Title: Different Tensor Factorization (Decomposition) Techniques for
RDF Tensors (Three-Mode-Tensors)
Description: Different Tensor Factorization techniques suitable for RDF Tensors.
RDF Tensors are three-mode-tensors, binary tensors and usually very sparse.
Currently implemented methods are
'RESCAL' Maximilian Nickel, Volker Tresp, and Hans-Peter Kriegel (2012) <doi:10.1145/2187836.2187874>,
'NMU' Daniel D. Lee and H. Sebastian Seung (1999) <doi:10.1038/44565>,
'ALS', Alternating Least Squares
'parCube' Papalexakis, Evangelos, C. Faloutsos, and N. Sidiropoulos (2012) <doi:10.1007/978-3-642-33460-3_39>,
'CP_APR' C. Chi and T. G. Kolda (2012) <doi:10.1137/110859063>.
The code is mostly converted from MATLAB and Python implementations of these methods.
The package also contains functions to get Boolean (Binary) transformation of the real-number-decompositions.
These methods also are for general tensors, so with few modifications they can be applied for other types of tensor.
Author: Abdelmoneim Amer Desouki
Maintainer: Abdelmoneim Amer Desouki <desouki@hhu.de>
Diff between RDFTensor versions 1.2 dated 2020-05-31 and 1.3 dated 2021-01-13
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/RDFTensor-Demo.html | 22 +++++++++++----------- man/RescalReconstructBack.Rd | 3 ++- man/inv_rescal_sf_prd_chnkgrp.Rd | 3 ++- man/recon_1prd_topn_par.Rd | 3 ++- man/scRescal.Rd | 3 ++- 10 files changed, 43 insertions(+), 31 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<https://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the 'GBIF'
tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 3.4.2 dated 2021-01-06 and 3.5.0 dated 2021-01-13
DESCRIPTION | 10 +- LICENSE | 2 MD5 | 40 ++++---- NAMESPACE | 4 NEWS.md | 13 ++ R/bbox.R | 3 R/check_wkt.r | 6 - R/download_predicate_dsl.R | 31 +++++- R/gbif_citation.R | 4 R/geometry_utils.R | 48 +++++----- R/occ_download_meta.R | 6 + R/rgbif-package.r | 2 man/check_wkt.Rd | 2 man/download_predicate_dsl.Rd | 11 +- man/gbif_citation.Rd | 4 man/occ_data.Rd | 2 man/occ_search.Rd | 2 tests/testthat/test-occ_data.R | 144 ++++++++++++++++--------------- tests/testthat/test-occ_search.r | 32 ++++-- tests/testthat/test-predicate_builders.R | 20 ++++ tests/testthat/test-wkt_parse.R | 6 - 21 files changed, 239 insertions(+), 153 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureStor versions 3.3.0 dated 2020-10-12 and 3.4.0 dated 2021-01-13
DESCRIPTION | 8 - MD5 | 26 ++- NAMESPACE | 10 + NEWS.md | 12 + R/transfer_format_utils.R |only README.md | 19 ++ inst/doc/intro.html | 230 +++++++++++++++++---------------- inst/doc/intro.rmd | 19 ++ man/delete_storage_account.Rd | 88 ++++++------ man/get_storage_account.Rd | 102 +++++++------- man/lease.Rd | 94 ++++++------- man/properties.Rd | 132 +++++++++--------- man/storage_save.Rd |only man/storage_write.Rd |only tests/testthat/test14_format_helpers.R |only vignettes/intro.rmd | 19 ++ 16 files changed, 423 insertions(+), 336 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 3.0.4 dated 2019-06-27 and 3.1.4 dated 2021-01-13
rfishbase-3.0.4/rfishbase/R/taxonomy.R |only rfishbase-3.0.4/rfishbase/data/datalist |only rfishbase-3.0.4/rfishbase/inst/doc/tutorial.R |only rfishbase-3.0.4/rfishbase/inst/doc/tutorial.Rmd |only rfishbase-3.0.4/rfishbase/inst/doc/tutorial.html |only rfishbase-3.0.4/rfishbase/man/clear_cache.Rd |only rfishbase-3.0.4/rfishbase/man/taxonomy.Rd |only rfishbase-3.0.4/rfishbase/vignettes/tutorial.Rmd |only rfishbase-3.1.4/rfishbase/DESCRIPTION | 40 - rfishbase-3.1.4/rfishbase/MD5 | 172 ++-- rfishbase-3.1.4/rfishbase/NAMESPACE | 15 rfishbase-3.1.4/rfishbase/NEWS.md | 12 rfishbase-3.1.4/rfishbase/R/00-endpoint.R | 106 ++- rfishbase-3.1.4/rfishbase/R/common_names.R | 50 - rfishbase-3.1.4/rfishbase/R/cran-hacks.R |only rfishbase-3.1.4/rfishbase/R/distribution.R | 111 ++- rfishbase-3.1.4/rfishbase/R/docs.R | 2 rfishbase-3.1.4/rfishbase/R/fb_tbl.R | 94 +- rfishbase-3.1.4/rfishbase/R/fishbase.R | 4 rfishbase-3.1.4/rfishbase/R/load_taxa.R | 170 +--- rfishbase-3.1.4/rfishbase/R/local_db.R |only rfishbase-3.1.4/rfishbase/R/refs.R | 8 rfishbase-3.1.4/rfishbase/R/species.R | 18 rfishbase-3.1.4/rfishbase/R/species_list.R | 24 rfishbase-3.1.4/rfishbase/R/species_names.R | 7 rfishbase-3.1.4/rfishbase/R/synonyms.R | 108 +-- rfishbase-3.1.4/rfishbase/R/trophic_ecology.R | 19 rfishbase-3.1.4/rfishbase/R/zzz.R | 2 rfishbase-3.1.4/rfishbase/README.md | 349 ++++------ rfishbase-3.1.4/rfishbase/build/vignette.rds |binary rfishbase-3.1.4/rfishbase/inst/CITATION | 2 rfishbase-3.1.4/rfishbase/inst/WORDLIST |only rfishbase-3.1.4/rfishbase/inst/doc/rfishbase.Rmd |only rfishbase-3.1.4/rfishbase/inst/doc/rfishbase.html |only rfishbase-3.1.4/rfishbase/man/brains.Rd | 13 rfishbase-3.1.4/rfishbase/man/c_code.Rd | 12 rfishbase-3.1.4/rfishbase/man/common_names.Rd | 22 rfishbase-3.1.4/rfishbase/man/common_to_sci.Rd | 14 rfishbase-3.1.4/rfishbase/man/country.Rd | 13 rfishbase-3.1.4/rfishbase/man/countrysub.Rd | 13 rfishbase-3.1.4/rfishbase/man/countrysubref.Rd | 13 rfishbase-3.1.4/rfishbase/man/default_db.Rd |only rfishbase-3.1.4/rfishbase/man/diet.Rd | 13 rfishbase-3.1.4/rfishbase/man/diet_items.Rd | 13 rfishbase-3.1.4/rfishbase/man/distribution.Rd | 13 rfishbase-3.1.4/rfishbase/man/docs.Rd | 2 rfishbase-3.1.4/rfishbase/man/ecology.Rd | 15 rfishbase-3.1.4/rfishbase/man/ecosystem.Rd | 13 rfishbase-3.1.4/rfishbase/man/estimate.Rd | 13 rfishbase-3.1.4/rfishbase/man/faoareas.Rd | 13 rfishbase-3.1.4/rfishbase/man/fecundity.Rd | 13 rfishbase-3.1.4/rfishbase/man/fishbase.Rd | 3 rfishbase-3.1.4/rfishbase/man/fooditems.Rd | 13 rfishbase-3.1.4/rfishbase/man/genetics.Rd | 13 rfishbase-3.1.4/rfishbase/man/introductions.Rd | 13 rfishbase-3.1.4/rfishbase/man/larvae.Rd | 13 rfishbase-3.1.4/rfishbase/man/length_freq.Rd | 13 rfishbase-3.1.4/rfishbase/man/length_length.Rd | 13 rfishbase-3.1.4/rfishbase/man/length_weight.Rd | 13 rfishbase-3.1.4/rfishbase/man/load_taxa.Rd | 15 rfishbase-3.1.4/rfishbase/man/maturity.Rd | 13 rfishbase-3.1.4/rfishbase/man/morphology.Rd | 13 rfishbase-3.1.4/rfishbase/man/morphometrics.Rd | 13 rfishbase-3.1.4/rfishbase/man/oxygen.Rd | 13 rfishbase-3.1.4/rfishbase/man/popchar.Rd | 13 rfishbase-3.1.4/rfishbase/man/popgrowth.Rd | 13 rfishbase-3.1.4/rfishbase/man/popqb.Rd | 13 rfishbase-3.1.4/rfishbase/man/predators.Rd | 13 rfishbase-3.1.4/rfishbase/man/ration.Rd | 13 rfishbase-3.1.4/rfishbase/man/reexports.Rd | 2 rfishbase-3.1.4/rfishbase/man/references.Rd | 13 rfishbase-3.1.4/rfishbase/man/reproduction.Rd | 13 rfishbase-3.1.4/rfishbase/man/rfishbase-package.Rd | 4 rfishbase-3.1.4/rfishbase/man/sealifebase.Rd | 3 rfishbase-3.1.4/rfishbase/man/spawning.Rd | 13 rfishbase-3.1.4/rfishbase/man/species.Rd | 13 rfishbase-3.1.4/rfishbase/man/species_by_ecosystem.Rd |only rfishbase-3.1.4/rfishbase/man/species_fields.Rd | 3 rfishbase-3.1.4/rfishbase/man/species_list.Rd | 16 rfishbase-3.1.4/rfishbase/man/species_names.Rd | 11 rfishbase-3.1.4/rfishbase/man/speed.Rd | 13 rfishbase-3.1.4/rfishbase/man/stocks.Rd | 13 rfishbase-3.1.4/rfishbase/man/swimming.Rd | 13 rfishbase-3.1.4/rfishbase/man/synonyms.Rd | 24 rfishbase-3.1.4/rfishbase/man/validate_names.Rd | 14 rfishbase-3.1.4/rfishbase/tests/spelling.R |only rfishbase-3.1.4/rfishbase/tests/testthat/setup-test_db.R |only rfishbase-3.1.4/rfishbase/tests/testthat/test-db_create.R |only rfishbase-3.1.4/rfishbase/tests/testthat/test_distribution.R | 9 rfishbase-3.1.4/rfishbase/tests/testthat/test_endpoint.R | 15 rfishbase-3.1.4/rfishbase/tests/testthat/test_list_fields.R | 1 rfishbase-3.1.4/rfishbase/tests/testthat/test_load_taxa.R | 13 rfishbase-3.1.4/rfishbase/tests/testthat/test_species_list.R | 5 rfishbase-3.1.4/rfishbase/tests/testthat/test_synonyms.R | 14 rfishbase-3.1.4/rfishbase/tests/testthat/test_trophic_ecology.R | 4 rfishbase-3.1.4/rfishbase/vignettes/rfishbase.Rmd |only rfishbase-3.1.4/rfishbase/vignettes/rfishbase.Rmd.og |only 97 files changed, 1266 insertions(+), 710 deletions(-)
Title: Shiny Apps on Crunch
Description: To facilitate building custom dashboards on the Crunch data
platform <https://crunch.io/>, the 'crunchy' package provides tools for
working with 'shiny'. These tools include utilities to manage authentication
and authorization automatically and custom stylesheets to help match the
look and feel of the Crunch web application. The package also includes
several gadgets for use in 'RStudio'.
Author: Greg Freedman Ellis [aut, cre],
Neal Richardson [aut],
Jonathan Keane [aut],
Gordon Shotwell [aut],
Mike Malecki [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crunchy versions 0.3.2 dated 2020-07-20 and 0.3.3 dated 2021-01-13
DESCRIPTION | 6 MD5 | 6 inst/doc/flexdashboards.html | 350 +++++++++--------------------------------- tests/testthat/test-gadgets.R | 1 4 files changed, 83 insertions(+), 280 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 1.1.0 dated 2020-09-04 and 1.1.1 dated 2021-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/visvow.R | 13 ++++++++++++- build/partial.rdb |binary build/vignette.rds |binary 5 files changed, 19 insertions(+), 8 deletions(-)
Title: Joint Analysis and Imputation of Incomplete Data
Description: Joint analysis and imputation of incomplete data in the Bayesian
framework, using (generalized) linear (mixed) models and extensions there of,
survival models, or joint models for longitudinal and survival data.
Incomplete covariates, if present, are automatically imputed.
The package performs some preprocessing of the data and creates a 'JAGS'
model, which will then automatically be passed to 'JAGS'
<http://mcmc-jags.sourceforge.net/> with the help of
the package 'rjags'.
Author: Nicole S. Erler [aut, cre] (<https://orcid.org/0000-0002-9370-6832>)
Maintainer: Nicole S. Erler <n.erler@erasmusmc.nl>
Diff between JointAI versions 1.0.1 dated 2020-11-16 and 1.0.2 dated 2021-01-13
JointAI-1.0.1/JointAI/inst/doc/AfterFitting.R |only JointAI-1.0.1/JointAI/inst/doc/ModelSpecification.R |only JointAI-1.0.1/JointAI/inst/doc/SelectingParameters.R |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models.data_list..rds |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models.jagsmodel..txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.GR_crit.multiva.txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.MC_error..txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.coef..txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.confint..txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.function.x.coef.txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.print..txt |only JointAI-1.0.1/JointAI/tests/testthat/testout/CLMM_Models_lapply.models0.summary..txt |only 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Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of
isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>),
SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
and fair-cut forest (Cortes (2019) <arXiv:1911.06646>),
for isolation-based outlier detection, clustered outlier detection, distance or similarity
approximation (Cortes (2019) <arXiv:1910.12362>),
and imputation of missing values (Cortes (2019) <arXiv:1911.06646>),
based on random or guided decision tree splitting. Provides simple heuristics for fitting the model to
categorical columns and handling missing data, and offers options for varying between random and guided
splits, and for using different splitting criteria.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between isotree versions 0.1.24 dated 2020-12-10 and 0.1.28 dated 2021-01-13
DESCRIPTION | 8 - LICENSE | 2 MD5 | 39 ++++----- NAMESPACE | 4 R/RcppExports.R | 8 + R/isoforest.R | 85 ++++++++++++++++---- man/add.isolation.tree.Rd | 3 man/append.trees.Rd | 3 man/deepcopy.isotree.Rd |only man/isolation.forest.Rd | 14 --- man/print.isolation_forest.Rd | 2 man/unpack.isolation.forest.Rd | 3 src/RcppExports.cpp | 36 ++++---- src/Rwrapper.cpp | 109 +++++++++++++++++++++----- src/dist.cpp | 26 ++++++ src/extended.cpp | 1 src/fit_model.cpp | 47 ++++------- src/isoforest.cpp | 1 src/isotree.h | 37 ++++++++- src/serialize.cpp | 166 +++++++++++++++++++++++++++++++++++++---- src/utils.cpp | 63 +++++++++++++++ 21 files changed, 513 insertions(+), 144 deletions(-)
Title: Data Import, Cleaning, and Conversions for Swimming Results
Description: The goal for of the 'SwimmeR' package is to provide means of acquiring, and then analyzing, data from swimming (and diving) competitions. To that end 'SwimmeR' allows results to be read in from .html sources, like 'Hy-Tek' real time results pages, '.pdf' files, 'ISL' results, and (on a development basis) '.hy3' files. Once read in, 'SwimmeR' can convert swimming times (performances) between the computationally useful format of seconds reported to the '100ths' place (e.g. 95.37), and the conventional reporting format (1:35.37) used in the swimming community. 'SwimmeR' can also score meets in a variety of formats with user defined point values, convert times between courses ('LCM', 'SCM', 'SCY') and draw single elimination brackets, as well as providing a suite of tools for working cleaning swimming data. This is a developmental package, not yet mature.
