Title: Parallel Dynamic Web-Scraping Using 'RSelenium'
Description: A system to increase the efficiency of dynamic web-scraping with 'RSelenium'
by leveraging parallel processing. You provide a function wrapper for your 'RSelenium'
scraping routine with a set of inputs, and 'parsel' runs it in several browser instances.
Chunked input processing as well as error catching and logging ensures seamless
execution and minimal data loss, even when unforeseen 'RSelenium' errors occur.
Author: Till Tietz [cre, aut]
Maintainer: Till Tietz <ttietz2014@gmail.com>
Diff between parsel versions 0.2.0 dated 2022-06-08 and 0.2.1 dated 2022-08-15
DESCRIPTION | 8 +++--- MD5 | 18 +++++++------- NEWS.md | 6 ++++ R/constructors_elements.R | 34 +++++++++++++-------------- R/constructors_navigation.R | 12 ++++----- R/parscrape.R | 10 +++++--- README.md | 55 ++++++++++++++++++++------------------------ man/click.Rd | 2 - man/get_element.Rd | 8 +++--- man/type.Rd | 4 +-- 10 files changed, 80 insertions(+), 77 deletions(-)
Title: Barycenter Methods for Spatial Point Patterns
Description: Computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns. The result is an approximate barycenter (also known as Fréchet mean or prototype) based on a transport-transform metric. Possible choices include Optimal SubPattern Assignment (OSPA) and Spike Time metrics. Details can be found in Müller, Schuhmacher and Mateu (2020) <doi:10.1007/s11222-020-09932-y>.
Author: Raoul Mueller [aut],
Dominic Schuhmacher [aut, cre]
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between ttbary versions 0.2-2 dated 2022-02-19 and 0.3-0 dated 2022-08-15
DESCRIPTION | 10 - MD5 | 41 ++--- NAMESPACE | 4 NEWS | 19 ++ R/RcppExports.R | 16 + R/kmeansbary.R | 191 +++++++++++++++++------ R/ppdist.R | 2 build/partial.rdb |binary man/drezner.Rd |only man/kmeansbary.Rd | 16 + man/kmeansbaryeps.Rd | 8 man/kmeansbarynet.Rd | 5 man/kmeansbaryweightnet.Rd | 5 man/ppdist.Rd | 2 src/RcppExports.cpp | 51 +++++- src/clustercenter.cpp | 363 +++++++++++++++++++++++++++++++++++++++++++++ src/clustercenter.h | 17 ++ src/distcomp.cpp | 32 +++ src/distcomp.h | 2 src/kmeansbary.cpp | 51 +++++- src/multimatching.cpp | 74 ++++++--- src/multimatching.h | 3 22 files changed, 783 insertions(+), 129 deletions(-)
Title: Pulls Information from Prov.Json Files
Description: R functions to access provenance information collected by 'rdt' or
'rdtLite'. The information is stored inside a 'ProvInfo' object and can be
accessed through a collection of functions that will return the requested
data. The exact format of the JSON created by 'rdt' and 'rdtLite' is described
in <https://github.com/End-to-end-provenance/ExtendedProvJson>.
Author: Orenna Brand [aut],
Joseph Wonsil [aut],
Emery Boose [aut],
Barbara Lerner [cre]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provParseR versions 0.3 dated 2020-06-16 and 1.0 dated 2022-08-15
DESCRIPTION | 11 MD5 | 16 - R/provParse.R | 48 ++- inst/testdata/ddg.json | 10 inst/testdata/prov.json | 552 +++++++++++++++++++++++++++++--------- inst/testscripts/airt-vs-prec.pdf |binary tests/testthat/test_provParse.R | 4 tests/testthat/test_provParse2.R | 26 - tests/testthat/test_provParse4.R | 4 9 files changed, 507 insertions(+), 164 deletions(-)
Title: Motif-Based Spectral Clustering of Weighted Directed Networks
Description: Tools for spectral clustering of weighted directed networks using motif
adjacency matrices. Methods perform well on large and sparse networks, and
random sampling methods for generating weighted directed networks are also
provided. Based on methodology detailed in Underwood, Elliott and Cucuringu
(2020) <arXiv:2004.01293>.
Author: William George Underwood [aut, cre]
Maintainer: William George Underwood <wgu2@princeton.edu>
Diff between motifcluster versions 0.2.1 dated 2022-07-01 and 0.2.2 dated 2022-08-15
DESCRIPTION | 8 ++--- MD5 | 15 +++++----- NEWS.md | 4 ++ inst/doc/motifcluster_vignette.pdf |binary tests/testthat/test_indicators.R | 40 ++++++++++++++-------------- tests/testthat/test_motifadjacency.R | 50 ++++++++++++++++------------------- tests/testthat/test_sampling.R | 8 ++--- tests/testthat/test_spectral.R | 12 ++++---- vignettes/auto |only 9 files changed, 70 insertions(+), 67 deletions(-)
Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM'
Formats
Description: Read and write labelled sparse matrices in text format as used by
software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM',
and others. Supports labelled data for regression, classification (binary, multi-class, multi-label),
and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between readsparse versions 0.1.5-2 dated 2022-08-06 and 0.1.5-3 dated 2022-08-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/read_sparse.R | 4 ++++ tests/testthat/test-read-write.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a non-negative low-rank approximate factorization of a sparse counts matrix by maximizing Poisson
likelihood with L1/L2 regularization (e.g. for implicit-feedback recommender systems or bag-of-words-based topic modeling)
(Cortes, (2018) <arXiv:1811.01908>), which usually leads to very sparse user and item factors (over 90% zero-valued).
Similar to hierarchical Poisson factorization (HPF), but follows an optimization-based approach with regularization
instead of a hierarchical prior, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph],
Jean-Sebastien Roy [cph] ,
Stephen Nash [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.4.0 dated 2022-02-25 and 0.4.0-1 dated 2022-08-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/poismf.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces.
Playing surfaces are drawn pursuant to rule-book specifications.
This package should be used as a baseline plot for displaying player
tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>
Diff between sportyR versions 1.0.1 dated 2021-04-20 and 2.0.0 dated 2022-08-15
sportyR-1.0.1/sportyR/R/baseball-mlb-features.R |only sportyR-1.0.1/sportyR/R/basketball-fiba-features.R |only sportyR-1.0.1/sportyR/R/basketball-nba-features.R |only sportyR-1.0.1/sportyR/R/basketball-ncaa-bb-features.R |only sportyR-1.0.1/sportyR/R/basketball-wnba-features.R |only sportyR-1.0.1/sportyR/R/football-ncaa-football-features.R |only sportyR-1.0.1/sportyR/R/football-nfl-features.R |only sportyR-1.0.1/sportyR/R/hockey-iihf-features.R |only sportyR-1.0.1/sportyR/R/hockey-ncaa-hockey-features.R |only sportyR-1.0.1/sportyR/R/hockey-nhl-features.R |only sportyR-1.0.1/sportyR/R/hockey-nwhl-features.R |only sportyR-1.0.1/sportyR/R/soccer-fifa-features.R |only sportyR-1.0.1/sportyR/R/soccer-mls-features.R |only sportyR-1.0.1/sportyR/R/soccer-ncaa-soccer-features.R |only sportyR-1.0.1/sportyR/R/soccer-nwsl-features.R |only sportyR-1.0.1/sportyR/R/soccer-premier-league-features.R |only sportyR-1.0.1/sportyR/R/sport-baseball.R |only sportyR-1.0.1/sportyR/R/sport-basketball.R |only sportyR-1.0.1/sportyR/R/sport-football.R |only sportyR-1.0.1/sportyR/R/sport-hockey.R |only sportyR-1.0.1/sportyR/R/sport-soccer.R |only sportyR-1.0.1/sportyR/man/translate.Rd |only sportyR-2.0.0/sportyR/DESCRIPTION | 32 sportyR-2.0.0/sportyR/MD5 | 236 +++- sportyR-2.0.0/sportyR/NAMESPACE | 3 sportyR-2.0.0/sportyR/NEWS.md | 87 + sportyR-2.0.0/sportyR/R/cani-functions.R | 495 ++++++---- sportyR-2.0.0/sportyR/R/coordinate-transformations.R | 67 - sportyR-2.0.0/sportyR/R/create-shapes.R | 60 - sportyR-2.0.0/sportyR/R/data.R | 27 sportyR-2.0.0/sportyR/R/features-baseball.R |only sportyR-2.0.0/sportyR/R/features-basketball.R |only sportyR-2.0.0/sportyR/R/features-curling.R |only sportyR-2.0.0/sportyR/R/features-football.R |only sportyR-2.0.0/sportyR/R/features-hockey.R |only