidthOverTime.Rd | 62 +++--- man/plotTable.Rd | 87 +++++---- man/plotTableRaw.Rd | 46 ++-- man/plot_CalibratedMSErr.Rd | 90 +++++---- man/plot_Charge.Rd | 62 +++--- man/plot_ContEVD.Rd | 62 +++--- man/plot_ContUser.Rd | 74 +++---- man/plot_ContUserScore.Rd | 68 +++---- man/plot_ContsPG.Rd | 46 ++-- man/plot_CountData.Rd | 64 +++--- man/plot_IDRate.Rd | 82 ++++---- man/plot_IDsOverRT.Rd | 78 ++++---- man/plot_IonInjectionTimeOverRT.Rd | 66 +++---- man/plot_MBRAlign.Rd | 96 +++++----- man/plot_MBRIDtransfer.Rd | 80 ++++---- man/plot_MBRgain.Rd | 74 +++---- man/plot_MS2Decal.Rd | 54 ++--- man/plot_MS2Oversampling.Rd | 52 ++--- man/plot_MissedCleavages.Rd | 66 +++---- man/plot_RTPeakWidth.Rd | 58 +++--- man/plot_RatiosPG.Rd | 76 ++++---- man/plot_ScanIDRate.Rd | 50 ++--- man/plot_TIC.Rd | 58 +++--- man/plot_TopN.Rd | 48 ++--- man/plot_TopNoverRT.Rd | 54 ++--- man/plot_UncalibratedMSErr.Rd | 92 +++++---- man/pointsPutX.Rd | 50 ++--- man/print.PTXQC_table.Rd | 30 +-- man/printWithFooter.Rd | 40 ++-- man/qcMetric-class.Rd | 124 ++++++------- man/qcMetric_MSMSScans_TopNoverRT-class.Rd | 20 +- man/qualBestKS.Rd | 42 ++-- man/qualCentered.Rd | 46 ++-- man/qualCenteredRef.Rd | 50 ++--- man/qualGaussDev.Rd | 42 ++-- man/qualHighest.Rd | 66 +++---- man/qualLinThresh.Rd | 44 ++-- man/qualMedianDist.Rd | 38 ++-- man/qualUniform.Rd | 92 ++++----- man/read.MQ.Rd | 69 ++++--- man/renameFile.Rd | 38 ++-- man/repEach.Rd | 46 ++-- man/scale01linear.Rd | 36 +-- man/scale_x_discrete_reverse.Rd | 38 ++-- man/scale_y_discrete_reverse.Rd | 38 ++-- man/shortenStrings.Rd | 73 +++---- man/simplifyNames.Rd | 92 +++++---- man/supCount.Rd | 58 +++--- man/theme_blank.Rd | 26 +- man/thinOut.Rd | 46 ++-- man/thinOutBatch.Rd | 48 ++--- man/wait_for_writable.Rd | 58 +++--- 132 files changed, 3490 insertions(+), 3399 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Package implements projection based methods for preprocessing,
exploring and analysis of multivariate data used in chemometrics.
Author: Sergey Kucheryavskiy
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.10.1 dated 2020-03-01 and 0.10.3 dated 2020-03-28
DESCRIPTION | 8 - MD5 | 33 +++--- NEWS.md | 14 ++ R/mdaplot.R | 8 - R/misc.R | 1 R/pls.R | 48 +++++---- R/prep.R | 219 +++++++++++++++++++++++------------------- R/regmodel.R | 3 R/regres.R | 4 README.md | 6 - man/mdaplot.Rd | 8 - man/pls.cal.Rd | 2 man/prep.autoscale.Rd | 5 man/prep.msc.Rd | 11 -- man/prep.norm.Rd | 2 tests/testthat/test-pls.R | 6 - tests/testthat/test-plsbugs.R |only tests/testthat/test-prep.R | 106 +++++++++++++++++--- 18 files changed, 306 insertions(+), 178 deletions(-)
Title: Isotope Origin Clustering and Assignment Tools
Description: This resource provides tools to create, compare, and post-process
spatial isotope assignment models of animal origin. It generates
probability-of-origin maps for individuals based on user-provided tissue and
environment isotope values (e.g., as generated by IsoMAP, Bowen [2010]
<doi:10.1111/2041-210X.12147>) using the framework established in Bowen
(2014) <doi:10.1111/2041-210X.12147>. The package 'isocat' can then
quantitatively compare and cluster these maps to group individuals by
similar origin. It also includes techniques for applying four approaches
(cumulative sum, odds ratio, quantile only, and quantile simulation) with
which users can summarize geographic origins and probable distance traveled
by individuals.
Author: Caitlin Campbell [aut, cre]
Maintainer: Caitlin Campbell <caitjcampbell@gmail.com>
Diff between isocat versions 0.2.4 dated 2019-12-10 and 0.2.5 dated 2020-03-28
DESCRIPTION | 13 MD5 | 43 - NAMESPACE | 5 NEWS.md | 17 R/CumSumSuite.R | 8 R/getPrecisionPar.R | 2 R/isotopeAssignmentModel.R | 301 ++++++---- R/meanAggregateClusterProbability.R | 2 README.md | 2 inst/doc/isocat.R | 3 inst/doc/isocat.Rmd | 3 inst/doc/isocat.html | 25 man/dot-assignmentMaker.Rd |only man/dot-compareMyRasters.Rd |only man/dot-findProductThenNormalize.Rd |only man/isotopeAssignmentModel.Rd | 34 - vignettes/isocat.Rmd | 3 vignettes/isocat_files/figure-html/Create_mean_aggregate_surfaces-1.png |binary vignettes/isocat_files/figure-html/eval_odds_ratio_surface-1.png |binary vignettes/isocat_files/figure-html/eval_quantile_surface-1.png |binary vignettes/isocat_files/figure-html/eval_quantsim_surface-1.png |binary vignettes/isocat_files/figure-html/example_surface-1.png |binary vignettes/isocat_files/figure-html/plot_cumulative_sum_surface-1.png |binary vignettes/isocat_files/figure-html/prob_of_orgin_surface-1.png |binary 24 files changed, 310 insertions(+), 151 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with
spatially correlated errors by robust and Gaussian (Restricted)
Maximum Likelihood and for computing robust and customary point
and block external-drift Kriging predictions, along with utility
functions for variogram modelling in ad hoc geostatistical analyses,
model building, model evaluation by cross-validation, (conditional)
simulation of Gaussian processes, unbiased back-transformation of
Kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.3-12 dated 2020-02-16 and 0.3-13 dated 2020-03-28
ChangeLog | 7 + DESCRIPTION | 8 - MD5 | 26 +-- NEWS | 1 R/georob_S3methods.R | 19 +- R/georob_exported_functions.R | 9 - R/georob_private_functions.R | 45 +++++- R/georob_variogram.R | 280 ++++++++++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/georob_vignette.pdf |binary man/fit.variogram.model.Rd | 35 ++++- man/georobObject.Rd | 19 ++ man/georobS3methods.Rd | 18 +- 14 files changed, 309 insertions(+), 158 deletions(-)
Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays.
Author: Stephane Karasiewicz
Maintainer: Stephane Karasiewicz <skaraz.science@gmail.com>
Diff between subniche versions 1.0 dated 2020-03-16 and 1.1 dated 2020-03-28
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/subarea.R | 54 ++++++++++++++++++++++++++++++++++++++---------------- 3 files changed, 45 insertions(+), 22 deletions(-)
Title: A Method for Creating Xylophone-Like Frequency Density Plots
Description: Methods for plotting multiple xylophone-style histograms
using base graphics.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between xyloplot versions 1.6 dated 2018-05-09 and 2.0 dated 2020-03-28
xyloplot-1.6/xyloplot/man/xyloplot.character.Rd |only xyloplot-1.6/xyloplot/man/xyloplot.factor.Rd |only xyloplot-1.6/xyloplot/man/xyloplot.list.Rd |only xyloplot-1.6/xyloplot/man/xyloplot.numeric.Rd |only xyloplot-2.0/xyloplot/DESCRIPTION | 14 xyloplot-2.0/xyloplot/MD5 | 28 - xyloplot-2.0/xyloplot/NAMESPACE | 4 xyloplot-2.0/xyloplot/NEWS.md | 4 xyloplot-2.0/xyloplot/R/functions.R | 383 ++++++++++++++---------- xyloplot-2.0/xyloplot/build/vignette.rds |binary xyloplot-2.0/xyloplot/inst/doc/Examples.R | 40 +- xyloplot-2.0/xyloplot/inst/doc/Examples.Rmd | 60 +++ xyloplot-2.0/xyloplot/inst/doc/Examples.html | 84 +++-- xyloplot-2.0/xyloplot/man/left_right_xylo.Rd |only xyloplot-2.0/xyloplot/man/plot.xyloplot.Rd |only xyloplot-2.0/xyloplot/man/xylo_positions.Rd | 6 xyloplot-2.0/xyloplot/man/xyloplot.Rd | 58 ++- xyloplot-2.0/xyloplot/vignettes/Examples.Rmd | 60 +++ 18 files changed, 491 insertions(+), 250 deletions(-)
Title: Standardize Plant Names According to World Flora Online
Taxonomic Backbone
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between WorldFlora versions 1.4 dated 2020-02-20 and 1.5 dated 2020-03-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/WFO.match.R | 40 ++++++++++++++++++++++++++++++++++++++-- R/WFO.one.R | 14 +++++++++++++- inst/ChangeLog | 13 +++++++++++++ man/WFO.match.Rd | 9 +++++++-- 6 files changed, 80 insertions(+), 14 deletions(-)
Title: General Purpose Optimization in R using C++
Description: Perform general purpose optimization in R using C++. A unified
wrapper interface is provided to call C functions of the five optimization
algorithms ('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B' and 'SANN') underlying
optim().
Author: Yi Pan [aut, cre]
Maintainer: Yi Pan <ypan1988@gmail.com>
Diff between roptim versions 0.1.2 dated 2018-11-12 and 0.1.3 dated 2020-03-28
DESCRIPTION | 6 MD5 | 14 - R/RcppExports.R | 364 +++++++++++++++++++++++++------------------------- build/vignette.rds |binary inst/doc/article.pdf |binary inst/include/roptim.h | 6 src/Makevars | 6 src/Makevars.win | 6 8 files changed, 202 insertions(+), 200 deletions(-)
Title: Visualizing Social Science Data with 'ggplot2'
Description: A 'ggplot2' extension for implementing parliament charts and several other useful visualizations.
Author: Frederik Tiedemann [aut, cre]
Maintainer: Frederik Tiedemann <fj.tiedemann@googlemail.com>
Diff between ggpol versions 0.0.5 dated 2019-03-14 and 0.0.6 dated 2020-03-28
DESCRIPTION | 14 - MD5 | 28 +- NAMESPACE | 22 ++ NEWS.md | 6 R/facet_share.R | 488 ++++++++++++++++++++++++++++++------------------ R/geom_boxjitter.R | 89 +++++--- README.md | 8 man/GeomConfmat.Rd | 64 ++++-- man/facet_share.Rd | 62 +----- man/geom_arcbar.Rd | 47 +++- man/geom_bartext.Rd | 35 ++- man/geom_boxjitter.Rd | 68 ++++-- man/geom_circle.Rd | 45 +++- man/geom_parliament.Rd | 49 +++- man/geom_tshighlight.Rd | 28 +- 15 files changed, 668 insertions(+), 385 deletions(-)
Title: Analyze Cricketers and Cricket Teams Based on ESPN Cricinfo
Statsguru
Description: Tools for analyzing performances of cricketers based on stats in
ESPN Cricinfo Statsguru. The toolset can be used for analysis of Tests,ODIs
and Twenty20 matches of both batsmen and bowlers. The package can also be used to
analyze team performances.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between cricketr versions 0.0.22 dated 2019-07-12 and 0.0.23 dated 2020-03-28
DESCRIPTION | 10 - MD5 | 14 +- NAMESPACE | 33 ++--- R/getPlayerData.R | 181 ++++++++++++++-------------- R/getPlayerDataOD.R | 201 +++++++++++++++---------------- R/getPlayerDataTT.R | 199 +++++++++++++++--------------- R/getTeamData.R | 336 ++++++++++++++++++++++++++-------------------------- build/partial.rdb |binary 8 files changed, 490 insertions(+), 484 deletions(-)
Title: Get Data from the 'KOF Datenservice' API
Description: Read Swiss time series data from the 'KOF Datenservice' API, <https://datenservice.kof.ethz.ch>. The API provides macroeconomic survey data, business cycle and further macro economic time series about Switzerland. The package itself is a set of wrappers around the 'KOF Datenservice' API. The 'kofdata' package is able to consume public information as well as data that requires an API token.
