Title: Phylogenetic Analysis with Discrete Character Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Author: Martin R. Smith [aut, cre, cph]
,
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 1.1.2 dated 2022-05-11 and 1.2.0 dated 2022-08-10
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Title: Sub-National Geospatial Data Archive: Geoprocessing Toolkit
Description: Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.
Author: Jason Byers, Marty Davidson, Yuri M. Zhukov
Maintainer: Yuri M. Zhukov <zhukov@umich.edu>
Diff between SUNGEO versions 0.2.288 dated 2022-01-31 and 0.2.291 dated 2022-08-10
DESCRIPTION | 8 +++--- MD5 | 18 ++++++------- R/nesting.R | 66 ++++++++++++++++++++++++++++++++++++++++++++------- R/point2poly_krige.R | 18 ++++++------- R/point2poly_simp.R | 10 +++---- R/point2poly_tess.R | 4 +-- R/poly2poly_ap.R | 4 +-- R/sf2raster.R | 4 +-- README.md | 2 - man/nesting.Rd | 17 ++++++++++--- 10 files changed, 104 insertions(+), 47 deletions(-)
Title: Subset- And Name-Aware Array Utility Functions
Description: Stacking arrays according to dimension names, subset-aware
splitting and mapping of functions, intersecting along arbitrary
dimensions, converting to and from data.frames, and many other helper
functions.
Author: Michael Schubert <mschu.dev@gmail.com>
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between narray versions 0.4.1.1 dated 2021-05-10 and 0.5.0 dated 2022-08-10
DESCRIPTION | 16 - MD5 | 62 +++--- NAMESPACE | 2 NEWS.md |only R/RcppExports.R |only R/construct.r | 2 R/intersect_list.r | 2 R/lambda.r | 16 + R/mask.r | 10 - R/melt.r | 5 R/narray-package.r |only R/stack.r | 64 ------ R/translate.r | 5 R/util.r | 2 build/vignette.rds |binary inst/doc/narray.R | 4 inst/doc/narray.Rmd | 14 - inst/doc/narray.html | 382 ++++++++++++++++++++++++++++++---------- man/filter.Rd | 3 man/lambda.Rd | 5 man/map.Rd | 3 man/mask.Rd | 4 man/match.Rd | 4 man/melt.Rd | 3 man/narray.Rd |only man/translate.Rd | 5 src |only tests/testthat/test-construct.r | 14 + tests/testthat/test-dimnames.r | 5 tests/testthat/test-intersect.r | 3 tests/testthat/test-mask.r | 17 + tests/testthat/test-melt.r | 8 tests/testthat/test-stack.r | 65 +++++- vignettes/narray.Rmd | 14 - 34 files changed, 511 insertions(+), 228 deletions(-)
Title: Iterated Function Systems
Description: Iterated Function Systems Estimator as in Iacus and La Torre (2005) <doi:10.1155/JAMDS.2005.33>.
Author: S. M. Iacus
Maintainer: Stefano M. Iacus <siacus@iq.harvard.edu>
Diff between ifs versions 0.1.5 dated 2015-08-21 and 0.1.9 dated 2022-08-10
DESCRIPTION | 11 - MD5 | 10 - NAMESPACE | 3 NEWS |only README.md |only man/ifsm.w.maps.Rd | 2 src/ifs.c | 353 ++++++++++++++++++++++++++--------------------------- 7 files changed, 191 insertions(+), 188 deletions(-)
Title: API Client for the 'ClimMob' Platform
Description: API client for 'ClimMob', an open source software for decentralized
large-N trials with the 'tricot' approach <https://climmob.net/>.
Developed by van Etten et al. (2016) <doi:10.1017/S0014479716000739>, it turns the
research paradigm on its head; instead of a few researchers designing complicated
trials to compare several technologies in search of the best solutions for the
target environment, it enables many participants to carry out reasonably simple
experiments that taken together can offer even more information. 'ClimMobTools'
enables project managers to deep explore and analyse their 'ClimMob' data in R.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
Brandon Madriz [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between ClimMobTools versions 0.4.5 dated 2022-02-18 and 0.4.6 dated 2022-08-10
DESCRIPTION | 25 +-- MD5 | 38 +++-- NAMESPACE | 1 NEWS.md | 9 + R/AAA-getDataCM.R | 2 R/as.data.frame-climmob_list.R | 9 - R/getProjectProgress.R | 2 R/getProjectsCM.R | 16 -- R/getTraitList.R |only R/internal_functions.R | 219 --------------------------------- R/randomise.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.html | 269 ++++++++++++++++++++++++++++++++++++++--- inst/vector |only man/ClimMobTools.Rd | 4 man/getDataCM.Rd | 4 man/getProjectProgress.Rd | 4 man/getProjectsCM.Rd | 4 man/getTraitList.Rd |only man/randomise.Rd | 4 21 files changed, 316 insertions(+), 299 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut, cre],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [ctb] ,
Jeffrey Wong [ctb [...truncated...]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 8.0.0 dated 2022-05-10 and 9.0.0 dated 2022-08-10
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Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.4.1 dated 2022-06-16 and 3.4.2 dated 2022-08-10
DESCRIPTION | 12 MD5 | 94 +-- NAMESPACE | 1 R/DBgetEvalid.R | 2 R/DBgetPlots.R | 208 ++++--- R/ISAinternal.R | 4 R/aaa.R | 1 R/check.auxiliary.R | 48 + R/check.popdata.R | 244 +++++--- R/check.rowcol.R | 2 R/datSumTree.R | 2 R/modGBarea.R | 5 R/modGBpop.R | 110 ++-- R/modMAarea.R | 14 R/modMApop.R | 21 R/modMAtree.R | 14 R/modSAarea.R | 11 R/modSApop.R | 38 + R/modSAtree.R | 11 R/popTableIDs.R | 4 R/popTables.R | 5 R/spExtractRast.R | 19 R/spGetAuxiliary.R | 302 ++++++----- R/spGetPlots.R | 954 +++++++++++++++++++++-------------- R/spGetSAdoms.R | 24 R/spGetXY.R | 9 R/spMakeSpatialPoints.R | 2 R/spZonalRast.R | 13 inst/doc/FIESTA_tutorial_GB.R | 1 inst/doc/FIESTA_tutorial_GB.Rmd | 1 inst/doc/FIESTA_tutorial_GB.html | 535 ++++++++++--------- inst/doc/FIESTA_tutorial_MA.html | 22 inst/doc/FIESTA_tutorial_PB.html | 32 - inst/doc/FIESTA_tutorial_SA.R | 4 inst/doc/FIESTA_tutorial_SA.Rmd | 4 inst/doc/FIESTA_tutorial_SA.html | 82 +-- inst/extdata/ref_data/ref_domain.csv | 1 man/DBgetPlots.Rd | 10 man/modGBpop.Rd | 4 man/modSAarea.Rd | 2 man/modSAtree.Rd | 2 man/popTableIDs.Rd | 3 man/popTables.Rd | 4 man/ref_domain.Rd | 2 man/spGetAuxiliary.Rd | 5 man/spGetPlots.Rd | 15 vignettes/FIESTA_tutorial_GB.Rmd | 1 vignettes/FIESTA_tutorial_SA.Rmd | 4 48 files changed, 1746 insertions(+), 1162 deletions(-)
Title: Creates Simultaneous Testing Bands for QQ-Plots
Description: Provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous
testing bands to asses significance of sample deviation from a reference distribution.
Author: Eric Weine [aut, cre],
Mary Sara McPeek [aut],
Abney Mark [aut]
Maintainer: Eric Weine <ericweine15@gmail.com>
Diff between qqconf versions 1.2.3 dated 2022-03-28 and 1.3.0 dated 2022-08-10
DESCRIPTION | 13 - MD5 | 32 +- NAMESPACE | 5 R/ppplot.R | 263 ++++++++++------------ R/qqplot.R | 280 +++++++++++------------- R/two_sided.R | 275 ++++++++++++++++++++--- R/utils.R |only inst/doc/qqconf_introduction.html | 36 +-- man/between.Rd |only man/estimate_params_from_data.Rd |only man/get_best_available_prob_pts_method.Rd |only man/get_bounds_two_sided.Rd | 10 man/get_extended_quantile.Rd |only man/get_mass_name_from_distr.Rd |only man/get_qq_band.Rd |only man/get_qq_distribution_from_pp_distribution.Rd |only man/monte_carlo_two_sided.Rd | 2 man/pp_conf_plot.Rd | 30 +- man/qq_conf_plot.Rd | 36 ++- src/Makevars.in | 11 src/Makevars.win | 14 - 21 files changed, 594 insertions(+), 413 deletions(-)
Title: Makes 'R' Easier for Everyone
Description: A meta-package that aims to make 'R' easier for everyone,
especially programmers who have a background in 'SAS®' software.
This set of packages brings many useful concepts to 'R', including
data libraries, data dictionaries, formats
and format catalogs, a data step, and a traceable log. The 'flagship'
package is a reporting package that can output in text, rich text, 'PDF' and
'HTML' file formats.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between sassy versions 1.0.7 dated 2022-01-19 and 1.0.8 dated 2022-08-10
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Title: Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Description: Finds the critical sample size ("critical point of stability") for a
correlation to stabilize in Schoenbrodt and Perugini's definition of
sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between fastpos versions 0.4.1 dated 2020-09-29 and 0.5.0 dated 2022-08-10
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Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and
exploration of data from environmental monitoring programs.
The package name stands for "water quality" and reflects the
original focus on time series data for physical and chemical
properties of water, as well as the biota. Intended for
programs that sample approximately monthly, quarterly or
annually at discrete stations, a feature of many legacy data
sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject
matter.