sportyR-2.0.0/sportyR/R/features-soccer.R |only sportyR-2.0.0/sportyR/R/features-tennis.R |only sportyR-2.0.0/sportyR/R/geom-baseball.R |only sportyR-2.0.0/sportyR/R/geom-basketball.R |only sportyR-2.0.0/sportyR/R/geom-curling.R |only sportyR-2.0.0/sportyR/R/geom-football.R |only sportyR-2.0.0/sportyR/R/geom-hockey.R |only sportyR-2.0.0/sportyR/R/geom-soccer.R |only sportyR-2.0.0/sportyR/R/geom-tennis.R |only sportyR-2.0.0/sportyR/R/math-functions.R | 38 sportyR-2.0.0/sportyR/R/plot-helpers.R | 270 +++-- sportyR-2.0.0/sportyR/R/sysdata.rda |binary sportyR-2.0.0/sportyR/R/unit-conversions.R | 227 ++-- sportyR-2.0.0/sportyR/R/utils.R |only sportyR-2.0.0/sportyR/build |only sportyR-2.0.0/sportyR/inst |only sportyR-2.0.0/sportyR/man/baseball_base.Rd |only sportyR-2.0.0/sportyR/man/baseball_batters_box.Rd |only sportyR-2.0.0/sportyR/man/baseball_catchers_box.Rd |only sportyR-2.0.0/sportyR/man/baseball_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/baseball_foul_line.Rd |only sportyR-2.0.0/sportyR/man/baseball_home_plate.Rd |only sportyR-2.0.0/sportyR/man/baseball_infield_dirt.Rd |only sportyR-2.0.0/sportyR/man/baseball_infield_grass.Rd |only sportyR-2.0.0/sportyR/man/baseball_pitchers_mound.Rd |only sportyR-2.0.0/sportyR/man/baseball_pitchers_plate.Rd |only sportyR-2.0.0/sportyR/man/baseball_running_lane.Rd |only sportyR-2.0.0/sportyR/man/basketball_backboard.Rd |only sportyR-2.0.0/sportyR/man/basketball_basket_ring.Rd |only sportyR-2.0.0/sportyR/man/basketball_center_circle_fill.Rd |only sportyR-2.0.0/sportyR/man/basketball_center_circle_outline.Rd |only sportyR-2.0.0/sportyR/man/basketball_court_apron.Rd |only sportyR-2.0.0/sportyR/man/basketball_division_line.Rd |only sportyR-2.0.0/sportyR/man/basketball_endline.Rd |only sportyR-2.0.0/sportyR/man/basketball_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/basketball_free_throw_circle.Rd |only sportyR-2.0.0/sportyR/man/basketball_free_throw_circle_dash.Rd |only sportyR-2.0.0/sportyR/man/basketball_free_throw_circle_fill.Rd |only sportyR-2.0.0/sportyR/man/basketball_free_throw_lane_boundary.Rd |only sportyR-2.0.0/sportyR/man/basketball_half_court.Rd |only sportyR-2.0.0/sportyR/man/basketball_inbounding_line.Rd |only sportyR-2.0.0/sportyR/man/basketball_lane_space_mark.Rd |only sportyR-2.0.0/sportyR/man/basketball_lower_defensive_box_mark.Rd |only sportyR-2.0.0/sportyR/man/basketball_net.Rd |only sportyR-2.0.0/sportyR/man/basketball_painted_area.Rd |only sportyR-2.0.0/sportyR/man/basketball_restricted_arc.Rd |only sportyR-2.0.0/sportyR/man/basketball_sideline.Rd |only sportyR-2.0.0/sportyR/man/basketball_substitution_line.Rd |only sportyR-2.0.0/sportyR/man/basketball_team_bench_line.Rd |only sportyR-2.0.0/sportyR/man/basketball_three_point_line.Rd |only sportyR-2.0.0/sportyR/man/basketball_two_point_range.Rd |only sportyR-2.0.0/sportyR/man/cani_color_league_features.Rd | 8 sportyR-2.0.0/sportyR/man/cani_plot_league.Rd | 12 sportyR-2.0.0/sportyR/man/cani_plot_sport.Rd | 16 sportyR-2.0.0/sportyR/man/convert_units.Rd | 8 sportyR-2.0.0/sportyR/man/curling_back_line.Rd |only sportyR-2.0.0/sportyR/man/curling_button.Rd |only sportyR-2.0.0/sportyR/man/curling_centre_line.Rd |only sportyR-2.0.0/sportyR/man/curling_centre_zone.Rd |only sportyR-2.0.0/sportyR/man/curling_courtesy_line.Rd |only sportyR-2.0.0/sportyR/man/curling_end.Rd |only sportyR-2.0.0/sportyR/man/curling_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/curling_hack_foothold.Rd |only sportyR-2.0.0/sportyR/man/curling_hack_line.Rd |only sportyR-2.0.0/sportyR/man/curling_hog_line.Rd |only sportyR-2.0.0/sportyR/man/curling_house_ring.Rd |only sportyR-2.0.0/sportyR/man/curling_sheet_apron.Rd |only sportyR-2.0.0/sportyR/man/curling_tee_line.Rd |only sportyR-2.0.0/sportyR/man/football_coaching_box.Rd |only sportyR-2.0.0/sportyR/man/football_coaching_box_line.Rd |only sportyR-2.0.0/sportyR/man/football_directional_arrow.Rd |only sportyR-2.0.0/sportyR/man/football_end_line.Rd |only sportyR-2.0.0/sportyR/man/football_endzone.Rd |only sportyR-2.0.0/sportyR/man/football_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/football_field_apron.Rd |only sportyR-2.0.0/sportyR/man/football_field_border.Rd |only sportyR-2.0.0/sportyR/man/football_field_border_outline.Rd |only sportyR-2.0.0/sportyR/man/football_goal_line.Rd |only sportyR-2.0.0/sportyR/man/football_half_field.Rd |only sportyR-2.0.0/sportyR/man/football_major_yard_line.Rd |only sportyR-2.0.0/sportyR/man/football_minor_yard_line.Rd |only sportyR-2.0.0/sportyR/man/football_restricted_area.Rd |only sportyR-2.0.0/sportyR/man/football_sideline.Rd |only sportyR-2.0.0/sportyR/man/football_team_bench_area.Rd |only sportyR-2.0.0/sportyR/man/football_team_bench_area_outline.Rd |only sportyR-2.0.0/sportyR/man/football_try_mark.Rd |only sportyR-2.0.0/sportyR/man/geom_baseball.Rd | 72 + sportyR-2.0.0/sportyR/man/geom_basketball.Rd | 227 ++++ sportyR-2.0.0/sportyR/man/geom_curling.Rd |only sportyR-2.0.0/sportyR/man/geom_football.Rd | 128 ++ sportyR-2.0.0/sportyR/man/geom_hockey.Rd | 96 + sportyR-2.0.0/sportyR/man/geom_soccer.Rd | 100 +- sportyR-2.0.0/sportyR/man/geom_tennis.Rd |only sportyR-2.0.0/sportyR/man/grapes-or-grapes.Rd |only sportyR-2.0.0/sportyR/man/hockey_boards.Rd |only sportyR-2.0.0/sportyR/man/hockey_center_faceoff_circle.Rd |only sportyR-2.0.0/sportyR/man/hockey_center_faceoff_spot.Rd |only sportyR-2.0.0/sportyR/man/hockey_center_line.Rd |only sportyR-2.0.0/sportyR/man/hockey_defensive_zone.Rd |only sportyR-2.0.0/sportyR/man/hockey_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/hockey_goal_crease_fill.Rd |only sportyR-2.0.0/sportyR/man/hockey_goal_crease_outline.Rd |only sportyR-2.0.0/sportyR/man/hockey_goal_frame.Rd |only sportyR-2.0.0/sportyR/man/hockey_goal_frame_fill.Rd |only sportyR-2.0.0/sportyR/man/hockey_goal_line.Rd |only sportyR-2.0.0/sportyR/man/hockey_goaltenders_restricted_area.Rd |only sportyR-2.0.0/sportyR/man/hockey_neutral_zone.Rd |only sportyR-2.0.0/sportyR/man/hockey_nodzone_faceoff_spot_ring.Rd |only sportyR-2.0.0/sportyR/man/hockey_nodzone_faceoff_spot_stripe.Rd |only sportyR-2.0.0/sportyR/man/hockey_odzone_faceoff_circle.Rd |only sportyR-2.0.0/sportyR/man/hockey_odzone_faceoff_lines.Rd |only sportyR-2.0.0/sportyR/man/hockey_off_ice_officials_box.Rd |only sportyR-2.0.0/sportyR/man/hockey_offensive_zone.Rd |only sportyR-2.0.0/sportyR/man/hockey_penalty_box_fill.Rd |only sportyR-2.0.0/sportyR/man/hockey_penalty_box_outline.Rd |only sportyR-2.0.0/sportyR/man/hockey_player_bench_area_fill.Rd |only sportyR-2.0.0/sportyR/man/hockey_player_bench_outline.Rd |only sportyR-2.0.0/sportyR/man/hockey_referee_crease.Rd |only sportyR-2.0.0/sportyR/man/hockey_zone_line.Rd |only sportyR-2.0.0/sportyR/man/reflect.Rd | 2 sportyR-2.0.0/sportyR/man/rotate_coords.Rd | 13 sportyR-2.0.0/sportyR/man/soccer_center_circle.Rd |only sportyR-2.0.0/sportyR/man/soccer_center_mark.Rd |only sportyR-2.0.0/sportyR/man/soccer_corner_arc.Rd |only sportyR-2.0.0/sportyR/man/soccer_corner_defensive_marks.Rd |only sportyR-2.0.0/sportyR/man/soccer_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/soccer_goal.Rd |only sportyR-2.0.0/sportyR/man/soccer_goal_box.Rd |only sportyR-2.0.0/sportyR/man/soccer_goal_line.Rd |only sportyR-2.0.0/sportyR/man/soccer_half_pitch.Rd |only sportyR-2.0.0/sportyR/man/soccer_halfway_line.Rd |only sportyR-2.0.0/sportyR/man/soccer_penalty_box.Rd |only sportyR-2.0.0/sportyR/man/soccer_penalty_mark.Rd |only sportyR-2.0.0/sportyR/man/soccer_pitch_apron.Rd |only sportyR-2.0.0/sportyR/man/soccer_touchline.Rd |only sportyR-2.0.0/sportyR/man/surface_dimensions.Rd |only sportyR-2.0.0/sportyR/man/tennis_backcourt.Rd |only sportyR-2.0.0/sportyR/man/tennis_baseline.Rd |only sportyR-2.0.0/sportyR/man/tennis_center_mark.Rd |only sportyR-2.0.0/sportyR/man/tennis_center_serviceline.Rd |only sportyR-2.0.0/sportyR/man/tennis_court_apron.Rd |only sportyR-2.0.0/sportyR/man/tennis_doubles_alley.Rd |only sportyR-2.0.0/sportyR/man/tennis_features_set_colors.Rd |only sportyR-2.0.0/sportyR/man/tennis_frontcourt_half.Rd |only sportyR-2.0.0/sportyR/man/tennis_net.Rd |only sportyR-2.0.0/sportyR/man/tennis_serviceline.Rd |only sportyR-2.0.0/sportyR/man/tennis_sideline.Rd |only sportyR-2.0.0/sportyR/tests/testthat/test-cani-functions.R | 109 +- sportyR-2.0.0/sportyR/tests/testthat/test-coordinate-transforms.R | 86 + sportyR-2.0.0/sportyR/tests/testthat/test-math-functions.R |only sportyR-2.0.0/sportyR/tests/testthat/test-no-league-error.R | 6 sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-baseball.R |only sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-basketball.R |only sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-curling.R |only sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-football.R |only sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-hockey.R |only sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-soccer.R |only sportyR-2.0.0/sportyR/tests/testthat/test-plots-and-features-tennis.R |only sportyR-2.0.0/sportyR/tests/testthat/test-shapes.R | 18 sportyR-2.0.0/sportyR/tests/testthat/test-unit-conversions.R | 205 ++-- sportyR-2.0.0/sportyR/vignettes |only 196 files changed, 1846 insertions(+), 802 deletions(-)
Title: Rank Normal Transformation Omnibus Test
Description: Inverse normal transformation (INT) based genetic association testing. These tests are recommend for continuous traits with non-normally distributed residuals. INT-based tests robustly control the type I error in settings where standard linear regression does not, as when the residual distribution exhibits excess skew or kurtosis. Moreover, INT-based tests dominate standard linear regression in terms of power. These tests may be classified into two types. In direct INT (D-INT), the phenotype is itself transformed. In indirect INT (I-INT), phenotypic residuals are transformed. The omnibus test (O-INT) adaptively combines D-INT and I-INT into a single robust and statistically powerful approach. See McCaw ZR, Lane JM, Saxena R, Redline S, Lin X. "Operating characteristics of the rank-based inverse normal transformation for quantitative trait analysis in genome-wide association studies" <doi:10.1111/biom.13214>.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>
Diff between RNOmni versions 1.0.0 dated 2020-10-05 and 1.0.1 dated 2022-08-15
RNOmni-1.0.0/RNOmni/man/BAT.ScoreTest.Rd |only RNOmni-1.0.0/RNOmni/man/BAT.WaldTest.Rd |only RNOmni-1.0.0/RNOmni/man/IINT.ScoreTest.Rd |only RNOmni-1.0.0/RNOmni/man/SchurC.Rd |only RNOmni-1.0.0/RNOmni/man/ScoreStat.Rd |only RNOmni-1.0.0/RNOmni/man/WaldStat.Rd |only RNOmni-1.0.0/RNOmni/man/fitOLS.Rd |only RNOmni-1.0.0/RNOmni/man/matIP.Rd |only RNOmni-1.0.0/RNOmni/man/matInv.Rd |only RNOmni-1.0.1/RNOmni/DESCRIPTION | 26 - RNOmni-1.0.1/RNOmni/MD5 | 67 ++-- RNOmni-1.0.1/RNOmni/NAMESPACE | 5 RNOmni-1.0.1/RNOmni/NEWS.md |only RNOmni-1.0.1/RNOmni/R/BAT.R | 93 +----- RNOmni-1.0.1/RNOmni/R/CauchyCombination.R |only RNOmni-1.0.1/RNOmni/R/DINT.R | 21 + RNOmni-1.0.1/RNOmni/R/IINT.R | 42 +- RNOmni-1.0.1/RNOmni/R/InputCheck.R |only RNOmni-1.0.1/RNOmni/R/OINT.R | 109 +------ RNOmni-1.0.1/RNOmni/R/PackageHelp.R | 2 RNOmni-1.0.1/RNOmni/R/RN.R | 23 - RNOmni-1.0.1/RNOmni/R/RcppExports.R | 16 - RNOmni-1.0.1/RNOmni/build/vignette.rds |binary RNOmni-1.0.1/RNOmni/inst/doc/RNOmni.html | 416 ++++++++++++++++------------ RNOmni-1.0.1/RNOmni/man/BAT.Rd | 6 RNOmni-1.0.1/RNOmni/man/BasicInputChecks.Rd | 7 RNOmni-1.0.1/RNOmni/man/CauchyToP.Rd | 2 RNOmni-1.0.1/RNOmni/man/DINT.Rd | 18 - RNOmni-1.0.1/RNOmni/man/FitOLS.Rd |only RNOmni-1.0.1/RNOmni/man/IINT.Rd | 10 RNOmni-1.0.1/RNOmni/man/OINT.Rd | 14 RNOmni-1.0.1/RNOmni/man/OmniP.Rd | 6 RNOmni-1.0.1/RNOmni/man/PtoCauchy.Rd | 2 RNOmni-1.0.1/RNOmni/man/RankNorm.Rd | 12 RNOmni-1.0.1/RNOmni/src/LinReg.cpp | 16 - RNOmni-1.0.1/RNOmni/src/MatrixOps.cpp | 21 + RNOmni-1.0.1/RNOmni/src/RcppExports.cpp | 35 +- RNOmni-1.0.1/RNOmni/tests |only 38 files changed, 514 insertions(+), 455 deletions(-)
Title: Compare Provenance Collections to Explain Changed Script Outputs
Description: Inspects provenance collected by the 'rdt' or 'rdtLite' packages,
or other tools providing compatible PROV JSON output created by
the execution of a script, and find differences between two provenance
collections. Factors under examination included the hardware and
software used to execute the script, versions of attached libraries,
use of global variables, modified inputs and outputs, and changes
in main and sourced scripts. Based on detected changes, 'provExplainR'
can be used to study how these factors affect the behavior of
the script and generate a promising diagnosis of the causes of different
script results. More information about 'rdtLite' and associated tools is available
at <https://github.com/End-to-end-provenance/> and Barbara Lerner,
Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi:10.3390/informatics5010012>.
Author: Barbara Lerner [cre],
Emery Boose [aut],
Khanh Ngo [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provExplainR versions 1.1 dated 2021-07-15 and 1.1.1 dated 2022-08-15
DESCRIPTION | 10 +++--- MD5 | 8 ++--- R/provExplainR.R | 57 ++++++++++++++++++++++++++++---------- man/explain.Rd | 9 ++++-- tests/testthat/testScriptChange.R | 8 ----- 5 files changed, 57 insertions(+), 35 deletions(-)
Title: Reading Ontologies into R
Description: Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017 <doi:10.1093/bioinformatics/btw763>.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyIndex versions 2.7 dated 2021-02-03 and 2.9 dated 2022-08-15
DESCRIPTION | 12 MD5 | 34 +- NEWS.md | 5 R/data.R | 64 ++- R/descendants.R | 10 R/sets.R | 12 build/vignette.rds |binary data/datalist | 6 data/go.RData |binary data/hpo.RData |binary data/mpo.RData |binary inst/doc/intro-to-ontologyX.R | 56 +-- inst/doc/intro-to-ontologyX.html | 658 +++++++++++++++++++++++++-------------- inst/doc/reading-ontologies.R | 58 +-- inst/doc/reading-ontologies.Rmd | 4 inst/doc/reading-ontologies.html | 658 +++++++++++++++++++++++++-------------- man/get_ontology.Rd | 16 vignettes/reading-ontologies.Rmd | 4 18 files changed, 1041 insertions(+), 556 deletions(-)
Title: Sequence Generalization Through Similarity Network
Description: Proposes an application for sequence prediction generalizing the similarity within the network of previous sequences.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between segen versions 1.0.0 dated 2022-06-28 and 1.1.0 dated 2022-08-15
DESCRIPTION | 9 - MD5 | 10 - NAMESPACE | 1 NEWS.md | 4 R/main.R | 346 +++++++++++++++++++++++++++++------------------------------ man/segen.Rd | 4 6 files changed, 188 insertions(+), 186 deletions(-)
Title: Apply Mapping Functions in Parallel using Futures
Description: Implementations of the family of map() functions from 'purrr'
that can be resolved using any 'future'-supported backend, e.g.
parallel on the local machine or distributed on a compute cluster.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut],
RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between furrr versions 0.3.0 dated 2022-05-04 and 0.3.1 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ man/furrr-package.Rd | 2 +- man/future_map2.Rd | 5 +---- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Shape Selection for Landsat Time Series of Forest Dynamics
Description: Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <https://landsat.gsfc.nasa.gov/>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal [...truncated...]