Author: Matthias Bannert [aut, cre],
Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>
Diff between kofdata versions 0.1.3.3 dated 2019-08-05 and 0.1.3.4 dated 2020-03-28
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 1 + R/get_dataset.R | 16 +++++++++------- R/get_time_series.R | 22 +++++++++++++--------- R/json_to_ts.R | 4 +++- man/get_metadata.Rd | 4 ++-- man/get_time_series.Rd | 5 +++-- 8 files changed, 43 insertions(+), 33 deletions(-)
Title: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Description: A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.
Author: Daniel Greene, Sylvia Richardson and Ernest Turro
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between BeviMed versions 5.3 dated 2017-08-21 and 5.7 dated 2020-03-28
BeviMed-5.3/BeviMed/man/exact_evidence.Rd |only BeviMed-5.3/BeviMed/man/lower_bound_gamma1_evidence.Rd |only BeviMed-5.3/BeviMed/man/region_association_evidence.Rd |only BeviMed-5.7/BeviMed/DESCRIPTION | 12 BeviMed-5.7/BeviMed/MD5 | 99 - BeviMed-5.7/BeviMed/NAMESPACE | 77 - BeviMed-5.7/BeviMed/R/RcppExports.R | 14 BeviMed-5.7/BeviMed/R/convenience.R | 11 BeviMed-5.7/BeviMed/R/functions.R | 178 --- BeviMed-5.7/BeviMed/R/generics.R | 6 BeviMed-5.7/BeviMed/build/vignette.rds |binary BeviMed-5.7/BeviMed/inst/doc/Guide.R | 142 +- BeviMed-5.7/BeviMed/inst/doc/Guide.Rnw | 4 BeviMed-5.7/BeviMed/inst/doc/Guide.pdf |binary BeviMed-5.7/BeviMed/inst/doc/Intro.R | 44 BeviMed-5.7/BeviMed/inst/doc/Intro.html | 507 +++------- BeviMed-5.7/BeviMed/inst/doc/vcf.R | 26 BeviMed-5.7/BeviMed/inst/doc/vcf.html | 366 ++----- BeviMed-5.7/BeviMed/man/BeviMed-package.Rd | 10 BeviMed-5.7/BeviMed/man/CI_gamma1_evidence.Rd | 48 BeviMed-5.7/BeviMed/man/bevimed.Rd | 78 - BeviMed-5.7/BeviMed/man/bevimed_m.Rd | 180 +-- BeviMed-5.7/BeviMed/man/bevimed_polytomous.Rd | 80 - BeviMed-5.7/BeviMed/man/call_cpp.Rd | 167 +-- BeviMed-5.7/BeviMed/man/conditional_prob_pathogenic.Rd | 40 BeviMed-5.7/BeviMed/man/expected_explained.Rd | 40 BeviMed-5.7/BeviMed/man/explaining_variants.Rd | 40 BeviMed-5.7/BeviMed/man/extract_conditional_prob_pathogenic.Rd | 40 BeviMed-5.7/BeviMed/man/extract_expected_explained.Rd | 40 BeviMed-5.7/BeviMed/man/extract_explaining_variants.Rd | 40 BeviMed-5.7/BeviMed/man/extract_gamma1_evidence.Rd | 40 BeviMed-5.7/BeviMed/man/extract_prob_association.Rd | 44 BeviMed-5.7/BeviMed/man/extract_prob_pathogenic.Rd | 44 BeviMed-5.7/BeviMed/man/gamma0_evidence.Rd | 44 BeviMed-5.7/BeviMed/man/gamma1_evidence.Rd | 40 BeviMed-5.7/BeviMed/man/log_BF.Rd | 48 BeviMed-5.7/BeviMed/man/print.BeviMed.Rd | 44 BeviMed-5.7/BeviMed/man/print.BeviMed_m.Rd | 44 BeviMed-5.7/BeviMed/man/print.BeviMed_summary.Rd | 44 BeviMed-5.7/BeviMed/man/prob_association.Rd | 44 BeviMed-5.7/BeviMed/man/prob_association_m.Rd | 52 - BeviMed-5.7/BeviMed/man/prob_pathogenic.Rd | 44 BeviMed-5.7/BeviMed/man/stack_BeviMeds.Rd | 34 BeviMed-5.7/BeviMed/man/stop_chain.Rd | 94 - BeviMed-5.7/BeviMed/man/subset_variants.Rd | 36 BeviMed-5.7/BeviMed/man/sum_ML_over_PP.Rd | 38 BeviMed-5.7/BeviMed/man/summary.BeviMed.Rd | 62 - BeviMed-5.7/BeviMed/man/summary.BeviMed_m.Rd | 96 - BeviMed-5.7/BeviMed/man/tune_proposal_sds.Rd | 72 - BeviMed-5.7/BeviMed/man/tune_temperatures.Rd | 43 BeviMed-5.7/BeviMed/src/sampling.cpp | 12 BeviMed-5.7/BeviMed/vignettes/Guide.Rnw | 4 52 files changed, 1479 insertions(+), 1833 deletions(-)
Title: Tidy Output from Regular Expression Matching
Description: Wrappers on 'regexpr' and 'gregexpr' to return the match
results in tidy data frames.
Author: Gábor Csárdi [aut, cre],
Matthew Lincoln [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rematch2 versions 2.1.0 dated 2019-07-11 and 2.1.1 dated 2020-03-28
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/bind_re_match.R | 4 ++++ R/exec-all.R | 10 ++++++++-- README.md | 2 +- man/bind_re_match.Rd | 5 +++++ man/re_exec.Rd | 9 ++++++--- man/re_exec_all.Rd | 9 ++++++--- man/re_match.Rd | 7 +++++-- man/re_match_all.Rd | 9 ++++++--- man/rematch2.Rd | 1 - tests/testthat/helper.R | 2 +- 13 files changed, 63 insertions(+), 32 deletions(-)
Title: Compose Half-Half Plots Using Your Favourite Geoms
Description: A 'ggplot2' extension for easy plotting of half-half geom combinations. Think half boxplot and half jitterplot, or half violinplot and half dotplot.
Author: Frederik Tiedemann [aut, cre]
Maintainer: Frederik Tiedemann <fj.tiedemann@googlemail.com>
Diff between gghalves versions 0.0.1 dated 2019-09-23 and 0.1.0 dated 2020-03-28
DESCRIPTION | 14 +++-- MD5 | 31 +++++++----- NAMESPACE | 7 ++ NEWS.md | 19 +++++++ R/geom_half_boxplot.R | 29 ++++++++--- R/geom_half_point.R | 106 ++++++++++++++++++++++++++++++++----------- R/geom_half_point_panel.R |only R/geom_half_violin.R | 13 +++-- R/stat-half-point.R | 2 build |only inst |only man/geom_half_boxplot.Rd | 4 + man/geom_half_dotplot.Rd | 2 man/geom_half_point.Rd | 11 ++-- man/geom_half_point_panel.Rd |only man/geom_half_violin.Rd | 8 ++- man/gghalves-extensions.Rd | 6 +- vignettes |only 18 files changed, 184 insertions(+), 68 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>),
Omar Benites Alfaro [aut] (<https://orcid.org/0000-0002-6852-9598>),
Denise Garcia de Santana [ctb],
Marli A. Ranal [ctb],
Marcelo F. Pompelli [aut, ths]
(<https://orcid.org/0000-0002-4408-6374>),
Federal University of Pernambuco [cph] (Register of application),
Federal Rural University of Pernambuco [cph] (Post Graduate Program)
Maintainer: Flavio Lozano Isla <flavjack@gmail.com>
Diff between GerminaR versions 1.4 dated 2020-03-01 and 1.4.2 dated 2020-03-28
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- R/processing.R | 6 +- R/utils.R | 10 ++-- README.md | 26 ++---------- build/vignette.rds |binary inst/doc/GerminaR.html | 6 +- man/metamorphosis.Rd | 4 - man/web_table.Rd | 4 - vignettes/GerminaR_files/figure-html/unnamed-chunk-16-1.png |binary 10 files changed, 34 insertions(+), 50 deletions(-)
More information about extraterrestrial at CRAN
Permanent link
Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and model diagnostics, in the univariate
and the multivariate case.
Author: Adelchi Azzalini [aut, cre] (<https://orcid.org/0000-0002-7583-1269>)
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.5-5 dated 2020-01-30 and 1.6-0 dated 2020-03-28
DESCRIPTION | 15 MD5 | 26 - NAMESPACE | 9 NEWS | 8 R/sn-funct.R | 749 +++++++++++++++++++++++++++++++++---------- R/sn_S4.R | 4 R/zzz.R | 2 man/dp2cp.Rd | 2 man/fournum.Rd |only man/galton_moors2alpha_nu.Rd |only man/matrix-op.Rd | 3 man/overview.Rd | 11 man/pprodt2.Rd |only man/profile.selm.Rd | 4 man/sn-st.cumulants.Rd | 6 man/st.prelimFit.Rd |only 16 files changed, 638 insertions(+), 201 deletions(-)
Title: Information Decomposition of Two-Phase Experiments
Description: The main purpose of this package is to generate the structure of the analysis of variance
(ANOVA) table of the two-phase experiments. The user only need to input the design and the
relationships of the random and fixed factors using the Wilkinson-Rogers' syntax,
this package can then quickly generate the structure of the ANOVA table with the
coefficients of the variance components for the expected mean squares.
Thus, the balanced incomplete block design and provides the efficiency
factors of the fixed effects can also be studied and compared much easily.