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>),
Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>
Diff between SwimmeR versions 0.6.0 dated 2020-11-22 and 0.7.2 dated 2021-01-13
SwimmeR-0.6.0/SwimmeR/R/parse_hy3.R |only SwimmeR-0.6.0/SwimmeR/inst/extdata/Meet-Results-2019-CIF-SWIMMING-AND-DIVING-CHAMPIONSHIPS-10May2019-001.hy3 |only SwimmeR-0.6.0/SwimmeR/man/parse_hy3.Rd |only SwimmeR-0.7.2/SwimmeR/DESCRIPTION | 8 SwimmeR-0.7.2/SwimmeR/LICENSE | 4 SwimmeR-0.7.2/SwimmeR/MD5 | 204 SwimmeR-0.7.2/SwimmeR/NAMESPACE | 158 SwimmeR-0.7.2/SwimmeR/NEWS.md | 129 SwimmeR-0.7.2/SwimmeR/R/Course_Convert.R | 182 SwimmeR-0.7.2/SwimmeR/R/Course_Convert_DF.R | 208 SwimmeR-0.7.2/SwimmeR/R/King200Breast.R | 28 SwimmeR-0.7.2/SwimmeR/R/Read_Results.R | 126 SwimmeR-0.7.2/SwimmeR/R/SwimR.R | 12 SwimmeR-0.7.2/SwimmeR/R/Swim_Parse.R | 2231 +++------- SwimmeR-0.7.2/SwimmeR/R/add_row_numbers.R | 36 SwimmeR-0.7.2/SwimmeR/R/collect_relay_swimmers.R | 245 - SwimmeR-0.7.2/SwimmeR/R/collect_relay_swimmers_2.R |only SwimmeR-0.7.2/SwimmeR/R/discard_errors.R | 44 SwimmeR-0.7.2/SwimmeR/R/dive_place.R | 76 SwimmeR-0.7.2/SwimmeR/R/draw_bracket.R | 632 +- SwimmeR-0.7.2/SwimmeR/R/event_parse.R | 135 SwimmeR-0.7.2/SwimmeR/R/event_parse_ISL.R | 124 SwimmeR-0.7.2/SwimmeR/R/fill_down.R | 40 SwimmeR-0.7.2/SwimmeR/R/fill_left.R | 42 SwimmeR-0.7.2/SwimmeR/R/fold.R | 60 SwimmeR-0.7.2/SwimmeR/R/format_results.R |only SwimmeR-0.7.2/SwimmeR/R/get_mode.R | 92 SwimmeR-0.7.2/SwimmeR/R/globals.R | 158 SwimmeR-0.7.2/SwimmeR/R/hy3_parse.R |only SwimmeR-0.7.2/SwimmeR/R/hy3_places.R | 154 SwimmeR-0.7.2/SwimmeR/R/hy3_times.R | 160 SwimmeR-0.7.2/SwimmeR/R/interleave_results.R | 72 SwimmeR-0.7.2/SwimmeR/R/is_link_broken.R | 46 SwimmeR-0.7.2/SwimmeR/R/lines_sort.R | 108 SwimmeR-0.7.2/SwimmeR/R/list_transform.R | 38 SwimmeR-0.7.2/SwimmeR/R/mmss_format.R | 52 SwimmeR-0.7.2/SwimmeR/R/not_in.R | 48 SwimmeR-0.7.2/SwimmeR/R/relay_aggregate.R | 16 SwimmeR-0.7.2/SwimmeR/R/results_score.R | 752 +-- SwimmeR-0.7.2/SwimmeR/R/samms_parse.R |only SwimmeR-0.7.2/SwimmeR/R/sec_format.R | 54 SwimmeR-0.7.2/SwimmeR/R/sec_format_helper.R | 57 SwimmeR-0.7.2/SwimmeR/R/splits_parse.R | 473 +- SwimmeR-0.7.2/SwimmeR/R/splits_parse_ISL.R | 376 - SwimmeR-0.7.2/SwimmeR/R/splits_reform.R | 72 SwimmeR-0.7.2/SwimmeR/R/swim_parse_ISL.R | 794 +-- SwimmeR-0.7.2/SwimmeR/R/swim_parse_old.R |only SwimmeR-0.7.2/SwimmeR/R/swim_place.R | 64 SwimmeR-0.7.2/SwimmeR/R/tie_rescore.R | 82 SwimmeR-0.7.2/SwimmeR/R/utils-pipe.R | 22 SwimmeR-0.7.2/SwimmeR/README.md | 282 - SwimmeR-0.7.2/SwimmeR/build/vignette.rds |binary SwimmeR-0.7.2/SwimmeR/inst/CITATION | 30 SwimmeR-0.7.2/SwimmeR/inst/doc/SwimmeR.R | 271 - SwimmeR-0.7.2/SwimmeR/inst/doc/SwimmeR.Rmd | 557 +- SwimmeR-0.7.2/SwimmeR/inst/doc/SwimmeR.html | 1361 +++--- SwimmeR-0.7.2/SwimmeR/inst/extdata/df_standard.rds |binary SwimmeR-0.7.2/SwimmeR/man/King200Breast.Rd | 38 SwimmeR-0.7.2/SwimmeR/man/Read_Results.Rd | 64 SwimmeR-0.7.2/SwimmeR/man/Swim_Parse.Rd | 140 SwimmeR-0.7.2/SwimmeR/man/SwimmeR.Rd | 26 SwimmeR-0.7.2/SwimmeR/man/add_row_numbers.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/collect_relay_swimmers.Rd | 50 SwimmeR-0.7.2/SwimmeR/man/collect_relay_swimmers_2.Rd |only SwimmeR-0.7.2/SwimmeR/man/course_convert.Rd | 76 SwimmeR-0.7.2/SwimmeR/man/course_convert_DF.Rd | 92 SwimmeR-0.7.2/SwimmeR/man/discard_errors.Rd | 44 SwimmeR-0.7.2/SwimmeR/man/dive_place.Rd | 50 SwimmeR-0.7.2/SwimmeR/man/draw_bracket.Rd | 124 SwimmeR-0.7.2/SwimmeR/man/event_parse.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/event_parse_ISL.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/fill_down.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/fill_left.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/fold.Rd | 52 SwimmeR-0.7.2/SwimmeR/man/format_results.Rd |only SwimmeR-0.7.2/SwimmeR/man/get_mode.Rd | 82 SwimmeR-0.7.2/SwimmeR/man/grapes-notin-grapes.Rd | 60 SwimmeR-0.7.2/SwimmeR/man/hy3_parse.Rd |only SwimmeR-0.7.2/SwimmeR/man/hy3_places.Rd | 56 SwimmeR-0.7.2/SwimmeR/man/hy3_times.Rd | 50 SwimmeR-0.7.2/SwimmeR/man/interleave_results.Rd | 54 SwimmeR-0.7.2/SwimmeR/man/is_link_broken.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/lines_sort.Rd | 50 SwimmeR-0.7.2/SwimmeR/man/list_transform.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/mmss_format.Rd | 60 SwimmeR-0.7.2/SwimmeR/man/pipe.Rd | 24 SwimmeR-0.7.2/SwimmeR/man/results_score.Rd | 174 SwimmeR-0.7.2/SwimmeR/man/samms_parse.Rd |only SwimmeR-0.7.2/SwimmeR/man/sec_format.Rd | 62 SwimmeR-0.7.2/SwimmeR/man/sec_format_helper.Rd | 34 SwimmeR-0.7.2/SwimmeR/man/splits_parse.Rd | 50 SwimmeR-0.7.2/SwimmeR/man/splits_parse_ISL.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/splits_reform.Rd | 46 SwimmeR-0.7.2/SwimmeR/man/swim_parse_ISL.Rd | 78 SwimmeR-0.7.2/SwimmeR/man/swim_parse_old.Rd |only SwimmeR-0.7.2/SwimmeR/man/swim_place.Rd | 50 SwimmeR-0.7.2/SwimmeR/man/tie_rescore.Rd | 54 SwimmeR-0.7.2/SwimmeR/tests/testthat.R | 8 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-Course_Convert.R | 6 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-Course_Convert_DF.R | 22 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-ISL.R | 122 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-Read_Results_works.R | 44 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-Swim_Parse_Old_works.R |only SwimmeR-0.7.2/SwimmeR/tests/testthat/test-Swim_Parse_works.R | 396 + SwimmeR-0.7.2/SwimmeR/tests/testthat/test-get_mode.R | 20 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-hy3_parse_works.R | 20 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-relay_swimmers_works.R |only SwimmeR-0.7.2/SwimmeR/tests/testthat/test-results_score_works.R | 176 SwimmeR-0.7.2/SwimmeR/tests/testthat/test-samms_works.R |only SwimmeR-0.7.2/SwimmeR/tests/testthat/test-splits.R | 190 SwimmeR-0.7.2/SwimmeR/vignettes/SwimmeR.Rmd | 557 +- 111 files changed, 7015 insertions(+), 7569 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Metapackage for implementing a variety of event-based models, with
a focus on spatially explicit models. These include raster-based,
event-based, and agent-based models. The core simulation components
(provided by 'SpaDES.core') are built upon a discrete event simulation (DES;
see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>)
framework that facilitates modularity, and easily enables the user to
include additional functionality by running user-built simulation modules
(see also 'SpaDES.tools'). Included are numerous tools to visualize rasters
and other maps (via 'quickPlot'), and caching methods for reproducible
simulations (via 'reproducible'). Tools for running simulation experiments are
provided by 'SpaDES.experiment'. Additional functionality is provided by
the 'SpaDES.addins' and 'SpaDES.shiny' packages.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>),
Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>),
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES versions 2.0.4 dated 2019-09-17 and 2.0.6 dated 2021-01-13
SpaDES-2.0.4/SpaDES/.aspell |only SpaDES-2.0.6/SpaDES/DESCRIPTION | 23 +- SpaDES-2.0.6/SpaDES/MD5 | 26 +- SpaDES-2.0.6/SpaDES/NEWS.md | 12 + SpaDES-2.0.6/SpaDES/R/spades-package.R | 12 - SpaDES-2.0.6/SpaDES/R/zzz.R | 10 SpaDES-2.0.6/SpaDES/README.md | 79 +++++-- SpaDES-2.0.6/SpaDES/build/vignette.rds |binary SpaDES-2.0.6/SpaDES/inst/WORDLIST | 52 ++-- SpaDES-2.0.6/SpaDES/inst/doc/getting-started.R | 2 SpaDES-2.0.6/SpaDES/inst/doc/getting-started.Rmd | 2 SpaDES-2.0.6/SpaDES/inst/doc/getting-started.html | 233 ++-------------------- SpaDES-2.0.6/SpaDES/man/SpaDES-package.Rd | 14 - SpaDES-2.0.6/SpaDES/man/pkgEnv.Rd | 4 SpaDES-2.0.6/SpaDES/vignettes/getting-started.Rmd | 2 15 files changed, 176 insertions(+), 295 deletions(-)
Title: Mapping Fisheries Data and Spatial Analysis Tools
Description: This software has evolved from fisheries research conducted at the
Pacific Biological Station (PBS) in 'Nanaimo', British Columbia, Canada. It
extends the R language to include two-dimensional plotting features similar
to those commonly available in a Geographic Information System (GIS).
Embedded C code speeds algorithms from computational geometry, such as
finding polygons that contain specified point events or converting between
longitude-latitude and Universal Transverse Mercator (UTM) coordinates.
Additionally, we include 'C++' code developed by Angus Johnson for the
'Clipper' library, data for a global shoreline, and other data sets in the
public domain. Under the user's R library directory '.libPaths()',
specifically in './PBSmapping/doc', a complete user's guide is offered and
should be consulted to use package functions effectively.
Author: Jon T. Schnute [aut],
Nicholas Boers [aut],
Rowan Haigh [aut, cre],
Alex Couture-Beil [ctb],
Denis Chabot [ctb],
Chris Grandin [ctb],
Angus Johnson [ctb],
Paul Wessel [ctb],
Franklin Antonio [ctb],
Nicholas J. Lewin-Koh [ctb],
Roger Bivand [ctb]
Maintainer: Rowan Haigh <rowan.haigh@dfo-mpo.gc.ca>
Diff between PBSmapping versions 2.72.1 dated 2019-03-15 and 2.73.0 dated 2021-01-13
DESCRIPTION | 10 - MD5 | 23 ++-- R/PBSmapping.r | 2 R/extraFuns.r | 262 +++++++++++++++++++++++++++++++++++++++---------- inst/doc/ChangeLog.txt | 7 + inst/doc/Links.html | 22 ++-- man/RGB2RYB.Rd |only man/addBubbles.Rd | 71 +++++++------ man/addCompass.Rd | 38 ++++--- man/bcBathymetry.Rd | 43 ++++---- man/importGSHHS.Rd | 40 ++++--- man/joinPolys.Rd | 117 +++++++++++---------- man/makeTopography.Rd | 35 +++--- 13 files changed, 437 insertions(+), 233 deletions(-)
Title: Tools to Read and Manipulate Fisheries Data
Description: Set of tools to read and manipulate various data formats for fisheries. Mainly
catered towards scientific trawl survey sampling ('biotic') data, acoustic
trawl data, and commercial fishing catch ('landings') data. Among the
supported data formats are the data products from the Norwegian Institute
Marine Research ('IMR') and the International Council for the Exploration of
the Sea (ICES).
Author: Ibrahim Umar [cre, aut],
Sindre Vatnehol [aut],
Arne Johannes Holmin [aut],
Edvin Fuglebakk [aut],
Espen Johnsen [aut],
Norwegian Institute of Marine Research [cph, fnd]
Maintainer: Ibrahim Umar <ibrahim.umar@hi.no>
Diff between RstoxData versions 1.0.17 dated 2020-11-23 and 1.0.23 dated 2021-01-13
RstoxData-1.0.17/RstoxData/man/WriteICESAcoustic.Rd |only RstoxData-1.0.17/RstoxData/man/WriteICESBiotic.Rd |only RstoxData-1.0.17/RstoxData/man/WriteICESDatras.Rd |only RstoxData-1.0.23/RstoxData/DESCRIPTION | 13 RstoxData-1.0.23/RstoxData/MD5 | 75 RstoxData-1.0.23/RstoxData/NAMESPACE | 25 RstoxData-1.0.23/RstoxData/NEWS.md | 19 RstoxData-1.0.23/RstoxData/R/DefineAndUpdateVariables.R | 57 RstoxData-1.0.23/RstoxData/R/Definitions.R | 19 RstoxData-1.0.23/RstoxData/R/RcppExports.R | 4 RstoxData-1.0.23/RstoxData/R/Read.R | 187 + RstoxData-1.0.23/RstoxData/R/RstoxData-package.R | 51 RstoxData-1.0.23/RstoxData/R/StoxAcoustic.R | 103 RstoxData-1.0.23/RstoxData/R/StoxBiotic.R | 74 RstoxData-1.0.23/RstoxData/R/StoxExport.R | 1669 +++++----- RstoxData-1.0.23/RstoxData/R/Utilities.R | 43 RstoxData-1.0.23/RstoxData/R/backwardCompatibility.R |only RstoxData-1.0.23/RstoxData/R/data.R | 99 RstoxData-1.0.23/RstoxData/R/fdirParsing.R | 317 - RstoxData-1.0.23/RstoxData/R/icesParsing.R |only RstoxData-1.0.23/RstoxData/R/stoxFunctionAttributes.R | 72 RstoxData-1.0.23/RstoxData/inst/extdata/functionArguments.rds |binary RstoxData-1.0.23/RstoxData/inst/testresources/intercatch_example.csv |only RstoxData-1.0.23/RstoxData/man/AddToStoxBiotic.Rd | 9 RstoxData-1.0.23/RstoxData/man/ConvertStoxBiotic.Rd | 2 RstoxData-1.0.23/RstoxData/man/ICESAcoustic.Rd |only RstoxData-1.0.23/RstoxData/man/ICESAcousticData.Rd |only RstoxData-1.0.23/RstoxData/man/ICESBiotic.Rd |only RstoxData-1.0.23/RstoxData/man/ICESBioticData.Rd |only RstoxData-1.0.23/RstoxData/man/ICESDatras.Rd |only RstoxData-1.0.23/RstoxData/man/ICESDatrasData.Rd |only RstoxData-1.0.23/RstoxData/man/ModelData.Rd | 6 RstoxData-1.0.23/RstoxData/man/ReadAcoustic.Rd | 8 RstoxData-1.0.23/RstoxData/man/ReadBiotic.Rd | 7 RstoxData-1.0.23/RstoxData/man/ReportICESAcoustic.Rd |only RstoxData-1.0.23/RstoxData/man/ReportICESAcousticData.Rd |only RstoxData-1.0.23/RstoxData/man/ReportICESBiotic.Rd |only RstoxData-1.0.23/RstoxData/man/ReportICESBioticData.Rd |only RstoxData-1.0.23/RstoxData/man/ReportICESDatras.Rd |only RstoxData-1.0.23/RstoxData/man/ReportICESDatrasData.Rd |only RstoxData-1.0.23/RstoxData/man/StoxAcoustic.Rd | 4 RstoxData-1.0.23/RstoxData/man/StoxBiotic.Rd | 4 RstoxData-1.0.23/RstoxData/man/backwardCompatibility.Rd |only RstoxData-1.0.23/RstoxData/man/parseInterCatch.Rd |only RstoxData-1.0.23/RstoxData/man/processPropertyFormats.Rd | 2 RstoxData-1.0.23/RstoxData/man/readLssFile.Rd | 2 RstoxData-1.0.23/RstoxData/man/stoxFunctionAttributes.Rd | 2 RstoxData-1.0.23/RstoxData/tests/testthat/test-StoxExport.R | 35 RstoxData-1.0.23/RstoxData/tests/testthat/test-icesParsing.R |only 49 files changed, 1735 insertions(+), 1173 deletions(-)
Title: Testing Infrastructure for Broom Model Generics
Description: Provides a number of testthat tests that can be
used to verify that tidy(), glance() and augment() methods meet
consistent specifications. This allows methods for the same generic to
be spread across multiple packages, since all of those packages can
make the same guarantees to users about returned objects.
Author: Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>),
Simon Couch [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between modeltests versions 0.1.3 dated 2020-09-11 and 0.1.4 dated 2021-01-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 6 ++++++ README.md | 22 +++++++++++----------- data/column_glossary.rda |binary man/modeltests-package.Rd | 4 ++-- 6 files changed, 29 insertions(+), 23 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between magick versions 2.5.2 dated 2020-11-10 and 2.6.0 dated 2021-01-13
DESCRIPTION | 6 MD5 | 44 - NAMESPACE | 1 NEWS | 5 R/RcppExports.R | 4 R/animation.R | 2 R/edges.R | 2 R/edit.R | 6 R/init.R | 2 R/morphology.R | 2 R/options.R | 6 inst/doc/intro.Rmd | 2 inst/doc/intro.html | 1456 ++-------------------------------------------------- man/animation.Rd | 2 man/edges.Rd | 2 man/editing.Rd | 5 man/morphology.Rd | 2 man/options.Rd | 3 src/Makevars.win | 3 src/RcppExports.cpp | 9 src/config.cc | 12 src/edit.cpp | 12 vignettes/intro.Rmd | 2 23 files changed, 165 insertions(+), 1425 deletions(-)
Title: Index Numbers in Social Sciences
Description: We provide an R tool for teaching in Social Sciences. It allows the computation of index numbers. It is a measure of the evolution of a fixed magnitude for only a product of for several products. It is very useful in Social Sciences. Among others, we obtain simple index numbers (in chain or in serie), index numbers for not only a product or weighted index numbers as the Laspeyres index (Laspeyres, 1864), the Paasche index (Paasche, 1874) or the Fisher index (Lapedes, 1978).
Author: Alejandro Saavedra-Nieves, Paula Saavedra-Nieves
Maintainer: Alejandro Saavedra-Nieves <alejandro.saavedra.nieves@gmail.com>
Diff between IndexNumber versions 1.3 dated 2021-01-07 and 1.3.1 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary man/edgeworth.index.number.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Principal Component Analysis in High-Dimensional Data
Description: In high-dimensional settings:
Estimate the number of distant spikes based on the Generalized Spiked Population (GSP) model.
Estimate the population eigenvalues, angles between the sample and population eigenvectors, correlations between the sample and population PC scores, and the asymptotic shrinkage factors.
Adjust the shrinkage bias in the predicted PC scores.
Dey, R. and Lee, S. (2019) <doi:10.1016/j.jmva.2019.02.007>.