Author: Xiyue Liao [aut, cre] ,
Mary Meyer [aut],
Elizabeth Freeman [aut],
Gretchen Moisen [aut]
Maintainer: Xiyue Liao <xiyue.liao@csulb.edu>
Diff between ShapeSelectForest versions 1.4 dated 2020-03-27 and 1.5 dated 2022-08-15
ChangeLog | 3 +++ DESCRIPTION | 26 ++++++++++++++++---------- MD5 | 10 +++++----- R/shape.R | 3 ++- inst/CITATION | 38 ++++++++++++++++++-------------------- man/plotshape.Rd | 2 +- 6 files changed, 45 insertions(+), 37 deletions(-)
More information about ShapeSelectForest at CRAN
Permanent link
Title: The (Adaptive) Elastic Net and Lasso Penalized Sparse Asymmetric
Least Squares (SALES) and Coupled Sparse Asymmetric Least
Squares (COSALES) using Coordinate Descent and Proximal
Gradient Algorithms
Description: A coordinate descent algorithm for computing the solution paths of
the sparse and coupled sparse asymmetric least squares, including the
(adaptive) elastic net and Lasso penalized SALES and COSALES regressions.
Author: Yuwen Gu <yuwen.gu@uconn.edu>, Hui Zou <zouxx019@umn.edu>
Maintainer: Yuwen Gu <yuwen.gu@uconn.edu>
Diff between SALES versions 1.0.0 dated 2016-01-12 and 1.0.2 dated 2022-08-15
ChangeLog | 18 + DESCRIPTION | 26 +- MD5 | 105 +++++----- NAMESPACE | 71 +++--- R/alspath.R | 44 ++-- R/coef.alspath.R | 40 ++- R/coef.cpalspath.R | 57 ++--- R/coef.cpernet.R | 58 +++++ R/coef.cv.cpernet.R | 66 +++++- R/coef.cv.ernet.R | 64 +++++- R/coef.ernet.R | 73 ++++++- R/cpalspath.R | 56 ++--- R/cpernet.R | 268 ++++++++++++++++++------- R/cv.alspath.R | 8 R/cv.cpalspath.R | 13 - R/cv.cpernet.R | 158 +++++++++++---- R/cv.ernet.R | 153 +++++++++++--- R/ernet.R | 254 ++++++++++++++++++------ R/plot.cpernet.R | 104 +++++++--- R/plot.cv.cpernet.R | 93 ++++++-- R/plot.cv.ernet.R | 92 ++++++-- R/plot.ernet.R | 87 ++++++-- R/predict.alspath.R | 36 +-- R/predict.cpalspath.R | 62 +++-- R/predict.cpernet.R | 56 +++++ R/predict.cv.cpernet.R | 66 +++++- R/predict.cv.ernet.R | 65 +++++- R/predict.ernet.R | 59 +++++ R/print.cpernet.R | 44 ++++ R/print.ernet.R | 44 +++- R/utilities.R | 100 +++++---- man/coef.Rd |only man/coef.cpernet.Rd | 62 +++-- man/coef.cv.cpernet.Rd | 67 +++--- man/coef.cv.ernet.Rd | 65 +++--- man/coef.ernet.Rd | 60 +++-- man/cpernet.Rd | 217 ++++++++++++++------ man/cv.cpernet.Rd | 131 ++++++++---- man/cv.ernet.Rd | 119 +++++++---- man/ernet.Rd | 200 +++++++++++++------ man/plot.cpernet.Rd | 53 +++-- man/plot.cv.cpernet.Rd | 48 ++-- man/plot.cv.ernet.Rd | 46 ++-- man/plot.ernet.Rd | 48 ++-- man/predict.Rd |only man/predict.cpernet.Rd | 67 +++--- man/predict.cv.cpernet.Rd | 68 ++++-- man/predict.cv.ernet.Rd | 66 +++--- man/predict.ernet.Rd | 60 +++-- man/print.cpernet.Rd | 48 ++-- man/print.ernet.Rd | 45 ++-- src/alslassoNET.f90 | 477 +++++++++++++++++++++++----------------------- src/auxiliary.f90 | 91 ++++---- src/cpalslassoNet.f90 | 343 +++++++++++++++++---------------- src/init.c |only 55 files changed, 3171 insertions(+), 1650 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb], [...truncated...]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.7-2 dated 2022-01-05 and 2.8-0 dated 2022-08-15
Rcmdr-2.7-2/Rcmdr/build/partial.rdb |only Rcmdr-2.8-0/Rcmdr/DESCRIPTION | 13 Rcmdr-2.8-0/Rcmdr/MD5 | 113 Rcmdr-2.8-0/Rcmdr/NAMESPACE | 12 Rcmdr-2.8-0/Rcmdr/NEWS | 24 Rcmdr-2.8-0/Rcmdr/R/CR-AV-Plot3D.R |only Rcmdr-2.8-0/Rcmdr/R/cluster.R | 918 - Rcmdr-2.8-0/Rcmdr/R/commander.R | 3202 ++--- Rcmdr-2.8-0/Rcmdr/R/data-menu.R | 227 Rcmdr-2.8-0/Rcmdr/R/distributions-menu.R | 1165 - Rcmdr-2.8-0/Rcmdr/R/distributions-plotDistributions-menu.R | 682 - Rcmdr-2.8-0/Rcmdr/R/distributions-sample.R | 334 Rcmdr-2.8-0/Rcmdr/R/file-menu.R | 17 Rcmdr-2.8-0/Rcmdr/R/globals.R | 123 Rcmdr-2.8-0/Rcmdr/R/graphs-menu.R | 6071 +++++----- Rcmdr-2.8-0/Rcmdr/R/model-menu.R | 2909 ++-- Rcmdr-2.8-0/Rcmdr/R/statistics-dimensional-menu.R | 765 - Rcmdr-2.8-0/Rcmdr/R/statistics-means-menu.R | 8 Rcmdr-2.8-0/Rcmdr/R/statistics-models-menu.R | 1837 +-- Rcmdr-2.8-0/Rcmdr/R/statistics-nonparametric-menu.R | 544 Rcmdr-2.8-0/Rcmdr/R/statistics-proportions-menu.R | 4 Rcmdr-2.8-0/Rcmdr/R/statistics-summaries-menu.R | 1354 +- Rcmdr-2.8-0/Rcmdr/R/statistics-tables-menu.R | 714 - Rcmdr-2.8-0/Rcmdr/R/statistics-variances-menu.R | 366 Rcmdr-2.8-0/Rcmdr/R/utilities.R | 454 Rcmdr-2.8-0/Rcmdr/build/vignette.rds |binary Rcmdr-2.8-0/Rcmdr/inst/CITATION | 4 Rcmdr-2.8-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.Rnw | 2987 ++-- Rcmdr-2.8-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary Rcmdr-2.8-0/Rcmdr/inst/etc/Rcmdr-RMarkdown-Template.Rmd | 11 Rcmdr-2.8-0/Rcmdr/inst/etc/Rcmdr-menus.txt | 12 Rcmdr-2.8-0/Rcmdr/inst/etc/Rcmdr-model-capabilities.txt | 23 Rcmdr-2.8-0/Rcmdr/inst/etc/Rcmdr-operations.txt |only Rcmdr-2.8-0/Rcmdr/inst/etc/error.gif |only Rcmdr-2.8-0/Rcmdr/inst/etc/info.gif |only Rcmdr-2.8-0/Rcmdr/inst/etc/question.gif |only Rcmdr-2.8-0/Rcmdr/inst/etc/warning.gif |only Rcmdr-2.8-0/Rcmdr/inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/inst/po/ko/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/inst/po/ro/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/inst/po/ru/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.8-0/Rcmdr/man/Commander.Rd | 14 Rcmdr-2.8-0/Rcmdr/man/Rcmdr-package.Rd | 6 Rcmdr-2.8-0/Rcmdr/man/Rcmdr.Utilities.Rd | 24 Rcmdr-2.8-0/Rcmdr/man/RecodeDialog.Rd | 9 Rcmdr-2.8-0/Rcmdr/man/generalizedLinearModel.Rd | 104 Rcmdr-2.8-0/Rcmdr/man/linearModel.Rd | 86 Rcmdr-2.8-0/Rcmdr/po/R-Rcmdr.pot | 461 Rcmdr-2.8-0/Rcmdr/po/R-es.po | 489 Rcmdr-2.8-0/Rcmdr/po/R-ja.po | 765 - Rcmdr-2.8-0/Rcmdr/po/R-ko.po | 804 + Rcmdr-2.8-0/Rcmdr/po/R-ro.po | 2864 ++-- Rcmdr-2.8-0/Rcmdr/po/R-ru.po | 477 Rcmdr-2.8-0/Rcmdr/po/R-sl.po | 772 + Rcmdr-2.8-0/Rcmdr/po/R-zh.po | 848 + Rcmdr-2.8-0/Rcmdr/vignettes/Getting-Started-with-the-Rcmdr.Rnw | 2987 ++-- Rcmdr-2.8-0/Rcmdr/vignettes/Rcmdr-Manual.bib | 11 Rcmdr-2.8-0/Rcmdr/vignettes/Rcmdr-menus | 635 - 61 files changed, 20699 insertions(+), 15550 deletions(-)
Title: Bayesian Inference for A|B and Bandit Marketing Tests
Description: Uses simple Bayesian conjugate prior update rules to calculate
the win probability of each option, value remaining in the test, and
percent lift over the baseline for various marketing objectives.