Author: Alan Jassby [aut],
James Cloern [ctb],
Jemma Stachelek [ctb, cre]
Maintainer: Jemma Stachelek <jemma.stachelek@gmail.com>
Diff between wql versions 0.4.9 dated 2017-07-08 and 1.0.0 dated 2022-08-10
DESCRIPTION | 14 - MD5 | 54 ++--- NEWS.md | 6 R/plotSeason.R | 136 +++++++------ R/wql-package.R | 255 ++++++++++++------------- README.md | 118 +++++++----- build/vignette.rds |binary build/wql.pdf |binary inst/doc/wql-package.R | 76 +++---- inst/doc/wql-package.Rmd | 4 inst/doc/wql-package.html | 452 +++++++++++++++++++++++++++------------------- man/WqData-class.Rd | 13 - man/decompTs.Rd | 8 man/interpTs.Rd | 9 man/mannKen.Rd | 11 - man/phenoAmp.Rd | 4 man/phenoPhase.Rd | 10 - man/plotSeason.Rd | 20 +- man/plotTs.Rd | 10 - man/plotTsTile.Rd | 15 + man/seaKen.Rd | 12 + man/seaRoll.Rd | 13 + man/seasonTrend.Rd | 3 man/sfbay.Rd | 8 man/tsMake.Rd | 20 +- man/wqData.Rd | 10 - man/years.Rd | 12 - vignettes/wql-package.Rmd | 4 28 files changed, 739 insertions(+), 558 deletions(-)
Title: 'Too Many, Too Improbable' (TMTI) Test Procedures
Description: Methods for computing joint tests, controlling the Familywise Error Rate (FWER) and getting lower bounds on the number of false hypotheses in a set. The methods implemented here are described in Mogensen and Markussen (2021) <arXiv:2108.04731>.
Author: Phillip B. Mogensen
Maintainer: Phillip B. Mogensen <pbm@math.ku.dk>
Diff between TMTI versions 1.0.0 dated 2022-08-07 and 1.0.1 dated 2022-08-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/cppfunctions.cpp | 23 ++++++++++++----------- 3 files changed, 17 insertions(+), 16 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb],
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb],
Benjamin Nutter [ctb],
Andrew Peters [ctb],
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip Cha [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.0.0 dated 2021-07-22 and 1.1.0 dated 2022-08-10
DESCRIPTION | 36 MD5 | 202 ++- NAMESPACE | 5 NEWS.md | 48 R/REDCapR-package.R | 2 R/constant.R | 2 R/helpers-testing.R | 10 R/kernel-api.R | 13 R/metadata-utilities.R | 2 R/project-dag-write.R |only R/project-delete-multiple-arm.R |only R/project-delete-single-arm.R |only R/project-simple.R | 4 R/redcap-arm-export.R |only R/redcap-delete.R |only R/redcap-event-instruments.R |only R/redcap-instruments.R |only R/redcap-metadata-read.R | 28 R/redcap-read-dag.R |only R/redcap-read-oneshot-eav.R | 8 R/redcap-read-oneshot.R | 20 R/redcap-read.R | 53 R/redcap-users-export.R | 5 R/redcap-version.R | 2 R/retrieve-credential.R | 37 R/sanitize-token.R | 10 R/skippers.R |only R/validate.R | 2 README.md | 22 build/vignette.rds |binary inst/WORDLIST |only inst/doc/BasicREDCapROperations.R | 2 inst/doc/BasicREDCapROperations.Rmd | 2 inst/doc/BasicREDCapROperations.html | 511 ++++++-- inst/doc/SecurityDatabase.html | 273 +++- inst/doc/TroubleshootingApiCalls.Rmd | 2 inst/doc/TroubleshootingApiCalls.html | 634 ++++++++-- inst/doc/advanced-redcapr-operations.R | 4 inst/doc/advanced-redcapr-operations.Rmd | 4 inst/doc/advanced-redcapr-operations.html | 509 ++++++-- inst/doc/workflow-read.R | 4 inst/doc/workflow-read.Rmd | 32 inst/doc/workflow-read.html | 465 ++++++- inst/misc/example.credentials | 14 inst/misc/validation-transformation.yml |only inst/test-data/decimal-comma |only inst/test-data/decimal-comma-and-dot |only inst/test-data/decimal-dot |only inst/test-data/delete-multiple-arm |only inst/test-data/delete-single-arm |only inst/test-data/longitudinal-single-arm |only inst/test-data/project-color-boxes/Readme.md | 4 inst/test-data/project-longitudinal/arm.csv |only inst/test-data/specific-redcapr/delete |only inst/test-data/specific-redcapr/event-instruments |only inst/test-data/specific-redcapr/instruments |only inst/test-data/specific-redcapr/read-batch-repeating-sparse |only inst/test-data/specific-redcapr/read-batch-simple/specify-fields-zero-length.R |only inst/test-data/specific-redcapr/read-batch-simple/specify-fields.R |only inst/test-data/specific-redcapr/read-batch-simple/specify-records-zero-length.R |only inst/test-data/specific-redcapr/read-batch-simple/specify-records.R |only inst/test-data/specific-redcapr/read-dag |only inst/test-data/specific-redcapr/read-oneshot/specify-fields-zero-length.R |only inst/test-data/specific-redcapr/read-oneshot/specify-fields.R |only inst/test-data/specific-redcapr/read-oneshot/specify-records-zero-length.R |only inst/test-data/specific-redcapr/read-oneshot/specify-records.R |only inst/test-data/specific-redcapr/users-export/with-dags--user.R | 26 inst/test-data/specific-redcapr/users-export/with-dags--user_form.R | 4 inst/test-data/specific-redcapr/users-export/without-dags--user.R | 26 inst/test-data/specific-redcapr/users-export/without-dags--user_form.R | 2 inst/test-data/specific-redcapr/write-dag |only inst/test-data/super-wide-3 |only inst/test-data/super-wide-metadata |only inst/test-data/validation-types-v1 |only man/REDCapR-package.Rd | 2 man/constant.Rd | 2 man/kernel_api.Rd | 2 man/metadata_utilities.Rd | 2 man/redcap_arm_export.Rd |only man/redcap_dag_read.Rd |only man/redcap_delete.Rd |only man/redcap_event_instruments.Rd |only man/redcap_instruments.Rd |only man/redcap_next_free_record_name.Rd | 6 man/redcap_read.Rd | 15 man/redcap_read_oneshot.Rd | 11 man/redcap_users_export.Rd | 6 man/retrieve_credential.Rd | 20 man/sanitize_token.Rd | 8 tests/spelling.R |only tests/testthat/test-arm-export.R |only tests/testthat/test-column-sanitize.R | 2 tests/testthat/test-dag-read.R |only tests/testthat/test-delete.R |only tests/testthat/test-event-instruments.R |only tests/testthat/test-file-oneshot.R | 1 tests/testthat/test-instruments-metadata.R |only tests/testthat/test-metadata-read.R | 37 tests/testthat/test-read-batch-repeating-sparse.R |only tests/testthat/test-read-batch-simple.R | 119 + tests/testthat/test-read-dag.R |only tests/testthat/test-read-decimal-comma.R |only tests/testthat/test-read-decimal-dot.R |only tests/testthat/test-read-errors.R | 62 tests/testthat/test-read-oneshot-eav.R | 4 tests/testthat/test-read-oneshot.R | 124 + tests/testthat/test-read-superwide.R | 84 + tests/testthat/test-retrieve-credential-local.R | 29 tests/testthat/test-retrieve-credential-mssql.R | 14 tests/testthat/test-sanitize.R | 9 tests/testthat/test-skippers.R |only tests/testthat/test-version.R | 2 tests/testthat/test-write-batch.R | 12 tests/testthat/test-write-dag.R |only tests/testthat/test-write-error.R | 15 tests/testthat/test-write-oneshot.R | 12 vignettes/BasicREDCapROperations.Rmd | 2 vignettes/TroubleshootingApiCalls.Rmd | 2 vignettes/advanced-redcapr-operations.Rmd | 4 vignettes/workflow-read.Rmd | 32 120 files changed, 2984 insertions(+), 685 deletions(-)
Title: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Description: Functions for the input/output and visualization of
medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI'
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [aut],
Karsten Tabelow [ctb],
Jon Clayden [ctb],
John Muschelli [aut]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>
Diff between oro.nifti versions 0.11.3 dated 2022-08-09 and 0.11.4 dated 2022-08-10
DESCRIPTION | 39 +++++++++++---------------------------- MD5 | 9 +++++---- NEWS.md | 4 ++++ R/plot.R | 20 +++++++++++++++----- man/orthographic-methods.Rd | 11 +++++++++++ tests/testthat/test-plotting.R |only 6 files changed, 46 insertions(+), 37 deletions(-)
Title: Tools for Working with the National Hydrography Dataset
Description: Tools for working with the National Hydrography Dataset, with
functions for querying, downloading, and networking both the NHD
<https://www.usgs.gov/national-hydrography>
and NHDPlus <https://www.epa.gov/waterdata/nhdplus-national-hydrography-dataset-plus> datasets.