Author: Rounak Dey, Seunggeun Lee
Maintainer: Rounak Dey <deyrnk@umich.edu>
Diff between hdpca versions 1.1.3 dated 2019-10-23 and 1.1.5 dated 2021-01-13
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/hapmap.rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Detrend Images
Description: Detrend fluorescence microscopy image series for
fluorescence fluctuation and correlation spectroscopy ('FCS' and
'FFS') analysis. This package contains functionality published in a
2016 paper <doi:10.1093/bioinformatics/btx434> but it has been
extended since then with the Robin Hood algorithm and thus contains
unpublished work.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths, cph]
(<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between detrendr versions 0.6.9 dated 2020-09-03 and 0.6.11 dated 2021-01-13
DESCRIPTION | 19 ++++++------- MD5 | 14 ++++----- NEWS.md | 12 ++++++++ inst/WORDLIST | 39 ++++++++++++++------------- inst/doc/batch-mode.html | 52 +++++++++++++++++++++++++++++++++++- inst/doc/linescan-data.html | 48 +++++++++++++++++++++++++++++++++ inst/doc/single-images.html | 54 +++++++++++++++++++++++++++++++++++--- tests/testthat/test-dir-detrend.R | 20 ++++++++++---- 8 files changed, 212 insertions(+), 46 deletions(-)
Title: Capture Hi-C Analysis Engine
Description: Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Author: Erle Holgersen [aut, cre],
Olivia Leavy [aut],
Olivia Fletcher [aut],
Frank Dudbridge [aut],
Syed Haider [aut]
Maintainer: Erle Holgersen <erle.holgersen@gmail.com>
Diff between chicane versions 0.1.2 dated 2020-07-27 and 0.1.3 dated 2021-01-13
chicane-0.1.2/chicane/inst/doc/Introduction.R |only chicane-0.1.2/chicane/inst/doc/Introduction.Rmd |only chicane-0.1.2/chicane/inst/doc/Introduction.html |only chicane-0.1.2/chicane/vignettes/Introduction.Rmd |only chicane-0.1.3/chicane/DESCRIPTION | 10 - chicane-0.1.3/chicane/MD5 | 52 +++---- chicane-0.1.3/chicane/NAMESPACE | 3 chicane-0.1.3/chicane/NEWS | 26 ++- chicane-0.1.3/chicane/R/check.model.numerical.fit.R | 1 chicane-0.1.3/chicane/R/create.locus.plot.R | 21 +-- chicane-0.1.3/chicane/R/create.modelfit.plot.R | 16 +- chicane-0.1.3/chicane/R/get.combination.count.R | 1 chicane-0.1.3/chicane/R/multiple.testing.correct.R | 6 chicane-0.1.3/chicane/R/prepare.data.R | 3 chicane-0.1.3/chicane/R/run.model.fitting.R | 23 +++ chicane-0.1.3/chicane/build/vignette.rds |binary chicane-0.1.3/chicane/inst/doc/Getting_Started.R |only chicane-0.1.3/chicane/inst/doc/Getting_Started.Rmd |only chicane-0.1.3/chicane/inst/doc/Getting_Started.html |only chicane-0.1.3/chicane/inst/doc/Visualising_Interactions.R | 16 +- chicane-0.1.3/chicane/inst/doc/Visualising_Interactions.Rmd | 20 +- chicane-0.1.3/chicane/inst/doc/Visualising_Interactions.html | 28 ++-- chicane-0.1.3/chicane/man/create.locus.plot.Rd | 9 + chicane-0.1.3/chicane/man/create.modelfit.plot.Rd | 2 chicane-0.1.3/chicane/man/multiple.testing.correct.Rd | 6 chicane-0.1.3/chicane/tests/testthat/test_chicane.R | 75 ++++------- chicane-0.1.3/chicane/tests/testthat/test_fit.model.R | 52 +++---- chicane-0.1.3/chicane/tests/testthat/test_test.enrichment.R | 2 chicane-0.1.3/chicane/vignettes/Getting_Started.Rmd |only chicane-0.1.3/chicane/vignettes/Visualising_Interactions.Rmd | 20 +- chicane-0.1.3/chicane/vignettes/bibliography.bib | 20 ++ 31 files changed, 230 insertions(+), 182 deletions(-)
Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureGraph versions 1.1.2 dated 2020-10-12 and 1.2.0 dated 2021-01-13
AzureGraph-1.1.2/AzureGraph/tests/testthat/test04_aad_v2.R |only AzureGraph-1.2.0/AzureGraph/DESCRIPTION | 12 AzureGraph-1.2.0/AzureGraph/LICENSE | 2 AzureGraph-1.2.0/AzureGraph/MD5 | 80 +++-- AzureGraph-1.2.0/AzureGraph/NAMESPACE | 11 AzureGraph-1.2.0/AzureGraph/NEWS.md | 7 AzureGraph-1.2.0/AzureGraph/R/AzureGraph.R | 2 AzureGraph-1.2.0/AzureGraph/R/az_app.r | 3 AzureGraph-1.2.0/AzureGraph/R/az_device.R | 4 AzureGraph-1.2.0/AzureGraph/R/az_dir_role.R |only AzureGraph-1.2.0/AzureGraph/R/az_group.R | 18 - AzureGraph-1.2.0/AzureGraph/R/az_object.R | 113 -------- AzureGraph-1.2.0/AzureGraph/R/az_svc_principal.R | 5 AzureGraph-1.2.0/AzureGraph/R/az_user.R | 19 - AzureGraph-1.2.0/AzureGraph/R/call_graph.R | 41 -- AzureGraph-1.2.0/AzureGraph/R/format.R | 22 + AzureGraph-1.2.0/AzureGraph/R/graph_login.R | 166 +++++++++--- AzureGraph-1.2.0/AzureGraph/R/is.R | 19 + AzureGraph-1.2.0/AzureGraph/R/ms_graph.R | 14 - AzureGraph-1.2.0/AzureGraph/R/ms_object.R |only AzureGraph-1.2.0/AzureGraph/R/utils.R |only AzureGraph-1.2.0/AzureGraph/R/zzz_class_directory.R |only AzureGraph-1.2.0/AzureGraph/build/vignette.rds |binary AzureGraph-1.2.0/AzureGraph/inst/doc/extend.Rmd |only AzureGraph-1.2.0/AzureGraph/inst/doc/extend.html |only AzureGraph-1.2.0/AzureGraph/inst/doc/intro.Rmd | 2 AzureGraph-1.2.0/AzureGraph/inst/doc/intro.html | 2 AzureGraph-1.2.0/AzureGraph/man/az_app.Rd | 8 AzureGraph-1.2.0/AzureGraph/man/az_device.Rd | 10 AzureGraph-1.2.0/AzureGraph/man/az_directory_role.Rd |only AzureGraph-1.2.0/AzureGraph/man/az_group.Rd | 10 AzureGraph-1.2.0/AzureGraph/man/az_object.Rd | 10 AzureGraph-1.2.0/AzureGraph/man/az_service_principal.Rd | 10 AzureGraph-1.2.0/AzureGraph/man/az_user.Rd | 12 AzureGraph-1.2.0/AzureGraph/man/call_graph.Rd | 6 AzureGraph-1.2.0/AzureGraph/man/format.Rd |only AzureGraph-1.2.0/AzureGraph/man/graph_login.Rd | 39 +- AzureGraph-1.2.0/AzureGraph/man/info.Rd | 10 AzureGraph-1.2.0/AzureGraph/man/ms_graph.Rd | 14 - AzureGraph-1.2.0/AzureGraph/man/ms_object.Rd |only AzureGraph-1.2.0/AzureGraph/man/register_graph_class.Rd |only AzureGraph-1.2.0/AzureGraph/man/utils.Rd |only AzureGraph-1.2.0/AzureGraph/tests/testthat/test00_class.R |only AzureGraph-1.2.0/AzureGraph/tests/testthat/test01_auth.R | 55 +++ AzureGraph-1.2.0/AzureGraph/tests/testthat/test02_app_sp.R | 4 AzureGraph-1.2.0/AzureGraph/tests/testthat/test03_usergrp.R | 7 AzureGraph-1.2.0/AzureGraph/vignettes/extend.Rmd |only AzureGraph-1.2.0/AzureGraph/vignettes/intro.Rmd | 2 48 files changed, 404 insertions(+), 335 deletions(-)
Title: Parse 'ActiGraph' 'GT3X'/'GT3X+' 'Accelerometer' Data
Description: Implements a high performance C++ parser
for 'ActiGraph' 'GT3X'/'GT3X+' data format (with extension '.gt3x')
for 'accelerometer' samples. Activity samples can be easily read into a
matrix or data.frame. This allows for storing the raw 'accelerometer'
samples in the original binary format to reserve space.
Author: Tuomo Nieminen [aut, cre],
John Muschelli [aut] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: Tuomo Nieminen <tuomo.a.nieminen@gmail.com>
Diff between read.gt3x versions 1.0.1 dated 2021-01-08 and 1.0.2 dated 2021-01-13
DESCRIPTION | 8 - MD5 | 10 - NEWS.md | 6 R/gt3x_sample_data.R | 12 + build/vignette.rds |binary inst/doc/read_gt3x.html | 290 ++++++++++++++++++++++++++---------------------- 6 files changed, 187 insertions(+), 139 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre],
R Consortium [fnd],
RStudio [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between hms versions 0.5.3 dated 2020-01-08 and 1.0.0 dated 2021-01-13
hms-0.5.3/hms/R/compat-lifecycle.R |only hms-0.5.3/hms/build |only hms-0.5.3/hms/tests/testthat/helper-pillar.R |only hms-0.5.3/hms/tests/testthat/out |only hms-1.0.0/hms/DESCRIPTION | 22 +- hms-1.0.0/hms/LICENSE |only hms-1.0.0/hms/MD5 | 62 +++----- hms-1.0.0/hms/NAMESPACE | 9 - hms-1.0.0/hms/NEWS.md | 26 +++ hms-1.0.0/hms/R/cast.R | 11 - hms-1.0.0/hms/R/coerce.R | 33 ---- hms-1.0.0/hms/R/hms.R | 25 ++- hms-1.0.0/hms/R/round.R | 44 +++++ hms-1.0.0/hms/README.md | 124 ++++++++-------- hms-1.0.0/hms/man/Deprecated.Rd | 5 hms-1.0.0/hms/man/hms-package.Rd | 4 hms-1.0.0/hms/man/hms.Rd | 5 hms-1.0.0/hms/man/round_hms.Rd | 11 + hms-1.0.0/hms/man/vec_cast.hms.Rd | 4 hms-1.0.0/hms/man/vec_ptype2.hms.Rd | 4 hms-1.0.0/hms/tests/testthat/_snaps |only hms-1.0.0/hms/tests/testthat/test-arith.R | 9 - hms-1.0.0/hms/tests/testthat/test-coercion-deprecated.R | 34 ++-- hms-1.0.0/hms/tests/testthat/test-coercion.R | 4 hms-1.0.0/hms/tests/testthat/test-colformat.R | 29 --- hms-1.0.0/hms/tests/testthat/test-combine.R | 11 - hms-1.0.0/hms/tests/testthat/test-construct.R | 16 +- hms-1.0.0/hms/tests/testthat/test-lubridate.R | 2 hms-1.0.0/hms/tests/testthat/test-output.R | 2 hms-1.0.0/hms/tests/testthat/test-parse.R | 2 hms-1.0.0/hms/tests/testthat/test-round.R | 28 +++ hms-1.0.0/hms/tests/testthat/test-subset.R | 5 hms-1.0.0/hms/tests/testthat/test-update.R | 2 33 files changed, 280 insertions(+), 253 deletions(-)
Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.9.2 dated 2020-04-07 and 0.9.4 dated 2021-01-13
geojsonio-0.9.2/geojsonio/README.md |only geojsonio-0.9.2/geojsonio/build |only geojsonio-0.9.2/geojsonio/inst/doc |only geojsonio-0.9.2/geojsonio/inst/js/README.md |only geojsonio-0.9.2/geojsonio/inst/vign |only geojsonio-0.9.2/geojsonio/vignettes |only geojsonio-0.9.4/geojsonio/DESCRIPTION | 20 geojsonio-0.9.4/geojsonio/LICENSE | 2 geojsonio-0.9.4/geojsonio/MD5 | 121 ++--- geojsonio-0.9.4/geojsonio/NAMESPACE | 1 geojsonio-0.9.4/geojsonio/NEWS.md | 9 geojsonio-0.9.4/geojsonio/R/as.json.R | 21 geojsonio-0.9.4/geojsonio/R/file_to_geojson.r | 4 geojsonio-0.9.4/geojsonio/R/geojson_json.R | 213 ++++++---- geojsonio-0.9.4/geojsonio/R/geojson_list.R | 29 - geojsonio-0.9.4/geojsonio/R/geojson_read.R | 14 geojsonio-0.9.4/geojsonio/R/geojson_sp.R | 6 geojsonio-0.9.4/geojsonio/R/geojson_style.R | 2 geojsonio-0.9.4/geojsonio/R/geojson_write.r | 9 geojsonio-0.9.4/geojsonio/R/geojsonio-package.r | 3 geojsonio-0.9.4/geojsonio/R/postgis.R | 4 geojsonio-0.9.4/geojsonio/R/projections.r | 16 geojsonio-0.9.4/geojsonio/R/topojson_list.R | 2 geojsonio-0.9.4/geojsonio/R/topojson_read.R | 7 geojsonio-0.9.4/geojsonio/R/zzz.r | 7 geojsonio-0.9.4/geojsonio/man/as.json.Rd | 8 geojsonio-0.9.4/geojsonio/man/figures/unnamed-chunk-14-1.png |only geojsonio-0.9.4/geojsonio/man/figures/unnamed-chunk-20-1.png |only geojsonio-0.9.4/geojsonio/man/figures/unnamed-chunk-21-1.png |only geojsonio-0.9.4/geojsonio/man/figures/unnamed-chunk-22-1.png |binary geojsonio-0.9.4/geojsonio/man/figures/unnamed-chunk-23-1.png |only geojsonio-0.9.4/geojsonio/man/figures/unnamed-chunk-24-1.png |binary geojsonio-0.9.4/geojsonio/man/file_to_geojson.Rd | 4 geojsonio-0.9.4/geojsonio/man/geojson_json.Rd | 58 ++ geojsonio-0.9.4/geojsonio/man/geojson_list.Rd | 10 geojsonio-0.9.4/geojsonio/man/geojson_sp.Rd | 2 geojsonio-0.9.4/geojsonio/man/geojson_style.Rd | 2 geojsonio-0.9.4/geojsonio/man/geojson_write.Rd | 4 geojsonio-0.9.4/geojsonio/man/geojsonio.Rd | 2 geojsonio-0.9.4/geojsonio/man/postgis.Rd | 4 geojsonio-0.9.4/geojsonio/man/topojson_json.Rd | 2 geojsonio-0.9.4/geojsonio/man/topojson_list.Rd | 4 geojsonio-0.9.4/geojsonio/man/topojson_read.Rd | 4 geojsonio-0.9.4/geojsonio/man/topojson_write.Rd | 4 geojsonio-0.9.4/geojsonio/tests/testthat/helper-geojsonio.R | 23 + geojsonio-0.9.4/geojsonio/tests/testthat/test-as.json.R | 23 + geojsonio-0.9.4/geojsonio/tests/testthat/test-file_to_geojson.R | 4 geojsonio-0.9.4/geojsonio/tests/testthat/test-geojson_atomize.R | 1 geojsonio-0.9.4/geojsonio/tests/testthat/test-geojson_json.R | 55 ++ geojsonio-0.9.4/geojsonio/tests/testthat/test-geojson_read.R | 2 geojsonio-0.9.4/geojsonio/tests/testthat/test-onload.R | 2 geojsonio-0.9.4/geojsonio/tests/testthat/test-projections.R | 8 geojsonio-0.9.4/geojsonio/tests/testthat/test-spatial_methods.R | 2 geojsonio-0.9.4/geojsonio/tests/testthat/test-topojson_read.R | 10 geojsonio-0.9.4/geojsonio/tests/testthat/test-topojson_write.R | 1 55 files changed, 464 insertions(+), 265 deletions(-)
Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models.
Author: Matthew C. Fitzpatrick, Karel Mokany, Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@umces.edu>
Diff between gdm versions 1.4.2 dated 2020-04-22 and 1.4.2.1 dated 2021-01-13
DESCRIPTION | 9 +--- MD5 | 8 +-- R/GDM_Table_Funcs.R | 102 ++++++++++++++++++++++++++++++-------------------- build/vignette.rds |binary man/formatsitepair.Rd | 93 +++++++++++++++++++++++++++++---------------- 5 files changed, 130 insertions(+), 82 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values.
Many times large experimental datasets need some additional filtering, adequate functions are provided.
Batch reading (or writing) of sets of files and combining data to arrays is supported, too.
Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrMisc versions 1.5.0 dated 2020-12-07 and 1.5.1 dated 2021-01-13
DESCRIPTION | 8 +-- MD5 | 30 +++++++------- R/moderTest2grp.R | 69 ++++++++++++++++++++++----------- R/moderTestXgrp.R | 78 ++++++++++++++++++++++++++++--------- R/ratioAllComb.R | 15 ++++--- R/stableMode.R | 87 +++++++++++++++++++++++++++++------------- R/stdErrMedBoot.R | 14 +++--- R/writeCsv.R | 9 ++-- inst/doc/wrMiscVignette1.Rmd | 13 ++++++ inst/doc/wrMiscVignette1.html | 43 +++++++++++++------- man/moderTest2grp.Rd | 5 +- man/moderTestXgrp.Rd | 7 +-- man/ratioAllComb.Rd | 11 ++++- man/stableMode.Rd | 18 +++++--- man/writeCsv.Rd | 3 - vignettes/wrMiscVignette1.Rmd | 13 ++++++ 16 files changed, 294 insertions(+), 129 deletions(-)
Title: Shiny/R Wrapper for 'clipboard.js'
Description: Leverages the functionality of 'clipboard.js', a JavaScript library
for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com>
for more information), and provides a reactive copy-to-clipboard UI button
component, called 'rclipButton', for 'shiny' R applications.
Author: Sebastien Bihorel
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between rclipboard versions 0.1.2 dated 2019-07-02 and 0.1.3 dated 2021-01-13
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 8 ++++---- R/rclipButton.R | 2 +- README.md | 6 ++++-- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Boolean Matrix Factorization
Description: Provides four boolean matrix factorization (BMF) methods.
BMF has many applications like data mining and categorical data
analysis. BMF is also known as boolean matrix decomposition (BMD)
and was found to be an NP-hard (non-deterministic polynomial-time)
problem. Currently implemented methods are
'Asso' Miettinen, Pauli and others (2008)
<doi:10.1109/TKDE.2008.53>,
'GreConD' R. Belohlavek, V. Vychodil (2010)
<doi:10.1016/j.jcss.2009.05.002> ,
'GreConDPlus' R. Belohlavek, V. Vychodil (2010)
<doi:10.1016/j.jcss.2009.05.002> ,
'topFiberM' A. Desouki, M. Roeder, A. Ngonga (2019)
<arXiv:1903.10326>.
Author: Abdelmoneim Amer Desouki
Maintainer: Abdelmoneim Amer Desouki <desouki@hhu.de>
Diff between rBMF versions 1.0 dated 2020-06-25 and 1.1 dated 2021-01-13
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS | 7 +++++++ build/partial.rdb |binary data/Chess.RData |binary data/DBLP.RData |binary 6 files changed, 20 insertions(+), 13 deletions(-)
Title: Prediction Model Selection and Performance Evaluation in
Multiple Imputed Datasets
Description: Pooling, backward and forward selection of logistic and Cox regression models in
multiply imputed datasets. Backward and forward selection can be done
from the pooled model using Rubin's Rules (RR), the D1, D2, D3 and
the median p-values method. This is also possible for Mixed models.
The models can contain continuous, dichotomous, categorical and restricted
cubic spline predictors and interaction terms between all these type of predictors.
The stability of the models can be evaluated using bootstrapping and cluster
bootstrapping. The package further contains functions to pool the model performance
as ROC/AUC, R-squares, scaled Brier score and calibration plots for logistic
regression models. Internal validation can be done with cross-validation or bootstrapping.
The adjusted intercept after shrinkage of pooled regression coefficients can be obtained.
Backward and forward selection as part of internal validation is possible.
A function to externally validate logistic prediction models in multiple imputed
datasets is available and a function to compare models.
Eekhout (2017) <doi:10.1186/s12874-017-0404-7>.
Wiel (2009) <doi:10.1093/biostatistics/kxp011>.
Marshall (2009) <doi:10.1186/1471-2288-9-57>.