Author: Kevin Chang [aut, cre],
Katya Ruggiero [aut]
Maintainer: Kevin Chang <k.chang@auckland.ac.nz>
Diff between infoDecompuTE versions 0.6.1 dated 2018-05-29 and 0.6.2 dated 2020-03-28
DESCRIPTION | 11 +++-- MD5 | 84 ++++++++++++++++++++++----------------------- NEWS.md | 7 +++ R/adjustMissingLevels.r | 19 +++++----- R/data.R | 23 ++++++++++-- R/getCoefVC.onePhase.R | 4 +- R/getCoefVC.twoPhase.R | 2 - R/getEffFactor.R | 6 +-- R/getFixedEF.onePhase.R | 2 - R/getTrtCoef.R | 2 - R/getTrtRep.R | 2 - R/getVMat.onePhase.R | 2 - R/getVMat.twoPhase.R | 2 - R/infoDecompMat.R | 2 - R/makeBlkDesMat.R | 2 - R/makeContrMat.R | 2 - R/makeOrthProjectors.R | 2 - R/makeOverDesMat.R | 2 - R/summaryAovOnePhase.R | 8 ++-- R/summaryAovTwoPhase.R | 11 +++-- R/toLatexTable.r | 2 - README.md | 14 +++---- man/adjustMissingLevels.Rd | 2 - man/chrisEx1.Rd | 16 ++++++-- man/chrisEx2.Rd | 11 ++++- man/chrisEx3.Rd | 11 ++++- man/getCoefVC.onePhase.Rd | 13 +++++- man/getCoefVC.twoPhase.Rd | 11 ++++- man/getEffFactor.Rd | 2 - man/getFixedEF.onePhase.Rd | 14 +++++-- man/getFixedEF.twoPhase.Rd | 12 +++++- man/getTrtCoef.Rd | 2 - man/getTrtRep.Rd | 2 - man/getVMat.onePhase.Rd | 2 - man/getVMat.twoPhase.Rd | 2 - man/infoDecompMat.Rd | 2 - man/makeBlkDesMat.Rd | 2 - man/makeContrMat.Rd | 2 - man/makeOrthProjectors.Rd | 2 - man/makeOverDesMat.Rd | 2 - man/summaryAovOnePhase.Rd | 19 ++++++++-- man/summaryAovTwoPhase.Rd | 24 +++++++++--- man/toLatexTable.Rd | 2 - 43 files changed, 235 insertions(+), 131 deletions(-)
Title: A Framework for Building HTTP API
Description: Allows to easily create high-performance full featured HTTP APIs from R
functions. Provides high-level classes such as 'Request', 'Response',
'Application', 'Middleware' in order to streamline server side
application development. Out of the box allows to serve requests using
'Rserve' package, but flexible enough to integrate with other HTTP servers
such as 'httpuv'.
Author: Dmitriy Selivanov [aut, cre] (<https://orcid.org/0000-0001-5413-1506>),
Artem Klevtsov [aut] (<https://orcid.org/0000-0003-0492-6647>),
rexy.ai [cph, fnd]
Maintainer: Dmitriy Selivanov <ds@rexy.ai>
Diff between RestRserve versions 0.2.0.2 dated 2020-03-09 and 0.2.1 dated 2020-03-28
DESCRIPTION | 16 MD5 | 102 ++-- NEWS.md | 4 R/Application.R | 199 ++++---- R/AuthBackend.R | 36 - R/AuthBackendBasic.R | 30 - R/AuthBackendBearer.R | 29 - R/AuthMiddleware.R | 28 - R/Backend.R | 17 R/BackendRserve.R | 121 ++--- R/CORSMiddleware.R | 24 - R/ContentHandlersFactory.R |only R/EncodeDecodeMiddleware.R | 201 -------- R/HTTPDate.R | 8 R/HTTPError.R | 326 +++++++------- R/Middleware.R | 67 -- R/RcppExports.R | 8 R/Request.R | 213 +++------ R/Response.R | 186 +++----- R/RestRserve-package.R |only R/Router.R | 49 -- R/logging.R | 127 ++--- R/utils.R | 12 README.md | 1 inst/doc/ContentHandlers.html | 4 inst/doc/Logging.html | 6 inst/doc/Middleware.html | 16 inst/examples/multipart |only inst/tinytest/test-parse-headers.R | 5 inst/tinytest/test-url-encoding.R | 4 man/Application.Rd | 415 ++++++++++++++---- man/ApplicationProcess.Rd |only man/AuthBackend.Rd | 88 ++- man/AuthBackendBasic.Rd | 105 +++- man/AuthBackendBearer.Rd | 104 +++- man/AuthMiddleware.Rd | 84 ++- man/Backend.Rd |only man/BackendRserve.Rd | 168 +++++-- man/CORSMiddleware.Rd | 73 ++- man/ContentHandlers.Rd | 163 +++++-- man/EncodeDecodeMiddleware.Rd | 77 ++- man/HTTPError.Rd | 848 ++++++++++++++++++++++++++++++++----- man/Logger.Rd | 272 +++++++++-- man/Middleware.Rd | 103 ++-- man/Request.Rd | 388 ++++++++++++---- man/Response.Rd | 480 +++++++++++++++++--- man/RestRserve-package.Rd |only man/Router.Rd | 134 ++++- man/openapi.Rd | 19 man/to_json.Rd | 2 src/RcppExports.cpp | 24 + src/parse_headers.cpp | 4 src/url_decode.cpp | 1 src/url_encode.cpp | 1 src/utils.cpp | 10 55 files changed, 3584 insertions(+), 1818 deletions(-)
Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.0.2-1 dated 2020-02-24 and 1.1.0 dated 2020-03-28
PoissonBinomial-1.0.2-1/PoissonBinomial/man/Poisson-Binomial-Distribution.Rd |only PoissonBinomial-1.0.2-1/PoissonBinomial/man/Poisson-Binomial-package.Rd |only PoissonBinomial-1.1.0/PoissonBinomial/DESCRIPTION | 16 PoissonBinomial-1.1.0/PoissonBinomial/MD5 | 57 PoissonBinomial-1.1.0/PoissonBinomial/NAMESPACE | 4 PoissonBinomial-1.1.0/PoissonBinomial/NEWS.md | 11 PoissonBinomial-1.1.0/PoissonBinomial/R/PoissonBinomial.R | 35 PoissonBinomial-1.1.0/PoissonBinomial/R/RcppExports.R | 40 PoissonBinomial-1.1.0/PoissonBinomial/R/gpbinom.R |only PoissonBinomial-1.1.0/PoissonBinomial/R/pbinom.R | 64 PoissonBinomial-1.1.0/PoissonBinomial/R/utility.R |only PoissonBinomial-1.1.0/PoissonBinomial/build/vignette.rds |binary PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/intro.R | 70 PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/intro.Rmd | 186 + PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/intro.html | 292 +- PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/proc_approx.R | 106 PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/proc_approx.Rmd | 162 + PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/proc_approx.html | 1295 ++++++---- PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/proc_exact.R | 87 PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/proc_exact.Rmd | 146 - PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/proc_exact.html | 636 +++- PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/use_with_rcpp.Rmd | 69 PoissonBinomial-1.1.0/PoissonBinomial/inst/doc/use_with_rcpp.html | 71 PoissonBinomial-1.1.0/PoissonBinomial/inst/include/PoissonBinomial_RcppExports.h | 176 + PoissonBinomial-1.1.0/PoissonBinomial/man/GenPoissonBinomial-Distribution.Rd |only PoissonBinomial-1.1.0/PoissonBinomial/man/PoissonBinomial-Distribution.Rd |only PoissonBinomial-1.1.0/PoissonBinomial/man/PoissonBinomial-package.Rd |only PoissonBinomial-1.1.0/PoissonBinomial/src/PoissonBinomial.cpp | 443 +++ PoissonBinomial-1.1.0/PoissonBinomial/src/RcppExports.cpp | 322 ++ PoissonBinomial-1.1.0/PoissonBinomial/vignettes/intro.Rmd | 186 + PoissonBinomial-1.1.0/PoissonBinomial/vignettes/proc_approx.Rmd | 162 + PoissonBinomial-1.1.0/PoissonBinomial/vignettes/proc_exact.Rmd | 146 - PoissonBinomial-1.1.0/PoissonBinomial/vignettes/use_with_rcpp.Rmd | 69 33 files changed, 3830 insertions(+), 1021 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Request <https://openblender.io> API Services
Description: Interface to make HTTP requests to 'OpenBlender' API services. Go to <https://openblender.io> for more information.
Author: Open Blender Inc. [cph],
Daniel V. Pinacho [aut, cre]
Maintainer: Daniel V. Pinacho <danielvpinacho@gmail.com>
Diff between openblender versions 0.5.6 dated 2020-03-25 and 0.5.7 dated 2020-03-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/utils.R | 14 ++++++++++---- tests/testthat.R | 43 +++++++++++++++++++++---------------------- 4 files changed, 37 insertions(+), 32 deletions(-)
Title: Multivariate Version of the Diebold-Mariano Test
Description: Allows to perform the multivariate version of the Diebold-Mariano test for equal predictive ability of multiple forecast comparison. Main reference: Mariano, R.S., Preve, D. (2012) <doi:10.1016/j.jeconom.2012.01.014>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University
of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between multDM versions 1.1 dated 2020-03-26 and 1.1.1 dated 2020-03-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/TB_MA.R | 2 +- man/TB_MA.Rd | 2 -- man/oilforecasts.Rd | 5 ++++- 6 files changed, 22 insertions(+), 13 deletions(-)
Title: Multivariate Fay Herriot Models for Small Area Estimation
Description: Implements multivariate Fay-Herriot models for small area estimation. It uses empirical best linear unbiased prediction (EBLUP) estimator. Multivariate models consider the correlation of several target variables and borrow strength from auxiliary variables to improve the effectiveness of a domain sample size. Models which accommodated by this package are univariate model with several target variables (model 0), multivariate model (model 1), autoregressive multivariate model (model 2), and heteroscedastic autoregressive multivariate model (model 3). Functions provide EBLUP estimators and mean squared error (MSE) estimator for each model. These models were developed by Roberto Benavent and Domingo Morales (2015) <doi:10.1016/j.csda.2015.07.013>.
Author: Novia Permatasari, Azka Ubaidillah
Maintainer: Novia Permatasari <16.9335@stis.ac.id>
Diff between msae versions 0.1.0 dated 2020-03-20 and 0.1.1 dated 2020-03-28
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/data3.R | 2 +- R/df2matR.R | 2 +- R/eblupMFH1.R | 45 +++++++++++++++++++++++++++++++-------------- R/eblupMFH2.R | 40 ++++++++++++++++++++++++++++------------ R/eblupMFH3.R | 39 +++++++++++++++++++++++++++------------ R/eblupUFH.R | 31 ++++++++++++++++++++++++------- R/msae-package.R | 2 +- man/datasae3.Rd | 2 +- man/df2matR.Rd | 2 +- man/eblupMFH1.Rd | 27 ++++++++++++++++++++++----- man/eblupMFH2.Rd | 27 ++++++++++++++++++++++----- man/eblupMFH3.Rd | 31 ++++++++++++++++++++++++------- man/eblupUFH.Rd | 31 ++++++++++++++++++++++++------- man/msae.Rd | 2 +- 16 files changed, 227 insertions(+), 94 deletions(-)
Title: Design of Optimum-Path Forest Classifiers
Description: The 'LibOPF' is a framework to develop pattern recognition techniques based on optimum-path forests (OPF), João P. Papa and Alexandre X. Falcão (2008) <doi:10.1007/978-3-540-89639-5_89>, with methods for supervised learning and data clustering.
Author: Rafael Junqueira Martarelli [aut, cre],
João Paulo Papa [aut],
Alexandre Xavier Falcão [cph]
Maintainer: Rafael Junqueira Martarelli <rfel.jm@gmail.com>
Diff between LibOPF versions 2.4.0 dated 2020-03-26 and 2.5.0 dated 2020-03-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Makevars | 4 +++- src/Makevars.win | 4 +++- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames
for chromosome data and optionally mark data.
Supports micrometers, cM and Mb.