References:
Fink, Daniel (1997) "A Compendium of Conjugate Priors" <https://www.johndcook.com/CompendiumOfConjugatePriors.pdf>.
Stucchio, Chris (2015) "Bayesian A/B Testing at VWO" <https://cdn2.hubspot.net/hubfs/310840/VWO_SmartStats_technical_whitepaper.pdf>.
Author: Ryan Angi
Maintainer: Ryan Angi <rangi@redventures.com>
Diff between grizbayr versions 1.3.1 dated 2020-11-11 and 1.3.2 dated 2022-08-15
DESCRIPTION | 11 MD5 | 20 NEWS.md | 7 R/rdirichlet.R | 2 R/sample_session_duration.R | 2 R/sysdata.R |only build/vignette.rds |binary inst/WORDLIST | 29 inst/doc/intro.html | 1093 +++++++++++++++++++------------------ man/distribution_column_mapping.Rd |only man/rdirichlet.Rd | 2 man/sample_session_duration.Rd | 2 12 files changed, 609 insertions(+), 559 deletions(-)
Title: Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Description: Finds the critical sample size ("critical point of stability") for a
correlation to stabilize in Schoenbrodt and Perugini's definition of
sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between fastpos versions 0.5.0 dated 2022-08-10 and 0.5.1 dated 2022-08-15
DESCRIPTION | 10 - MD5 | 15 +- NAMESPACE | 2 NEWS.md | 8 + R/fastpos.R | 18 ++- README.md | 199 +++++++++++++++++++++++++++---------- man/figures/README-parallel4-1.png |only man/figures/README-sim2-1.png |binary man/find_critical_pos.Rd | 3 9 files changed, 184 insertions(+), 71 deletions(-)
Title: Monochrome Bitmap Font Tools
Description: Provides functions for creating and modifying bitmaps with special emphasis on bitmap fonts and their glyphs. Provides native read/write support for the 'hex' and 'yaff' bitmap font formats and if 'Python' is installed can also read/write several more bitmap font formats using an embedded version of 'monobit'.
Author: Trevor L Davis [aut, cre] ,
Rob Hagemans [cph] ,
Frederic Cambus [cph]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between bittermelon versions 0.2.1 dated 2021-11-01 and 1.0.0 dated 2022-08-15
bittermelon-0.2.1/bittermelon/inst/monobit/monobit/__pycache__ |only bittermelon-0.2.1/bittermelon/inst/monobit/monobit/base/__pycache__ |only bittermelon-0.2.1/bittermelon/inst/monobit/monobit/codecs/__pycache__ |only bittermelon-1.0.0/bittermelon/DESCRIPTION | 13 +- bittermelon-1.0.0/bittermelon/MD5 | 60 +--------- bittermelon-1.0.0/bittermelon/NEWS.md | 5 bittermelon-1.0.0/bittermelon/R/Ops.bm_object.R | 1 bittermelon-1.0.0/bittermelon/R/bm_mask.R | 2 bittermelon-1.0.0/bittermelon/man/Ops.bm_object.Rd | 10 - bittermelon-1.0.0/bittermelon/man/bittermelon.Rd | 4 bittermelon-1.0.0/bittermelon/man/bm_mask.Rd | 2 11 files changed, 29 insertions(+), 68 deletions(-)
Title: Analysis of MHC Data in Non-Model Species
Description: Twelve tools for bioinformatical processing and analysis of major
histocompatibility complex (MHC) data. The functions are tailored for amplicon data
sets that have been filtered using the 'dada2' method (for more information on
'dada2', visit <https://benjjneb.github.io/dada2/> ), but even other types of data
sets can be analyzed.
The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise
comparisons of all sequences in a data set, and mean distances of all pairwise
comparisons within each sample in a data set. The function additionally outputs five
tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for
each amino acid position in all sequences in the data set. These tables may be useful
for further downstream analyses, such as estimation of MHC supertypes.
The BootKmeans() function is a wrapper for the kmeans() function of the 'stats'
package, which allows for bootstrapping. Bootstrapping k-estimates may be
desirable in dat [...truncated...]
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.4.2 dated 2022-05-23 and 1.4.3 dated 2022-08-15
MHCtools-1.4.2/MHCtools/R/HpltFind_func_20200915.R |only MHCtools-1.4.3/MHCtools/DESCRIPTION | 10 - MHCtools-1.4.3/MHCtools/LICENSE | 2 MHCtools-1.4.3/MHCtools/MD5 | 56 ++++---- MHCtools-1.4.3/MHCtools/NEWS.md | 89 ++++++------- MHCtools-1.4.3/MHCtools/R/BootKmeans_func_20210910.R | 4 MHCtools-1.4.3/MHCtools/R/ClusterMatch_func_20210910.R | 4 MHCtools-1.4.3/MHCtools/R/CreateFas_func_20170924.R | 4 MHCtools-1.4.3/MHCtools/R/CreateSamplesFas_func_20170924.R | 4 MHCtools-1.4.3/MHCtools/R/DistCalc_func_20200902.R | 10 - MHCtools-1.4.3/MHCtools/R/GetHpltStats_func_20200915.R | 4 MHCtools-1.4.3/MHCtools/R/GetHpltTable_func_20200915.R | 4 MHCtools-1.4.3/MHCtools/R/GetReplStats_func_20200914.R | 4 MHCtools-1.4.3/MHCtools/R/GetReplTable_func_20200914.R | 4 MHCtools-1.4.3/MHCtools/R/HpltFind_func_20220802.R |only MHCtools-1.4.3/MHCtools/R/PapaDiv_func_20200915.R | 4 MHCtools-1.4.3/MHCtools/R/ReplMatch_func_20200914.R | 4 MHCtools-1.4.3/MHCtools/README.md | 6 MHCtools-1.4.3/MHCtools/man/BootKmeans.Rd | 4 MHCtools-1.4.3/MHCtools/man/ClusterMatch.Rd | 4 MHCtools-1.4.3/MHCtools/man/CreateFas.Rd | 4 MHCtools-1.4.3/MHCtools/man/CreateSamplesFas.Rd | 4 MHCtools-1.4.3/MHCtools/man/DistCalc.Rd | 10 - MHCtools-1.4.3/MHCtools/man/GetHpltStats.Rd | 4 MHCtools-1.4.3/MHCtools/man/GetHpltTable.Rd | 4 MHCtools-1.4.3/MHCtools/man/GetReplStats.Rd | 4 MHCtools-1.4.3/MHCtools/man/GetReplTable.Rd | 4 MHCtools-1.4.3/MHCtools/man/HpltFind.Rd | 20 ++ MHCtools-1.4.3/MHCtools/man/PapaDiv.Rd | 4 MHCtools-1.4.3/MHCtools/man/ReplMatch.Rd | 4 30 files changed, 145 insertions(+), 138 deletions(-)
Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite
overwhelming with palettes spread over many packages with many
different API's. This packages aims to collect all color palettes
across the R ecosystem under the same package with a streamlined API.
Author: See AUTHORS file.