Author: Jemma Stachelek [aut, cre]
Maintainer: Jemma Stachelek <jemma.stachelek@gmail.com>
Diff between nhdR versions 0.5.7 dated 2022-01-03 and 0.5.8 dated 2022-08-10
nhdR-0.5.7/nhdR/R/traverse.R |only nhdR-0.5.8/nhdR/DESCRIPTION | 12 nhdR-0.5.8/nhdR/MD5 | 53 - nhdR-0.5.8/nhdR/NAMESPACE | 138 ++-- nhdR-0.5.8/nhdR/NEWS.md | 120 ++-- nhdR-0.5.8/nhdR/R/get.R | 2 nhdR-0.5.8/nhdR/R/load.R | 714 ++++++++++++------------- nhdR-0.5.8/nhdR/R/query.R | 678 +++++++++++------------ nhdR-0.5.8/nhdR/R/utils.R | 794 ++++++++++++++-------------- nhdR-0.5.8/nhdR/README.md | 474 ++++++++-------- nhdR-0.5.8/nhdR/build/vignette.rds |binary nhdR-0.5.8/nhdR/inst/CITATION | 36 - nhdR-0.5.8/nhdR/inst/doc/demo.R | 32 - nhdR-0.5.8/nhdR/inst/doc/demo.html | 354 ++++++------ nhdR-0.5.8/nhdR/inst/doc/flow.R | 104 +-- nhdR-0.5.8/nhdR/inst/doc/flow.html | 439 +++++++-------- nhdR-0.5.8/nhdR/inst/doc/network.R | 68 +- nhdR-0.5.8/nhdR/inst/doc/network.html | 393 ++++++------- nhdR-0.5.8/nhdR/man/find_state.Rd | 44 - nhdR-0.5.8/nhdR/man/nhd_dl_state.Rd | 86 +-- nhdR-0.5.8/nhdR/man/nhd_load.Rd | 124 ++-- nhdR-0.5.8/nhdR/man/nhd_plus_load.Rd | 166 ++--- nhdR-0.5.8/nhdR/man/nhd_plus_query.Rd | 144 ++--- nhdR-0.5.8/nhdR/man/nhd_query.Rd | 126 ++-- nhdR-0.5.8/nhdR/man/select_point_overlay.Rd | 68 +- nhdR-0.5.8/nhdR/tests/testthat/test-list.R | 50 - nhdR-0.5.8/nhdR/tests/testthat/test-load.R | 188 +++--- nhdR-0.5.8/nhdR/tests/testthat/test-query.R | 176 +++--- 28 files changed, 2801 insertions(+), 2782 deletions(-)
Title: Stepwise Regression with Assumptions Checking
Description: The stepwise regression with assumptions checking and the possible Box-Cox transformation.
Author: Thidarat Thongsri [aut, cre],
Klairung Samart [aut]
Maintainer: Thidarat Thongsri <k.th.thidarat@gmail.com>
Diff between mlrpro versions 0.1.1 dated 2022-06-17 and 0.1.2 dated 2022-08-10
mlrpro-0.1.1/mlrpro/inst/WORDLIST |only mlrpro-0.1.1/mlrpro/tests/spelling.R |only mlrpro-0.1.2/mlrpro/DESCRIPTION | 9 mlrpro-0.1.2/mlrpro/MD5 | 8 mlrpro-0.1.2/mlrpro/R/mlrpro.R | 1580 ++++++++++++++++++++++++++++------- mlrpro-0.1.2/mlrpro/tests/testthat.R | 8 6 files changed, 1313 insertions(+), 292 deletions(-)
Title: Provides an R Interface to 'Enrichr'
Description: Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.
Author: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <wj241@alumni.cam.ac.uk>
Diff between enrichR versions 3.0 dated 2021-02-01 and 3.1 dated 2022-08-10
enrichR-3.0/enrichR/tools/README-unnamed-chunk-13-1.png |only enrichR-3.0/enrichR/tools/README-unnamed-chunk-14-1.png |only enrichR-3.1/enrichR/DESCRIPTION | 10 - enrichR-3.1/enrichR/MD5 | 16 -- enrichR-3.1/enrichR/NAMESPACE | 1 enrichR-3.1/enrichR/NEWS.md | 2 enrichR-3.1/enrichR/R/functions.R | 22 +-- enrichR-3.1/enrichR/README.md | 2 enrichR-3.1/enrichR/build/vignette.rds |binary enrichR-3.1/enrichR/inst/doc/enrichR.html | 117 +++++++++++----- 10 files changed, 114 insertions(+), 56 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2007-06-11 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-26 0.2-1.1
2014-09-10 0.2-1
2014-08-29 0.2-0
2012-03-23 0.1-8
2010-07-25 0.1-7
2009-12-28 0.1-6
2008-08-11 0.1-5
2008-02-17 0.1-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-20 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-08 2.1.1
2013-08-20 2.0.2
2013-08-19 2.0.0
2011-02-04 1.1.0
2010-03-10 1.0.0
Title: Stepwise Procedure for Beta, Beta-Binomial and Negative Binomial
Regression Models
Description: Starting from a Regression Model, it provides a stepwise
procedure to select the linear predictor.
Author: Sergio Garofalo
Maintainer: Sergio Garofalo <sergio.garofalo96@gmail.com>
Diff between StepBeta versions 2.0.1 dated 2022-07-14 and 2.1.0 dated 2022-08-10
DESCRIPTION | 15 - MD5 | 16 - NAMESPACE | 5 R/Check_formual_terms.R | 16 - R/Combination_terms.R |only R/Step_AIC_BetaBinomial_regression.R |only R/Step_Aic_beta_regression.R | 493 +++++++++++++++++------------------ man/Combination_Terms.Rd |only man/StepBeta.Rd | 4 man/Step_glimML.Rd |only man/check_formula_terms.Rd | 4 11 files changed, 284 insertions(+), 269 deletions(-)
Title: Using Apache 'Kafka' Messaging Queue Through 'R'
Description: Apache 'Kafka' is an open-source message broker project developed by the Apache Software Foundation which can be thought of as a distributed, partitioned, replicated commit log service.At a high level, producers send messages over the network to the 'Kafka' cluster which in turn serves them up to consumers.See <https://kafka.apache.org/> for more information.Functions included in this package enable:1.Creating 'Kafka' producer 2.Writing messages to a topic 3.Closing 'Kafka' producer 4.Creating 'Kafka' consumer 5.Reading messages from a topic 6.Closing 'Kafka' consumer. The jars required for this package are included in a separate package 'rkafkajars'.
Author: Shruti Gupta[aut,cre]
Maintainer: Shruti Gupta <shrutigupta34@gmail.com>
Diff between rkafka versions 1.3 dated 2021-12-05 and 1.4 dated 2022-08-10
rkafka-1.3/rkafka/inst/doc/rkafka-manual.pdf |only rkafka-1.4/rkafka/DESCRIPTION | 8 ++++---- rkafka-1.4/rkafka/MD5 | 12 ++++++------ rkafka-1.4/rkafka/build/vignette.rds |binary rkafka-1.4/rkafka/inst/doc/rkafka.Rnw | 4 ++-- rkafka-1.4/rkafka/inst/doc/rkafka.pdf |binary rkafka-1.4/rkafka/inst/doc/rkafka.synctex.gz |only rkafka-1.4/rkafka/vignettes/rkafka.Rnw | 4 ++-- 8 files changed, 14 insertions(+), 14 deletions(-)
Title: Flexible Binding for Complex Function Evaluation with the Base R
|> Pipe
Description: Provides a simple function to bind a piped object to a placeholder
symbol to enable complex function evaluation with the base R |> pipe.
Author: Brenton M. Wiernik [cre, aut]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between pipebind versions 0.1.0 dated 2022-04-29 and 0.1.1 dated 2022-08-10
DESCRIPTION | 12 ++-- MD5 | 14 ++--- NEWS.md | 10 ++- R/pipebind.R | 128 +++++++++++++++++++++++++++----------------------- README.md | 148 +++++++++++++++++++++++++++++++--------------------------- inst/CITATION | 30 +++++------ inst/WORDLIST | 2 man/bind.Rd | 25 +++++---- 8 files changed, 202 insertions(+), 167 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.18.1 dated 2022-05-29 and 0.18.2 dated 2022-08-10
parameters-0.18.1/parameters/inst/WORDLIST |only parameters-0.18.1/parameters/man/model_parameters.glht.Rd |only parameters-0.18.1/parameters/man/model_parameters.lavaan.Rd |only parameters-0.18.1/parameters/man/model_parameters.t1way.Rd |only parameters-0.18.1/parameters/tests/spelling.R |only parameters-0.18.2/parameters/DESCRIPTION | 52 parameters-0.18.2/parameters/MD5 | 349 ++-- parameters-0.18.2/parameters/NAMESPACE | 8 parameters-0.18.2/parameters/NEWS.md | 51 parameters-0.18.2/parameters/R/1_model_parameters.R | 106 - parameters-0.18.2/parameters/R/2_ci.R | 6 parameters-0.18.2/parameters/R/3_p_value.R | 1 parameters-0.18.2/parameters/R/backports.R | 10 parameters-0.18.2/parameters/R/check_factorstructure.R | 2 parameters-0.18.2/parameters/R/ci_generic.R | 19 parameters-0.18.2/parameters/R/ci_profile_boot.R | 3 parameters-0.18.2/parameters/R/cluster_analysis.R | 16 parameters-0.18.2/parameters/R/cluster_centers.R | 3 parameters-0.18.2/parameters/R/cluster_meta.R | 28 parameters-0.18.2/parameters/R/compare_parameters.R | 2 parameters-0.18.2/parameters/R/dof_kenward.R | 2 parameters-0.18.2/parameters/R/dominance_analysis.R |only parameters-0.18.2/parameters/R/equivalence_test.R | 4 parameters-0.18.2/parameters/R/extract_parameters.R | 126 + parameters-0.18.2/parameters/R/extract_parameters_anova.R | 27 parameters-0.18.2/parameters/R/extract_random_variances.R | 807 +++------- parameters-0.18.2/parameters/R/factor_analysis.R | 1 parameters-0.18.2/parameters/R/format.R | 194 +- parameters-0.18.2/parameters/R/format_p_adjust.R | 3 parameters-0.18.2/parameters/R/format_parameters.R | 77 parameters-0.18.2/parameters/R/methods_BayesFactor.R | 6 