Author: Martijn Heymans [cre, aut] (<https://orcid.org/0000-0002-3889-0921>),
Iris Eekhout [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>
Diff between psfmi versions 0.5.0 dated 2020-09-24 and 0.7.1 dated 2021-01-13
psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.html |only psfmi-0.5.0/psfmi/vignettes/psfmi_valext.Rmd |only psfmi-0.7.1/psfmi/DESCRIPTION | 32 psfmi-0.7.1/psfmi/MD5 | 164 + psfmi-0.7.1/psfmi/NAMESPACE | 20 psfmi-0.7.1/psfmi/NEWS.md | 11 psfmi-0.7.1/psfmi/R/MI_cv_naive.R | 7 psfmi-0.7.1/psfmi/R/RR_diff_prop.R |only psfmi-0.7.1/psfmi/R/bw_single.R | 35 psfmi-0.7.1/psfmi/R/cv_MI.R | 7 psfmi-0.7.1/psfmi/R/mivalext_lr.R | 5 psfmi-0.7.1/psfmi/R/pool_auc.R | 31 psfmi-0.7.1/psfmi/R/pool_compare_models.R |only psfmi-0.7.1/psfmi/R/pool_reclassification.R |only psfmi-0.7.1/psfmi/R/psfmi_coxr.R | 2 psfmi-0.7.1/psfmi/R/psfmi_coxr_bw.R | 12 psfmi-0.7.1/psfmi/R/psfmi_coxr_fw.R | 8 psfmi-0.7.1/psfmi/R/psfmi_lr.R | 6 psfmi-0.7.1/psfmi/R/psfmi_lr_bw.R | 16 psfmi-0.7.1/psfmi/R/psfmi_lr_fw.R | 16 psfmi-0.7.1/psfmi/R/psfmi_mm.R | 2 psfmi-0.7.1/psfmi/R/psfmi_perform.R | 12 psfmi-0.7.1/psfmi/R/scaled_brier.R | 2 psfmi-0.7.1/psfmi/README.md | 20 psfmi-0.7.1/psfmi/build/vignette.rds |binary psfmi-0.7.1/psfmi/data/anderson.rda |only psfmi-0.7.1/psfmi/data/aortadis.rda |only psfmi-0.7.1/psfmi/data/bmd.rda |only psfmi-0.7.1/psfmi/data/chlrform.rda |only psfmi-0.7.1/psfmi/data/chol_long.rda |only psfmi-0.7.1/psfmi/data/chol_wide.rda |only psfmi-0.7.1/psfmi/data/day2_dataset4_mi.rda |only psfmi-0.7.1/psfmi/data/hipstudy.rda |only psfmi-0.7.1/psfmi/data/hipstudy_external.rda |only psfmi-0.7.1/psfmi/data/hoorn_basic.rda |only psfmi-0.7.1/psfmi/data/infarct.rda |only psfmi-0.7.1/psfmi/data/lbpmilr.rda |binary psfmi-0.7.1/psfmi/data/lungvolume.rda |only psfmi-0.7.1/psfmi/data/mammaca.rda |only psfmi-0.7.1/psfmi/data/men.rda |only psfmi-0.7.1/psfmi/data/sbp_age.rda |only psfmi-0.7.1/psfmi/data/sbp_qas.rda |only psfmi-0.7.1/psfmi/data/smoking.rda |only psfmi-0.7.1/psfmi/data/weight.rda |only psfmi-0.7.1/psfmi/inst/doc/MI_boot.R | 13 psfmi-0.7.1/psfmi/inst/doc/MI_boot.Rmd | 27 psfmi-0.7.1/psfmi/inst/doc/MI_boot.html | 607 +------ psfmi-0.7.1/psfmi/inst/doc/MI_cv_naive.Rmd | 4 psfmi-0.7.1/psfmi/inst/doc/MI_cv_naive.html | 552 +----- psfmi-0.7.1/psfmi/inst/doc/boot_MI.R | 16 psfmi-0.7.1/psfmi/inst/doc/boot_MI.Rmd | 29 psfmi-0.7.1/psfmi/inst/doc/boot_MI.html | 687 +------- psfmi-0.7.1/psfmi/inst/doc/cv_MI.Rmd | 4 psfmi-0.7.1/psfmi/inst/doc/cv_MI.html | 557 +----- psfmi-0.7.1/psfmi/inst/doc/cv_MI_RR.Rmd | 4 psfmi-0.7.1/psfmi/inst/doc/cv_MI_RR.html | 541 +----- psfmi-0.7.1/psfmi/inst/doc/development_workflow.R |only psfmi-0.7.1/psfmi/inst/doc/development_workflow.Rmd |only psfmi-0.7.1/psfmi/inst/doc/development_workflow.html |only psfmi-0.7.1/psfmi/inst/doc/psfmi_CoxModels.R | 2 psfmi-0.7.1/psfmi/inst/doc/psfmi_CoxModels.Rmd | 12 psfmi-0.7.1/psfmi/inst/doc/psfmi_CoxModels.html | 836 +++------ psfmi-0.7.1/psfmi/inst/doc/psfmi_LogisticModels.Rmd | 4 psfmi-0.7.1/psfmi/inst/doc/psfmi_LogisticModels.html | 944 +++-------- psfmi-0.7.1/psfmi/inst/doc/psfmi_StabilityAnalysis.Rmd | 4 psfmi-0.7.1/psfmi/inst/doc/psfmi_StabilityAnalysis.html | 1355 ++++++---------- psfmi-0.7.1/psfmi/inst/doc/psfmi_mice.Rmd | 4 psfmi-0.7.1/psfmi/inst/doc/psfmi_mice.html | 705 ++------ psfmi-0.7.1/psfmi/man/MI_cv_naive.Rd | 12 psfmi-0.7.1/psfmi/man/RR_diff_prop.Rd |only psfmi-0.7.1/psfmi/man/anderson.Rd |only psfmi-0.7.1/psfmi/man/aortadis.Rd |only psfmi-0.7.1/psfmi/man/bmd.Rd |only psfmi-0.7.1/psfmi/man/bw_single.Rd | 11 psfmi-0.7.1/psfmi/man/chlrform.Rd |only psfmi-0.7.1/psfmi/man/chol_long.Rd |only psfmi-0.7.1/psfmi/man/chol_wide.Rd |only psfmi-0.7.1/psfmi/man/cv_MI.Rd | 5 psfmi-0.7.1/psfmi/man/day2_dataset4_mi.Rd |only psfmi-0.7.1/psfmi/man/hipstudy.Rd |only psfmi-0.7.1/psfmi/man/hipstudy_external.Rd |only psfmi-0.7.1/psfmi/man/hoorn_basic.Rd |only psfmi-0.7.1/psfmi/man/infarct.Rd |only psfmi-0.7.1/psfmi/man/lungvolume.Rd |only psfmi-0.7.1/psfmi/man/mammaca.Rd |only psfmi-0.7.1/psfmi/man/men.Rd |only psfmi-0.7.1/psfmi/man/pool_auc.Rd | 2 psfmi-0.7.1/psfmi/man/pool_compare_models.Rd |only psfmi-0.7.1/psfmi/man/pool_reclassification.Rd |only psfmi-0.7.1/psfmi/man/psfmi_lr.Rd | 2 psfmi-0.7.1/psfmi/man/psfmi_perform.Rd | 7 psfmi-0.7.1/psfmi/man/sbp_age.Rd |only psfmi-0.7.1/psfmi/man/sbp_qas.Rd |only psfmi-0.7.1/psfmi/man/scaled_brier.Rd | 4 psfmi-0.7.1/psfmi/man/smoking.Rd |only psfmi-0.7.1/psfmi/man/weight.Rd |only psfmi-0.7.1/psfmi/vignettes/MI_boot.Rmd | 27 psfmi-0.7.1/psfmi/vignettes/MI_cv_naive.Rmd | 4 psfmi-0.7.1/psfmi/vignettes/boot_MI.Rmd | 29 psfmi-0.7.1/psfmi/vignettes/cv_MI.Rmd | 4 psfmi-0.7.1/psfmi/vignettes/cv_MI_RR.Rmd | 4 psfmi-0.7.1/psfmi/vignettes/development_workflow.Rmd |only psfmi-0.7.1/psfmi/vignettes/psfmi_CoxModels.Rmd | 12 psfmi-0.7.1/psfmi/vignettes/psfmi_LogisticModels.Rmd | 4 psfmi-0.7.1/psfmi/vignettes/psfmi_StabilityAnalysis.Rmd | 4 psfmi-0.7.1/psfmi/vignettes/psfmi_mice.Rmd | 4 108 files changed, 2381 insertions(+), 5069 deletions(-)
Title: Tidy Statistical Inference
Description: The objective of this package is to perform
inference using an expressive statistical grammar that coheres with
the tidy design framework.
Author: Andrew Bray [aut, cre],
Chester Ismay [aut] (<https://orcid.org/0000-0003-2820-2547>),
Evgeni Chasnovski [aut] (<https://orcid.org/0000-0002-1617-4019>),
Ben Baumer [aut] (<https://orcid.org/0000-0002-3279-0516>),
Mine Cetinkaya-Rundel [aut] (<https://orcid.org/0000-0001-6452-2420>),
Simon Couch [ctb],
Ted Laderas [ctb] (<https://orcid.org/0000-0002-6207-7068>),
Nick Solomon [ctb],
Johanna Hardin [ctb],
Albert Y. Kim [ctb] (<https://orcid.org/0000-0001-7824-306X>),
Neal Fultz [ctb],
Doug Friedman [ctb],
Richie Cotton [ctb] (<https://orcid.org/0000-0003-2504-802X>),
Brian Fannin [ctb]
Maintainer: Andrew Bray <abray@reed.edu>
Diff between infer versions 0.5.3 dated 2020-07-14 and 0.5.4 dated 2021-01-13
DESCRIPTION | 121 ++- MD5 | 76 - NAMESPACE | 2 NEWS.md | 14 R/calculate.R | 242 +++--- R/get_confidence_interval.R | 88 +- R/gss.R | 3 R/hypothesize.R | 3 R/infer.R | 8 R/rep_sample_n.R | 109 +- R/utils.R | 15 R/wrappers.R | 276 ++++-- inst/doc/anova.html | 48 + inst/doc/chi_squared.html | 48 + inst/doc/infer.R | 4 inst/doc/infer.Rmd | 4 inst/doc/infer.html | 52 + inst/doc/observed_stat_examples.R | 21 inst/doc/observed_stat_examples.Rmd | 35 inst/doc/observed_stat_examples.html | 952 +++++++++++++----------- inst/doc/t_test.html | 48 + man/calculate.Rd | 16 man/chisq_stat.Rd | 10 man/chisq_test.Rd | 6 man/get_confidence_interval.Rd | 52 - man/gss.Rd | 3 man/infer.Rd | 22 man/prop_test.Rd | 50 + man/rep_sample_n.Rd | 70 + man/t_test.Rd | 2 tests/testthat/helper-data.R | 5 tests/testthat/test-calculate.R | 173 ++-- tests/testthat/test-rep_sample_n.R | 96 ++ tests/testthat/test-shade_confidence_interval.R | 3 tests/testthat/test-shade_p_value.R | 3 tests/testthat/test-visualize.R | 1 tests/testthat/test-wrappers.R | 173 ++-- vignettes/infer.Rmd | 4 vignettes/observed_stat_examples.Rmd | 35 39 files changed, 1841 insertions(+), 1052 deletions(-)
Title: Bayesian Network Meta-Analysis using 'JAGS'
Description: Network meta-analyses using Bayesian framework following Dias et al. (2013) <DOI:10.1177/0272989X12458724>. Based on the data input, creates prior, model file, and initial values needed to run models in 'rjags'. Able to handle binomial, normal and multinomial arm-level data. Can handle multi-arm trials and includes methods to incorporate covariate and baseline risk effects. Includes standard diagnostics and visualization tools to evaluate the results.
Author: Michael Seo [aut, cre],
Christopher Schmid [aut]
Maintainer: Michael Seo <swj8874@gmail.com>
Diff between bnma versions 1.3.0 dated 2020-08-27 and 1.4.0 dated 2021-01-13
DESCRIPTION | 12 MD5 | 82 + NAMESPACE | 6 NEWS.md | 8 R/bnma.R | 45 - R/contrast.network.R | 8 R/network.data.R | 8 R/network.inits.R | 77 + R/network.rjags.R | 10 R/network.run.R | 60 + R/network.summary.R | 200 ++-- R/nodesplit.network.R | 2 R/preprocess.data.R | 7 R/ume.network.R | 56 - build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 38 inst/doc/my-vignette.R | 41 inst/doc/my-vignette.Rmd | 56 + inst/doc/my-vignette.html | 1552 +++++++++++++++++++++---------------- man/blocker.Rd | 33 man/bnma-package.Rd | 26 man/calculate.contrast.deviance.Rd | 4 man/calculate.deviance.Rd | 2 man/cardiovascular.Rd | 44 - man/certolizumab.Rd | 6 man/contrast.network.data.Rd | 4 man/network.data.Rd | 6 man/network.forest.plot.Rd | 2 man/network.gelman.diag.Rd | 2 man/network.inconsistency.plot.Rd |only man/network.leverage.plot.Rd | 6 man/network.run.Rd | 2 man/nodesplit.network.data.Rd | 2 man/parkinsons.Rd | 6 man/parkinsons_contrast.Rd | 6 man/smoking.Rd | 8 man/statins.Rd | 6 man/sucra.Rd | 2 man/thrombolytic.Rd | 6 man/ume.network.data.Rd | 12 man/ume.network.run.Rd | 1 vignettes/my-vignette.Rmd | 56 + 43 files changed, 1513 insertions(+), 997 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between rscorecard versions 0.17.0 dated 2020-12-05 and 0.18.0 dated 2021-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/sysdata.rda |binary 4 files changed, 10 insertions(+), 6 deletions(-)
Title: R Scripts in the Google Cloud via Cloud Run, Cloud Build and
Cloud Scheduler
Description: Tools to easily enable R scripts in the Google Cloud Platform.
Utilise cloud services such as Cloud Run <https://cloud.google.com/run/> for R over HTTP,
Cloud Build <https://cloud.google.com/cloud-build/> for Continuous Delivery
and Integration services and
Cloud Scheduler <https://cloud.google.com/scheduler/> for scheduled scripts.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>),
Sunholo Ltd [cph]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between googleCloudRunner versions 0.3.0 dated 2020-09-10 and 0.4.0 dated 2021-01-13
googleCloudRunner-0.3.0/googleCloudRunner/inst/shiny/image_talker/app/auth.json |only googleCloudRunner-0.3.0/googleCloudRunner/inst/shiny/shiny_cloudrun/app/mark-edmondson-gde-web-client.json |only googleCloudRunner-0.4.0/googleCloudRunner/DESCRIPTION | 17 - googleCloudRunner-0.4.0/googleCloudRunner/MD5 | 72 +++---- googleCloudRunner-0.4.0/googleCloudRunner/NAMESPACE | 22 ++ googleCloudRunner-0.4.0/googleCloudRunner/NEWS.md | 15 + googleCloudRunner-0.4.0/googleCloudRunner/R/buildsteps_templates.R | 7 googleCloudRunner-0.4.0/googleCloudRunner/R/buildtriggers.R | 100 +++++++++- googleCloudRunner-0.4.0/googleCloudRunner/R/cloudbuild.R | 3 googleCloudRunner-0.4.0/googleCloudRunner/R/cloudscheduler.R | 30 +-- googleCloudRunner-0.4.0/googleCloudRunner/R/deploy-buildtriggers.R | 2 googleCloudRunner-0.4.0/googleCloudRunner/R/jwt-requests.R |only googleCloudRunner-0.4.0/googleCloudRunner/R/plumber.R | 4 googleCloudRunner-0.4.0/googleCloudRunner/R/setup_buildemail.R | 21 +- googleCloudRunner-0.4.0/googleCloudRunner/R/setup_parts.R | 43 ++-- googleCloudRunner-0.4.0/googleCloudRunner/R/setup_tests.R | 58 ++++- googleCloudRunner-0.4.0/googleCloudRunner/R/yaml.R | 1 googleCloudRunner-0.4.0/googleCloudRunner/README.md | 1 googleCloudRunner-0.4.0/googleCloudRunner/inst/docker/parallel_cloudrun |only googleCloudRunner-0.4.0/googleCloudRunner/inst/example/Dockerfile | 4 googleCloudRunner-0.4.0/googleCloudRunner/inst/example/api.R | 2 googleCloudRunner-0.4.0/googleCloudRunner/inst/example/server.R |only googleCloudRunner-0.4.0/googleCloudRunner/man/BuildTrigger.Rd | 3 googleCloudRunner-0.4.0/googleCloudRunner/man/GitHubEventsConfig.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_copy.Rd |only googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_delete.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_edit.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_get.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_list.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_repo.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_buildtrigger_run.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_deploy_run_website.Rd | 2 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_jwt_create.Rd |only googleCloudRunner-0.4.0/googleCloudRunner/man/cr_plumber_pubsub.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_run.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_run_get.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_run_list.Rd | 1 googleCloudRunner-0.4.0/googleCloudRunner/man/cr_schedule_get.Rd | 2 39 files changed, 320 insertions(+), 101 deletions(-)
More information about googleCloudRunner at CRAN
Permanent link
Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut] (<https://orcid.org/0000-0002-6813-3200>),
Natacha Turck [aut],
Alexandre Hainard [aut],
Natalia Tiberti [aut],
Frédérique Lisacek [aut],
Jean-Charles Sanchez [aut],
Markus Müller [aut],
Stefan Siegert [ctb] (Fast DeLong code),
Matthias Doering [ctb] (Hand & Till Multiclass)
Maintainer: Xavier Robin <pROC-cran@xavier.robin.name>
Diff between pROC versions 1.16.2 dated 2020-03-19 and 1.17.0.1 dated 2021-01-13
DESCRIPTION | 8 MD5 | 160 NAMESPACE | 1 NEWS | 13 R/auc.R | 4 R/bootstrap.R | 46 R/coords.R | 326 R/ggroc.R | 10 R/lines.roc.R | 2 R/multiclass.R | 5 R/plot.roc.R | 6 R/power.roc.test.R | 22 R/roc.R | 6 R/roc.utils.R | 135 R/smooth.R | 40 README.md | 4 build |only man/aSAH.Rd | 4 man/auc.Rd | 8 man/ci.Rd | 2 man/ci.auc.Rd | 8 man/ci.coords.Rd | 12 man/ci.se.Rd | 8 man/ci.sp.Rd | 8 man/ci.thresholds.Rd | 8 man/coords.Rd | 113 man/coords_transpose.Rd | 18 man/cov.Rd | 10 man/ggroc.Rd | 26 man/multiclass.Rd | 4 man/pROC-package.Rd | 15 man/plot.ci.Rd | 2 man/plot.roc.Rd | 2 man/power.roc.test.Rd | 14 man/roc.Rd | 6 man/roc.test.Rd | 10 man/smooth.Rd | 37 man/var.Rd | 10 tests/figs/deps.txt | 2 tests/figs/ggroc/ggroc-list-extra-aes-screenshot.svg | 6 tests/figs/ggroc/ggroc-list-multi-aes.svg | 6 tests/figs/ggroc/ggroc-list-scale-colour-manual.svg |only tests/figs/ggroc/ggroc-list-screenshot.svg | 6 tests/figs/ggroc/ggroc-smooth-list-screenshot.svg |only tests/figs/ggroc/ggroc-smooth-screenshot.svg |only tests/figs/plot/advanced-screenshot-1.svg | 4 tests/figs/plot/advanced-screenshot-2.svg | 4 tests/figs/plot/advanced-screenshot-3.svg | 6 tests/figs/plot/advanced-screenshot-4.svg | 4 tests/figs/plot/advanced-screenshot-5.svg | 4 tests/figs/plot/advanced-screenshot-6.svg | 4 tests/figs/plot/basic-ndka.svg | 4 tests/figs/plot/basic-s100b.svg | 4 tests/figs/plot/basic-wfns.svg | 4 tests/figs/plot/legacy-axes.svg | 4 tests/figs/plot/plot-formula.svg | 4 tests/testthat/helper-coords-expected-smooth.R |only tests/testthat/helper-expectations.R |only tests/testthat/helper-roc-expected.R | 3433 +--------- tests/testthat/helper-roc.utils-expected.R |only tests/testthat/helper-skip.R |only tests/testthat/helper-vdiffr.R |only tests/testthat/print_output/r.ndka.ci.auc |only tests/testthat/print_output/r.ndka.ci.coords |only tests/testthat/print_output/r.ndka.ci.se |only tests/testthat/print_output/r.ndka.ci.sp |only tests/testthat/print_output/r.ndka.ci.thresholds |only tests/testthat/print_output/roc.test-venkatraman.paired |only tests/testthat/print_output/roc.test-venkatraman.unpaired |only tests/testthat/print_output/roc.test-venkatraman.unpaired.unstratified |only tests/testthat/print_output/roc.test-venkatraman.unstratified |only tests/testthat/test-are-paired.R | 3 tests/testthat/test-ci.auc.R | 19 tests/testthat/test-ci.formula.R |only tests/testthat/test-ci.se.R |only tests/testthat/test-ci.sp.R |only tests/testthat/test-ci.thresholds.R |only tests/testthat/test-coords.R | 68 tests/testthat/test-cov.R | 68 tests/testthat/test-ggroc.R | 33 tests/testthat/test-large.R | 2 tests/testthat/test-numeric-accuracy.R | 2 tests/testthat/test-onload.R | 8 tests/testthat/test-plot.R | 37 tests/testthat/test-power.roc.test.R | 29 tests/testthat/test-print.R | 54 tests/testthat/test-roc.R | 9 tests/testthat/test-roc.test-venkatraman.R |only tests/testthat/test-roc.test.R | 88 tests/testthat/test-roc.utils.R | 56 tests/testthat/test-roc.utils.percent.R | 2 tests/testthat/test-smooth.R |only tests/testthat/test-var.R | 19 93 files changed, 1672 insertions(+), 3437 deletions(-)
Title: Utilities for Japanese Mesh Code
Description: Helpful functions for using mesh code (80km to 100m) data in Japan. Visualize mesh code using 'ggplot2' and 'leaflet', etc.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpmesh versions 2.0.0 dated 2020-11-26 and 2.0.1 dated 2021-01-13
DESCRIPTION | 12 - MD5 | 17 +- NEWS.md | 6 inst/doc/usage.html | 250 +----------------------------- tests/testthat/helper-vdiffr.R |only tests/testthat/test-administration_mesh.R | 12 - tests/testthat/test-data.R | 2 tests/testthat/test-export_mesh.R | 2 tests/testthat/test-find.R | 10 - tests/testthat/test-fine_separate.R | 6 10 files changed, 46 insertions(+), 271 deletions(-)
Title: Download and Manage Open Data from INEGI
Description: Download and manage data sets of statistical projects and geographic data created by Instituto Nacional de Estadistica y Geografia (INEGI). See <https://www.inegi.org.mx/>.