Four styles of marks are available: square, dots, cM, cenStyle, upArrow, downArrow;
its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in
concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964)
<doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999)
<doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes
by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 1.14.2 dated 2020-02-27 and 1.14.7 dated 2020-03-28
idiogramFISH-1.14.2/idiogramFISH/inst/doc/BplotIdiogramsHoloVig.R |only idiogramFISH-1.14.2/idiogramFISH/inst/doc/BplotIdiogramsHoloVig.Rmd |only idiogramFISH-1.14.2/idiogramFISH/inst/doc/BplotIdiogramsHoloVig.html |only idiogramFISH-1.14.2/idiogramFISH/inst/extdata/sequence.gb |only idiogramFISH-1.14.2/idiogramFISH/man/figures/nostoSmall.jpg |only idiogramFISH-1.14.2/idiogramFISH/vignettes/BplotIdiogramsHoloVig.Rmd |only idiogramFISH-1.14.7/idiogramFISH/DESCRIPTION | 19 idiogramFISH-1.14.7/idiogramFISH/MD5 | 106 idiogramFISH-1.14.7/idiogramFISH/NEWS.md | 15 idiogramFISH-1.14.7/idiogramFISH/R/arrowPlotMark.R |only idiogramFISH-1.14.7/idiogramFISH/R/genBankReadIF.R | 67 idiogramFISH-1.14.7/idiogramFISH/R/insertInList.R |only idiogramFISH-1.14.7/idiogramFISH/R/makeNumCols.R | 11 idiogramFISH-1.14.7/idiogramFISH/R/mapXYCen.R |only idiogramFISH-1.14.7/idiogramFISH/R/mimicCenPlotMark.R |only idiogramFISH-1.14.7/idiogramFISH/R/orientation.R | 70 idiogramFISH-1.14.7/idiogramFISH/R/plotIdiograms.R | 929 +++ idiogramFISH-1.14.7/idiogramFISH/R/roundPlotMark.R | 28 idiogramFISH-1.14.7/idiogramFISH/R/rulerTitle.R | 5 idiogramFISH-1.14.7/idiogramFISH/README.md | 37 idiogramFISH-1.14.7/idiogramFISH/build/vignette.rds |binary idiogramFISH-1.14.7/idiogramFISH/inst/doc/AplotIdiogramsVig.R | 868 +-- idiogramFISH-1.14.7/idiogramFISH/inst/doc/AplotIdiogramsVig.Rmd | 1105 ++- idiogramFISH-1.14.7/idiogramFISH/inst/doc/AplotIdiogramsVig.html | 2868 +++++++--- idiogramFISH-1.14.7/idiogramFISH/inst/doc/BcircularVig.R |only idiogramFISH-1.14.7/idiogramFISH/inst/doc/BcircularVig.Rmd |only idiogramFISH-1.14.7/idiogramFISH/inst/doc/BcircularVig.html |only idiogramFISH-1.14.7/idiogramFISH/inst/doc/DphylogenyVig.Rmd | 18 idiogramFISH-1.14.7/idiogramFISH/inst/doc/DphylogenyVig.html | 20 idiogramFISH-1.14.7/idiogramFISH/inst/doc/EhumanVig.Rmd | 16 idiogramFISH-1.14.7/idiogramFISH/inst/doc/EhumanVig.html | 18 idiogramFISH-1.14.7/idiogramFISH/inst/doc/index.R | 32 idiogramFISH-1.14.7/idiogramFISH/inst/doc/index.Rmd | 64 idiogramFISH-1.14.7/idiogramFISH/inst/doc/index.html | 46 idiogramFISH-1.14.7/idiogramFISH/man/arrowPlotMark.Rd |only idiogramFISH-1.14.7/idiogramFISH/man/figures/NEWS.svg |only idiogramFISH-1.14.7/idiogramFISH/man/figures/README-example-1.png |binary idiogramFISH-1.14.7/idiogramFISH/man/figures/README-example2-1.png |binary idiogramFISH-1.14.7/idiogramFISH/man/figures/README-unnamed-chunk-17-1.png |binary idiogramFISH-1.14.7/idiogramFISH/man/figures/crandownload.svg | 4 idiogramFISH-1.14.7/idiogramFISH/man/figures/cranmanualbookdown.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/figures/cranversion.svg | 4 idiogramFISH-1.14.7/idiogramFISH/man/figures/develmanualpkgdown.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/figures/develmanualvignette.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/figures/gitbadge.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/figures/manual.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/figures/nostoc.jpg |binary idiogramFISH-1.14.7/idiogramFISH/man/figures/nostocSmall.jpg |only idiogramFISH-1.14.7/idiogramFISH/man/figures/pkgdownver.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/figures/readme.svg | 2 idiogramFISH-1.14.7/idiogramFISH/man/genBankReadIF.Rd | 4 idiogramFISH-1.14.7/idiogramFISH/man/idiogramFISH-package.Rd | 6 idiogramFISH-1.14.7/idiogramFISH/man/insertInList.Rd |only idiogramFISH-1.14.7/idiogramFISH/man/makeNumCols.Rd | 4 idiogramFISH-1.14.7/idiogramFISH/man/mapXYCen.Rd |only idiogramFISH-1.14.7/idiogramFISH/man/mimicCenPlotMark.Rd |only idiogramFISH-1.14.7/idiogramFISH/man/plotIdiograms.Rd | 148 idiogramFISH-1.14.7/idiogramFISH/man/rulerTitle.Rd | 3 idiogramFISH-1.14.7/idiogramFISH/vignettes/AplotIdiogramsVig.Rmd | 1105 ++- idiogramFISH-1.14.7/idiogramFISH/vignettes/BcircularVig.Rmd |only idiogramFISH-1.14.7/idiogramFISH/vignettes/DphylogenyVig.Rmd | 18 idiogramFISH-1.14.7/idiogramFISH/vignettes/EhumanVig.Rmd | 16 idiogramFISH-1.14.7/idiogramFISH/vignettes/index.Rmd | 64 idiogramFISH-1.14.7/idiogramFISH/vignettes/refs/packages.bib | 9 64 files changed, 5338 insertions(+), 2403 deletions(-)
Title: Delineating Temporal Dataset Shifts in Electronic Health Records
Description: The 'EHRtemporalVariability' package contains functions to delineate temporal dataset shifts in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches. This is done through the estimation of data statistical distributions over time and their projection in non-parametric statistical manifolds uncovering the patterns of the data latent temporal variability. Dataset shifts can be explored and identified through visual analytics formats such as Data Temporal heatmaps and Information Geometric Temporal (IGT) plots. An additional 'EHRtemporalVariability' Shiny app can be used to load and explore the package results and even to allow the use of these functions to those users non-experienced in R coding.
Author: Carlos Sáez [aut, cre],
Alba Gutiérrez-Sacristán [aut],
Isaac Kohane [aut],
Juan M García-Gómez [aut],
Paul Avillach [aut],
Biomedical Data Science Lab, Universitat Politècnica de València
(Spain) [cph],
Department of Biomedical Informatics, Harvard Medical School [cph]
Maintainer: Carlos Sáez <carsaesi@upv.es>
Diff between EHRtemporalVariability versions 1.0.3 dated 2020-03-26 and 1.0.4 dated 2020-03-28
DESCRIPTION | 8 MD5 | 16 NEWS.md | 6 R/estimateDataTemporalMap.R | 2 build/vignette.rds |binary inst/doc/EHRtemporalVariability.Rmd | 2 inst/doc/EHRtemporalVariability.html | 2398 ++++++++++++++++++++++++++++++- vignettes/EHRtemporalVariability.Rmd | 2 vignettes/EHRtemporalVariabilityHelp.pdf |binary 9 files changed, 2384 insertions(+), 50 deletions(-)
More information about EHRtemporalVariability at CRAN
Permanent link
Title: Using the Theory of Belief Functions
Description: Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Claude Boivin, Stat.ASSQ <webapp.cb@gmail.com>
Maintainer: Claude Boivin <webapp.cb@gmail.com>
Diff between dst versions 1.4.0 dated 2019-08-20 and 1.4.1 dated 2020-03-28
dst-1.4.0/dst/inst/doc/Monty-hall-Example.R |only dst-1.4.0/dst/inst/doc/Monty-hall-Example.Rmd |only dst-1.4.0/dst/inst/doc/Monty-hall-Example.html |only dst-1.4.0/dst/vignettes/Monty-hall-Example.Rmd |only dst-1.4.1/dst/DESCRIPTION | 17 +- dst-1.4.1/dst/MD5 | 66 +++++++---- dst-1.4.1/dst/NAMESPACE | 1 dst-1.4.1/dst/NEWS | 16 ++ dst-1.4.1/dst/R/bcaPrint.R |only dst-1.4.1/dst/R/data.R |only dst-1.4.1/dst/R/dsrwon.R | 9 + dst-1.4.1/dst/R/extmin.R | 19 +++ dst-1.4.1/dst/R/nzdsr.R | 3 dst-1.4.1/dst/build/vignette.rds |binary dst-1.4.1/dst/data |only dst-1.4.1/dst/inst/doc/Captain_Example.R |only dst-1.4.1/dst/inst/doc/Captain_Example.Rmd |only dst-1.4.1/dst/inst/doc/Captain_Example.html |only dst-1.4.1/dst/inst/doc/Introduction_to_Belief_Functions.R |only dst-1.4.1/dst/inst/doc/Introduction_to_Belief_Functions.Rmd |only dst-1.4.1/dst/inst/doc/Introduction_to_Belief_Functions.html |only dst-1.4.1/dst/inst/doc/The_Monty_Hall_Game.R |only dst-1.4.1/dst/inst/doc/The_Monty_Hall_Game.Rmd |only dst-1.4.1/dst/inst/doc/The_Monty_Hall_Game.html |only dst-1.4.1/dst/inst/doc/Zadeh_Example.R |only dst-1.4.1/dst/inst/doc/Zadeh_Example.Rmd |only dst-1.4.1/dst/inst/doc/Zadeh_Example.html |only dst-1.4.1/dst/inst/dst.pdf |binary dst-1.4.1/dst/man/ads.Rd |only dst-1.4.1/dst/man/bca.Rd | 14 +- dst-1.4.1/dst/man/bcaPrint.Rd |only dst-1.4.1/dst/man/bcaRel.Rd | 6 - dst-1.4.1/dst/man/dlfm.Rd |only dst-1.4.1/dst/man/dst.Rd | 1 dst-1.4.1/dst/man/extmin.Rd | 2 dst-1.4.1/dst/man/fw.Rd |only dst-1.4.1/dst/man/mrf.Rd |only dst-1.4.1/dst/man/mrt.Rd |only dst-1.4.1/dst/man/nzdsr.Rd | 2 dst-1.4.1/dst/man/swr.Rd |only dst-1.4.1/dst/tests/testthat/test_bcaPrint.R |only dst-1.4.1/dst/tests/testthat/test_dsrwon.R | 7 + dst-1.4.1/dst/tests/testthat/test_extmin.R | 24 +++- dst-1.4.1/dst/vignettes/Captain_Example.Rmd |only dst-1.4.1/dst/vignettes/Introduction_to_Belief_Functions.Rmd |only dst-1.4.1/dst/vignettes/The_Monty_Hall_Game.Rmd |only dst-1.4.1/dst/vignettes/Zadeh_Example.Rmd |only 47 files changed, 141 insertions(+), 46 deletions(-)
Title: Calculates the Wavelet-Based Organization Index
Description: Calculates the wavelet-based organization index following Brune et al (2018) (<doi:10.1002/qj.3409>), the modified wavelet-based organization index and the local wavelet-based organization index of an arbitrary 2D array using Wavelet Transforms of the LS2W package by Eckley et al (2010) (<doi:10.1111/j.1467-9876.2009.00721.x>) and Eckley and Nason (2011) (<doi:10.18637/jss.v043.i03>). In Version 1.0.3 the calculation of LW is added.