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between paletteer versions 1.4.0 dated 2021-07-20 and 1.4.1 dated 2022-08-15
paletteer-1.4.0/paletteer/man/wrapper_c.Rd |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/cartography.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/ggthemes-ptol.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/ggthemes-solarized.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/taylor.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/tidyquant.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/trekcolors.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/tvthemes.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/unikn.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/vapeplot.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/vaporwave.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/werpals.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/wesanderson.svg |only paletteer-1.4.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/yarrr.svg |only paletteer-1.4.1/paletteer/DESCRIPTION | 8 +- paletteer-1.4.1/paletteer/MD5 | 38 +++------- paletteer-1.4.1/paletteer/NEWS.md | 4 + paletteer-1.4.1/paletteer/R/paletteer_c_wrappers.R | 7 + paletteer-1.4.1/paletteer/R/sysdata.rda |binary paletteer-1.4.1/paletteer/README.md | 4 - paletteer-1.4.1/paletteer/data/palettes_d.rda |binary paletteer-1.4.1/paletteer/data/palettes_d_names.rda |binary paletteer-1.4.1/paletteer/man/figures/README-unnamed-chunk-4-1.png |binary paletteer-1.4.1/paletteer/man/paletteer-package.Rd | 14 +-- paletteer-1.4.1/paletteer/man/palettes_d.Rd | 2 paletteer-1.4.1/paletteer/man/palettes_d_names.Rd | 2 paletteer-1.4.1/paletteer/tests/testthat/_snaps/vdiffr_palette_check/khroma.svg | 4 - 27 files changed, 34 insertions(+), 49 deletions(-)
Title: Datasets for Teaching Archaeology and Paleontology
Description: Datasets for teaching quantitative approaches and
modeling in archaeology and paleontology. This package provides
several types of data related to broad topics (cultural evolution,
radiocarbon dating, paleoenvironments, etc.), which can be used to
illustrate statistical methods in the classroom (multivariate data
analysis, compositional data analysis, diversity measurement, etc.).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb]
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between folio versions 1.1.0 dated 2022-05-05 and 1.2.0 dated 2022-08-15
DESCRIPTION | 8 ++--- MD5 | 33 ++++++++++++++--------- NEWS.md | 8 +++++ R/artefacts.R |only R/folio-package.R | 4 +- R/isotopes.R | 71 ++++++++++++++++++++++++++++++++++++++++++++++++--- build/partial.rdb |binary data/munsingen.rda |only data/ngrip2010.rda |only data/shipwrecks.rda |only inst/CITATION | 4 +- man/epica2008.Rd | 1 man/folio-package.Rd | 6 ++-- man/law2006.Rd | 1 man/lisiecki2005.Rd | 2 + man/munsingen.Rd |only man/ngrip2004.Rd | 10 ++++--- man/ngrip2010.Rd |only man/nydal1996.Rd | 1 man/shipwrecks.Rd |only man/spratt2016.Rd | 4 ++ 21 files changed, 119 insertions(+), 34 deletions(-)
Title: Robust Score Testing in GLMs, by Sign-Flip Contributions
Description: Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.
Author: Livio Finos, Jelle Goeman and Jesse Hemerik, with contribution of Riccardo De Santis.
Maintainer: Livio Finos <livio.finos@unipd.it>
Diff between flipscores versions 1.1.0 dated 2020-06-20 and 1.2.0 dated 2022-08-15
DESCRIPTION | 14 +-- MD5 | 24 ++--- NAMESPACE | 6 - R/anova_flipscores.R | 119 +++++++++++--------------- R/compute_scores.R | 159 +++++++++++++++++++++++++---------- R/flipscores.R | 155 +++++++++++++++++++++------------- R/flipscores_package.R | 13 +- R/utility_functions.R | 12 +- R/utiliy_score_functions.R | 202 ++++++++++++++++++++++++++++++++++++++++----- man/anova.flipscores.Rd | 27 ++---- man/compute_scores.Rd | 11 +- man/flipscores-package.Rd | 8 - man/flipscores.Rd | 18 ++-- 13 files changed, 510 insertions(+), 258 deletions(-)
Title: Efficiency Analysis Trees
Description: Functions are provided to determine production frontiers and technical
efficiency measures through non-parametric techniques based upon regression trees.
The package includes code for estimating radial input, output, directional and
additive measures, plotting graphical representations of the scores and the production
frontiers by means of trees, and determining rankings of importance of input variables
in the analysis. Additionally, an adaptation of Random Forest by a set of individual
Efficiency Analysis Trees for estimating technical efficiency is also included. More
details in: <doi:10.1016/j.eswa.2020.113783>.
Author: Miriam Esteve [cre, aut] ,
Victor Espana [aut] ,
Juan Aparicio [aut] ,
Xavier Barber [aut]
Maintainer: Miriam Esteve <mestevecampello@gmail.com>
Diff between eat versions 0.1.2 dated 2022-01-15 and 0.1.3 dated 2022-08-15
DESCRIPTION | 10 MD5 | 36 - NEWS.md | 7 R/eat_pkg.R | 7 R/efficiencyCEAT.R | 14 R/efficiencyEAT.R | 14 R/efficiency_plots.R | 14 R/plotEAT.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/EAT.html | 1212 ++++++++++++++++++++++++++++++------------------ man/RFEAT.Rd | 4 man/RandomEAT.Rd | 6 man/eat-package.Rd | 7 man/efficiencyCEAT.Rd | 14 man/efficiencyEAT.Rd | 14 man/efficiencyJitter.Rd | 14 man/layout.Rd | 2 man/plotEAT.Rd | 10 19 files changed, 857 insertions(+), 540 deletions(-)
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 2.2.0 dated 2022-07-03 and 2.2.1 dated 2022-08-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/GetProteinFunction.R | 2 +- R/GetProteomeFasta.R | 4 ++-- R/GetProteomeInfo.R | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Read Ethoscope Data
Description: Handling of behavioural data from the Ethoscope platform
(Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>).
Ethoscopes (<https://www.notion.so/giorgiogilestro/Ethoscope-User-Manual-a9739373ae9f4840aa45b277f2f0e3a7>) are an open source/open hardware framework made of
interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple
small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables
such as xy coordinates, dimensions and speed.
This package is part of the rethomics framework <https://rethomics.github.io/>.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between scopr versions 0.3.3 dated 2019-02-15 and 0.3.4 dated 2022-08-15
scopr-0.3.3/scopr/README.md |only scopr-0.3.4/scopr/DESCRIPTION | 16 ++-- scopr-0.3.4/scopr/MD5 | 23 +++--- scopr-0.3.4/scopr/R/build-query.R | 3 scopr-0.3.4/scopr/R/list-result-files.R | 4 - scopr-0.3.4/scopr/R/load-ethoscope.R | 33 ++++++---- scopr-0.3.4/scopr/R/parse-datetime.R | 9 ++ scopr-0.3.4/scopr/man/link_ethoscope_metadata.Rd | 12 ++- scopr-0.3.4/scopr/man/load_ethoscope.Rd | 22 +++++- scopr-0.3.4/scopr/man/no_region_id_metadata.Rd | 4 - scopr-0.3.4/scopr/man/region_id_metadata.Rd | 4 - scopr-0.3.4/scopr/tests/testthat/test-build_query.R | 26 +++++++ scopr-0.3.4/scopr/tests/testthat/test-link_ethoscope_metadata_remote.R | 2 13 files changed, 112 insertions(+), 46 deletions(-)
Title: Neighborhood Deprivation Indices
Description: Computes various metrics of socio-economic deprivation and disparity in
the United States. Some metrics are considered "spatial" because they
consider the values of neighboring (i.e., adjacent) census geographies in
their computation, while other metrics are "aspatial" because they only
consider the value within each census geography. Two types of aspatial
neighborhood deprivation indices (NDI) are available: including:
(1) based on Messer et al. (2006) <doi:10.1007/s11524-006-9094-x>
and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066>
and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002>
who use variables chosen by Roux and Mair (2010)
<doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition
of multiple demographic characteristics from the U.S. Census Bureau
American Community Survey 5-year estimates (ACS-5; 2010-2020). Using data
from the ACS-5 (2009-2020), the package can also (1) compute the spatial
Racial Isolation Index ( [...truncated...]
Author: Ian D. Buller [aut, cre, cph] ,
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@nih.gov>
Diff between ndi versions 0.1.0 dated 2022-08-13 and 0.1.1 dated 2022-08-15
DESCRIPTION | 29 + MD5 | 41 +- NAMESPACE | 7 NEWS.md | 11 R/anthopolos.R |only R/bravo.R |only R/gini.R |only R/globals.R | 2 R/messer.R | 4 R/package.R | 20 - R/powell_wiley.R | 4 README.md | 114 ++++++- inst/CITATION | 63 ++++ inst/doc/vignette.html | 575 ++++++++++++++++++++++++++++++------- man/anthopolos.Rd |only man/bravo.Rd |only man/gini.Rd |only man/messer.Rd | 2 man/ndi-package.Rd | 18 - man/powell_wiley.Rd | 2 tests/testthat/test-anthopolos.R |only tests/testthat/test-bravo.R |only tests/testthat/test-gini.R |only tests/testthat/test-messer.R | 4 tests/testthat/test-powell_wiley.R | 4 vignettes/vignette.Rmd | 292 +++++++++++++++--- 26 files changed, 982 insertions(+), 210 deletions(-)
Title: Helper Functions to Work with 'Moodle' Data
Description: A collection of functions to connect to a 'Moodle' database, cache relevant tables locally and generate learning analytics.
'Moodle' is an open source Learning Management System (LMS) developed by MoodleHQ. For more information about Moodle, visit <https://moodle.org>.