Author: Cesar Renteria [aut, cre]
Maintainer: Cesar Renteria <cesar.renteria@cide.edu>
Diff between importinegi versions 1.1.2 dated 2020-05-04 and 1.1.3 dated 2021-01-13
DESCRIPTION | 12 +++++------ MD5 | 16 +++++++------- R/censo_municipal.R | 2 - R/sig_caminos_descarga.R | 50 +++++++++++++++++++--------------------------- README.md | 6 ++--- inst/doc/importinegi.R | 8 +++---- inst/doc/importinegi.Rmd | 14 ++++++------ inst/doc/importinegi.html | 10 ++++----- vignettes/importinegi.Rmd | 14 ++++++------ 9 files changed, 62 insertions(+), 70 deletions(-)
Title: Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data
Description: Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data.
Includes Cauchit, Compl. Log-Log, Logistic, and Probit link functions for Bernoulli Distributed RR data.
RR Designs: Warner, Forced Response, Unrelated Question, Kuk, Crosswise, and Triangular.
Reference: Fox, J-P, Veen, D. and Klotzke, K. (2018). Generalized Linear Mixed Models for Randomized Responses. Methodology. <doi:10.1027/1614-2241/a000153>.
Author: Jean-Paul Fox [aut], Konrad Klotzke [aut], Duco Veen [aut]
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>
Diff between GLMMRR versions 0.2.0 dated 2016-08-08 and 0.5.0 dated 2021-01-13
GLMMRR-0.2.0/GLMMRR/R/hello.R |only GLMMRR-0.2.0/GLMMRR/man/hello.Rd |only GLMMRR-0.5.0/GLMMRR/DESCRIPTION | 18 +-- GLMMRR-0.5.0/GLMMRR/MD5 | 91 ++++++++------- GLMMRR-0.5.0/GLMMRR/NAMESPACE | 3 GLMMRR-0.5.0/GLMMRR/R/ETHBE.R |only GLMMRR-0.5.0/GLMMRR/R/MTURK.R |only GLMMRR-0.5.0/GLMMRR/R/Plagiarism.R | 41 +++---- GLMMRR-0.5.0/GLMMRR/R/RRglm.R | 5 GLMMRR-0.5.0/GLMMRR/R/RRglmGOF.R | 12 -- GLMMRR-0.5.0/GLMMRR/R/RRglmer.R | 9 - GLMMRR-0.5.0/GLMMRR/R/RRlink_cauchit.R | 2 GLMMRR-0.5.0/GLMMRR/R/RRlink_cloglog.R | 2 GLMMRR-0.5.0/GLMMRR/R/RRlink_logit.R | 2 GLMMRR-0.5.0/GLMMRR/R/RRlink_probit.R | 2 GLMMRR-0.5.0/GLMMRR/R/getMLPrevalence.R | 4 GLMMRR-0.5.0/GLMMRR/R/getRRparameters.R | 4 GLMMRR-0.5.0/GLMMRR/R/plot.R | 117 +++++++++++++------- GLMMRR-0.5.0/GLMMRR/R/print.R | 11 + GLMMRR-0.5.0/GLMMRR/R/residuals.R | 4 GLMMRR-0.5.0/GLMMRR/R/summary.R | 2 GLMMRR-0.5.0/GLMMRR/R/tools.R | 18 +-- GLMMRR-0.5.0/GLMMRR/build |only GLMMRR-0.5.0/GLMMRR/data/ETHBE.rda |only GLMMRR-0.5.0/GLMMRR/data/MTURK.rda |only GLMMRR-0.5.0/GLMMRR/man/ETHBE.Rd |only GLMMRR-0.5.0/GLMMRR/man/MTURK.Rd |only GLMMRR-0.5.0/GLMMRR/man/Plagiarism.Rd | 48 ++++---- GLMMRR-0.5.0/GLMMRR/man/RRbinomial.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/RRglm.Rd | 5 GLMMRR-0.5.0/GLMMRR/man/RRglmGOF.Rd | 17 +- GLMMRR-0.5.0/GLMMRR/man/RRglmer.Rd | 19 ++- GLMMRR-0.5.0/GLMMRR/man/RRlink.cauchit.Rd | 4 GLMMRR-0.5.0/GLMMRR/man/RRlink.cloglog.Rd | 4 GLMMRR-0.5.0/GLMMRR/man/RRlink.logit.Rd | 4 GLMMRR-0.5.0/GLMMRR/man/RRlink.probit.Rd | 4 GLMMRR-0.5.0/GLMMRR/man/getCellMeans.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/getCellSizes.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/getMLPrevalence.Rd | 5 GLMMRR-0.5.0/GLMMRR/man/getRRparameters.Rd | 5 GLMMRR-0.5.0/GLMMRR/man/getUniqueGroups.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/intDotplot.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/plot.RRglm.Rd | 18 +-- GLMMRR-0.5.0/GLMMRR/man/plot.RRglmerMod.Rd | 7 - GLMMRR-0.5.0/GLMMRR/man/print.RRglmGOF.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/print.summary.RRglm.Rd | 12 +- GLMMRR-0.5.0/GLMMRR/man/print.summary.RRglmerMod.Rd | 12 +- GLMMRR-0.5.0/GLMMRR/man/residuals.RRglm.Rd | 13 +- GLMMRR-0.5.0/GLMMRR/man/residuals.RRglmerMod.Rd | 12 +- GLMMRR-0.5.0/GLMMRR/man/summary.RRglm.Rd | 1 GLMMRR-0.5.0/GLMMRR/man/summary.RRglmerMod.Rd | 1 51 files changed, 290 insertions(+), 254 deletions(-)
Title: Best Subset Selection /Ridge Regression in Linear, Logistic,
Poisson and CoxPH Models
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
Author: Canhong Wen [aut, cre],
Aijun Zhang [aut],
Shijie Quan [aut],
Liyuan Hu [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Jin Zhu [aut],
Xueqin Wang [aut]
Maintainer: Canhong Wen <wencanhong@gmail.com>
Diff between BeSS versions 1.0.9 dated 2020-06-30 and 2.0.0 dated 2021-01-13
BeSS-1.0.9/BeSS/R/bess.cox.R |only BeSS-1.0.9/BeSS/R/bess.glm.R |only BeSS-1.0.9/BeSS/R/bess.lm.R |only BeSS-1.0.9/BeSS/R/gbess.cox.R |only BeSS-1.0.9/BeSS/R/gbess.glm.R |only BeSS-1.0.9/BeSS/R/gbess.lm.R |only BeSS-1.0.9/BeSS/R/print.bess.one.R |only BeSS-1.0.9/BeSS/R/summary.bess.one.R |only BeSS-1.0.9/BeSS/README |only BeSS-1.0.9/BeSS/data/SAheart.RData |only BeSS-1.0.9/BeSS/data/gravier.RData |only BeSS-1.0.9/BeSS/data/prostate.RData |only BeSS-1.0.9/BeSS/inst/CITATION |only BeSS-1.0.9/BeSS/inst/include |only BeSS-1.0.9/BeSS/man/SAheart.Rd |only BeSS-1.0.9/BeSS/man/aic.Rd |only BeSS-1.0.9/BeSS/man/bess-internal.Rd |only BeSS-1.0.9/BeSS/man/coef.bess.one.Rd |only BeSS-1.0.9/BeSS/man/deviance.bess.one.Rd |only BeSS-1.0.9/BeSS/man/gravier.Rd |only BeSS-1.0.9/BeSS/man/logLik.bess.one.Rd |only BeSS-1.0.9/BeSS/man/predict.bess.one.Rd |only BeSS-1.0.9/BeSS/man/print.bess.one.Rd |only BeSS-1.0.9/BeSS/man/prostate.Rd |only BeSS-1.0.9/BeSS/man/summary.bess.one.Rd |only BeSS-1.0.9/BeSS/src/group.cpp |only BeSS-2.0.0/BeSS/DESCRIPTION | 30 BeSS-2.0.0/BeSS/MD5 | 123 +- BeSS-2.0.0/BeSS/NAMESPACE | 75 + BeSS-2.0.0/BeSS/NEWS.md |only BeSS-2.0.0/BeSS/R/RcppExports.R | 32 BeSS-2.0.0/BeSS/R/aic.R | 88 +- BeSS-2.0.0/BeSS/R/bess.R | 1301 +++++++++++++++++-------------- BeSS-2.0.0/BeSS/R/bess.one.R | 340 ++++++-- BeSS-2.0.0/BeSS/R/coef.bess.R | 67 - BeSS-2.0.0/BeSS/R/data.R |only BeSS-2.0.0/BeSS/R/deviance.bess.R | 125 ++ BeSS-2.0.0/BeSS/R/deviance_all.R |only BeSS-2.0.0/BeSS/R/gen.data.R | 304 +++++-- BeSS-2.0.0/BeSS/R/logLik.bess.R | 102 +- BeSS-2.0.0/BeSS/R/package.R |only BeSS-2.0.0/BeSS/R/plot.bess.R | 527 +++++++++++- BeSS-2.0.0/BeSS/R/predict.bess.R | 258 +++--- BeSS-2.0.0/BeSS/R/print.bess.R | 101 ++ BeSS-2.0.0/BeSS/R/recover.R |only BeSS-2.0.0/BeSS/R/summary.bess.R | 172 +++- BeSS-2.0.0/BeSS/R/utilize.R |only BeSS-2.0.0/BeSS/README.md |only BeSS-2.0.0/BeSS/build |only BeSS-2.0.0/BeSS/data/duke.rda |only BeSS-2.0.0/BeSS/data/trim32.rda |only BeSS-2.0.0/BeSS/inst/doc |only BeSS-2.0.0/BeSS/man/BeSS-package.Rd |only BeSS-2.0.0/BeSS/man/bess.Rd | 502 ++++++++--- BeSS-2.0.0/BeSS/man/bess.one.Rd | 373 +++++--- BeSS-2.0.0/BeSS/man/coef.bess.Rd | 83 + BeSS-2.0.0/BeSS/man/deviance.bess.Rd | 68 + BeSS-2.0.0/BeSS/man/duke.Rd |only BeSS-2.0.0/BeSS/man/gen.data.Rd | 169 ++-- BeSS-2.0.0/BeSS/man/logLik.bess.Rd | 106 +- BeSS-2.0.0/BeSS/man/plot.bess.Rd | 80 + BeSS-2.0.0/BeSS/man/predict.bess.Rd | 117 ++ BeSS-2.0.0/BeSS/man/print.bess.Rd | 57 - BeSS-2.0.0/BeSS/man/summary.bess.Rd | 74 + BeSS-2.0.0/BeSS/man/trim32.Rd |only BeSS-2.0.0/BeSS/src/Algorithm.cpp |only BeSS-2.0.0/BeSS/src/Algorithm.h |only BeSS-2.0.0/BeSS/src/Data.cpp |only BeSS-2.0.0/BeSS/src/Data.h |only BeSS-2.0.0/BeSS/src/Makevars |only BeSS-2.0.0/BeSS/src/Makevars.win |only BeSS-2.0.0/BeSS/src/Metric.cpp |only BeSS-2.0.0/BeSS/src/Metric.h |only BeSS-2.0.0/BeSS/src/RcppExports.cpp | 355 -------- BeSS-2.0.0/BeSS/src/bess.cpp | 469 ++++++----- BeSS-2.0.0/BeSS/src/bess.h |only BeSS-2.0.0/BeSS/src/coxph.cpp |only BeSS-2.0.0/BeSS/src/coxph.h |only BeSS-2.0.0/BeSS/src/logistic.cpp |only BeSS-2.0.0/BeSS/src/logistic.h |only BeSS-2.0.0/BeSS/src/normalize.cpp |only BeSS-2.0.0/BeSS/src/normalize.h |only BeSS-2.0.0/BeSS/src/path.cpp |only BeSS-2.0.0/BeSS/src/path.h |only BeSS-2.0.0/BeSS/src/poisson.cpp |only BeSS-2.0.0/BeSS/src/poisson.h |only BeSS-2.0.0/BeSS/src/screening.cpp |only BeSS-2.0.0/BeSS/src/screening.h |only BeSS-2.0.0/BeSS/src/utilities.cpp |only BeSS-2.0.0/BeSS/src/utilities.h |only BeSS-2.0.0/BeSS/vignettes |only 91 files changed, 3995 insertions(+), 2103 deletions(-)
Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other random but perhaps useful functions.
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>
Diff between windex versions 2.0 dated 2020-10-19 and 2.0.1 dated 2021-01-13
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++------------- NAMESPACE | 4 ++-- R/mark.dist.R | 6 +++++- R/modSel.geiger.R |only R/modSelTab.R | 21 +++++++++++++++++++-- inst/CITATION | 2 +- man/error.bars.Rd | 2 +- man/mark.dist.Rd | 9 ++++++++- man/modSel.geiger.Rd |only man/modSel.rayDISC.Rd | 4 ++-- man/modSelTab.Rd | 15 +++++++++------ man/sample.data.Rd | 2 +- man/sample.tree.Rd | 2 +- man/test.windex.Rd | 4 ++-- man/windex-package.Rd | 2 +- 16 files changed, 72 insertions(+), 39 deletions(-)
Title: Data-Driven Identification of SVAR Models
Description: Implements data-driven identification methods for structural vector autoregressive (SVAR) models.
Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural
impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>), patterns of GARCH (Normadin, M., Phaneuf, L. (2004) <doi:10.1016/j.jmoneco.2003.11.002>),
independent component analysis (Matteson, D. S, Tsay, R. S., (2013) <doi:10.1080/01621459.2016.1150851>), least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>),
smooth transition in variances (Luetkepohl, H., Netsunajev, A. (2017) <doi:10.1016/j.jedc.2017.09.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>)).
Author: Alexander Lange [aut, cre],
Bernhard Dalheimer [aut],
Helmut Herwartz [aut],
Simone Maxand [aut],
Hannes Riebl [ctb]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>
Diff between svars versions 1.3.5 dated 2020-11-23 and 1.3.6 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/cf.R | 2 +- inst/doc/svars.pdf |binary tests/testthat/test-cf.R |only 5 files changed, 9 insertions(+), 8 deletions(-)
Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness. We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between politeness versions 0.7.5 dated 2020-11-16 and 0.7.6 dated 2021-01-13
DESCRIPTION | 8 ++--- MD5 | 9 +++-- R/getTokenSets.R | 4 +- R/textTools.R | 18 +++++++++++ inst/doc/politeness.html | 72 +++-------------------------------------------- man/cleanpunct.Rd |only 6 files changed, 35 insertions(+), 76 deletions(-)
Title: Difference Benchmarking for Multivariate Small Area Estimation
Description: Implements Benchmarking Method for Multivariate Small Area Estimation under Fay Herriot Model. Multivariate Small Area Estimation (MSAE) is a development of Univariate Small Area Estimation that considering the correlation among response variables and borrowing the strength from related areas and auxiliary variables to increase the effectiveness of sample size, the multivariate model in this package is based on multivariate model 1 proposed by Roberto Benavent and Domingo Morales (2015) <doi:10.1016/j.csda.2015.07.013>. Benchmarking in Small Area Estimation is a modification of Small Area Estimation model to guarantee that the aggregate weighted mean of the county predictors equals the corresponding weighted mean of survey estimates. Difference Benchmarking is the simplest benchmarking method but widely used by multiplying empirical best linear unbiased prediction (EBLUP) estimator by the common adjustment factors (J.N.K Rao and Isabel Molina, 2015).