Author: Sebastian Brune, Sebastian Buschow, Florian Kapp, Petra Friederichs
Maintainer: Sebastian Brune <sbrune@uni-bonn.de>
Diff between calcWOI versions 1.0.2 dated 2019-04-04 and 1.0.3 dated 2020-03-28
DESCRIPTION | 13 +++++++------ MD5 | 8 +++++--- NAMESPACE | 1 + R/LW.R |only man/LW.Rd |only man/calcWOI-package.Rd | 32 ++++++++++++++++++++++---------- 6 files changed, 35 insertions(+), 19 deletions(-)
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),
Mattan S. Ben-Shachar [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathon Love [ctb],
Russell Lenth [ctb],
Rune Haubo Bojesen Christensen [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between afex versions 0.26-0 dated 2020-01-16 and 0.27-2 dated 2020-03-28
DESCRIPTION | 13 +-- MD5 | 92 +++++++++++++----------- NAMESPACE | 1 NEWS | 29 +++++++ R/aov_car.R | 6 + R/mixed.R | 16 ++-- R/nice.R | 22 ++++- R/round_ps.R | 40 ++++++++-- R/zzz.R | 3 README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/afex_anova_example.html | 116 +++++++++++++++---------------- inst/doc/afex_mixed_example.html | 94 ++++++++++++------------- inst/doc/afex_plot_introduction.R | 10 +- inst/doc/afex_plot_introduction.Rmd | 11 +- inst/doc/afex_plot_introduction.html | 51 ++++++------- inst/doc/afex_plot_supported_models.html | 10 +- inst/doc/introduction-mixed-models.pdf |binary inst/extdata/freeman_models.rda |binary inst/extdata/freeman_reduced_model.rda |binary inst/extdata/plots_brms.rda |binary inst/extdata/plots_rstanarm.rda |binary inst/extdata/tmb_example_fit.rda |binary man/afex-package.Rd | 2 man/afex_aov-methods.Rd | 11 -- man/afex_plot.Rd | 10 ++ man/aov_car.Rd | 105 ++++++++++++++-------------- man/fhch2010.Rd | 20 ++--- man/figures |only man/ks2013.3.Rd | 4 - man/md_12.1.Rd | 4 - man/md_15.1.Rd | 4 - man/md_16.1.Rd | 4 - man/md_16.4.Rd | 4 - man/mixed.Rd | 34 +++++---- man/nice.Rd | 12 ++- man/obk.long.Rd | 4 - man/round_ps.Rd | 31 ++++++-- man/sk2011.1.Rd | 4 - man/sk2011.2.Rd | 12 ++- tests/testthat/test-afex_plot-vignette.R | 7 + tests/testthat/test-aov_car-structural.R | 3 tests/testthat/test-mixed-bugs.R | 45 ++++++++++++ tests/testthat/test-mixed-structure.R | 6 + vignettes/afex_plot_introduction.Rmd | 11 +- 46 files changed, 523 insertions(+), 328 deletions(-)
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions for some common tasks,
such as data partition, variable selection, woe binning, scorecard scaling,
performance evaluation and report generation. These functions can also used
in the development of machine learning models.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.2.8.1 dated 2019-12-11 and 0.2.9 dated 2020-03-28
scorecard-0.2.8.1/scorecard/tests/testthat/test.R |only scorecard-0.2.9/scorecard/DESCRIPTION | 8 - scorecard-0.2.9/scorecard/MD5 | 38 ++++----- scorecard-0.2.9/scorecard/NAMESPACE | 2 scorecard-0.2.9/scorecard/NEWS.md | 9 ++ scorecard-0.2.9/scorecard/R/condition_fun.R | 78 ++++++++++++------- scorecard-0.2.9/scorecard/R/perf.R | 33 +++++--- scorecard-0.2.9/scorecard/R/refs.R | 3 scorecard-0.2.9/scorecard/R/scorecard.R | 3 scorecard-0.2.9/scorecard/R/split_df.R | 34 +++++--- scorecard-0.2.9/scorecard/R/var_filter.R | 2 scorecard-0.2.9/scorecard/R/woebin.R | 26 ++---- scorecard-0.2.9/scorecard/README.md | 5 - scorecard-0.2.9/scorecard/build/vignette.rds |binary scorecard-0.2.9/scorecard/inst/doc/demo.Rmd | 2 scorecard-0.2.9/scorecard/inst/doc/demo.html | 14 +-- scorecard-0.2.9/scorecard/man/perf_eva.Rd | 12 +- scorecard-0.2.9/scorecard/man/split_df.Rd | 12 +- scorecard-0.2.9/scorecard/tests/testthat.R | 28 ++++++ scorecard-0.2.9/scorecard/tests/testthat/test_init.R |only scorecard-0.2.9/scorecard/vignettes/demo.Rmd | 2 21 files changed, 196 insertions(+), 115 deletions(-)
Title: Neo4j to R
Description: The aim of the neo2R is to provide simple and low level connectors
for querying neo4j graph databases (<https://neo4j.com/>).
The objects returned by the query functions are either lists or data.frames
with very few post-processing.
It allows fast processing of queries returning many records.
And it let the user handle post-processing according to the data model
and his needs.
Author: Patrice Godard
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between neo2R versions 2.0.0 dated 2020-02-17 and 2.1.0 dated 2020-03-28
DESCRIPTION | 6 - MD5 | 11 +- NAMESPACE | 1 R/cypher.R | 222 +++++++++++++++++++++++++++++++++++++++++++---------- R/import_from_df.R | 5 - man/cypher.Rd | 3 man/multicypher.Rd |only 7 files changed, 200 insertions(+), 48 deletions(-)
Title: Attraction Indian Buffet Distribution
Description: An implementation of probability mass function and sampling algorithms is provided for the attraction Indian buffet distribution (AIBD), originally from Dahl (2016) <https://ww2.amstat.org/meetings/jsm/2016/onlineprogram/ActivityDetails.cfm?SessionID=213038>.
Author: David B. Dahl [aut, cre],
Richard Warr [aut],
Jeremy Meyer [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between aibd versions 0.1.7 dated 2020-03-11 and 0.1.8 dated 2020-03-28
DESCRIPTION | 10 ++--- MD5 | 52 +++++++++++++++--------------- NAMESPACE | 2 + NEWS | 3 + R/aibd.R | 6 --- R/enumerateFeatureAllocations.R | 9 ++--- R/expectedPairwiseAllocationMatrix.R | 8 ++-- R/ibp.R | 6 --- R/internal-utils.R | 13 ------- R/logLikelihoodLGLFM.R | 11 ++---- R/logPosteriorLGLFM.R | 4 -- R/logProbabilityFeatureAllocation.R | 26 ++------------- R/onLoad.R | 57 +++++++++++++++++---------------- R/sampleFeatureAllocation.R | 11 +----- R/samplePosteriorLGLFM.R | 6 +-- inst/java/scala-2.11/aibd.jar |binary inst/java/scala-2.12/aibd.jar |binary inst/java/scala-2.13/aibd.jar |binary java/aibd-source.jar |binary man/aibd.Rd | 6 --- man/ibp.Rd | 6 --- man/logLikelihoodLGLFM.Rd | 4 -- man/logPosteriorLGLFM.Rd | 4 -- man/logProbabilityFeatureAllocation.Rd | 4 -- man/sampleFeatureAllocation.Rd | 5 -- man/samplePosteriorLGLFM.Rd | 4 -- tests/testthat/setup-instance.R | 11 +----- 27 files changed, 90 insertions(+), 178 deletions(-)
Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides:
'%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return),
'build_frame()'/'draw_frame()' ('data.frame' example tools),
'qc()' (quoting concatenate),
':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard
evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.9.6 dated 2020-01-26 and 2.0.0 dated 2020-03-28
wrapr-1.9.6/wrapr/R/CapturePipeline.R |only wrapr-1.9.6/wrapr/R/UnaryFunctions.R |only wrapr-1.9.6/wrapr/R/as_dot_fn.R |only wrapr-1.9.6/wrapr/R/locum.R |only wrapr-1.9.6/wrapr/inst/doc/Function_Objects.R |only wrapr-1.9.6/wrapr/inst/doc/Function_Objects.Rmd |only wrapr-1.9.6/wrapr/inst/doc/Function_Objects.html |only wrapr-1.9.6/wrapr/inst/unit_tests/test_assoc.R |only wrapr-1.9.6/wrapr/inst/unit_tests/test_fn_composition.R |only wrapr-1.9.6/wrapr/man/ApplyTo.Rd |only wrapr-1.9.6/wrapr/man/Collector.Rd |only wrapr-1.9.6/wrapr/man/PartialFunction-class.Rd |only wrapr-1.9.6/wrapr/man/PartialNamedFn-class.Rd |only wrapr-1.9.6/wrapr/man/SrcFunction-class.Rd |only wrapr-1.9.6/wrapr/man/UnaryFn-class.Rd |only wrapr-1.9.6/wrapr/man/UnaryFnList-class.Rd |only wrapr-1.9.6/wrapr/man/apply_left.Collector.Rd |only wrapr-1.9.6/wrapr/man/apply_left.UnaryFn.Rd |only wrapr-1.9.6/wrapr/man/apply_left.locum.Rd |only wrapr-1.9.6/wrapr/man/apply_right.UnaryFn.Rd |only wrapr-1.9.6/wrapr/man/apply_right.locum.Rd |only wrapr-1.9.6/wrapr/man/as.UnaryFn.Rd |only wrapr-1.9.6/wrapr/man/as.character.locum.Rd |only wrapr-1.9.6/wrapr/man/as.list.UnaryFn.Rd |only wrapr-1.9.6/wrapr/man/as.list.UnaryFnList.Rd |only wrapr-1.9.6/wrapr/man/as_dot_fn.Rd |only wrapr-1.9.6/wrapr/man/as_fn.Rd |only wrapr-1.9.6/wrapr/man/as_fnlist.Rd |only wrapr-1.9.6/wrapr/man/c.UnaryFn.Rd |only wrapr-1.9.6/wrapr/man/concat_items_rev.Rd |only wrapr-1.9.6/wrapr/man/eval_dot_sequence.Rd |only wrapr-1.9.6/wrapr/man/fnlist.Rd |only wrapr-1.9.6/wrapr/man/format.PartialFunction.Rd |only wrapr-1.9.6/wrapr/man/format.PartialNamedFn.Rd |only wrapr-1.9.6/wrapr/man/format.SrcFunction.Rd |only wrapr-1.9.6/wrapr/man/format.UnaryFnList.Rd |only wrapr-1.9.6/wrapr/man/format.locum.Rd |only wrapr-1.9.6/wrapr/man/locum.Rd |only wrapr-1.9.6/wrapr/man/pkgfn.Rd |only wrapr-1.9.6/wrapr/man/print.locum.Rd |only wrapr-1.9.6/wrapr/man/sequence_as_function.Rd |only wrapr-1.9.6/wrapr/man/show-PartialFunction-method.Rd |only wrapr-1.9.6/wrapr/man/show-PartialNamedFn-method.Rd |only wrapr-1.9.6/wrapr/man/show-SrcFunction-method.Rd |only wrapr-1.9.6/wrapr/man/show-UnaryFnList-method.Rd |only wrapr-1.9.6/wrapr/man/srcfn.Rd |only wrapr-1.9.6/wrapr/man/wrapfn.Rd |only