Author: Aleksander Dietrichson [aut, cre],
Chi Square Laboratories [cph],
Darko Miletic [ctb],
Pablo Pagnone [ctb],
Alex Ondrus [ctb]
Maintainer: Aleksander Dietrichson <dietrichson@gmail.com>
Diff between moodleR versions 1.0.0 dated 2022-03-25 and 1.0.1 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/vignette.rds |binary man/moodleR-package.Rd | 19 ++++--------------- 5 files changed, 16 insertions(+), 23 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984) <isbn:978-0-12-299050-2> and Lebart et al.
(2006) <isbn:978-2-10-049616-7>.
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [ctb]
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.2.2 dated 2021-09-18 and 0.3.0 dated 2022-08-15
dimensio-0.2.2/dimensio/R/jackknife.R |only dimensio-0.2.2/dimensio/R/joint.R |only dimensio-0.2.2/dimensio/inst/examples/ex-jackknife.R |only dimensio-0.2.2/dimensio/man/figures/README-plot-coord-1.png |only dimensio-0.2.2/dimensio/man/figures/README-plot-coord-2.png |only dimensio-0.2.2/dimensio/man/figures/README-plot-coord-3.png |only dimensio-0.2.2/dimensio/man/figures/README-plot-eig-3.png |only dimensio-0.2.2/dimensio/man/figures/README-plot-eig-4.png |only dimensio-0.2.2/dimensio/man/figures/README-plot-ind-3.png |only dimensio-0.2.2/dimensio/man/figures/README-plot-valid-1.png |only dimensio-0.2.2/dimensio/man/jackknife.Rd |only dimensio-0.2.2/dimensio/man/mutator.Rd |only dimensio-0.2.2/dimensio/tests/testthat/_snaps/jackknife.md |only dimensio-0.2.2/dimensio/tests/testthat/_snaps/plot-ca/ca-coord-all.svg |only dimensio-0.2.2/dimensio/tests/testthat/test-jackknife.R |only dimensio-0.3.0/dimensio/DESCRIPTION | 45 dimensio-0.3.0/dimensio/MD5 | 194 +-- dimensio-0.3.0/dimensio/NAMESPACE | 18 dimensio-0.3.0/dimensio/NEWS.md | 26 dimensio-0.3.0/dimensio/R/AllClasses.R | 13 dimensio-0.3.0/dimensio/R/AllGenerics.R | 621 ++++++---- dimensio-0.3.0/dimensio/R/bootstrap.R | 99 - dimensio-0.3.0/dimensio/R/data.R |only dimensio-0.3.0/dimensio/R/dimensio-package.R | 10 dimensio-0.3.0/dimensio/R/ggplot2.R |only dimensio-0.3.0/dimensio/R/helpers.R | 16 dimensio-0.3.0/dimensio/R/mutators.R | 114 + dimensio-0.3.0/dimensio/R/pca.R | 2 dimensio-0.3.0/dimensio/R/plot.R | 493 +++++-- dimensio-0.3.0/dimensio/R/svd.R | 2 dimensio-0.3.0/dimensio/R/tidy.R |only dimensio-0.3.0/dimensio/R/wrap.R |only dimensio-0.3.0/dimensio/README.md | 147 -- dimensio-0.3.0/dimensio/build/partial.rdb |binary dimensio-0.3.0/dimensio/data |only dimensio-0.3.0/dimensio/inst/CITATION | 9 dimensio-0.3.0/dimensio/inst/examples/ex-biplot.R |only dimensio-0.3.0/dimensio/inst/examples/ex-bootstrap.R | 47 dimensio-0.3.0/dimensio/inst/examples/ex-ca.R | 18 dimensio-0.3.0/dimensio/inst/examples/ex-coordinates.R |only dimensio-0.3.0/dimensio/inst/examples/ex-pca.R | 12 dimensio-0.3.0/dimensio/inst/examples/ex-plot.R | 22 dimensio-0.3.0/dimensio/inst/examples/ex-subset.R | 12 dimensio-0.3.0/dimensio/inst/examples/ex-summary.R | 6 dimensio-0.3.0/dimensio/inst/examples/ex-wrap.R |only dimensio-0.3.0/dimensio/man/CA-class.Rd | 18 dimensio-0.3.0/dimensio/man/PCA-class.Rd | 12 dimensio-0.3.0/dimensio/man/benthos.Rd |only dimensio-0.3.0/dimensio/man/biplot.Rd |only dimensio-0.3.0/dimensio/man/bootstrap.Rd | 115 - dimensio-0.3.0/dimensio/man/ca.Rd | 27 dimensio-0.3.0/dimensio/man/colours.Rd |only dimensio-0.3.0/dimensio/man/countries.Rd |only dimensio-0.3.0/dimensio/man/dimensio-package.Rd | 14 dimensio-0.3.0/dimensio/man/envelopes.Rd |only dimensio-0.3.0/dimensio/man/figures/README-biplot-1.png |only dimensio-0.3.0/dimensio/man/figures/README-plot-eig-1.png |binary dimensio-0.3.0/dimensio/man/figures/README-plot-eig-2.png |binary dimensio-0.3.0/dimensio/man/figures/README-plot-ind-1.png |binary dimensio-0.3.0/dimensio/man/figures/README-plot-ind-2.png |binary dimensio-0.3.0/dimensio/man/figures/README-plot-var-1.png |binary dimensio-0.3.0/dimensio/man/figures/README-plot-var-2.png |binary dimensio-0.3.0/dimensio/man/get_contributions.Rd |only dimensio-0.3.0/dimensio/man/get_coordinates.Rd |only dimensio-0.3.0/dimensio/man/get_data.Rd |only dimensio-0.3.0/dimensio/man/get_distances.Rd |only dimensio-0.3.0/dimensio/man/get_eigenvalues.Rd |only dimensio-0.3.0/dimensio/man/mutators.Rd |only dimensio-0.3.0/dimensio/man/pca.Rd | 20 dimensio-0.3.0/dimensio/man/plot_contributions.Rd | 33 dimensio-0.3.0/dimensio/man/plot_coordinates.Rd | 141 +- dimensio-0.3.0/dimensio/man/plot_eigenvalues.Rd | 37 dimensio-0.3.0/dimensio/man/subset.Rd | 23 dimensio-0.3.0/dimensio/man/summary.Rd | 6 dimensio-0.3.0/dimensio/man/tidy.Rd |only dimensio-0.3.0/dimensio/tests/testthat/_snaps/biplot-ca |only dimensio-0.3.0/dimensio/tests/testthat/_snaps/biplot-pca |only dimensio-0.3.0/dimensio/tests/testthat/_snaps/bootstrap |only dimensio-0.3.0/dimensio/tests/testthat/_snaps/bootstrap.md | 114 + dimensio-0.3.0/dimensio/tests/testthat/_snaps/ca.md |only dimensio-0.3.0/dimensio/tests/testthat/_snaps/pca.md |only dimensio-0.3.0/dimensio/tests/testthat/_snaps/plot-ca/ca-eig-0-0.svg | 85 - 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Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cm [...truncated...]
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 3.4.3 dated 2022-06-28 and 3.4.4 dated 2022-08-15
DESCRIPTION | 9 MD5 | 36 NAMESPACE | 10 NEWS.md | 151 R/cmsaf.R | 58 R/get_grid.R | 8 R/release_questions.R | 36 R/run_toolbox.R | 42 build/partial.rdb |binary inst/WORDLIST | 90 inst/toolbox/ColorspacePrivates.R | 1260 +-- inst/toolbox/global.R | 706 - inst/toolbox/server.R |15198 +++++++++++++++++++------------------- inst/toolbox/ui.R | 1548 +-- inst/toolbox/www/style.css | 532 - man/cmsaf.Rd | 76 man/run_toolbox.Rd | 36 tests/spelling.R | 6 tests/spelling.Rout.save | 50 19 files changed, 9928 insertions(+), 9924 deletions(-)
Title: Downloads and Organizes Financial Data from Yahoo Finance
Description: Facilitates download of financial data from Yahoo Finance <https://finance.yahoo.com/>,
a vast repository of stock price data across multiple financial exchanges. The package offers a local caching system
and support for parallel computation.