parameters-0.18.2/parameters/R/methods_FactoMineR.R | 1 parameters-0.18.2/parameters/R/methods_MCMCglmm.R | 2 parameters-0.18.2/parameters/R/methods_PMCMRplus.R | 2 parameters-0.18.2/parameters/R/methods_aod.R | 1 parameters-0.18.2/parameters/R/methods_aov.R | 16 parameters-0.18.2/parameters/R/methods_averaging.R | 8 parameters-0.18.2/parameters/R/methods_bamlss.R | 8 parameters-0.18.2/parameters/R/methods_bayesQR.R | 3 parameters-0.18.2/parameters/R/methods_bbmle.R | 1 parameters-0.18.2/parameters/R/methods_bfsl.R | 1 parameters-0.18.2/parameters/R/methods_brglm2.R | 1 parameters-0.18.2/parameters/R/methods_brms.R | 8 parameters-0.18.2/parameters/R/methods_car.R | 15 parameters-0.18.2/parameters/R/methods_censReg.R | 1 parameters-0.18.2/parameters/R/methods_cgam.R | 38 parameters-0.18.2/parameters/R/methods_coda.R | 1 parameters-0.18.2/parameters/R/methods_cplm.R | 15 parameters-0.18.2/parameters/R/methods_emmeans.R | 17 parameters-0.18.2/parameters/R/methods_epi2x2.R | 1 parameters-0.18.2/parameters/R/methods_fitdistr.R | 6 parameters-0.18.2/parameters/R/methods_gamlss.R | 1 parameters-0.18.2/parameters/R/methods_ggeffects.R | 1 parameters-0.18.2/parameters/R/methods_gjrm.R | 1 parameters-0.18.2/parameters/R/methods_glmm.R | 1 parameters-0.18.2/parameters/R/methods_glmmTMB.R | 24 parameters-0.18.2/parameters/R/methods_hclust.R | 2 parameters-0.18.2/parameters/R/methods_htest.R | 22 parameters-0.18.2/parameters/R/methods_ivfixed.R | 1 parameters-0.18.2/parameters/R/methods_ivprobit.R | 1 parameters-0.18.2/parameters/R/methods_kmeans.R | 3 parameters-0.18.2/parameters/R/methods_lavaan.R | 77 parameters-0.18.2/parameters/R/methods_lme4.R | 20 parameters-0.18.2/parameters/R/methods_lmodel2.R | 1 parameters-0.18.2/parameters/R/methods_lmtest.R | 1 parameters-0.18.2/parameters/R/methods_logistf.R | 1 parameters-0.18.2/parameters/R/methods_lqmm.R | 2 parameters-0.18.2/parameters/R/methods_lrm.R | 13 parameters-0.18.2/parameters/R/methods_marginaleffects.R | 59 parameters-0.18.2/parameters/R/methods_margins.R | 6 parameters-0.18.2/parameters/R/methods_mass.R | 3 parameters-0.18.2/parameters/R/methods_maxLik.R | 2 parameters-0.18.2/parameters/R/methods_mediate.R | 7 parameters-0.18.2/parameters/R/methods_merTools.R | 1 parameters-0.18.2/parameters/R/methods_metafor.R | 3 parameters-0.18.2/parameters/R/methods_metaplus.R | 19 parameters-0.18.2/parameters/R/methods_mfx.R | 12 parameters-0.18.2/parameters/R/methods_mgcv.R | 1 parameters-0.18.2/parameters/R/methods_mhurdle.R | 1 parameters-0.18.2/parameters/R/methods_mice.R | 1 parameters-0.18.2/parameters/R/methods_mixed.R | 1 parameters-0.18.2/parameters/R/methods_mixmod.R | 1 parameters-0.18.2/parameters/R/methods_mjoint.R | 9 parameters-0.18.2/parameters/R/methods_mlm.R | 35 parameters-0.18.2/parameters/R/methods_model_fit.R | 1 parameters-0.18.2/parameters/R/methods_multcomp.R | 3 parameters-0.18.2/parameters/R/methods_mvord.R | 1 parameters-0.18.2/parameters/R/methods_nlme.R | 2 parameters-0.18.2/parameters/R/methods_ordinal.R | 1 parameters-0.18.2/parameters/R/methods_other.R | 2 parameters-0.18.2/parameters/R/methods_panelr.R | 11 parameters-0.18.2/parameters/R/methods_plm.R | 6 parameters-0.18.2/parameters/R/methods_posterior.R | 2 parameters-0.18.2/parameters/R/methods_pscl.R | 3 parameters-0.18.2/parameters/R/methods_psych.R | 80 parameters-0.18.2/parameters/R/methods_quantreg.R | 3 parameters-0.18.2/parameters/R/methods_robustlmm.R | 1 parameters-0.18.2/parameters/R/methods_rstan.R | 8 parameters-0.18.2/parameters/R/methods_rstanarm.R | 10 parameters-0.18.2/parameters/R/methods_scam.R | 1 parameters-0.18.2/parameters/R/methods_selection.R | 1 parameters-0.18.2/parameters/R/methods_sem.R | 1 parameters-0.18.2/parameters/R/methods_spaMM.R | 1 parameters-0.18.2/parameters/R/methods_stats4.R | 1 parameters-0.18.2/parameters/R/methods_survey.R | 1 parameters-0.18.2/parameters/R/methods_systemfit.R | 1 parameters-0.18.2/parameters/R/methods_varest.R | 1 parameters-0.18.2/parameters/R/methods_vgam.R | 1 parameters-0.18.2/parameters/R/methods_wrs2.R | 4 parameters-0.18.2/parameters/R/n_clusters_easystats.R | 6 parameters-0.18.2/parameters/R/n_factors.R | 42 parameters-0.18.2/parameters/R/parameters_type.R | 2 parameters-0.18.2/parameters/R/pool_parameters.R | 57 parameters-0.18.2/parameters/R/principal_components.R | 4 parameters-0.18.2/parameters/R/print.parameters_model.R | 26 parameters-0.18.2/parameters/R/print_html.R | 8 parameters-0.18.2/parameters/R/print_md.R | 8 parameters-0.18.2/parameters/R/reduce_parameters.R | 8 parameters-0.18.2/parameters/R/robust_estimation.R | 2 parameters-0.18.2/parameters/R/sort_parameters.R | 8 parameters-0.18.2/parameters/R/standardize_info.R | 6 parameters-0.18.2/parameters/R/standardize_parameters.R | 10 parameters-0.18.2/parameters/R/standardize_posteriors.R | 2 parameters-0.18.2/parameters/R/utils.R | 3 parameters-0.18.2/parameters/R/utils_clustering.R | 2 parameters-0.18.2/parameters/R/utils_format.R | 10 parameters-0.18.2/parameters/R/utils_model_parameters.R | 76 parameters-0.18.2/parameters/R/utils_pca_efa.R | 7 parameters-0.18.2/parameters/README.md | 16 parameters-0.18.2/parameters/build/partial.rdb |binary parameters-0.18.2/parameters/build/vignette.rds |binary parameters-0.18.2/parameters/man/cluster_analysis.Rd | 12 parameters-0.18.2/parameters/man/cluster_meta.Rd | 3 parameters-0.18.2/parameters/man/compare_parameters.Rd | 21 parameters-0.18.2/parameters/man/dominance_analysis.Rd |only parameters-0.18.2/parameters/man/format_parameters.Rd | 8 parameters-0.18.2/parameters/man/model_parameters.Rd | 65 parameters-0.18.2/parameters/man/model_parameters.aov.Rd | 115 + parameters-0.18.2/parameters/man/model_parameters.averaging.Rd | 741 ++++++++- parameters-0.18.2/parameters/man/model_parameters.cgam.Rd | 110 + parameters-0.18.2/parameters/man/model_parameters.default.Rd | 80 parameters-0.18.2/parameters/man/model_parameters.htest.Rd | 15 parameters-0.18.2/parameters/man/model_parameters.merMod.Rd | 219 ++ parameters-0.18.2/parameters/man/model_parameters.mira.Rd | 126 + parameters-0.18.2/parameters/man/model_parameters.mlm.Rd | 31 parameters-0.18.2/parameters/man/model_parameters.principal.Rd | 211 ++ parameters-0.18.2/parameters/man/model_parameters.rma.Rd | 21 parameters-0.18.2/parameters/man/model_parameters.stanreg.Rd | 224 ++ parameters-0.18.2/parameters/man/model_parameters.zcpglm.Rd | 100 + parameters-0.18.2/parameters/man/pool_parameters.Rd | 31 parameters-0.18.2/parameters/man/print.parameters_model.Rd | 33 parameters-0.18.2/parameters/man/reduce_parameters.Rd | 4 parameters-0.18.2/parameters/man/standardize_parameters.Rd | 2 parameters-0.18.2/parameters/tests/testthat/test-GLMMadaptive.R | 6 parameters-0.18.2/parameters/tests/testthat/test-Hmisc.R |only parameters-0.18.2/parameters/tests/testthat/test-compare_parameters.R | 10 parameters-0.18.2/parameters/tests/testthat/test-dominance_analysis.R |only parameters-0.18.2/parameters/tests/testthat/test-glmer.R | 14 parameters-0.18.2/parameters/tests/testthat/test-glmmTMB.R | 130 - parameters-0.18.2/parameters/tests/testthat/test-marginaleffects.R | 64 parameters-0.18.2/parameters/tests/testthat/test-mlm.R | 1 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.anova.R | 23 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.aov_es_ci.R | 1 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.blmerMod.R | 2 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.cgam.R | 119 - parameters-0.18.2/parameters/tests/testthat/test-model_parameters.glm.R | 21 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.lqmm.R | 1 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.mixed.R | 8 parameters-0.18.2/parameters/tests/testthat/test-model_parameters.vgam.R | 2 parameters-0.18.2/parameters/tests/testthat/test-model_parameters_df.R | 2 parameters-0.18.2/parameters/tests/testthat/test-model_parameters_random_pars.R | 37 parameters-0.18.2/parameters/tests/testthat/test-model_parameters_robust.R | 1 parameters-0.18.2/parameters/tests/testthat/test-p_value.R | 2 parameters-0.18.2/parameters/tests/testthat/test-panelr.R | 8 parameters-0.18.2/parameters/tests/testthat/test-quantreg.R | 25 parameters-0.18.2/parameters/tests/testthat/test-random_effects_ci-glmmTMB.R | 229 +- parameters-0.18.2/parameters/tests/testthat/test-random_effects_ci.R | 280 ++- parameters-0.18.2/parameters/tests/testthat/test-robust.R | 3 parameters-0.18.2/parameters/tests/testthat/test-standardize_info.R | 2 parameters-0.18.2/parameters/tests/testthat/test-wrs2.R | 1 180 files changed, 4091 insertions(+), 1905 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations,