wrapr-1.9.6/wrapr/vignettes/Function_Objects.Rmd |only wrapr-2.0.0/wrapr/DESCRIPTION | 15 wrapr-2.0.0/wrapr/MD5 | 191 ++----- wrapr-2.0.0/wrapr/NAMESPACE | 55 -- wrapr-2.0.0/wrapr/NEWS.md | 15 wrapr-2.0.0/wrapr/R/Reduce.R | 32 - wrapr-2.0.0/wrapr/R/as_named_list.R | 38 - wrapr-2.0.0/wrapr/R/bpipe.R | 68 ++ wrapr-2.0.0/wrapr/R/bquotefn.R | 135 +++-- wrapr-2.0.0/wrapr/R/lambda.R | 18 wrapr-2.0.0/wrapr/R/namedMapBuilder.R | 83 --- wrapr-2.0.0/wrapr/R/orderv.R | 4 wrapr-2.0.0/wrapr/R/qae.R | 11 wrapr-2.0.0/wrapr/R/string_interpolation.R | 164 +++++- wrapr-2.0.0/wrapr/R/unpack.R | 154 +++-- wrapr-2.0.0/wrapr/README.md | 103 ++- wrapr-2.0.0/wrapr/build/vignette.rds |binary wrapr-2.0.0/wrapr/inst/doc/CornerCases.html | 12 wrapr-2.0.0/wrapr/inst/doc/DebugFnW.html | 14 wrapr-2.0.0/wrapr/inst/doc/FrameTools.html | 12 wrapr-2.0.0/wrapr/inst/doc/Named_Arguments.html | 12 wrapr-2.0.0/wrapr/inst/doc/QuotingConcatinate.html | 12 wrapr-2.0.0/wrapr/inst/doc/SubstitutionModes.html | 12 wrapr-2.0.0/wrapr/inst/doc/bquote.R | 42 - wrapr-2.0.0/wrapr/inst/doc/bquote.Rmd | 54 +- wrapr-2.0.0/wrapr/inst/doc/bquote.html | 105 ++-- wrapr-2.0.0/wrapr/inst/doc/dot_pipe.Rmd | 2 wrapr-2.0.0/wrapr/inst/doc/dot_pipe.html | 13 wrapr-2.0.0/wrapr/inst/doc/lambda.R | 3 wrapr-2.0.0/wrapr/inst/doc/lambda.Rmd | 9 wrapr-2.0.0/wrapr/inst/doc/lambda.html | 28 - wrapr-2.0.0/wrapr/inst/doc/let.html | 12 wrapr-2.0.0/wrapr/inst/doc/multi_assign.R | 25 wrapr-2.0.0/wrapr/inst/doc/multi_assign.Rmd | 46 + wrapr-2.0.0/wrapr/inst/doc/multi_assign.html | 340 ++++++------- wrapr-2.0.0/wrapr/inst/doc/named_map_builder.html | 12 wrapr-2.0.0/wrapr/inst/doc/unpack_multiple_assignment.R | 6 wrapr-2.0.0/wrapr/inst/doc/unpack_multiple_assignment.Rmd | 13 wrapr-2.0.0/wrapr/inst/doc/unpack_multiple_assignment.html | 23 wrapr-2.0.0/wrapr/inst/doc/wrapr_Eager.html | 12 wrapr-2.0.0/wrapr/inst/doc/wrapr_applicable.html | 12 wrapr-2.0.0/wrapr/inst/unit_tests/test_as_named_list.R |only wrapr-2.0.0/wrapr/inst/unit_tests/test_named_map_builder.R | 6 wrapr-2.0.0/wrapr/inst/unit_tests/test_pipe.R | 2 wrapr-2.0.0/wrapr/inst/unit_tests/test_str_stuff.R | 7 wrapr-2.0.0/wrapr/inst/unit_tests/test_unpack.R | 23 wrapr-2.0.0/wrapr/man/UnpackerF.Rd | 5 wrapr-2.0.0/wrapr/man/UnpackerP.Rd | 5 wrapr-2.0.0/wrapr/man/as_named_list.Rd | 8 wrapr-2.0.0/wrapr/man/bquote_call.Rd | 12 wrapr-2.0.0/wrapr/man/bquote_call_args.Rd | 21 wrapr-2.0.0/wrapr/man/bquote_function.Rd | 24 wrapr-2.0.0/wrapr/man/evalb.Rd | 21 wrapr-2.0.0/wrapr/man/grab_assignments_from_dots.Rd | 19 wrapr-2.0.0/wrapr/man/grapes-less-than-s-grapes.Rd |only wrapr-2.0.0/wrapr/man/grapes-s-greater-than-grapes.Rd |only wrapr-2.0.0/wrapr/man/lambda.Rd | 7 wrapr-2.0.0/wrapr/man/makeFunction_se.Rd | 12 wrapr-2.0.0/wrapr/man/named_map_builder.Rd | 23 wrapr-2.0.0/wrapr/man/orderv.Rd | 2 wrapr-2.0.0/wrapr/man/pipe_impl.Rd | 66 ++ wrapr-2.0.0/wrapr/man/qae.Rd | 4 wrapr-2.0.0/wrapr/man/qe.Rd | 4 wrapr-2.0.0/wrapr/man/reduceexpand.Rd | 33 - wrapr-2.0.0/wrapr/man/si.Rd |only wrapr-2.0.0/wrapr/man/sinterp.Rd | 9 wrapr-2.0.0/wrapr/man/strsplit_capture.Rd | 3 wrapr-2.0.0/wrapr/man/subset-.Unpacker.Rd | 13 wrapr-2.0.0/wrapr/man/to.Rd | 14 wrapr-2.0.0/wrapr/man/unpack.Rd | 16 wrapr-2.0.0/wrapr/tools/README-unnamed-chunk-3-1.png |only wrapr-2.0.0/wrapr/vignettes/bquote.Rmd | 54 +- wrapr-2.0.0/wrapr/vignettes/dot_pipe.Rmd | 2 wrapr-2.0.0/wrapr/vignettes/lambda.Rmd | 9 wrapr-2.0.0/wrapr/vignettes/multi_assign.Rmd | 46 + wrapr-2.0.0/wrapr/vignettes/unpack_multiple_assignment.Rmd | 13 123 files changed, 1408 insertions(+), 992 deletions(-)
Title: Group Animal Relocation Data by Spatial and Temporal
Relationship
Description: Detects spatial and temporal groups in GPS relocations.
It can be used to convert GPS relocations to
gambit-of-the-group format to build proximity-based social networks.
In addition, the randomizations function provides data-stream
randomization methods suitable for GPS data.
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>),
Quinn Webber [aut] (<https://orcid.org/0000-0002-0434-9360>),
Eric Vander Wal [aut] (<https://orcid.org/0000-0002-8534-4317>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Diff between spatsoc versions 0.1.9 dated 2019-05-14 and 0.1.13 dated 2020-03-28
DESCRIPTION | 16 +++-- MD5 | 96 ++++++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 24 ++++++-- R/build_lines.R | 2 R/build_polys.R | 2 R/dyads.R |only R/edge_dist.R | 98 +++++++++++++++++++++++++-------- R/edge_nn.R | 110 +++++++++++++++++++++++++++---------- R/extdata.R | 14 ++-- R/get_gbi.R | 41 +++++++++----- R/group_lines.R | 85 +++++++++++++++++++++-------- R/group_polys.R | 64 ++++++++++++++++----- R/group_pts.R | 76 ++++++++++++++++++-------- R/group_times.R | 91 ++++++++++++++++++------------- R/randomizations.R | 101 +++++++++++++++++++--------------- R/spatsoc.R | 32 ++++------ build/vignette.rds |binary inst/CITATION | 12 ++-- inst/doc/faq.R | 24 ++++---- inst/doc/faq.Rmd | 23 +++++-- inst/doc/faq.html | 20 +++++- inst/doc/intro-spatsoc.R | 42 +++++++------- inst/doc/intro-spatsoc.html | 76 ++++++++++++++------------ inst/doc/using-edge-and-dyad.R |only inst/doc/using-edge-and-dyad.Rmd |only inst/doc/using-edge-and-dyad.html |only inst/doc/using-in-sna.R | 32 +++++----- inst/doc/using-in-sna.Rmd | 14 +++- inst/doc/using-in-sna.html | 8 +- man/DT.Rd | 14 ++-- man/build_lines.Rd | 21 +++++-- man/build_polys.Rd | 21 +++++-- man/dyad_id.Rd |only man/edge_dist.Rd | 93 ++++++++++++++++++++++++------- man/edge_nn.Rd | 93 +++++++++++++++++++++++-------- man/figures |only man/get_gbi.Rd | 36 ++++++++---- man/group_lines.Rd | 104 ++++++++++++++++++++++++++--------- man/group_polys.Rd | 80 ++++++++++++++++++++------- man/group_pts.Rd | 77 +++++++++++++++++++------- man/group_times.Rd | 83 +++++++++++++++++----------- man/randomizations.Rd | 111 ++++++++++++++++++++++---------------- man/spatsoc.Rd | 39 +++++-------- tests/testthat/test-dyad.R |only tests/testthat/test-edge-dist.R | 76 ++++++++++++++++++++++++-- tests/testthat/test-edge-nn.R | 105 +++++++++++++++++++++++++++++++++-- tests/testthat/test-pts.R | 22 +++++-- vignettes/faq.Rmd | 23 +++++-- vignettes/using-edge-and-dyad.Rmd |only vignettes/using-in-sna.Rmd | 14 +++- 51 files changed, 1451 insertions(+), 665 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. Either version 2 or 3 of the
'Protocol Buffers' 'API' is supported.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.16 dated 2020-03-19 and 0.4.17 dated 2020-03-28
ChangeLog | 18 +++++++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- README.md | 10 +++++++--- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS.Rd | 11 +++++++++++ inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/tinytest/test_addressbook.R | 6 ++++++ src/wrapper_Message.cpp | 10 +++++++++- 12 files changed, 75 insertions(+), 30 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.5-4 dated 2019-10-23 and 1.6-0 dated 2020-03-28
RBesT-1.5-4/RBesT/inst/sbc/launch_sbc.sh |only RBesT-1.6-0/RBesT/DESCRIPTION | 16 RBesT-1.6-0/RBesT/MD5 | 93 - RBesT-1.6-0/RBesT/R/EM_bmm_ab.R | 46 RBesT-1.6-0/RBesT/R/EM_plot.R | 20 RBesT-1.6-0/RBesT/R/automixfit.R | 2 RBesT-1.6-0/RBesT/R/decision2S_boundary.R | 8 RBesT-1.6-0/RBesT/R/forest_plot.R | 1 RBesT-1.6-0/RBesT/R/integrate_logit_log.R | 35 RBesT-1.6-0/RBesT/R/mixess.R | 26 RBesT-1.6-0/RBesT/R/mixfit.R | 7 RBesT-1.6-0/RBesT/R/mixplot.R | 5 RBesT-1.6-0/RBesT/R/sysdata.rda |binary RBesT-1.6-0/RBesT/R/zzz.R | 1 RBesT-1.6-0/RBesT/build/vignette.rds |binary RBesT-1.6-0/RBesT/data/AS.rda |binary RBesT-1.6-0/RBesT/data/colitis.rda |binary RBesT-1.6-0/RBesT/data/crohn.rda |binary RBesT-1.6-0/RBesT/data/transplant.rda |binary RBesT-1.6-0/RBesT/demo |only RBesT-1.6-0/RBesT/inst/NEWS | 19 RBesT-1.6-0/RBesT/inst/doc/PoS_codata.html | 437 ++++---- RBesT-1.6-0/RBesT/inst/doc/PoS_interim.html | 146 +- RBesT-1.6-0/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.6-0/RBesT/inst/doc/customizing_plots.R | 5 RBesT-1.6-0/RBesT/inst/doc/customizing_plots.Rmd | 5 RBesT-1.6-0/RBesT/inst/doc/customizing_plots.html | 299 ++--- RBesT-1.6-0/RBesT/inst/doc/introduction.html | 310 +++--- RBesT-1.6-0/RBesT/inst/doc/introduction_normal.html | 360 +++---- RBesT-1.6-0/RBesT/inst/doc/robustMAP.R | 4 RBesT-1.6-0/RBesT/inst/doc/robustMAP.Rmd | 4 RBesT-1.6-0/RBesT/inst/doc/robustMAP.html | 177 +-- RBesT-1.6-0/RBesT/inst/doc/variances_MAP.R | 2 RBesT-1.6-0/RBesT/inst/doc/variances_MAP.Rmd | 29 RBesT-1.6-0/RBesT/inst/doc/variances_MAP.html | 213 ++-- RBesT-1.6-0/RBesT/inst/sbc/calibration.md5 | 6 RBesT-1.6-0/RBesT/inst/sbc/make_reference_rankhist.R | 22 RBesT-1.6-0/RBesT/inst/sbc/sbc_report.R | 64 - RBesT-1.6-0/RBesT/inst/sbc/sbc_report.html | 950 +++++++++++++++++-- RBesT-1.6-0/RBesT/inst/sbc/sbc_tools.R | 23 RBesT-1.6-0/RBesT/man/mixfit.Rd | 7 RBesT-1.6-0/RBesT/tests/testthat/test-EM.R | 37 RBesT-1.6-0/RBesT/tests/testthat/test-oc2S.R | 25 RBesT-1.6-0/RBesT/tests/testthat/test-utils.R | 12 RBesT-1.6-0/RBesT/tools/build.sh | 10 RBesT-1.6-0/RBesT/vignettes/customizing_plots.Rmd | 5 RBesT-1.6-0/RBesT/vignettes/robustMAP.Rmd | 4 RBesT-1.6-0/RBesT/vignettes/variances_MAP.Rmd | 29 48 files changed, 2220 insertions(+), 1244 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages. These