Author: Zaza Yuda Perwira, Azka Ubaidillah
Maintainer: Zaza Yuda Perwira <221710086@stis.ac.id>
Diff between msaeDB versions 0.1.0 dated 2021-01-09 and 0.1.1 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/msaeDB-Package.R | 10 +++++----- README.md | 36 ++++++++++++++++++------------------ 4 files changed, 30 insertions(+), 30 deletions(-)
Title: Keyboard and Mouse Input Simulation for Windows OS
Description: Control your keyboard and mouse with R code by simulating key presses and mouse clicks. The input simulation is implemented with the Windows API.
Author: Jim Chen [aut, cre],
Jeff Keller [aut, ctb],
Garry Hopwood [ctb],
Chieh Hsu [ctb]
Maintainer: Jim Chen <jim71183@gmail.com>
Diff between KeyboardSimulator versions 2.5.1 dated 2020-07-10 and 2.6.0 dated 2021-01-13
DESCRIPTION | 10 +++++----- MD5 | 19 +++++++++++-------- R/RcppExports.R | 12 ++++++++++++ R/main.R | 18 +++++++++++++----- README.md | 9 +++++++-- man/keybd.type_string.Rd | 42 +++++++++++++++++++++--------------------- man/mouse.click.Rd | 4 ++-- man/mouse.release.Rd | 2 +- src/RcppExports.cpp | 30 ++++++++++++++++++++++++++++++ src/mouse_M.cpp |only src/mouse_M_hold.cpp |only src/mouse_M_release.cpp |only 12 files changed, 102 insertions(+), 44 deletions(-)
More information about KeyboardSimulator at CRAN
Permanent link
Title: Dose Rate Estimation from in-Situ Gamma-Ray Spectrometry
Measurements
Description: Process in-situ Gamma-Ray Spectrometry for
Luminescence Dating. This package allows to import, inspect and
correct the energy shifts of Gamma-ray spectra. It provides methods
for estimating the gamma dose rate by the use of a calibration curve.
The package only supports Canberra CNF and TKA files.
Author: Nicolas Frerebeau [aut] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [aut, cre] (<https://orcid.org/0000-0001-7503-8685>),
Guilhem Paradol [aut] (<https://orcid.org/0000-0002-8561-4903>),
Magali Rizza [ctb] (<https://orcid.org/0000-0003-2364-5621>),
Christelle Lahaye [ctb] (<https://orcid.org/0000-0003-2215-9015>),
Université Bordeaux Montaigne [cph, fnd],
CNRS [fnd],
LabEx Sciences archéologiques de Bordeaux [fnd],
Idex Aix-Marseille [fnd]
Maintainer: Brice Lebrun
<brice.lebrun@u-bordeaux-montaigne.fr>
Diff between gamma versions 1.0.0 dated 2020-09-18 and 1.0.1 dated 2021-01-13
DESCRIPTION | 11 ++++--- MD5 | 39 ++++++++++++++------------- NEWS.md | 10 ++++++- R/AllGenerics.R | 23 ++++++++-------- R/baseline_rubberband.R | 3 ++ R/baseline_snip.R | 6 ++-- R/gamma-package.R | 6 ++-- README.md | 26 +++++++++++++++--- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 36 ++++++++++++++----------- inst/doc/doserate.html | 58 ++++++++++++++++++++++++----------------- inst/doc/gamma.html | 28 +++++++++++++------ man/baseline.Rd | 13 +++++---- man/doserate.Rd | 2 - man/figures/README-calib-1.png |binary man/figures/README-usage-1.png |binary man/gamma-package.Rd | 6 ++-- man/integrate.Rd | 2 - man/smooth.Rd | 6 +--- tests/testthat/test-plot.R | 6 ++++ 21 files changed, 173 insertions(+), 108 deletions(-)
Title: Measuring Concreteness in Natural Language
Description: Models for detecting concreteness in natural language. This package is built in support of Yeomans (2021) <doi:10.1016/j.obhdp.2020.10.008>, which reviews linguistic models of concreteness in several domains. Here, we provide an implementation of the best-performing domain-general model (from Brysbaert et al., (2014) <doi:10.3758/s13428-013-0403-5>) as well as two pre-trained models for the feedback and plan-making domains.
Author: Mike Yeomans
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between doc2concrete versions 0.5.0 dated 2020-11-16 and 0.5.2 dated 2021-01-13
DESCRIPTION | 10 ++-- MD5 | 16 ++++--- R/doc2concrete.R | 94 ++++++++++++++++++++------------------------- R/domainModels.R |only R/ngramComponents.R | 18 ++++++++ inst/doc/doc2concrete.html | 68 +------------------------------- man/adviceModel.Rd | 15 ++++++- man/cleanpunct.Rd |only man/doc2concrete.Rd | 4 - man/planModel.Rd | 15 ++++++- 10 files changed, 107 insertions(+), 133 deletions(-)
Title: 'R Markdown' Format for Scientific and Technical Writing
Description: Scientific and technical article format for the web. 'Distill' articles
feature attractive, reader-friendly typography, flexible layout options
for visualizations, and full support for footnotes and citations.
Author: JJ Allaire [aut, cre] (<https://orcid.org/0000-0003-0174-9868>),
Rich Iannone [aut],
Alison Presmanes Hill [aut] (<https://orcid.org/0000-0002-8082-1890>),
Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Google LLC [ctb, cph] (https://distill.pub/guide/),
Nick Williams [ctb, cph] (https://wicky.nillia.ms/headroom.js/),
Denis Demchenko [ctb, cph] (https://github.com/lancedikson/bowser),
The Polymer Authors [ctb, cph]
(https://www.webcomponents.org/polyfills/),
Gábor Csárdi [ctb, cph] (whoami),
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between distill versions 1.1 dated 2020-12-02 and 1.2 dated 2021-01-13
DESCRIPTION | 8 MD5 | 50 ++-- NEWS.md | 18 + R/collections.R | 73 +++++ R/create.R | 35 ++ R/dependencies.R | 22 + R/distill_article.R | 118 ++++++--- R/distill_website.R | 123 +++++++++- R/import.R | 2 R/metadata.R | 1 R/navigation.R | 9 R/site_includes.R | 58 +++- R/sitemap.R | 38 +-- R/theme.R | 12 R/utils.R | 6 inst/rmarkdown/templates/distill_article/resources/alt-format.html |only inst/rmarkdown/templates/distill_article/resources/base-style.css | 66 +++-- inst/rmarkdown/templates/distill_article/resources/distill.html | 32 ++ inst/rmarkdown/templates/distill_article/resources/navbar.html | 6 inst/rmarkdown/templates/distill_article/resources/search.html | 13 - inst/www/popper |only inst/www/tippy |only man/create_article.Rd | 14 + man/create_post.Rd | 3 man/distill_article.Rd | 7 tests/testthat/_snaps/theme.md | 8 26 files changed, 561 insertions(+), 161 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-12 1.1.1
2020-12-16 1.1.0
2020-08-31 0.1.0
Title: Cycle-Free Flux Balance Analysis (CycleFreeFlux)
Description: Implement cycle-Free flux balance analysis (CycleFreeFlux), cycle-free flux variability, and Random Sampling of solution space.
Desouki, A. A., Jarre, F., Gelius-Dietrich, G., & Lercher, M. J. (2015). CycleFreeFlux: efficient removal of thermodynamically
infeasible loops from flux distributions. Bioinformatics, 31(13), 2159-2165. <doi:10.1093/bioinformatics/btv096>.
Flux balance analysis is a technique to find fluxes in metabolic models at steady state.
It is described in Orth, J.D., Thiele, I. and Palsson, B.O. What is flux balance analysis? Nat. Biotech. 28, 245-248 (2010).
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>
Diff between sybilcycleFreeFlux versions 2.0.1 dated 2019-12-15 and 2.0.2 dated 2021-01-13
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS | 4 ++++ data/iAF1260.RData |binary data/iMM904.RData |binary 5 files changed, 14 insertions(+), 10 deletions(-)
More information about sybilcycleFreeFlux at CRAN
Permanent link
Title: Single Cell mRNA Soup eXterminator
Description: Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.
Author: Matthew Daniel Young
Maintainer: Matthew Daniel Young <my4@sanger.ac.uk>
Diff between SoupX versions 1.4.8 dated 2020-10-15 and 1.5.0 dated 2021-01-13
DESCRIPTION | 12 +++---- MD5 | 20 ++++++------ R/load10X.R | 7 ++-- README.md | 16 ++++++++- build/vignette.rds |binary inst/CITATION | 10 +++--- inst/doc/pbmcTutorial.R | 74 ++++++++++++++++++++++----------------------- inst/doc/pbmcTutorial.html | 67 +++++++++++++++++++--------------------- man/PBMC_metaData.Rd | 4 +- man/PBMC_sc.Rd | 4 +- man/scToy.Rd | 4 +- 11 files changed, 117 insertions(+), 101 deletions(-)
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre]
(<https://orcid.org/0000-0001-9397-0900>),
Grigorios Papageorgiou [aut],
Pedro Miranda Afonso [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.1-1 dated 2021-01-11 and 0.1-2 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/help_functions.R | 3 ++- R/jm.R | 2 ++ R/jm_fit.R | 20 -------------------- man/JMbayes2.Rd | 4 ++-- src/JMbayes2_D.h | 4 ++-- src/JMbayes2_LogDens.h | 2 +- 9 files changed, 27 insertions(+), 38 deletions(-)
Title: Modeling Spatially Varying Coefficients
Description: Implements a maximum likelihood estimation (MLE)
method for estimation and prediction of Gaussian process-based
spatially varying coefficient (SVC) models
(Dambon et al. (2021a) <doi:10.1016/j.spasta.2020.100470>).
Covariance tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can
be applied such that the method scales to large data. Further, it implements
a joint variable selection of the fixed and random effects (Dambon et al.
(2021b) <arXiv:2101.01932>).
Author: Jakob A. Dambon [aut, cre] (<https://orcid.org/0000-0001-5855-2017>),
Fabio Sigrist [ctb] (<https://orcid.org/0000-0002-3994-2244>),
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>)
Maintainer: Jakob A. Dambon <jakob.dambon@math.uzh.ch>
Diff between varycoef versions 0.2.12 dated 2020-07-18 and 0.3.0 dated 2021-01-13
DESCRIPTION | 25 MD5 | 32 NAMESPACE | 20 R/BIC-SVC_mle.R |only R/SVC_mle.R | 37 - R/SVC_selection.R |only R/eff_dof.R |only R/logLik-SVC_mle.R | 6 R/varycoef.R | 56 + build/partial.rdb |binary inst/CITATION | 59 + inst/doc/example.html | 1585 +++++++++++++++++++++++-------------------- inst/doc/manual.html | 28 man/IC.SVC_mle.Rd |only man/SVC_mle.Rd | 14 man/SVC_selection.Rd |only man/SVC_selection_control.Rd |only man/predict.SVC_mle.Rd | 6 man/varycoef.Rd | 57 + vignettes/bibliography.bib | 27 20 files changed, 1152 insertions(+), 800 deletions(-)
Title: Data Frame Class for Tracking Data
Description: Data frame class for storing collective movement data (e.g. fish
schools, ungulate herds, baboon troops) collected from GPS trackers or
computer vision tracking software.
Author: Simon Garnier [aut, cre] (<https://orcid.org/0000-0002-3886-3974>)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between trackdf versions 0.2.1 dated 2019-08-04 and 0.2.2 dated 2021-01-13
DESCRIPTION | 10 MD5 | 36 +-- NEWS.md | 14 + R/track.R | 117 ++++++----- build/vignette.rds |binary inst/doc/z1_install.Rmd | 2 inst/doc/z1_install.html | 237 +++------------------- inst/doc/z2_build.R | 16 - inst/doc/z2_build.html | 348 ++++++++------------------------- inst/doc/z3_manipulate.R | 48 ++-- inst/doc/z3_manipulate.html | 455 ++++++++++++++------------------------------ man/conversions.Rd | 3 man/is_track.Rd | 4 man/rbind_track.Rd | 6 man/short_tracks.Rd | 6 man/sub-.track.Rd | 12 - man/track_.Rd | 39 ++- man/tracks.Rd | 6 vignettes/z1_install.Rmd | 2 19 files changed, 449 insertions(+), 912 deletions(-)
Title: Survey Sampling
Description: Functions to draw random samples using different sampling schemes are available. Functions are also provided to obtain (generalized) calibration weights, different estimators, as well some variance estimators.
Author: Yves Till<e9> <yves.tille@unine.ch>, Alina Matei <alina.matei@unine.ch>
Maintainer: Alina Matei <alina.matei@unine.ch>
Diff between sampling versions 2.8 dated 2016-12-22 and 2.9 dated 2021-01-13
DESCRIPTION | 11 ++--- MD5 | 79 +++++++++++++++++++------------------- R/UPminimalsupport.R | 2 R/UPrandompivotal.R | 2 R/UPrandomsystematic.R | 2 R/calib.r | 25 +++++++++--- R/checkcalibration.R | 31 +++++++++----- R/fastflightcube.R | 4 - R/gencalib.R | 29 ++++++++----- R/mstage.r | 4 - R/srswor.R | 2 R/strata.r | 2 build/vignette.rds |binary data/MU284.rda |binary data/rec99.rda |only inst/doc/HT_Hajek_estimators.R | 1 inst/doc/HT_Hajek_estimators.Snw | 10 ++-- inst/doc/HT_Hajek_estimators.pdf |binary inst/doc/UPexamples.R | 5 +- inst/doc/UPexamples.Snw | 4 + inst/doc/UPexamples.pdf |binary inst/doc/calibration.R | 13 ++---- inst/doc/calibration.Snw | 23 +++++------ inst/doc/calibration.pdf |binary man/UPmaxentropy.Rd | 2 man/UPmultinomial.Rd | 13 +++--- man/UPtille.Rd | 3 - man/balancedstratification.Rd | 21 ---------- man/belgianmunicipalities.Rd | 3 - man/calib.Rd | 9 +--- man/checkcalibration.Rd | 2 man/gencalib.Rd | 2 man/rec99.Rd |only man/regest.Rd | 2 man/regest_strata.Rd | 2 man/samplecube.Rd | 10 ++-- man/srswr.Rd | 2 man/varest.Rd | 2 src/init.c |only vignettes/HT_Hajek_estimators.Snw | 10 ++-- vignettes/UPexamples.Snw | 4 + vignettes/calibration.Snw | 23 +++++------ 42 files changed, 190 insertions(+), 169 deletions(-)
Title: Read and Write 'MTrackJ Data Files'
Description: 'MTrackJ' is an 'ImageJ' plugin for motion tracking and analysis (see
<https://imagescience.org/meijering/software/mtrackj/>). This package reads
and writes 'MTrackJ Data Files' ('.mdf', see
<https://imagescience.org/meijering/software/mtrackj/format/>). It supports
2D data and read/writes cluster, point, and channel information. If desired,
generates track identifiers that are unique over the clusters.
See the project page for more information and examples.
Author: Gerhard Burger [aut, cre] (<https://orcid.org/0000-0003-1062-5576>)
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between mdftracks versions 0.2.0 dated 2017-02-06 and 0.2.1 dated 2021-01-13
DESCRIPTION | 20 LICENSE | 1348 +++++++++++++++++++++--------------------- MD5 | 32 NAMESPACE | 13 NEWS.md | 21 R/data.R | 32 R/mdftracks.R | 654 ++++++++++---------- README.md | 344 +++++----- inst/WORDLIST |only man/mdftracks.Rd | 29 man/mdftracks.example.data.Rd | 58 - man/read.mdf.Rd | 91 +- man/write.mdf.Rd | 161 ++--- tests/spelling.R |only tests/testthat.R | 8 tests/testthat/testReadMdf.R | 154 ++-- tests/testthat/testWriteMdf.R | 389 ++++++------ tests/testthat/test_mdf.mdf | 40 - 18 files changed, 1720 insertions(+), 1674 deletions(-)
Title: Matrix Exponential, Log, 'etc'
Description: Computation of the matrix exponential, logarithm, sqrt,
and related quantities, using traditional and modern methods.
Author: Vincent Goulet, Christophe Dutang, Martin Maechler,
David Firth, Marina Shapira, Michael Stadelmann
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between expm versions 0.999-5 dated 2020-07-20 and 0.999-6 dated 2021-01-13
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 31 ++++++++++++++++--------------- R/balance.R | 13 +++++++++++-- R/expm.R | 21 ++++++++++++--------- R/expm2.R | 3 +-- build/partial.rdb |only build/vignette.rds |binary demo/balanceTst.R | 18 +++++++++--------- inst/doc/expm.pdf |binary man/balance.Rd | 7 ++++--- man/expm.Higham08.Rd | 6 +++--- man/expm.Rd | 2 +- man/logm.Rd | 2 +- tests/bal-ex.R | 4 ++-- tests/ex.R | 10 +++++----- tests/exact-ex.R | 6 +++--- 17 files changed, 94 insertions(+), 60 deletions(-)
Title: Interactive Genomic Visualization of Biological Data
Description: Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions
of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces
a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data
associated with chromosome elements (like gene expression) in the form of heat colors which can be highly
advantageous in the scientific interpretations and research work. Because of the large size of the chromosomes,
it is impractical to visualize each element on the same plot. However, the plot provides a magnified view for each
of chromosome locus to render additional information and visualization specific for that location. You can map
thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings
(like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the
chromosome at a location showing each mapped element in sequential order. The package provide multiple features
like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling.
The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.