such as erosion and dilation, on data of arbitrary dimensionality. Can also
be used for finding connected components, resampling, filtering, smoothing
and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.6.1 dated 2020-03-03 and 1.6.2 dated 2022-08-10
DESCRIPTION | 10 +++++----- MD5 | 29 +++++++++++++++-------------- NEWS | 12 ++++++++++-- R/display.R | 2 +- R/morph.R | 3 +-- README.md | 24 ++++++++++++++---------- build |only inst/tinytest/test-30-distance.R | 4 ++++ man/gameOfLife.Rd | 3 ++- man/kernels.Rd | 3 ++- man/resample.Rd | 3 ++- man/sampleKernelFunction.Rd | 3 ++- man/skeletonise.Rd | 6 +++--- src/Distancer.cpp | 17 +++++++++-------- tools/figures/fan-distance-1.png |binary tools/figures/fan-distance-2.png |binary 16 files changed, 70 insertions(+), 49 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory models can be estimated with quadrature (EM)
or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modeling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models, including mixture and zero-inflated response models,
are supported.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.36.1 dated 2022-03-22 and 1.37.1 dated 2022-08-10
DESCRIPTION | 8 +- MD5 | 138 ++++++++++++++++++------------------ NEWS.md | 25 ++++++ R/02-item_methods.R | 72 ++++++++++++------ R/03-estimation.R | 2 R/06-LoadPars.R | 2 R/DIF.R | 23 +++++- R/DRF.R | 131 ++++++++++++++++++++++++---------- R/DTF.R | 2 R/Discrete-methods.R | 2 R/EMstep.group.R | 3 R/M2.R | 4 - R/MHRM.group.R | 1 R/MHRM.utils.R | 6 - R/Mixed-methods.R | 4 - R/Mixture-methods.R | 2 R/MultipleGroup-methods.R | 2 R/RCI.R | 9 +- R/SingleGroup-methods.R | 161 ++++++++++++++++++++++++------------------ R/areainfo.R | 2 R/bfactor.R | 4 - R/boot.LR.R | 6 - R/boot.mirt.R | 55 +++++++++++--- R/empirical_ES.R | 42 +++++++--- R/extract.mirt.R | 4 + R/fscores.R | 12 ++- R/fscores.internal.R | 86 ++++++++++++++-------- R/itemfit.R | 154 ++++++++++++++++++++++++---------------- R/marginal_rxx.R | 6 + R/mirt-package.R | 12 +-- R/mirt.R | 6 + R/mirtCluster.R | 35 ++++++--- R/mixedmirt.R | 2 R/multipleGroup.R | 14 ++- R/simdata.R | 2 R/utils.R | 36 ++++++--- R/wald.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary man/DIF.Rd | 17 +++- man/DRF.Rd | 43 +++++++++-- man/M2.Rd | 4 - man/RCI.Rd | 5 + man/SAT12.Rd | 12 +-- man/anova-method.Rd | 30 +++++-- man/bfactor.Rd | 4 - man/boot.LR.Rd | 2 man/boot.mirt.Rd | 27 ++++++- man/draw_parameters.Rd | 2 man/empirical_ES.Rd | 4 - man/empirical_plot.Rd | 4 - man/extract.mirt.Rd | 1 man/fscores.Rd | 7 + man/itemGAM.Rd | 4 - man/itemfit.Rd | 41 +++++----- man/itemplot.Rd | 4 - man/marginal_rxx.Rd | 5 + man/mirt.Rd | 6 + man/mirtCluster.Rd | 13 ++- man/multipleGroup.Rd | 13 ++- man/plot-method.Rd | 15 ++- man/print.mirt_df.Rd | 3 man/print.mirt_list.Rd | 3 man/print.mirt_matrix.Rd | 3 man/residuals-method.Rd | 6 + man/simdata.Rd | 2 man/summary-method.Rd | 4 + tests/tests/test-16-DCIRT.R | 15 ++- tests/tests/test-17-DIF_DRF.R | 6 - 70 files changed, 904 insertions(+), 480 deletions(-)
Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results.
Gerlovina et al. (2022) <doi:10.1101/2022.04.14.488406>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between dcifer versions 1.1.0 dated 2022-08-06 and 1.1.1 dated 2022-08-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/vignetteDcifer.pdf |binary src/logr.c | 6 ++++++ vignettes/dciferpkg.bib | 4 ++-- 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2019) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2020) <doi:10.1007/s10994-021-05960-5> (open access),
Raymaekers and Rousseeuw (2020) <doi:10.52933/jdssv.v1i3.18> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples", "DI_examples" and "cellMCD_examples".
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [ctb],
Mia Hubert [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between cellWise versions 2.2.6 dated 2022-03-16 and 2.4.0 dated 2022-08-10
DESCRIPTION | 14 - MD5 | 48 +++-- NAMESPACE | 10 - R/RcppExports.R | 12 + R/TVCN.R | 37 +++- R/cellHandler.R | 155 +++++++--------- R/cellMCD.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/DI_examples.Rmd | 2 inst/doc/DI_examples.html | 4 inst/doc/cellMCD_examples.R |only inst/doc/cellMCD_examples.Rmd |only inst/doc/cellMCD_examples.html |only inst/doc/transfo_examples.html | 67 +++++++ man/DDC.Rd | 2 man/DI.Rd | 3 man/cellHandler.Rd | 3 man/cellMCD.Rd |only man/data_VOC.Rd | 4 man/estLocScale.Rd | 2 man/plot_cellMCD.Rd |only man/transfo.Rd | 3 man/wrap.Rd | 2 src/Main.cpp | 375 ++++++++++++++++++++++++++--------------- src/RcppExports.cpp | 49 +++++ src/cellMCD.cpp |only src/cellMCD.h |only vignettes/DI_examples.Rmd | 2 vignettes/cellMCD_examples.Rmd |only 30 files changed, 524 insertions(+), 270 deletions(-)
Title: Bayesian Reliability Estimation
Description: Functionality for reliability estimates. For 'unidimensional' tests:
Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower
bound and coefficient omega_u ('unidimensional') in a Bayesian and a frequentist version.
For multidimensional tests: omega_t (total) and omega_h (hierarchical).
The results include confidence and credible intervals, the
probability of a coefficient being larger than a cutoff,
and a check for the factor models, necessary for the omega coefficients.
The method for the Bayesian 'unidimensional' estimates, except for omega_u,
is sampling from the posterior inverse 'Wishart' for the
covariance matrix based measures (see 'Murphy', 2007,
<https://groups.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>.
The Bayesian omegas (u, t, and h) are obtained by
'Gibbs' sampling from the conditional posterior distributions of
(1) the single factor model and (2) the second-order factor model
('Lee', 2007, <https://onlinelibrary.wiley.com/doi/book/10.1002/9780470024737>).
Author: Julius M. Pfadt [aut, cre],
Don van den Bergh [aut],
Joris Goosen [aut]
Maintainer: Julius M. Pfadt <julius.pfadt@gmail.com>
Diff between Bayesrel versions 0.7.4.2 dated 2022-06-27 and 0.7.4.3 dated 2022-08-10
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 1 R/genericFunctions.R | 206 ++++++++++++++++++++------------------------ R/omegaFit.R | 7 - R/omegasMultiLavaan.R | 5 + R/reliabilityMultiFreq.R | 10 +- build/partial.rdb |binary man/omegasCFA.Rd | 10 +- tests/testthat/testOmegas.R | 5 - 10 files changed, 131 insertions(+), 139 deletions(-)
Title: Fit GLM's with High-Dimensional k-Way Fixed Effects
Description: Provides a routine to partial out factors with many levels during the optimization of the log-likelihood function of the corresponding generalized linear model (glm). The package is based on the algorithm described in Stammann (2018) <arXiv:1707.01815> and is restricted to glm's that are based on maximum likelihood estimation and nonlinear. It also offers an efficient algorithm to recover estimates of the fixed effects in a post-estimation routine and includes robust and multi-way clustered standard errors. Further the package provides analytical bias corrections for binary choice models derived by Fernandez-Val and Weidner (2016) <doi:10.1016/j.jeconom.2015.12.014> and Hinz, Stammann, and Wanner (2020) <arXiv:2004.12655>.