include e.g. measures like r-squared, intraclass correlation coefficient
(Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>),
root mean squared error or functions to check models for overdispersion,
singularity or zero-inflation and more. Functions apply to a large variety of
regression models, including generalized linear models, mixed effects models
and Bayesian models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between performance versions 0.4.4 dated 2020-02-10 and 0.4.5 dated 2020-03-28
DESCRIPTION | 27 ++++-- MD5 | 78 ++++++++++-------- NAMESPACE | 32 +++++++ NEWS.md | 20 ++++ R/check_collinearity.R | 2 R/check_distribution.R | 7 + R/check_heteroscedasticity.R | 12 ++ R/check_homogeneity.R | 5 - R/check_model.R | 6 - R/check_model_diagnostics.R | 25 +++-- R/check_outliers.R | 66 ++++++++++----- R/compare_performance.R | 23 +++-- R/cronbachs_alpha.R | 2 R/helpers.R | 1 R/logLik.R | 15 +++ R/model_performance.R | 1 R/model_performance.bayesian.R | 2 R/model_performance.bife.R |only R/model_performance.lavaan.R | 4 R/model_performance.lm.R | 20 +++- R/model_performance.mixed.R | 2 R/model_performance.rma.R |only R/performance_aicc.R | 117 ++++++++++++++++++++++++++-- R/performance_rmse.R | 2 R/print-methods.R | 31 ++++++- R/r2.R | 72 +++++++++++++++++ R/r2_coxsnell.R | 21 +++++ R/r2_efron.R | 86 ++++++++++---------- R/r2_nagelkerke.R | 23 +++++ README.md | 50 +++++------ build/partial.rdb |binary inst/WORDLIST | 8 + man/classify_distribution.Rd | 28 +++--- man/compare_performance.Rd | 10 ++ man/cronbachs_alpha.Rd | 3 man/figures/unnamed-chunk-19-1.png |only man/model_performance.Rd | 1 man/model_performance.lavaan.Rd | 4 man/model_performance.lm.Rd | 91 ++++++++++----------- man/model_performance.rma.Rd |only tests/testthat/test-check_collinearity.R |only tests/testthat/test-check_overdispersion.R | 2 tests/testthat/test-model_performance.rma.R |only 43 files changed, 651 insertions(+), 248 deletions(-)
Title: Parallel Analysis and Other Non Graphical Solutions to the
Cattell Scree Test
Description: Indices, heuristics and strategies to help determine the number of factors/components to retain:
1. Acceleration factor (af with or without Parallel Analysis);
2. Optimal Coordinates (noc with or without Parallel Analysis);
3. Parallel analysis (components, factors and bootstrap);
4. lambda > mean(lambda) (Kaiser, CFA and related);
5. Cattell-Nelson-Gorsuch (CNG);
6. Zoski and Jurs multiple regression (b, t and p);
7. Zoski and Jurs standard error of the regression coeffcient (sescree);
8. Nelson R2;
9. Bartlett khi-2;
10. Anderson khi-2;
11. Lawley khi-2 and
12. Bentler-Yuan khi-2.
Author: Gilles Raiche (Universite du Quebec a Montreal) and David Magis (Universite de Liege)
Maintainer: Gilles Raiche <raiche.gilles@uqam.ca>
Diff between nFactors versions 2.3.3.1 dated 2019-08-31 and 2.4.1 dated 2020-03-28
nFactors-2.3.3.1/nFactors/inst |only nFactors-2.3.3.1/nFactors/man/bentlerParameters.rd |only nFactors-2.3.3.1/nFactors/man/componentAxis.rd |only nFactors-2.3.3.1/nFactors/man/corFA.rd |only nFactors-2.3.3.1/nFactors/man/diagReplace.rd |only nFactors-2.3.3.1/nFactors/man/eigenBootParallel.rd |only nFactors-2.3.3.1/nFactors/man/eigenComputes.rd |only nFactors-2.3.3.1/nFactors/man/eigenFrom.rd |only nFactors-2.3.3.1/nFactors/man/generateStructure.rd |only nFactors-2.3.3.1/nFactors/man/iterativePrincipalAxis.rd |only nFactors-2.3.3.1/nFactors/man/makeCor.rd |only nFactors-2.3.3.1/nFactors/man/moreStats.rd |only nFactors-2.3.3.1/nFactors/man/nBartlett.rd |only nFactors-2.3.3.1/nFactors/man/nBentler.rd |only nFactors-2.3.3.1/nFactors/man/nCng.rd |only nFactors-2.3.3.1/nFactors/man/nFactors-package.rd |only nFactors-2.3.3.1/nFactors/man/nFactors-parameters.rd |only nFactors-2.3.3.1/nFactors/man/nFactorsObjectMethods.rd |only nFactors-2.3.3.1/nFactors/man/nMreg.rd |only nFactors-2.3.3.1/nFactors/man/nScreeObjectMethods.rd |only nFactors-2.3.3.1/nFactors/man/nSeScree.rd |only nFactors-2.3.3.1/nFactors/man/principalAxis.rd |only nFactors-2.3.3.1/nFactors/man/principalComponents.rd |only nFactors-2.3.3.1/nFactors/man/rRecovery.rd |only nFactors-2.3.3.1/nFactors/man/structureSim.rd |only nFactors-2.3.3.1/nFactors/man/structureSimObjectMethods.rd |only nFactors-2.3.3.1/nFactors/man/studySim.rd |only nFactors-2.4.1/nFactors/DESCRIPTION | 25 - nFactors-2.4.1/nFactors/MD5 | 138 +++---- nFactors-2.4.1/nFactors/NAMESPACE | 113 +++-- nFactors-2.4.1/nFactors/NEWS | 239 ++++++------ nFactors-2.4.1/nFactors/R/aphabetical.R |only nFactors-2.4.1/nFactors/R/bentlerParameters.r | 165 ++++++++ nFactors-2.4.1/nFactors/R/componentAxis.r | 43 ++ nFactors-2.4.1/nFactors/R/corFA.r | 39 ++ nFactors-2.4.1/nFactors/R/data.R |only nFactors-2.4.1/nFactors/R/diagReplace.r | 37 + nFactors-2.4.1/nFactors/R/eigenBootParallel.r | 68 +++ nFactors-2.4.1/nFactors/R/eigenComputes.r | 52 ++ nFactors-2.4.1/nFactors/R/eigenFrom.r | 60 ++- nFactors-2.4.1/nFactors/R/generateStructure.r | 104 +++++ nFactors-2.4.1/nFactors/R/iterativePrincipalAxis.r | 79 ++++ nFactors-2.4.1/nFactors/R/makeCor.r | 33 + nFactors-2.4.1/nFactors/R/moreStats.r | 30 + nFactors-2.4.1/nFactors/R/nBartlett.r | 104 +++++ nFactors-2.4.1/nFactors/R/nBentler.r | 122 ++++++ nFactors-2.4.1/nFactors/R/nCng.r | 61 +++ nFactors-2.4.1/nFactors/R/nFactors.R |only nFactors-2.4.1/nFactors/R/nFactorsObjectMethods.r | 59 ++- nFactors-2.4.1/nFactors/R/nMreg.r | 61 +++ nFactors-2.4.1/nFactors/R/nScree.R | 159 +++++++- nFactors-2.4.1/nFactors/R/nScreeObjectMethods.r | 89 ++++ nFactors-2.4.1/nFactors/R/nSeScree.r | 83 ++++ nFactors-2.4.1/nFactors/R/parallel.R | 90 ++++ nFactors-2.4.1/nFactors/R/plotParallel.R | 81 +++- nFactors-2.4.1/nFactors/R/plotnScree.R | 70 +++ nFactors-2.4.1/nFactors/R/plotuScree.R | 35 + nFactors-2.4.1/nFactors/R/principalAxis.r | 65 +++ nFactors-2.4.1/nFactors/R/principalComponents.r | 56 ++ nFactors-2.4.1/nFactors/R/rRecovery.r | 68 +++ nFactors-2.4.1/nFactors/R/structureSim.r | 88 ++++ nFactors-2.4.1/nFactors/R/structureSimObjectMethods.r | 91 ++++ nFactors-2.4.1/nFactors/R/studySim.r | 82 ++++ nFactors-2.4.1/nFactors/TODO | 32 - nFactors-2.4.1/nFactors/data/dFactors.rda |binary nFactors-2.4.1/nFactors/man/bentlerParameters.Rd |only nFactors-2.4.1/nFactors/man/componentAxis.Rd |only nFactors-2.4.1/nFactors/man/corFA.Rd |only nFactors-2.4.1/nFactors/man/dFactors.Rd | 167 ++++---- nFactors-2.4.1/nFactors/man/diagReplace.Rd |only nFactors-2.4.1/nFactors/man/eigenBootParallel.Rd |only nFactors-2.4.1/nFactors/man/eigenComputes.Rd |only nFactors-2.4.1/nFactors/man/eigenFrom.Rd |only nFactors-2.4.1/nFactors/man/figures |only nFactors-2.4.1/nFactors/man/generateStructure.Rd |only nFactors-2.4.1/nFactors/man/iterativePrincipalAxis.Rd |only nFactors-2.4.1/nFactors/man/makeCor.Rd |only nFactors-2.4.1/nFactors/man/moreStats.Rd |only nFactors-2.4.1/nFactors/man/nBartlett.Rd |only nFactors-2.4.1/nFactors/man/nBentler.Rd |only nFactors-2.4.1/nFactors/man/nCng.Rd |only nFactors-2.4.1/nFactors/man/nFactors.Rd |only nFactors-2.4.1/nFactors/man/nFactorsObjectMethods.Rd |only nFactors-2.4.1/nFactors/man/nMreg.Rd |only nFactors-2.4.1/nFactors/man/nScree.Rd | 251 ++++++------- nFactors-2.4.1/nFactors/man/nScreeObjectMethods.Rd |only nFactors-2.4.1/nFactors/man/nSeScree.Rd |only nFactors-2.4.1/nFactors/man/parallel.Rd | 149 +++---- nFactors-2.4.1/nFactors/man/plotParallel.Rd | 111 ++--- nFactors-2.4.1/nFactors/man/plotnScree.Rd | 99 ++--- nFactors-2.4.1/nFactors/man/plotuScree.Rd | 91 ++-- nFactors-2.4.1/nFactors/man/principalAxis.Rd |only nFactors-2.4.1/nFactors/man/principalComponents.Rd |only nFactors-2.4.1/nFactors/man/rRecovery.Rd |only nFactors-2.4.1/nFactors/man/structureSim.Rd |only nFactors-2.4.1/nFactors/man/structureSimObjectMethods.Rd |only nFactors-2.4.1/nFactors/man/studySim.Rd |only 97 files changed, 2799 insertions(+), 790 deletions(-)
Title: Multiple Hot-Deck Imputation
Description: Performs multiple hot-deck imputation of categorical and continuous variables in a data frame.