Author: Lakshay Anand [aut, cre]
Maintainer: Lakshay Anand <lakshayanand15@gmail.com>
Diff between chromoMap versions 0.2 dated 2019-04-10 and 0.3 dated 2021-01-13
chromoMap-0.2/chromoMap/inst/htmlwidgets/lib/chromoMap-1.0 |only chromoMap-0.3/chromoMap/DESCRIPTION | 16 chromoMap-0.3/chromoMap/LICENSE | 4 chromoMap-0.3/chromoMap/MD5 | 33 chromoMap-0.3/chromoMap/R/chromoMap.R | 264 chromoMap-0.3/chromoMap/build/vignette.rds |binary chromoMap-0.3/chromoMap/inst/doc/chromoMap.R | 354 chromoMap-0.3/chromoMap/inst/doc/chromoMap.Rmd | 599 chromoMap-0.3/chromoMap/inst/doc/chromoMap.html |22667 ++++++++++++- chromoMap-0.3/chromoMap/inst/htmlwidgets/chromoMap.js | 10 chromoMap-0.3/chromoMap/inst/htmlwidgets/chromoMap.yaml | 6 chromoMap-0.3/chromoMap/inst/htmlwidgets/lib/chromoMap-3.0 |only chromoMap-0.3/chromoMap/man/chromoMap.Rd | 102 chromoMap-0.3/chromoMap/vignettes/chromoMap.Rmd | 599 chromoMap-0.3/chromoMap/vignettes/data |only 15 files changed, 24226 insertions(+), 428 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>),
Vector Exponential Smoothing (de Silva et al., 2010, <doi: 10.1177/1471082X0901000401>) in state space forms,
several simulation functions and intermittent demand state space models. It also allows dealing with
intermittent demand based on the iETS framework (Svetunkov & Boylan, 2017, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 3.0.0 dated 2020-12-09 and 3.0.1 dated 2021-01-13
smooth-3.0.0/smooth/R/gnorm.R |only smooth-3.0.1/smooth/DESCRIPTION | 10 smooth-3.0.1/smooth/MD5 | 135 +- smooth-3.0.1/smooth/NAMESPACE | 6 smooth-3.0.1/smooth/NEWS | 34 smooth-3.0.1/smooth/R/RcppExports.R | 24 smooth-3.0.1/smooth/R/adam.R | 957 ++++++++++++++------- smooth-3.0.1/smooth/R/adamGeneral.R | 301 +++++- smooth-3.0.1/smooth/R/autoadam.R | 180 ++- smooth-3.0.1/smooth/R/ces.R | 2 smooth-3.0.1/smooth/R/es.R | 4 smooth-3.0.1/smooth/R/gum.R | 2 smooth-3.0.1/smooth/R/msarima.R | 30 smooth-3.0.1/smooth/R/sma.R | 2 smooth-3.0.1/smooth/R/ssarima.R | 2 smooth-3.0.1/smooth/R/ssfunctions.R | 18 smooth-3.0.1/smooth/R/ves.R | 42 smooth-3.0.1/smooth/R/vssFunctions.R | 12 smooth-3.0.1/smooth/build/partial.rdb |binary smooth-3.0.1/smooth/inst/doc/adam.R | 2 smooth-3.0.1/smooth/inst/doc/adam.Rmd | 6 smooth-3.0.1/smooth/inst/doc/adam.html | 588 ++++++------ smooth-3.0.1/smooth/inst/doc/ces.html | 24 smooth-3.0.1/smooth/inst/doc/es.html | 222 ++-- smooth-3.0.1/smooth/inst/doc/gum.html | 66 - smooth-3.0.1/smooth/inst/doc/oes.R | 3 smooth-3.0.1/smooth/inst/doc/oes.Rmd | 10 smooth-3.0.1/smooth/inst/doc/oes.html | 158 +-- smooth-3.0.1/smooth/inst/doc/simulate.html | 80 - smooth-3.0.1/smooth/inst/doc/sma.html | 6 smooth-3.0.1/smooth/inst/doc/smooth.html | 4 smooth-3.0.1/smooth/inst/doc/ssarima.html | 42 smooth-3.0.1/smooth/inst/doc/ves.html | 20 smooth-3.0.1/smooth/man/adam.Rd | 58 - smooth-3.0.1/smooth/man/auto.ces.Rd | 3 smooth-3.0.1/smooth/man/auto.gum.Rd | 5 smooth-3.0.1/smooth/man/auto.msarima.Rd | 7 smooth-3.0.1/smooth/man/auto.ssarima.Rd | 7 smooth-3.0.1/smooth/man/ces.Rd | 7 smooth-3.0.1/smooth/man/es.Rd | 11 smooth-3.0.1/smooth/man/gum.Rd | 9 smooth-3.0.1/smooth/man/msarima.Rd | 31 smooth-3.0.1/smooth/man/sim.es.Rd | 2 smooth-3.0.1/smooth/man/sim.oes.Rd | 2 smooth-3.0.1/smooth/man/sim.sma.Rd | 2 smooth-3.0.1/smooth/man/sim.ssarima.Rd | 4 smooth-3.0.1/smooth/man/sim.ves.Rd | 2 smooth-3.0.1/smooth/man/sma.Rd | 2 smooth-3.0.1/smooth/man/smooth.Rd | 4 smooth-3.0.1/smooth/man/smoothCombine.Rd | 7 smooth-3.0.1/smooth/man/ssarima.Rd | 17 smooth-3.0.1/smooth/man/ves.Rd | 20 smooth-3.0.1/smooth/src/RcppExports.cpp | 42 smooth-3.0.1/smooth/src/adamGeneral.cpp | 57 - smooth-3.0.1/smooth/src/adamGeneral.h | 20 smooth-3.0.1/smooth/src/adamRefitter.cpp | 31 smooth-3.0.1/smooth/src/adamSimulator.cpp | 11 smooth-3.0.1/smooth/src/ssGeneral.cpp | 18 smooth-3.0.1/smooth/tests/testthat/test_adam.R | 365 ++++---- smooth-3.0.1/smooth/tests/testthat/test_ces.R | 7 smooth-3.0.1/smooth/tests/testthat/test_es.R | 17 smooth-3.0.1/smooth/tests/testthat/test_ges.R | 35 smooth-3.0.1/smooth/tests/testthat/test_oes.R | 23 smooth-3.0.1/smooth/tests/testthat/test_simulate.R | 46 - smooth-3.0.1/smooth/tests/testthat/test_ssarima.R | 51 - smooth-3.0.1/smooth/tests/testthat/test_ves.R | 32 smooth-3.0.1/smooth/vignettes/adam.Rmd | 6 smooth-3.0.1/smooth/vignettes/library.bib | 1 smooth-3.0.1/smooth/vignettes/oes.Rmd | 10 69 files changed, 2359 insertions(+), 1605 deletions(-)
Title: Data Access Tools for the Soil and Landscape Grid of Australia
Description: Provides access to soil and landscape grid of Australia raster datasets via existing open geospatial consortium web coverage services. See <https://www.clw.csiro.au/aclep/soilandlandscapegrid/index.html>.
Author: Lauren O'Brien [aut, cre] (<https://orcid.org/0000-0002-7336-2171>),
Ross Searle [ant] (<https://orcid.org/0000-0003-0256-1496>)
Maintainer: Lauren O'Brien <obrlsoilau@gmail.com>
Diff between slga versions 1.1.1 dated 2020-03-31 and 1.1.2 dated 2021-01-13
DESCRIPTION | 14 +-- MD5 | 30 ++++---- NAMESPACE | 2 NEWS.md | 5 + R/aoi_processing.R | 27 +------ R/get_data.R | 25 +++--- R/get_point_data.R | 9 +- R/raster_processing.R | 44 ++++++------ R/slga.R | 2 README.md | 11 +-- build/vignette.rds |binary inst/doc/slga.Rmd | 6 - inst/doc/slga.html | 128 +++++++++++++++++++++-------------- man/slga-package.Rd | 2 tests/testthat/test_aoi_processing.R | 17 ++-- vignettes/slga.Rmd | 6 - 16 files changed, 177 insertions(+), 151 deletions(-)
Title: Test Surveys by Simulating Spatially-Correlated Populations
Description: Simulate age-structured populations that vary in space and time and
explore the efficacy of a range of built-in or user-defined sampling
protocols to reproduce the population parameters of the known population.
(See Regular et al. (2020) <doi:10.1371/journal.pone.0232822> for more
details).
Author: Paul Regular [aut, cre] (<https://orcid.org/0000-0003-0318-2615>),
Jonathan Babyn [ctb],
Greg Robertson [ctb]
Maintainer: Paul Regular <Paul.Regular@dfo-mpo.gc.ca>
Diff between SimSurvey versions 0.1.2 dated 2020-09-09 and 0.1.3 dated 2021-01-13
DESCRIPTION | 12 +++++----- MD5 | 18 +++++++-------- NEWS.md | 9 +++++++ R/make_grid.R | 48 ++++++++++++++++-------------------------- R/sim_pop.R | 2 - R/zzz.R | 12 ++++++---- README.md | 5 +++- build/vignette.rds |binary inst/doc/custom_closures.html | 10 ++++++++ man/sim_R.Rd | 2 - 10 files changed, 66 insertions(+), 52 deletions(-)
Title: Simulate Survival Data
Description: Simulate survival times from standard parametric survival
distributions (exponential, Weibull, Gompertz), 2-component mixture
distributions, or a user-defined hazard, log hazard, cumulative hazard,
or log cumulative hazard function. Baseline covariates can be included
under a proportional hazards assumption.
Time dependent effects (i.e. non-proportional hazards) can be included by
interacting covariates with linear time or a user-defined function of time.
Clustered event times are also accommodated.
The 2-component mixture distributions can allow for a variety of flexible
baseline hazard functions reflecting those seen in practice.
If the user wishes to provide a user-defined
hazard or log hazard function then this is possible, and the resulting
cumulative hazard function does not need to have a closed-form solution.
For details see the supporting paper <doi:10.18637/jss.v097.i03>.
Note that this package is modelled on the 'survsim' package available in
the 'Stata' software (see Crowther and Lambert (2012)
<https://www.stata-journal.com/sjpdf.html?articlenum=st0275> or
Crowther and Lambert (2013) <doi:10.1002/sim.5823>).
Author: Sam Brilleman [cre, aut, cph],
Alessandro Gasparini [ctb]
Maintainer: Sam Brilleman <sam.brilleman@gmail.com>
Diff between simsurv versions 0.2.3 dated 2019-02-01 and 1.0.0 dated 2021-01-13
DESCRIPTION | 45 +- MD5 | 27 - NEWS.md | 22 + R/simsurv.R | 93 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/simsurv_technical.R | 2 inst/doc/simsurv_technical.Rmd | 8 inst/doc/simsurv_technical.html | 233 +++++++++++- inst/doc/simsurv_usage.R | 30 - inst/doc/simsurv_usage.html | 752 ++++++++++++++++++++++++++-------------- man/brcancer.Rd | 68 +-- man/simsurv.Rd | 717 ++++++++++++++++++++------------------ vignettes/simsurv_technical.Rmd | 8 15 files changed, 1294 insertions(+), 711 deletions(-)
Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this,
R developers can use variables, inheritance, and functions to generate
dynamic style sheets. The package uses the 'Sass CSS' extension language,
which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut],
Timothy Mastny [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>),
Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] (LibSass library),
Greter Marcel [ctb, cph] (LibSass library),
Mifsud Michael [ctb, cph] (LibSass library),
Hampton Catlin [ctb, cph] (LibSass library),
Natalie Weizenbaum [ctb, cph] (LibSass library),
Chris Eppstein [ctb, cph] (LibSass library),
Adams Joseph [ctb, cph] (json.cpp),
Trifunovic Nemanja [ctb, cph] (utf8.h)
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.2.0 dated 2020-03-18 and 0.3.0 dated 2021-01-13
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Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between rmdformats versions 1.0.0 dated 2020-11-23 and 1.0.1 dated 2021-01-13
rmdformats-1.0.0/rmdformats/inst/templates/readthedown/fonts/RobotoSlab-Regular.ttf |only rmdformats-1.0.0/rmdformats/inst/templates/readthedown/readthedown_fonts.css |only rmdformats-1.0.0/rmdformats/inst/templates/robobook/fonts/RobotoSlab-Regular.ttf |only rmdformats-1.0.0/rmdformats/man/knit_print.pilltabs.Rd |only rmdformats-1.0.0/rmdformats/man/print.pilltabs.Rd |only rmdformats-1.0.0/rmdformats/tools |only rmdformats-1.0.1/rmdformats/DESCRIPTION | 10 rmdformats-1.0.1/rmdformats/MD5 | 75 - rmdformats-1.0.1/rmdformats/NEWS | 12 rmdformats-1.0.1/rmdformats/R/downcute.R | 12 rmdformats-1.0.1/rmdformats/R/html_docco.R | 2 rmdformats-1.0.1/rmdformats/R/html_template.R | 3 rmdformats-1.0.1/rmdformats/R/pilltabs.R | 72 - rmdformats-1.0.1/rmdformats/R/readthedown.R | 8 rmdformats-1.0.1/rmdformats/R/robobook.R | 2 rmdformats-1.0.1/rmdformats/README.md | 20 rmdformats-1.0.1/rmdformats/inst/rmarkdown/templates/downcute/template.yaml | 2 rmdformats-1.0.1/rmdformats/inst/rmarkdown/templates/robobook/template.yaml | 2 rmdformats-1.0.1/rmdformats/inst/templates/downcute/downcute.css | 4 rmdformats-1.0.1/rmdformats/inst/templates/html_clean/clean.css | 12 rmdformats-1.0.1/rmdformats/inst/templates/html_docco/docco.css | 17 rmdformats-1.0.1/rmdformats/inst/templates/material/material.css | 8 rmdformats-1.0.1/rmdformats/inst/templates/material/material.html | 2 rmdformats-1.0.1/rmdformats/inst/templates/readthedown/readthedown.css | 62 - rmdformats-1.0.1/rmdformats/inst/templates/readthedown/readthedown_fonts_download.css |only rmdformats-1.0.1/rmdformats/inst/templates/readthedown/readthedown_fonts_embed.css |only rmdformats-1.0.1/rmdformats/inst/templates/robobook/robobook.css | 482 +++------- rmdformats-1.0.1/rmdformats/inst/templates/robobook/robobook_fonts_download.css | 2 rmdformats-1.0.1/rmdformats/inst/templates/robobook/robobook_fonts_embed.css | 7 rmdformats-1.0.1/rmdformats/inst/templates/template.html | 6 rmdformats-1.0.1/rmdformats/man/downcute.Rd | 12 rmdformats-1.0.1/rmdformats/man/figures |only rmdformats-1.0.1/rmdformats/man/html_docco.Rd | 2 rmdformats-1.0.1/rmdformats/man/pilltabs.Rd | 12 rmdformats-1.0.1/rmdformats/man/pilltabs_print.Rd |only rmdformats-1.0.1/rmdformats/man/readthedown.Rd | 2 rmdformats-1.0.1/rmdformats/man/robobook.Rd | 2 37 files changed, 397 insertions(+), 455 deletions(-)
Title: Processing METAR Weather Reports
Description: Allows to download current and historical METAR weather reports
extract and parse basic parameters and present main weather information.
Current reports are downloaded from Aviation Weather Center
<https://www.aviationweather.gov/metar> and historical reports from
Iowa Environmental Mesonet web page of Iowa State University
ASOS-AWOS-METAR <http://mesonet.agron.iastate.edu/AWOS/>.
Author: Pawel Cwiek [aut, cre],
David Megginson [ctb] (Author of data set with airports list
https://ourairports.com/data/),
Greg Thompson [ctb] (Author of data set with airports list
https://www.aviationweather.gov/docs/metar/stations.txt)
Maintainer: Pawel Cwiek <prc.altodato@gmail.com>
Diff between pmetar versions 0.2.7.0 dated 2020-09-09 and 0.3.0 dated 2021-01-13
DESCRIPTION | 6 MD5 | 73 +-- NAMESPACE | 1 R/metar_airport.R | 2 R/metar_cloud_coverage.R | 23 R/metar_day.R | 2 R/metar_decode.R | 28 - R/metar_dew_point.R | 2 R/metar_dir.R | 2 R/metar_get.R | 13 R/metar_get_historical.R | 27 - R/metar_gust.R | 2 R/metar_hour.R | 2 R/metar_iata_icao.R | 2 R/metar_location.R | 2 R/metar_pressure.R | 14 R/metar_rwy_visibility.R |only R/metar_speed.R | 15 R/metar_temp.R | 2 R/metar_time_zone.R | 2 R/metar_visibility.R | 2 R/metar_windshear.R | 2 R/metar_wx_codes.R | 12 README.md | 98 +++- build/vignette.rds |binary inst/doc/pmetar.R | 13 inst/doc/pmetar.Rmd | 27 - inst/doc/pmetar.html | 669 +++++++++++------------------ man/metar_decode.Rd | 13 man/metar_get.Rd | 1 man/metar_pressure.Rd | 4 man/metar_rwy_visibility.Rd |only man/metar_speed.Rd | 3 tests/testthat/test_metar_cloud_coverage.R | 5 tests/testthat/test_metar_get.R | 4 tests/testthat/test_metar_pressure.R | 15 tests/testthat/test_metar_rwy_visibility.R |only tests/testthat/test_metar_speed.R | 15 vignettes/pmetar.Rmd | 27 - 39 files changed, 565 insertions(+), 565 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.0.10 dated 2020-11-22 and 0.0.11 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre],
Sebastian Krantz [ctb]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between fixest versions 0.8.0 dated 2020-12-14 and 0.8.1 dated 2021-01-13
DESCRIPTION | 12 MD5 | 87 +-- NAMESPACE | 4 NEWS.md | 233 +++++---- R/ESTIMATION_FUNS.R | 90 ++- R/Lagging.R | 31 + R/Methods.R | 4 R/MiscFuns.R | 925 ++++++++++++++++++++++++++++--------- R/RcppExports.R | 4 R/coefplot.R | 11 R/etable.R | 121 ++-- R/fixest_env.R | 276 +++++++---- R/fixest_multi.R | 12 R/index.R | 1 inst/doc/exporting_tables.html | 187 +++---- inst/doc/fixest_walkthrough.R | 62 ++ inst/doc/fixest_walkthrough.Rmd | 80 +++ inst/doc/fixest_walkthrough.html | 352 +++++++++----- inst/doc/multiple_estimations.html | 176 +++---- inst/doc/standard_errors.html | 4 man/aggregate.fixest.Rd |only man/coef.fixest.Rd | 7 man/coeftable.Rd | 7 man/demean.Rd | 4 man/etable.Rd | 29 - man/feNmlm.Rd | 5 man/feglm.Rd | 9 man/femlm.Rd | 10 man/feols.Rd | 10 man/fitted.fixest.Rd | 7 man/fixest.Rd | 1 man/i.Rd | 44 + man/resid.fixest.Rd | 12 man/setFixest_estimation.Rd | 4 man/setFixest_se.Rd | 7 man/sigma.fixest.Rd | 2 man/stepwise.Rd | 31 - man/summary.fixest.Rd | 26 - man/summary.fixest_multi.Rd | 8 man/vcov.fixest.Rd | 4 man/weights.fixest.Rd | 2 src/RcppExports.cpp | 14 src/misc_funs.cpp | 52 ++ tests/fixest_tests.R | 146 +++++ vignettes/fixest_walkthrough.Rmd | 80 +++ 45 files changed, 2263 insertions(+), 930 deletions(-)
Title: Generate Alluvial Plots with a Single Line of Code
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data
over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in
Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694>
Their graphical grammar however is a bit more complex then that of a regular x/y
plots. The 'ggalluvial' package made a great job of translating that grammar into
'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial
plot, however there still remains a multi-layered complexity that makes it difficult
to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple
interface to this package that allows you to produce a decent alluvial plot from any
dataframe in either long or wide format from a single line of code while also handling
continuous data. It is meant to allow a quick visualisation of entire dataframes
with a focus on different colouring options that can make alluvial plots a great
tool for data exploration.