Author: Amrei Stammann [aut, cre],
Daniel Czarnowske [aut]
Maintainer: Amrei Stammann <amrei.stammann@rub.de>
Diff between alpaca versions 0.3.3 dated 2020-10-30 and 0.3.4 dated 2022-08-10
DESCRIPTION | 25 - MD5 | 71 ++-- NAMESPACE | 1 R/alpaca.R | 14 R/biasCorr.R | 140 +++++--- R/feglm.R | 142 +++++--- R/feglm.nb.R | 151 +++++---- R/feglmControl.R | 45 +- R/generics.R | 277 +++++++++------- R/getAPEs.R | 246 +++++++------- R/internals.R | 294 +++++++++++------ R/simGLM.R | 18 - build/vignette.rds |binary inst/CITATION | 4 inst/NEWS.Rd | 17 + inst/doc/howto.R | 68 ++-- inst/doc/howto.Rmd | 78 ++-- inst/doc/howto.html | 550 +++++++++++++++++++------------- inst/doc/trade.R | 206 +++++------- inst/doc/trade.Rmd | 232 ++++++------- inst/doc/trade.html | 770 ++++++++++++++++++++++++---------------------- man/alpaca-package.Rd | 14 man/biasCorr.Rd | 19 - man/coef.summary.APEs.Rd | 4 man/coef.summary.feglm.Rd | 4 man/feglm.Rd | 8 man/feglm.nb.Rd | 6 man/feglmControl.Rd | 10 man/getAPEs.Rd | 23 - man/simGLM.Rd | 2 man/vcov.APEs.Rd |only man/vcov.feglm.Rd | 10 src/CenterVariables.cpp | 43 +- src/GroupSums.cpp | 26 - src/RcppExports.cpp | 5 vignettes/howto.Rmd | 78 ++-- vignettes/trade.Rmd | 232 ++++++------- 37 files changed, 2116 insertions(+), 1717 deletions(-)
Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
Description: Provides plotting utilities supporting easystats-packages
(<https://github.com/easystats/easystats>) and some extra themes,
geoms, and scales for 'ggplot2'. Color scales are based on
<https://materialui.co/colors>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, inv] ,
Indrajeet Patil [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Jeffrey R. Stevens [ctb] ,
Matthew Smith [rev] ,
Jakob Bossek [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between see versions 0.7.1 dated 2022-06-20 and 0.7.2 dated 2022-08-10
DESCRIPTION | 18 +-- MD5 | 130 +++++++++++++------------- NAMESPACE | 8 + NEWS.md | 16 +++ R/coord_radar.R | 14 +- R/geom_binomdensity.R | 1 R/geom_from_list.R | 2 R/plot.binned_residuals.R | 9 + R/plot.check_model.R | 124 +++++++++++++++++------- R/plot.check_outliers_new.R | 20 ++-- R/plot.compare_performance.R | 3 R/plot.describe_distribution.R | 1 R/plot.equivalence_test.R | 14 +- R/plot.estimate_density.R | 1 R/plot.p_direction.R | 1 R/plot.p_significance.R | 1 R/plot.parameters_brms_meta.R | 3 R/plot.parameters_model.R | 27 +++-- R/plot.parameters_sem.R | 2 R/plot.parameters_simulate.R | 2 R/plot.point_estimates.R | 1 R/plot.visualisation_recipe.R | 4 R/plots.R | 22 ++++ R/print.check_model.R | 2 R/scale_color_bluebrown.R | 36 +++---- R/scale_color_flat.R | 45 ++++----- R/scale_color_material.R | 36 +++---- R/scale_color_metro.R | 36 +++---- R/scale_color_okabeito.R |only R/scale_color_pizza.R | 34 +++--- R/scale_color_see.R | 41 +++++++- R/scale_color_social.R | 36 +++---- R/theme_modern.R | 1 R/theme_radar.R | 6 - man/bluebrown_colors.Rd | 44 ++++---- man/coord_radar.Rd | 14 +- man/flat_colors.Rd | 2 man/material_colors.Rd | 2 man/metro_colors.Rd | 2 man/okabeito_colors.Rd |only man/palette_bluebrown.Rd | 2 man/palette_flat.Rd | 2 man/palette_material.Rd | 2 man/palette_metro.Rd | 2 man/palette_okabeito.Rd |only man/palette_see.Rd | 2 man/palette_social.Rd | 2 man/plot.see_effectsize_table.Rd | 50 +++++----- man/scale_color_bluebrown.Rd | 14 ++ man/scale_color_flat.Rd | 61 ++++++++++-- man/scale_color_material.Rd | 14 ++ man/scale_color_metro.Rd | 21 +++- man/scale_color_okabeito.Rd |only man/scale_color_pizza.Rd | 19 +++ man/scale_color_see.Rd | 70 ++++++++++++-- man/scale_color_social.Rd | 14 ++ man/see_colors.Rd | 2 man/social_colors.Rd | 2 man/theme_radar.Rd | 6 - tests/testthat.R | 35 ++----- tests/testthat/test-plot.check_normality.R | 2 tests/testthat/test-plot.cluster_analysis.R | 2 tests/testthat/test-plot.easycormatrix.R | 2 tests/testthat/test-plot.n_factors.R | 2 tests/testthat/test-vdiffr_bayestestr_plots.R | 2 tests/testthat/test-vdiffr_geoms_coords.R | 6 - tests/testthat/test-vdiffr_scale_color.R | 2 tests/testthat/test-vdiffr_themes.R | 6 - 68 files changed, 686 insertions(+), 419 deletions(-)
Title: Kantorovich Distance Between Probability Measures
Description: Computes the Kantorovich distance between two probability measures on a finite set. The Kantorovich distance is also known as the Monge-Kantorovich distance or the first Wasserstein distance.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between kantorovich versions 3.0.0 dated 2020-10-28 and 3.0.1 dated 2022-08-10
DESCRIPTION | 9 - MD5 | 12 - NEWS.md | 13 + R/kantorovich.R | 6 build/vignette.rds |binary inst/doc/kantorovich.html | 355 +++++++++++++++++++--------------------- tests/testthat/test-ejoinings.R | 4 7 files changed, 197 insertions(+), 202 deletions(-)
Title: A Method to Estimate the Accuracy and Biogeographical Status of
Georeferenced Biological Data
Description: Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).
Author: Eduardo Arle [aut, cre],
Alexander Zizka [aut],
Patrick Weigelt [ctb],
Sam Levin [ctb],
Carsten Meyer [ths]
Maintainer: Eduardo Arle <eduardo.arle@idiv.de>
Diff between bRacatus versions 1.0.7 dated 2021-12-08 and 1.0.8 dated 2022-08-10
DESCRIPTION | 6 ++--- MD5 | 20 +++++++++--------- NEWS.md | 14 +++++++------ R/biogeoStatus.R | 11 +++++++++- R/getOcc.R | 2 - R/giftRegions.R | 6 ++--- R/glonafRegions.R | 6 ++--- R/internal_functions.R | 2 - R/rangeMaps.R | 46 +++++++++++++++++++++++++------------------ R/signalCalculation.R | 4 +-- inst/doc/Using_bRacatus.html | 2 - 11 files changed, 69 insertions(+), 50 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 Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin Jullum [rev],
gjo11 [rev]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between performance versions 0.9.1 dated 2022-06-20 and 0.9.2 dated 2022-08-10
DESCRIPTION | 14 +-- MD5 | 109 ++++++++++++------------- NAMESPACE | 3 NEWS.md | 87 +++++++++++++------ R/binned_residuals.R | 2 R/check_convergence.R | 25 ++++- R/check_distribution.R | 16 +-- R/check_model.R | 78 ++++++++++++----- R/check_model_diagnostics.R | 76 ++++++----------- R/check_outliers.R | 6 - R/check_overdispersion.R | 6 - R/compare_performance.R | 37 +++++--- R/display.R | 7 + R/format.R | 4 R/get_gradients.R | 6 - R/helpers.R | 4 R/icc.R | 1 R/model_performance.R | 10 ++ R/model_performance.kmeans.R | 5 - R/model_performance_default.R | 1 R/performance_accuracy.R | 4 R/performance_cv.R | 52 ++++++----- R/performance_mae.R | 2 R/performance_rmse.R | 2 R/performance_score.R | 2 R/pp_check.R | 18 ++-- R/print_md.R | 30 ++++++ R/r2.R | 22 ++++- R/r2_bayes.R | 20 ++-- R/r2_efron.R | 2 R/residuals.R | 2 R/sysdata.rda |binary R/test_bf.R | 5 - R/test_likelihoodratio.R | 29 +++--- R/test_performance.R | 21 ++-- R/test_vuong.R | 1 R/test_wald.R | 2 README.md | 62 +++++++------- build/partial.rdb |binary man/check_autocorrelation.Rd | 72 ++++++++-------- man/check_convergence.Rd | 16 ++- man/check_model.Rd | 17 +++ man/classify_distribution.Rd | 15 --- man/display.performance_model.Rd | 19 ++++ man/figures/unnamed-chunk-14-1.png |binary man/figures/unnamed-chunk-20-1.png |binary man/r2_bayes.Rd | 13 +- man/reexports.Rd | 36 ++++---- man/test_performance.Rd | 10 +- tests/testthat/test-check_zeroinflation.R | 11 +- tests/testthat/test-icc.R | 18 ++-- tests/testthat/test-model_performance.kmeans.R | 20 ++-- tests/testthat/test-model_performance.lm.R | 12 ++ tests/testthat/test-pkg-estimatr.R |only tests/testthat/test-r2_nakagawa.R | 56 +++++++----- tests/testthat/test-test_performance.R | 1 56 files changed, 645 insertions(+), 444 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut] ,