Author: Skyler Cranmer, Jeff Gill, Natalie Jackson, Andreas Murr, Dave Armstrong
Maintainer: Dave Armstrong <dave@quantoid.net>
Diff between hot.deck versions 1.1-1 dated 2020-02-24 and 1.1-2 dated 2020-03-28
hot.deck-1.1-1/hot.deck/README.md |only hot.deck-1.1-2/hot.deck/DESCRIPTION | 10 +- hot.deck-1.1-2/hot.deck/MD5 | 13 +-- hot.deck-1.1-2/hot.deck/build/vignette.rds |binary hot.deck-1.1-2/hot.deck/inst/doc/Using_Hot_Deck_Data.R | 26 ------ hot.deck-1.1-2/hot.deck/inst/doc/Using_Hot_Deck_Data.Rnw | 54 +++++++------- hot.deck-1.1-2/hot.deck/inst/doc/Using_Hot_Deck_Data.pdf |binary hot.deck-1.1-2/hot.deck/vignettes/Using_Hot_Deck_Data.Rnw | 54 +++++++------- 8 files changed, 68 insertions(+), 89 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Alan O'Callaghan [aut] (https://github.com/Alanocallaghan),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 1.0.0 dated 2019-12-05 and 1.1.0 dated 2020-03-28
ChangeLog | 93 ++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++--- MD5 | 20 +++++----- NEWS | 21 ++++++++++ NEWS.md | 21 ++++++++++ R/heatmaply.R | 73 ++++++++++++++++++++----------------- R/plots.R | 92 ++++++++++++++++++++++++++--------------------- R/zzz.R | 1 README.md | 7 ++- inst/doc/heatmaply.html | 84 +++++++++++++++++++++---------------------- man/heatmaply.Rd | 16 ++++++-- 11 files changed, 302 insertions(+), 136 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.4.2 dated 2020-02-12 and 3.4.3 dated 2020-03-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/package.R | 44 ++++++++++++++++++++++++++++---------------- R/utils.R | 2 ++ tests/testthat.R | 2 +- 6 files changed, 44 insertions(+), 25 deletions(-)
Title: Multiple Heat Maps for Projected Coordinates
Description: Functions for displaying multiple images or scatterplots with a color
scale, i.e., heat maps, possibly with projected coordinates. The
package relies on the base graphics system, so graphics are
rendered rapidly.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between autoimage versions 2.0.1 dated 2019-06-20 and 2.1 dated 2020-03-28
DESCRIPTION | 12 MD5 | 73 +++-- NAMESPACE | 4 NEWS | 11 R/auto_functions_other.R | 6 R/auto_setup_functions_internal.R |only R/autopoints.R |only R/heat_ppoints.R |only build/vignette.rds |binary inst/doc/autoimage.R | 50 +-- inst/doc/autoimage.html | 519 ++++++++++++++++++++++++++------------ inst/doc/autopoints.R |only inst/doc/autopoints.Rmd |only inst/doc/autopoints.html |only inst/doc/ggplot2-comparison.R | 42 +-- inst/doc/ggplot2-comparison.html | 437 +++++++++++++++++++++++-------- man/autoimage.Rd | 452 ++++++++++++++++----------------- man/autolayout.Rd | 194 +++++++------- man/autolegend.Rd | 196 +++++++------- man/automar.Rd | 60 ++-- man/autopoints.Rd |only man/autosize.Rd | 54 +-- man/blank.plot.Rd | 44 +-- man/canada.Rd | 68 ++-- man/copoly.Rd | 64 ++-- man/dot-legend.scale.args.Rd | 26 - man/ggautoimage.Rd | 254 +++++++++--------- man/heat_ppoints.Rd |only man/inarccap.Rd | 46 +-- man/legend.scale.Rd | 167 ++++++------ man/narccap.Rd | 104 +++---- man/parrows.Rd | 94 +++--- man/paxes.Rd | 138 +++++----- man/pimage.Rd | 484 ++++++++++++++++++----------------- man/plines.Rd | 104 +++---- man/ppoints.Rd | 98 +++---- man/ppolygon.Rd | 94 +++--- man/psegments.Rd | 116 ++++---- man/ptext.Rd | 130 ++++----- man/reset.par.Rd | 46 +-- man/rotate.Rd | 60 ++-- vignettes/autopoints.Rmd |only 42 files changed, 2363 insertions(+), 1884 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-25 0.3.1
2019-01-03 0.3.0
2018-09-13 0.2.0
2018-03-17 0.1.1
2018-02-13 0.1.0
Title: Estimate Phenological Metrics using Presence-Only Data
Description: Generates Weibull-parameterized estimates of phenology for any percentile of
a distribution using the framework established in Cooke (1979)
<doi:10.1093/biomet/66.2.367>.. Extensive testing against other
estimators suggest the weib_percentile() function is especially useful in
generating more accurate and less biased estimates of onset and offset.
Non-parametric bootstrapping can be used to generate confidence intervals
around those estimates. Additionally, this package offers an easy way to
perform non-parametric bootstrapping to generate confidence intervals for
quantile estimates, mean estimates, or any statistical function of interest.
Author: Michael Belitz [aut, cre],
Caitlin Campbell [ctb],
Daijinag Li [ctb]
Maintainer: Michael Belitz <mbelitz@ufl.edu>
Diff between phenesse versions 0.1.0 dated 2019-12-22 and 0.1.1 dated 2020-03-28
DESCRIPTION | 26 MD5 | 40 NAMESPACE | 3 NEWS.md | 4 R/mean_ci.R | 33 R/quantile_ci.R | 31 R/utils.R |only R/weib_percentile.R | 63 R/weib_percentile_ci.R | 60 README.md | 5 build/vignette.rds |binary inst/doc/phenesse_vignette.R | 2 inst/doc/phenesse_vignette.Rmd | 5 inst/doc/phenesse_vignette.html | 3958 ++------------------------------------ man/estimate_ci.Rd |only man/inat_examples.Rd | 80 man/mean_ci.Rd | 92 man/quantile_ci.Rd | 102 man/weib_percentile.Rd | 98 man/weib_percentile_ci.Rd | 150 - tests/testthat/test-quantile_ci.R | 4 vignettes/phenesse_vignette.Rmd | 5 22 files changed, 638 insertions(+), 4123 deletions(-)
Title: Simulation of High-Dimensional Data and Parallelized Repeated
Penalized Regression
Description: Simulation of continuous, correlated high-dimensional data with
time to event or binary response, and parallelized functions for Lasso,
Ridge, and Elastic Net penalized regression with repeated starts and
two-dimensional tuning of the Elastic Net.
Author: Levi Waldron <lwaldron.research@gmail.com>
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between pensim versions 1.2.9 dated 2014-03-14 and 1.3.1 dated 2020-03-28
pensim-1.2.9/pensim/inst/doc/pensim.Rnw |only pensim-1.2.9/pensim/inst/doc/pensim.pdf |only pensim-1.2.9/pensim/vignettes/pensim.Rnw |only pensim-1.3.1/pensim/DESCRIPTION | 22 + pensim-1.3.1/pensim/MD5 | 29 +- pensim-1.3.1/pensim/NAMESPACE | 1 pensim-1.3.1/pensim/README.md |only pensim-1.3.1/pensim/build/vignette.rds |binary pensim-1.3.1/pensim/inst/doc/pensim.R | 295 +++++++++++-------------- pensim-1.3.1/pensim/inst/doc/pensim.Rmd |only pensim-1.3.1/pensim/inst/doc/pensim.html |only pensim-1.3.1/pensim/man/create.data.Rd | 43 +-- pensim-1.3.1/pensim/man/opt.nested.crossval.Rd | 134 ++++++----- pensim-1.3.1/pensim/man/opt.splitval.Rd | 45 ++- pensim-1.3.1/pensim/man/opt1D.Rd | 139 +++++++---- pensim-1.3.1/pensim/man/opt2D.Rd | 156 ++++++++----- pensim-1.3.1/pensim/man/pensim-package.Rd | 32 ++ pensim-1.3.1/pensim/man/scan.l1l2.Rd | 50 ++-- pensim-1.3.1/pensim/vignettes/pensim.Rmd |only 19 files changed, 543 insertions(+), 403 deletions(-)
Title: Movement Data Visualization
Description: Tools to visualize movement data (e.g. from GPS tracking) and temporal changes of environmental data (e.g. from remote sensing) by creating video animations.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>
Diff between moveVis versions 0.10.4-1 dated 2020-02-13 and 0.10.5 dated 2020-03-28
moveVis-0.10.4-1/moveVis/R/pipe.R |only moveVis-0.10.4-1/moveVis/man/pipe.Rd |only moveVis-0.10.5/moveVis/DESCRIPTION | 16 moveVis-0.10.5/moveVis/MD5 | 57 - moveVis-0.10.5/moveVis/NAMESPACE | 38 - moveVis-0.10.5/moveVis/NEWS.md | 21 moveVis-0.10.5/moveVis/R/add_northarrow.R | 8 moveVis-0.10.5/moveVis/R/add_progress.R | 3 moveVis-0.10.5/moveVis/R/add_scalebar.R | 31 moveVis-0.10.5/moveVis/R/add_text.R | 7 moveVis-0.10.5/moveVis/R/add_timestamps.R | 5 moveVis-0.10.5/moveVis/R/align_move.R | 4 moveVis-0.10.5/moveVis/R/animate_frames.R | 43 - moveVis-0.10.5/moveVis/R/frames_graph.R | 3 moveVis-0.10.5/moveVis/R/frames_spatial.R | 60 + moveVis-0.10.5/moveVis/R/moveVis-internal.R | 387 ++++++++---- moveVis-0.10.5/moveVis/R/reexports.R |only moveVis-0.10.5/moveVis/R/subset_move.R | 3 moveVis-0.10.5/moveVis/R/suggest_formats.R | 5 moveVis-0.10.5/moveVis/R/view_spatial.R | 18 moveVis-0.10.5/moveVis/README.md | 11 moveVis-0.10.5/moveVis/man/basemap_data.Rd | 4 moveVis-0.10.5/moveVis/man/frames_spatial.Rd | 11 moveVis-0.10.5/moveVis/man/move_data.Rd | 4 moveVis-0.10.5/moveVis/man/reexports.Rd |only moveVis-0.10.5/moveVis/man/whitestork_data.Rd | 8 moveVis-0.10.5/moveVis/tests/testthat/helper-vars.R | 20 moveVis-0.10.5/moveVis/tests/testthat/test-add_.R | 2 moveVis-0.10.5/moveVis/tests/testthat/test-frames_spatial.R | 20 moveVis-0.10.5/moveVis/tests/testthat/test-internal.R |only moveVis-0.10.5/moveVis/tests/testthat/test-settings.R | 8 moveVis-0.10.5/moveVis/tests/testthat/test-view_spatial.R | 12 32 files changed, 546 insertions(+), 263 deletions(-)