Author: Bjoern Koneswarakantha [aut, cre]
(<https://orcid.org/0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Diff between easyalluvial versions 0.2.3 dated 2020-05-07 and 0.3.0 dated 2021-01-13
easyalluvial-0.2.3/easyalluvial/README.md |only easyalluvial-0.3.0/easyalluvial/DESCRIPTION | 19 easyalluvial-0.3.0/easyalluvial/MD5 | 69 - easyalluvial-0.3.0/easyalluvial/NAMESPACE | 11 easyalluvial-0.3.0/easyalluvial/NEWS.md | 7 easyalluvial-0.3.0/easyalluvial/R/alluvial_model_response.R | 605 ++++++++-- easyalluvial-0.3.0/easyalluvial/R/alluvial_wide.R | 15 easyalluvial-0.3.0/easyalluvial/R/expect_doppelganger.R |only easyalluvial-0.3.0/easyalluvial/R/manip.R | 69 - easyalluvial-0.3.0/easyalluvial/R/plot_imp.R | 2 easyalluvial-0.3.0/easyalluvial/R/plot_marginal_hist.R | 14 easyalluvial-0.3.0/easyalluvial/R/utils-pipe.R |only easyalluvial-0.3.0/easyalluvial/man/add_imp_plot.Rd | 2 easyalluvial-0.3.0/easyalluvial/man/add_marginal_histograms.Rd | 2 easyalluvial-0.3.0/easyalluvial/man/alluvial_model_response.Rd | 10 easyalluvial-0.3.0/easyalluvial/man/alluvial_model_response_caret.Rd | 42 easyalluvial-0.3.0/easyalluvial/man/alluvial_model_response_parsnip.Rd |only easyalluvial-0.3.0/easyalluvial/man/check_pkg_installed.Rd |only easyalluvial-0.3.0/easyalluvial/man/figures/README-plot_long-1.png |binary easyalluvial-0.3.0/easyalluvial/man/figures/README-unnamed-chunk-3-1.png |binary easyalluvial-0.3.0/easyalluvial/man/figures/README-unnamed-chunk-5-1.png |binary easyalluvial-0.3.0/easyalluvial/man/figures/README-wide_plot-1.png |binary easyalluvial-0.3.0/easyalluvial/man/get_data_space.Rd | 2 easyalluvial-0.3.0/easyalluvial/man/get_pdp_predictions.Rd | 44 easyalluvial-0.3.0/easyalluvial/man/get_pdp_predictions_seq.Rd |only easyalluvial-0.3.0/easyalluvial/man/manip_bin_numerics.Rd | 6 easyalluvial-0.3.0/easyalluvial/man/manip_factor_2_numeric.Rd | 3 easyalluvial-0.3.0/easyalluvial/man/pdp_predictions.Rd |only easyalluvial-0.3.0/easyalluvial/man/pipe.Rd |only easyalluvial-0.3.0/easyalluvial/man/plot_all_hists.Rd | 2 easyalluvial-0.3.0/easyalluvial/man/tidy_imp.Rd | 10 easyalluvial-0.3.0/easyalluvial/tests/testthat/Rplots.pdf |binary easyalluvial-0.3.0/easyalluvial/tests/testthat/test_alluvial_long.R | 26 easyalluvial-0.3.0/easyalluvial/tests/testthat/test_alluvial_model_response.R | 260 +++- easyalluvial-0.3.0/easyalluvial/tests/testthat/test_alluvial_wide.R | 28 easyalluvial-0.3.0/easyalluvial/tests/testthat/test_manip.R | 18 easyalluvial-0.3.0/easyalluvial/tests/testthat/test_model.R |only easyalluvial-0.3.0/easyalluvial/tests/testthat/test_plot_condensation.R | 6 easyalluvial-0.3.0/easyalluvial/tests/testthat/test_plot_imp.R | 10 easyalluvial-0.3.0/easyalluvial/tests/testthat/test_plot_marginal_histograms.R | 54 40 files changed, 1029 insertions(+), 307 deletions(-)
Title: Data-Limited Methods Toolkit
Description: A collection of data-limited management procedures that can be evaluated
with management strategy evaluation with the MSEtool package, or applied to
fishery data to provide management recommendations.
Author: Tom Carruthers [aut],
Quang Huynh [aut],
Adrian Hordyk [aut, cre],
M. Bryan [ctb],
HF. Geremont [ctb],
C. Grandin [ctb],
W. Harford [ctb],
Q. Huynh [ctb],
C. Walters [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between DLMtool versions 5.4.5 dated 2020-06-16 and 6.0.0 dated 2021-01-13
DLMtool-5.4.5/DLMtool/R/Awatea2OM.R |only DLMtool-5.4.5/DLMtool/R/Blow_funcs.R |only DLMtool-5.4.5/DLMtool/R/DFO.R |only DLMtool-5.4.5/DLMtool/R/DLMtool-package.R |only DLMtool-5.4.5/DLMtool/R/Data2csv.R |only DLMtool-5.4.5/DLMtool/R/Data_Functions.R |only DLMtool-5.4.5/DLMtool/R/Data_Plotting.R |only DLMtool-5.4.5/DLMtool/R/Data_make_update.R |only DLMtool-5.4.5/DLMtool/R/DefineClasses.r |only DLMtool-5.4.5/DLMtool/R/Fease_Functions.R |only DLMtool-5.4.5/DLMtool/R/IOTC.R |only DLMtool-5.4.5/DLMtool/R/MPs_Reference.R |only DLMtool-5.4.5/DLMtool/R/MSC.R |only DLMtool-5.4.5/DLMtool/R/MSE_Plotting.R |only DLMtool-5.4.5/DLMtool/R/MSE_Plotting_PMs.R |only DLMtool-5.4.5/DLMtool/R/MSE_functions.R |only DLMtool-5.4.5/DLMtool/R/MSYplotDev.R |only DLMtool-5.4.5/DLMtool/R/Misc_Exported.R |only DLMtool-5.4.5/DLMtool/R/Misc_Internal.R |only DLMtool-5.4.5/DLMtool/R/OM_Plotting.R |only DLMtool-5.4.5/DLMtool/R/OM_functions.R |only DLMtool-5.4.5/DLMtool/R/OM_init_doc.R |only DLMtool-5.4.5/DLMtool/R/OMts_dev.R |only DLMtool-5.4.5/DLMtool/R/PMobjects.R |only DLMtool-5.4.5/DLMtool/R/PMtable.R |only DLMtool-5.4.5/DLMtool/R/Roxy_DataObjects.r |only DLMtool-5.4.5/DLMtool/R/SS2DLM.R |only DLMtool-5.4.5/DLMtool/R/SampleOM.R |only DLMtool-5.4.5/DLMtool/R/Sketch_Functions.R |only DLMtool-5.4.5/DLMtool/R/StochasticSRA.R |only DLMtool-5.4.5/DLMtool/R/Turing.R |only DLMtool-5.4.5/DLMtool/R/data2OMfunctions.r |only DLMtool-5.4.5/DLMtool/R/iSCAM2DLM.R |only DLMtool-5.4.5/DLMtool/R/popdyn.R |only DLMtool-5.4.5/DLMtool/R/popdynDEVELOP.R |only DLMtool-5.4.5/DLMtool/R/runMSE.r |only DLMtool-5.4.5/DLMtool/R/sysdata.rda |only DLMtool-5.4.5/DLMtool/data |only DLMtool-5.4.5/DLMtool/inst |only DLMtool-5.4.5/DLMtool/man/BlankSelPlot.Rd |only DLMtool-5.4.5/DLMtool/man/Blow_opt.Rd |only DLMtool-5.4.5/DLMtool/man/CALsimp.Rd |only DLMtool-5.4.5/DLMtool/man/CSRA.Rd |only DLMtool-5.4.5/DLMtool/man/CSRAfunc.Rd |only DLMtool-5.4.5/DLMtool/man/CalcMPDynamics.Rd |only 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Title: Managing, Querying and Analyzing Tokenized Text
Description: Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations).
Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences),
similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages,
and the possibility to reconstruct original text from tokens to facilitate interpretation.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between corpustools versions 0.4.4 dated 2021-01-07 and 0.4.5 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/search_dictionary.r | 16 ++++++---------- R/udpipe_coref.r | 19 +++++++++++++++---- R/udpipe_tqueries.r | 2 +- inst/doc/corpustools.html | 14 +++++++------- 6 files changed, 38 insertions(+), 31 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>
Diff between bbsBayes versions 2.3.5.2020 dated 2020-11-26 and 2.3.6.2020 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/generate-indices.R | 11 ++++++----- R/generate-trends.R | 7 ++++--- R/plot-indices.R | 11 ++++++++--- README.md | 4 ++-- man/generate_indices.Rd | 11 ++++++----- man/generate_trends.Rd | 4 ++-- 8 files changed, 39 insertions(+), 31 deletions(-)
Title: Convert Png Files into Animated Png
Description: Convert several png files into an animated png file.
This package exports only a single function `apng'. Call the
apng function with a vector of file names (which should be
png files) to convert them to a single animated png file.
Author: Quinten Stokkink
Maintainer: Quinten Stokkink <q.a.stokkink@tudelft.nl>
Diff between apng versions 1.0 dated 2017-05-25 and 1.1 dated 2021-01-13
apng-1.0/apng/README.md |only apng-1.1/apng/DESCRIPTION | 8 ++++---- apng-1.1/apng/MD5 | 9 ++++----- apng-1.1/apng/R/reading.R | 2 +- apng-1.1/apng/build/partial.rdb |binary apng-1.1/apng/man/apng.Rd | 13 ++++++++++--- 6 files changed, 19 insertions(+), 13 deletions(-)
Title: Analysis and Prediction of Bicycle Rental Amount
Description: Provides functions for analyzing citizens' bicycle usage pattern and predicting rental amount on specific conditions.
Functions on this package interacts with data on 'tashudata' package, a 'drat' repository.
'tashudata' package contains rental/return history on public bicycle system('Tashu'), weather for 3 years and bicycle station information.
To install this data package, see the instructions at <https://github.com/zeee1/Tashu_Rpackage>.
top10_stations(), top10_paths() function visualizes image showing the most used top 10 stations and paths.
daily_bike_rental() and monthly_bike_rental() shows daily, monthly amount of bicycle rental.
create_train_dataset(), create_test_dataset() is data processing function for prediction.
Bicycle rental history from 2013 to 2014 is used to create training dataset and that on 2015 is for test dataset.
Users can make random-forest prediction model by using create_train_model()
and predict amount of bicycle rental in 2015 by using predict_bike_rental().
Author: Jiwon Min [aut, cre]
Maintainer: Jiwon Min <miw5281@gmail.com>
Diff between tashu versions 0.1.0 dated 2019-09-04 and 0.1.1 dated 2021-01-13
DESCRIPTION | 8 - MD5 | 16 +-- R/create_test_dataset.R | 5 R/create_train_dataset.R | 5 R/daily_bicycle_rental.R | 7 - R/monthly_bicycle_rental.R | 10 - build/vignette.rds |binary inst/doc/tashu.R | 30 ++--- inst/doc/tashu.html | 237 ++++++++++++++++++++++++--------------------- 9 files changed, 168 insertions(+), 150 deletions(-)
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] (Methods for mutating vertical tabs &
updateMultiInput),
Wil Davis [ctb] (numericRangeInput function),
Spencer Matthews [ctb] (autoNumeric methods)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.5.4 dated 2020-10-06 and 0.5.5 dated 2021-01-13
DESCRIPTION | 6 +- MD5 | 59 +++++++++++--------- NAMESPACE | 3 + NEWS.md | 10 +++ R/dependencies.R | 23 +++++++ R/input-airDatepicker.R | 13 ++-- R/input-autonumeric.R | 9 ++- R/input-awesomecheckbox.R | 2 R/input-awesomeradio.R | 2 R/input-checkboxgroupbuttons.R | 2 R/input-materialswitch.R | 18 +++--- R/input-radiogroupbuttons.R | 4 + R/input-sliderText.R | 2 R/progressBars.R | 45 +++++++++------ R/shinyWidgetsGallery.R | 2 R/stati-card.R |only R/sweetalert.R | 31 +++++++--- inst/assets/air-datepicker/i18n/datepicker.it.js |only inst/assets/air-datepicker2/i18n/datepicker.it.js |only inst/assets/bounty |only inst/assets/progress-bars/progress-bars-bindings.js | 6 +- inst/assets/shinyWidgets-bindings.min.js | 2 inst/assets/stati |only inst/assets/tools.R | 2 inst/examples/shinyWidgets/global.R | 17 ++++- inst/examples/shinyWidgets/server.R | 11 ++- inst/examples/shinyWidgets/ui.R | 43 +++++++------- man/airDatepicker.Rd | 7 +- man/inputSweetAlert.Rd | 5 + man/stati-card.Rd |only man/sweetalert.Rd | 16 ++++- tests/testthat/test-shinyWidgetsGallery.R | 10 ++- tests/testthat/test-sliderText.R | 7 +- 33 files changed, 241 insertions(+), 116 deletions(-)
Title: Formula Interface to the Grammar of Graphics
Description: Provides a formula interface to 'ggplot2' graphics.
Author: Daniel Kaplan [aut],
Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@calvin.edu>
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Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM algorithm. It can be used to accelerate any smooth, linearly
convergent acceleration scheme. A tutorial style introduction
to this package is available in a vignette on the CRAN download
page or, when the package is loaded in an R session, with
vignette("SQUAREM"). Refer to the J Stat Software article: <doi:10.18637/jss.v092.i07>.
Author: Ravi Varadhan
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2020.5 dated 2020-10-21 and 2021.1 dated 2021-01-13
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NEWS | 8 +++++++- R/squarem.R | 29 +++++++++++++++++++++-------- man/fpiter.Rd | 16 ++++++++++------ man/squarem.Rd | 7 +++---- vignettes/SQUAREM.pdf |only vignettes/SQUAREM.tex |only 8 files changed, 52 insertions(+), 28 deletions(-)
Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using
a headless browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre],
Gábor Csárdi [aut],
Hadley Wickham [aut],
RStudio [cph, fnd],
Mango Solutions [cph, ccp]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinytest versions 1.4.0 dated 2020-06-18 and 1.5.0 dated 2021-01-13
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Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng [aut],
Winston Chang [aut, cre],
RStudio, PBC [cph],
Hector Corrada Bravo [ctb],
Jeroen Ooms [ctb]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between httpuv versions 1.5.4 dated 2020-06-06 and 1.5.5 dated 2021-01-13
DESCRIPTION | 8 +- MD5 | 44 ++++++------- NEWS.md | 12 +++ R/RcppExports.R | 4 - R/httpuv.R | 40 ++++++++++-- R/utils.R | 5 + README.md | 4 - man/PipeServer.Rd | 64 +++++++++---------- man/Server.Rd | 44 ++++++------- man/WebServer.Rd | 64 +++++++++---------- man/WebSocket.Rd | 54 ++++++++-------- man/encodeURI.Rd | 8 +- man/httpuv-package.Rd | 4 - man/logLevel.Rd | 4 - man/runServer.Rd | 2 man/startServer.Rd | 152 ++++++++++++++++++++++++++-------------------- man/staticPath.Rd | 2 man/staticPathOptions.Rd | 2 src/httpresponse.cpp | 6 + src/httpuv.cpp | 4 - src/sha1/sha1.c | 3 src/webapplication.cpp | 12 +++ tests/testthat/test-app.R | 94 ++++++++++++++++++++++++++++ 23 files changed, 406 insertions(+), 230 deletions(-)
Title: Mosquito Gene Drive Explorer 2
Description: A simulation modeling framework which significantly extends capabilities from the
'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets.
For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>.
Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations,
epidemiological dynamics, time-varying parameters, and a continuous-time simulation
framework with various sampling algorithms for both deterministic and stochastic interpretations.
'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we
suggest installing that package initially.
Author: Sean L. Wu [aut, cre],
Jared B. Bennett [aut],
Héctor Manuel Sánchez Castellanos [ctb],
Tomás M. León [ctb],
Andrew J. Dolgert [ctb],
John M. Marshall [aut]
Maintainer: Sean L. Wu <slwood89@gmail.com>
Diff between MGDrivE2 versions 1.0.1 dated 2020-10-24 and 1.1.0 dated 2021-01-13
DESCRIPTION | 6 - MD5 | 108 ++++++++++++++++---------------- NAMESPACE | 4 + NEWS.md | 12 +++ R/PN-lifecycle-network-T.R | 96 ++++++++++++++++------------- R/auxiliary-analysis.R | 36 ++++++---- R/auxiliary-batch.R |only R/equilibrium-lifecycle.R | 2 R/hazard-auxiliary.R | 17 +++++ R/hazard-functions-mosy.R | 4 - R/sampling-ODE.R | 32 ++------- R/sampling-trajectory-CSV.R | 77 ++++++++++++++++------- R/sampling-trajectory-R.R | 99 ++++++++++++++++++------------ build/vignette.rds |binary inst/doc/advanced_topics.R | 20 +++--- inst/doc/advanced_topics.Rmd | 20 +++--- inst/doc/advanced_topics.html | 132 +++++++++++++++++++++++++--------------- inst/doc/epi-SEIR.R | 8 +- inst/doc/epi-SEIR.Rmd | 8 +- inst/doc/epi-SEIR.html | 100 ++++++++++++++++++++---------- inst/doc/epi-network.R | 4 - inst/doc/epi-network.Rmd | 4 - inst/doc/epi-network.html | 94 +++++++++++++++++++--------- inst/doc/epi-node.R | 4 - inst/doc/epi-node.Rmd | 4 - inst/doc/epi-node.html | 96 +++++++++++++++++++---------- inst/doc/inhomogeneous.R | 8 +- inst/doc/inhomogeneous.Rmd | 8 +- inst/doc/inhomogeneous.html | 96 +++++++++++++++++++---------- inst/doc/lifecycle-network.R | 4 - inst/doc/lifecycle-network.Rmd | 4 - inst/doc/lifecycle-network.html | 92 ++++++++++++++++++--------- inst/doc/lifecycle-node.R | 8 +- inst/doc/lifecycle-node.Rmd | 8 +- inst/doc/lifecycle-node.html | 98 +++++++++++++++++++---------- inst/doc/output-storage.R | 6 - inst/doc/output-storage.Rmd | 6 - inst/doc/output-storage.html | 98 +++++++++++++++++++---------- man/base_sum_F.Rd | 2 man/batch_migration.Rd |only man/batch_migration_stage.Rd |only man/get_shape.Rd |only man/sim_trajectory_CSV.Rd | 10 +-- man/sim_trajectory_R.Rd | 12 +-- man/sim_trajectory_base_CSV.Rd | 6 - man/sim_trajectory_base_R.Rd | 6 - man/split_aggregate_CSV.Rd | 9 -- man/spn_T_lifecycle_network.Rd | 7 +- man/summarize_stats_CSV.Rd | 7 -- vignettes/advanced_topics.Rmd | 20 +++--- vignettes/epi-SEIR.Rmd | 8 +- vignettes/epi-network.Rmd | 4 - vignettes/epi-node.Rmd | 4 - vignettes/inhomogeneous.Rmd | 8 +- vignettes/lifecycle-network.Rmd | 4 - vignettes/lifecycle-node.Rmd | 8 +- vignettes/output-storage.Rmd | 6 - 57 files changed, 953 insertions(+), 591 deletions(-)