Vincent Arel-Bundock [aut, ctb]
,
Alex Hayes [rev]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.18.0 dated 2022-07-05 and 0.18.2 dated 2022-08-10
DESCRIPTION | 10 - MD5 | 135 +++++++++++++------------ NAMESPACE | 14 ++ NEWS.md | 25 ++++ R/all_equal_models.R | 5 R/clean_names.R | 4 R/compute_variances.R | 23 ++-- R/export_table.R | 8 - R/find_formula.R | 24 +++- R/find_parameter_zi.R | 2 R/find_parameters_other.R | 6 - R/find_terms.R | 8 + R/find_transformation.R | 6 + R/format_p.R | 10 - R/format_table.R | 27 +++-- R/format_value.R | 18 +++ R/get_data.R | 4 R/get_datagrid.R | 7 - R/get_df.R | 15 ++ R/get_modelmatrix.R | 12 ++ R/get_parameters.R | 6 - R/get_parameters_gam.R | 2 R/get_parameters_others.R | 5 R/get_parameters_zi.R | 2 R/get_predicted.R | 39 +++++-- R/get_predicted_args.R | 33 +++--- R/get_predicted_ci.R | 61 ++++++++++- R/get_predicted_gam.R | 27 ++++- R/get_predicted_methods.R | 21 ++- R/get_predicted_mixed.R | 2 R/get_predicted_ordinal.R | 22 +++- R/get_predicted_se.R | 91 +++++++++++++---- R/get_priors.R | 2 R/get_sigma.R | 27 +++++ R/get_statistic.R | 4 R/get_varcov.R | 8 - R/get_varcov_sandwich.R | 9 + R/is_converged.R |only R/print_parameters.R | 6 - R/standardize_names.R | 2 R/utils_get_data.R | 10 - R/utils_object.R | 11 +- build/vignette.rds |binary inst/doc/display.html | 180 +++++++++++++++++----------------- inst/doc/export.R | 4 inst/doc/export.Rmd | 4 inst/doc/export.html | 4 inst/doc/insight.Rmd | 2 man/find_interactions.Rd | 3 man/find_parameters.zeroinfl.Rd | 4 man/find_predictors.Rd | 4 man/format_table.Rd | 7 + man/format_value.Rd | 7 + man/get_parameters.betareg.Rd | 3 man/get_parameters.zeroinfl.Rd | 4 man/get_predicted.Rd | 14 ++ man/get_predicted_ci.Rd | 14 +- man/get_varcov.Rd | 5 man/is_converged.Rd |only tests/testthat/test-cgam.R | 9 + tests/testthat/test-get_predicted.R | 12 ++ tests/testthat/test-is_converged.R |only tests/testthat/test-marginaleffects.R | 2 tests/testthat/test-model_info.R | 3 tests/testthat/test-polr.R | 3 tests/testthat/test-rlmer.R | 12 +- tests/testthat/test-rq.R | 5 tests/testthat/test-rqss.R | 10 + vignettes/export.Rmd | 4 vignettes/insight.Rmd | 2 70 files changed, 735 insertions(+), 339 deletions(-)
Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>,
Sylvain Jasson <Sylvain.Jasson@inrae.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
Diff between gmp versions 0.6-5 dated 2022-03-17 and 0.6-6 dated 2022-08-10
ChangeLog | 3 ++ DESCRIPTION | 8 ++--- MD5 | 24 ++++++++--------- src/apply.cc | 4 +- src/bigintegerR.cc | 35 ++++++++++++------------- src/bigrationalR.cc | 37 +++++++++++--------------- src/extract_matrix.cc | 65 +---------------------------------------------- src/extract_matrix.h | 24 ++++++++--------- src/matrix.cc | 9 ++---- src/matrixq.cc | 8 ++--- tests/basic-ex.R | 2 + tests/gmp-test.R | 14 ++++++++++ tests/gmp-test.Rout.save | 30 ++++++++++++++++++++- 13 files changed, 118 insertions(+), 145 deletions(-)
Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between EnrichIntersect versions 0.1 dated 2022-07-21 and 0.2 dated 2022-08-10
DESCRIPTION | 16 ++++++++++------ MD5 | 28 +++++++++++++++++----------- NAMESPACE | 16 ++-------------- NEWS.md | 5 +++++ R/cancers_drug_groups.R | 2 ++ R/cancers_genes_drugs.R | 2 ++ R/enrichment.R | 10 +++++----- R/intersectSankey.R | 16 ++++++++-------- build |only inst |only man/cancers_drug_groups.Rd | 3 +++ man/cancers_genes_drugs.Rd | 3 +++ man/enrichment.Rd | 4 +++- man/intersectSankey.Rd | 1 + vignettes |only 15 files changed, 61 insertions(+), 45 deletions(-)
More information about EnrichIntersect at CRAN
Permanent link
Title: Linear Discriminant Function and Canonical Correlation Analysis
Description: Produces SPSS- and SAS-like output for linear discriminant
function analysis and canonical correlation analysis. The methods are described in
Manly & Alberto (2017, ISBN:9781498728966),
Rencher (2002, ISBN:0-471-41889-7), and
Tabachnik & Fidell (2019, ISBN:9780134790541).
Author: Brian P. O'Connor
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between DFA.CANCOR versions 0.2.3 dated 2022-01-03 and 0.2.5 dated 2022-08-10
DFA.CANCOR-0.2.3/DFA.CANCOR/data/data_CCA_De_Leo.rda |only DFA.CANCOR-0.2.3/DFA.CANCOR/data/data_CCA_Tabachnik.rda |only DFA.CANCOR-0.2.3/DFA.CANCOR/data/data_DFA_Field.rda |only DFA.CANCOR-0.2.3/DFA.CANCOR/data/data_DFA_Sherry.rda |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/data_CCA_De_Leo.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/data_CCA_Tabachnik.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/data_DFA_Field.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/data_DFA_Sherry.Rd |only DFA.CANCOR-0.2.5/DFA.CANCOR/DESCRIPTION | 10 DFA.CANCOR-0.2.5/DFA.CANCOR/MD5 | 39 - DFA.CANCOR-0.2.5/DFA.CANCOR/NAMESPACE | 5 DFA.CANCOR-0.2.5/DFA.CANCOR/R/CANCOR.R | 12 DFA.CANCOR-0.2.5/DFA.CANCOR/R/DFA.R | 369 ++++++++---- DFA.CANCOR-0.2.5/DFA.CANCOR/R/GROUP.DIFFS.R | 2 DFA.CANCOR-0.2.5/DFA.CANCOR/R/boc.R | 486 +++++++++++----- DFA.CANCOR-0.2.5/DFA.CANCOR/R/onAttach.R |only DFA.CANCOR-0.2.5/DFA.CANCOR/data/data_CANCOR.rda |only DFA.CANCOR-0.2.5/DFA.CANCOR/data/data_DFA.rda |only DFA.CANCOR-0.2.5/DFA.CANCOR/man/CANCOR.Rd | 47 + DFA.CANCOR-0.2.5/DFA.CANCOR/man/DFA.Rd | 226 +++++-- DFA.CANCOR-0.2.5/DFA.CANCOR/man/GROUP.DIFFS.Rd | 4 DFA.CANCOR-0.2.5/DFA.CANCOR/man/HOMOGENEITY.Rd | 4 DFA.CANCOR-0.2.5/DFA.CANCOR/man/LINEARITY.Rd | 6 DFA.CANCOR-0.2.5/DFA.CANCOR/man/NORMALITY.Rd | 6 DFA.CANCOR-0.2.5/DFA.CANCOR/man/PLOT_LINEARITY.Rd | 6 DFA.CANCOR-0.2.5/DFA.CANCOR/man/data_CANCOR.Rd |only DFA.CANCOR-0.2.5/DFA.CANCOR/man/data_DFA.Rd |only 27 files changed, 853 insertions(+), 369 deletions(-)
Title: Cases of COVID-19 in the United States
Description: A wrapper around the 'COVID Tracking Project API'
<https://covidtracking.com/api/> providing data on cases of COVID-19
in the US.
Author: Amanda Dobbyn [aut, cre]
Maintainer: Amanda Dobbyn <amanda.e.dobbyn@gmail.com>
Diff between covid19us versions 0.1.8 dated 2022-03-25 and 0.1.9 dated 2022-08-10
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/get.R | 2 +- R/utils.R | 2 +- tests/testthat/testthat-problems.rds |only 5 files changed, 9 insertions(+), 8 deletions(-)
Title: Tools for Clustering High-Dimensional Data
Description: Tools for clustering high-dimensional data.
In particular, it contains the methods described in
<doi:10.1093/bioinformatics/btaa243>,
<arXiv:2010.00950>.
Author: Jakob Raymaekers [aut, cre],
Ruben Zamar [aut]
Maintainer: Jakob Raymaekers <j.raymaekers@maastrichtuniversity.nl>
Diff between clusterHD versions 1.0.1 dated 2022-05-05 and 1.0.2 dated 2022-08-10
DESCRIPTION | 8 - MD5 | 8 - R/HTKmeans_code.R | 233 ++++++++++++++++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary man/HTKmeans.Rd | 18 +++- 5 files changed, 235 insertions(+), 32 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-25 0.1-1.3
Title: Indices of Effect Size and Standardized Parameters
Description: Provide utilities to work with indices of effect size and
standardized parameters for a wide variety of models (see list of
supported models using the function 'insight::supported_models()'),
allowing computation of and conversion between indices such as Cohen's
d, r, odds, etc.
Author: Mattan S. Ben-Shachar [aut, cre]
,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Jessica Burnett [rev] ,
Johannes Karreth [rev]
Maintainer: Mattan S. Ben-Shachar <matanshm@post.bgu.ac.il>
Diff between effectsize versions 0.7.0 dated 2022-05-26 and 0.7.0.5 dated 2022-08-10
effectsize-0.7.0.5/effectsize/DESCRIPTION | 23 - effectsize-0.7.0.5/effectsize/MD5 | 164 ++++---- effectsize-0.7.0.5/effectsize/NEWS.md | 13 effectsize-0.7.0.5/effectsize/R/cohens_d.R | 5 effectsize-0.7.0.5/effectsize/R/common_language.R | 23 - effectsize-0.7.0.5/effectsize/R/convert_between_OR_to_RR.R | 31 - effectsize-0.7.0.5/effectsize/R/convert_between_common_language.R | 22 - effectsize-0.7.0.5/effectsize/R/convert_between_odds_to_probs.R | 1 effectsize-0.7.0.5/effectsize/R/convert_stat_chisq.R | 34 + effectsize-0.7.0.5/effectsize/R/convert_stat_to_anova.R | 4 effectsize-0.7.0.5/effectsize/R/docs_extra.R | 4 effectsize-0.7.0.5/effectsize/R/effectsize.BFBayesFactor.R | 62 +-- effectsize-0.7.0.5/effectsize/R/effectsize.R | 7 effectsize-0.7.0.5/effectsize/R/effectsize.htest.R | 120 +++--- effectsize-0.7.0.5/effectsize/R/equivalence_test.R | 10 effectsize-0.7.0.5/effectsize/R/eta_squared.R | 193 +++++----- effectsize-0.7.0.5/effectsize/R/eta_squared_posterior.R | 12 effectsize-0.7.0.5/effectsize/R/format_standardize.R | 1 effectsize-0.7.0.5/effectsize/R/interpret.R | 2 effectsize-0.7.0.5/effectsize/R/interpret_bf.R | 3 effectsize-0.7.0.5/effectsize/R/interpret_cfa_fit.R | 14 effectsize-0.7.0.5/effectsize/R/interpret_cohens_d.R | 2 effectsize-0.7.0.5/effectsize/R/interpret_cohens_g.R | 5 effectsize-0.7.0.5/effectsize/R/interpret_icc.R | 2 effectsize-0.7.0.5/effectsize/R/interpret_pd.R | 2 effectsize-0.7.0.5/effectsize/R/interpret_vif.R | 6 effectsize-0.7.0.5/effectsize/R/is_effectsize_name.R | 24 - effectsize-0.7.0.5/effectsize/R/print.effectsize_table.R | 35 + effectsize-0.7.0.5/effectsize/R/print.rules.R | 8 effectsize-0.7.0.5/effectsize/R/rank_effectsizes.R | 59 ++- effectsize-0.7.0.5/effectsize/R/reexports.R | 2 effectsize-0.7.0.5/effectsize/R/sd_pooled.R | 2 effectsize-0.7.0.5/effectsize/R/utils.R | 12 effectsize-0.7.0.5/effectsize/R/utils_validate_input_data.R | 32 - effectsize-0.7.0.5/effectsize/R/utils_values_aov.R | 1 effectsize-0.7.0.5/effectsize/R/xtab.R | 57 +- effectsize-0.7.0.5/effectsize/R/zzz_deprecated.R | 2 effectsize-0.7.0.5/effectsize/README.md | 34 - effectsize-0.7.0.5/effectsize/build/partial.rdb |binary effectsize-0.7.0.5/effectsize/build/vignette.rds |binary effectsize-0.7.0.5/effectsize/inst/doc/anovaES.R | 13 effectsize-0.7.0.5/effectsize/inst/doc/anovaES.Rmd | 13 effectsize-0.7.0.5/effectsize/inst/doc/anovaES.html | 40 +- effectsize-0.7.0.5/effectsize/inst/doc/convert.html | 15 effectsize-0.7.0.5/effectsize/inst/doc/effectsize.R | 24 - effectsize-0.7.0.5/effectsize/inst/doc/effectsize.Rmd | 24 - effectsize-0.7.0.5/effectsize/inst/doc/effectsize.html | 179 ++++----- effectsize-0.7.0.5/effectsize/inst/doc/effectsize_API.R | 21 - effectsize-0.7.0.5/effectsize/inst/doc/effectsize_API.Rmd | 21 - effectsize-0.7.0.5/effectsize/inst/doc/effectsize_API.html | 36 - effectsize-0.7.0.5/effectsize/inst/doc/from_test_statistics.html | 32 - effectsize-0.7.0.5/effectsize/inst/doc/interpret.html | 33 - effectsize-0.7.0.5/effectsize/inst/doc/simple_htests.R | 26 - effectsize-0.7.0.5/effectsize/inst/doc/simple_htests.Rmd | 26 - effectsize-0.7.0.5/effectsize/inst/doc/simple_htests.html | 131 +++--- effectsize-0.7.0.5/effectsize/man/effectsize.Rd | 7 effectsize-0.7.0.5/effectsize/man/effectsize_CIs.Rd | 86 +--- effectsize-0.7.0.5/effectsize/man/equivalence_test.effectsize_table.Rd | 6 effectsize-0.7.0.5/effectsize/man/eta_squared.Rd | 40 +- effectsize-0.7.0.5/effectsize/man/interpret.Rd | 2 effectsize-0.7.0.5/effectsize/man/interpret_bf.Rd | 5 effectsize-0.7.0.5/effectsize/man/interpret_gfi.Rd | 6 effectsize-0.7.0.5/effectsize/man/interpret_icc.Rd | 2 effectsize-0.7.0.5/effectsize/man/interpret_pd.Rd | 2 effectsize-0.7.0.5/effectsize/man/oddsratio_to_riskratio.Rd | 6 effectsize-0.7.0.5/effectsize/man/phi.Rd | 50 +- effectsize-0.7.0.5/effectsize/man/rank_biserial.Rd | 22 - effectsize-0.7.0.5/effectsize/tests/testthat/test-convert_between.R | 26 - effectsize-0.7.0.5/effectsize/tests/testthat/test-effectsize.R | 82 ++-- effectsize-0.7.0.5/effectsize/tests/testthat/test-eta_squared.R | 162 ++++---- effectsize-0.7.0.5/effectsize/tests/testthat/test-eta_squared_posterior.R | 8 effectsize-0.7.0.5/effectsize/tests/testthat/test-helpers.R | 34 + effectsize-0.7.0.5/effectsize/tests/testthat/test-interpret.R | 2 effectsize-0.7.0.5/effectsize/tests/testthat/test-plot.R | 2 effectsize-0.7.0.5/effectsize/tests/testthat/test-printing.R | 6 effectsize-0.7.0.5/effectsize/tests/testthat/test-rankES.R | 64 ++- effectsize-0.7.0.5/effectsize/tests/testthat/test-standardized_differences.R | 13 effectsize-0.7.0.5/effectsize/tests/testthat/test-xtab.R | 3 effectsize-0.7.0.5/effectsize/vignettes/anovaES.Rmd | 13 effectsize-0.7.0.5/effectsize/vignettes/effectsize.Rmd | 24 - effectsize-0.7.0.5/effectsize/vignettes/effectsize_API.Rmd | 21 - effectsize-0.7.0.5/effectsize/vignettes/simple_htests.Rmd | 26 - effectsize-0.7.0/effectsize/inst/WORDLIST |only effectsize-0.7.0/effectsize/tests/spelling.R |only 84 files changed, 1331 insertions(+), 1056 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.31 dated 2022-05-10 and 0.32 dated 2022-08-10
DESCRIPTION | 10 ++++---- MD5 | 29 ++++++++++++----------- NAMESPACE | 2 + NEWS.md | 12 +++++++++ R/command.R | 4 --- R/image.R | 52 +++++++++++++++++++++++++++++++++++++++---- R/packages.R | 2 - R/paths.R | 19 ++++++++++++--- build/vignette.rds |binary inst/doc/xfun.html | 12 ++++----- man/Rscript_call.Rd | 3 -- man/cache_rds.Rd | 3 +- man/optipng.Rd | 6 ---- man/shrink_images.Rd |only man/tinify.Rd | 15 +++++++++--- tests/test-cran/test-paths.R | 3 ++ 16 files changed, 124 insertions(+), 48 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.2.1 dated 2022-07-19 and 1.2.2 dated 2022-08-10
DESCRIPTION | 8 MD5 | 34 - NEWS.md | 13 R/00_global_variables.R | 20 R/tidy_distribution_summary_tbl.R | 168 ++--- R/util-distribution-comparison.R | 650 +++++++++++--------- README.md | 24 inst/doc/getting-started.html | 40 - man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/tidy_distribution_comparison.Rd | 32 man/tidy_distribution_summary_tbl.Rd | 2 18 files changed, 556 insertions(+), 435 deletions(-)
Title: Statistical Inference in High Dimensional Regression
Description: Inference procedures in the high-dimensional setting for
(1) linear functionals in generalized linear regression ('Cai et al.' (2019) <arXiv:1904.12891>, 'Guo et al.' (2020) <arXiv:2012.07133>, 'Cai et al.' (2021)),
(2) individual treatment effects in generalized linear regression,
(3) quadratic functionals in linear regression ('Guo et al.' (2019) <arXiv:1909.01503>).
Author: Prabrisha Rakshit, Zhenyu Wang, Zijian Guo, Tony Cai
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>
Diff between SIHR versions 1.0.0 dated 2022-07-25 and 1.0.1 dated 2022-08-10
DESCRIPTION | 8 +- MD5 | 18 ++--- R/ITE.R | 14 ++-- R/LF.R | 19 +++-- R/QF.R | 18 ++--- R/check.R | 31 ++++++++- README.md | 194 ++++++++++++++++++++++++++++++++++++++++++++---------------- man/ITE.Rd | 10 ++- man/LF.Rd | 7 +- man/QF.Rd | 3 10 files changed, 228 insertions(+), 94 deletions(-)
Title: Path Diagrams and Visual Analysis of Various SEM Packages'
Output
Description: Path diagrams and visual analysis of various SEM packages' output.
Author: Sacha Epskamp [aut, cre],
Simon Stuber [ctb],
Jason Nak [ctb],
Myrthe Veenman [ctb],
Terrence D. Jorgensen [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between semPlot versions 1.1.5 dated 2022-03-08 and 1.1.6 dated 2022-08-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ man/modelMatrices.Rd | 2 +- man/semMatrixAlgebra.Rd | 2 +- man/semPaths.Rd | 4 ++-- 6 files changed, 15 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-08 1.2-22
2020-09-22 1.2-21.1
2018-11-27 1.2-20
2014-05-31 1.2-19
2013-10-31 1.2-18
2013-04-19 1.2-16
2013-04-18 1.2-15
2012-11-20 1.2-14
2011-05-12 1.2-12
2010-04-12 1.2-11
2009-01-26 1.2-10
2008-09-11 1.2-9
2008-09-08 1.2-8
2007-09-30 1.2-6
2006-04-05 1.2-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-20 0.1.3
2021-01-05 0.1.2
2020-08-26 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-21 0.1-5
2013-03-05 0.1-4
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.26.1 dated 2022-06-13 and 1.27.0 dated 2022-08-10
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-08 0.1.2
2021-11-03 0.1.1
2021-10-09 0.1.0
2021-10-03 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-04 1.2.3
2022-03-27 1.2.1
2022-03-21 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-08 1.0.0