Author: Marcelo Perlin [aut, cre],
Nic Crane [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/523>),
Alexander Fischer [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/523>)
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between yfR versions 1.0.0 dated 2022-06-30 and 1.0.1 dated 2022-08-15
DESCRIPTION | 8 +-- MD5 | 24 +++++----- NEWS.md | 5 ++ R/yf_get.R | 2 README.md | 26 +++++------ inst/WORDLIST | 1 inst/doc/diff-batchgetsymbols.html | 4 - inst/doc/getting-started.R | 7 +-- inst/doc/getting-started.Rmd | 7 +-- inst/doc/getting-started.html | 83 +++++++++++++++++++------------------ inst/doc/using-collections.html | 4 - man/yf_get.Rd | 2 vignettes/getting-started.Rmd | 7 +-- 13 files changed, 93 insertions(+), 87 deletions(-)
Title: Investigating the Functional Characteristics of Selected SNPs
and Their Vicinity Genomic Region
Description: To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 0.2.4.0 dated 2022-08-07 and 0.2.5.0 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/CADD.R | 3 +-- R/getVariantData.R | 11 +++++++---- R/runPipelineOnlist.R | 2 +- 5 files changed, 17 insertions(+), 15 deletions(-)
Title: Spatial Dependence for Simple Features
Description: An interface to 'spdep' to integrate with 'sf' objects and the 'tidyverse'.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between sfdep versions 0.1.0 dated 2022-04-20 and 0.2.0 dated 2022-08-15
sfdep-0.1.0/sfdep/NEWS.md |only sfdep-0.1.0/sfdep/R/utils-pipe.R |only sfdep-0.1.0/sfdep/man/pipe.Rd |only sfdep-0.2.0/sfdep/DESCRIPTION | 16 sfdep-0.2.0/sfdep/MD5 | 169 +++- sfdep-0.2.0/sfdep/NAMESPACE | 41 + sfdep-0.2.0/sfdep/R/apply.R | 1 sfdep-0.2.0/sfdep/R/as_matrix.R |only sfdep-0.2.0/sfdep/R/aspace-trig.R |only sfdep-0.2.0/sfdep/R/emerging-hostpot-analysis.R |only sfdep-0.2.0/sfdep/R/emerging-hostpot-classifications.R |only sfdep-0.2.0/sfdep/R/global-colocation-impl.R |only sfdep-0.2.0/sfdep/R/global-gini.R |only sfdep-0.2.0/sfdep/R/global-measures.R | 46 - sfdep-0.2.0/sfdep/R/global-moran-bv-impl.R | 17 sfdep-0.2.0/sfdep/R/joincount-uni-impl.R | 15 sfdep-0.2.0/sfdep/R/lisa.R | 1 sfdep-0.2.0/sfdep/R/local-colocation-quotient-impl.R |only sfdep-0.2.0/sfdep/R/local-moran-bv-impl.R | 19 sfdep-0.2.0/sfdep/R/localC.R | 17 sfdep-0.2.0/sfdep/R/localG-star.R | 11 sfdep-0.2.0/sfdep/R/localG.R | 8 sfdep-0.2.0/sfdep/R/nb-block-contiguity.R |only sfdep-0.2.0/sfdep/R/nb-complete-graph.R |only sfdep-0.2.0/sfdep/R/nb-match-test-impl.R | 3 sfdep-0.2.0/sfdep/R/neighbors.R | 18 sfdep-0.2.0/sfdep/R/pariwise-colocation-impl.R |only sfdep-0.2.0/sfdep/R/point-pattern-centers.R |only sfdep-0.2.0/sfdep/R/point-pattern_std-distance.R |only sfdep-0.2.0/sfdep/R/pp-ellipse.R |only sfdep-0.2.0/sfdep/R/pp-std_dev_ellipse.R |only sfdep-0.2.0/sfdep/R/sfnetworks.R | 31 sfdep-0.2.0/sfdep/R/spacetime-activate.R |only sfdep-0.2.0/sfdep/R/spacetime-constructor.R |only sfdep-0.2.0/sfdep/R/spacetime-cube-complete.R |only sfdep-0.2.0/sfdep/R/spacetime-cube-set-cols.R |only sfdep-0.2.0/sfdep/R/spacetime-cube-test.R |only sfdep-0.2.0/sfdep/R/spacetime-local-gistar-impl.R |only sfdep-0.2.0/sfdep/R/spacetime-methods.R |only sfdep-0.2.0/sfdep/R/spacetime-nb-wt.R |only sfdep-0.2.0/sfdep/R/utils-constants.R |only sfdep-0.2.0/sfdep/R/utils-kernels.R | 17 sfdep-0.2.0/sfdep/R/utils-self.R | 2 sfdep-0.2.0/sfdep/R/utils-set-operations.R |only sfdep-0.2.0/sfdep/R/utils.R | 12 sfdep-0.2.0/sfdep/R/weights-contiguity.R | 1 sfdep-0.2.0/sfdep/R/weights-kernel.R | 32 sfdep-0.2.0/sfdep/R/zzz.R |only sfdep-0.2.0/sfdep/README.md | 51 + sfdep-0.2.0/sfdep/build/partial.rdb |binary sfdep-0.2.0/sfdep/build/vignette.rds |binary sfdep-0.2.0/sfdep/inst/doc/basics-of-sfdep.html | 455 ++++++++++--- sfdep-0.2.0/sfdep/inst/doc/conditional-permutation.R | 27 sfdep-0.2.0/sfdep/inst/doc/conditional-permutation.Rmd | 55 + sfdep-0.2.0/sfdep/inst/doc/conditional-permutation.html | 305 +++++++- sfdep-0.2.0/sfdep/inst/doc/spacetime-s3.R |only sfdep-0.2.0/sfdep/inst/doc/spacetime-s3.Rmd |only sfdep-0.2.0/sfdep/inst/doc/spacetime-s3.html |only sfdep-0.2.0/sfdep/inst/doc/spdep-and-pysal.html | 197 +++++ sfdep-0.2.0/sfdep/inst/extdata/bos-ecometric.csv |only sfdep-0.2.0/sfdep/inst/extdata/bos-ecometric.geojson |only sfdep-0.2.0/sfdep/man/activate.Rd |only sfdep-0.2.0/sfdep/man/as_spacetime.Rd |only sfdep-0.2.0/sfdep/man/center_mean.Rd |only sfdep-0.2.0/sfdep/man/classify_hotspot.Rd |only sfdep-0.2.0/sfdep/man/complete_spacetime_cube.Rd |only sfdep-0.2.0/sfdep/man/cond_permute_nb.Rd | 2 sfdep-0.2.0/sfdep/man/critical_threshold.Rd | 4 sfdep-0.2.0/sfdep/man/ellipse.Rd |only sfdep-0.2.0/sfdep/man/emerging_hotspot_analysis.Rd |only sfdep-0.2.0/sfdep/man/figures/README-unnamed-chunk-8-1.png |binary sfdep-0.2.0/sfdep/man/global_colocation.Rd |only sfdep-0.2.0/sfdep/man/global_colocation_calc.Rd |only sfdep-0.2.0/sfdep/man/global_colocation_perm_impl.Rd |only sfdep-0.2.0/sfdep/man/global_jc_perm.Rd | 28 sfdep-0.2.0/sfdep/man/global_moran_bv.Rd | 13 sfdep-0.2.0/sfdep/man/include_self.Rd | 2 sfdep-0.2.0/sfdep/man/is_spacetime_cube.Rd |only sfdep-0.2.0/sfdep/man/kernels.Rd | 10 sfdep-0.2.0/sfdep/man/local_c.Rd | 17 sfdep-0.2.0/sfdep/man/local_colocation.Rd |only sfdep-0.2.0/sfdep/man/local_colocation_calc.Rd |only sfdep-0.2.0/sfdep/man/local_colocation_impl.Rd |only sfdep-0.2.0/sfdep/man/local_g.Rd | 2 sfdep-0.2.0/sfdep/man/local_g_spt.Rd |only sfdep-0.2.0/sfdep/man/local_gstar.Rd | 2 sfdep-0.2.0/sfdep/man/local_jc_uni.Rd | 13 sfdep-0.2.0/sfdep/man/local_moran.Rd | 1 sfdep-0.2.0/sfdep/man/local_moran_bv.Rd | 6 sfdep-0.2.0/sfdep/man/local_moran_bv_calc.Rd | 4 sfdep-0.2.0/sfdep/man/nb_match_test.Rd | 3 sfdep-0.2.0/sfdep/man/nb_union.Rd |only sfdep-0.2.0/sfdep/man/pairwise_colocation.Rd |only sfdep-0.2.0/sfdep/man/pairwise_colocation_calc.Rd |only sfdep-0.2.0/sfdep/man/pairwise_colocation_perm_impl.Rd |only sfdep-0.2.0/sfdep/man/pct_nonzero.Rd |only sfdep-0.2.0/sfdep/man/recreate_listw.Rd | 6 sfdep-0.2.0/sfdep/man/set_col.Rd |only sfdep-0.2.0/sfdep/man/sin_d.Rd |only sfdep-0.2.0/sfdep/man/spacetime.Rd |only sfdep-0.2.0/sfdep/man/spatial_gini.Rd |only sfdep-0.2.0/sfdep/man/spt_nb.Rd |only sfdep-0.2.0/sfdep/man/spt_order.Rd |only sfdep-0.2.0/sfdep/man/spt_update.Rd |only sfdep-0.2.0/sfdep/man/spt_wt.Rd |only sfdep-0.2.0/sfdep/man/st_as_edges.Rd | 38 - sfdep-0.2.0/sfdep/man/st_as_graph.Rd | 3 sfdep-0.2.0/sfdep/man/st_as_nodes.Rd | 1 sfdep-0.2.0/sfdep/man/st_block_nb.Rd |only sfdep-0.2.0/sfdep/man/st_complete_nb.Rd |only sfdep-0.2.0/sfdep/man/st_contiguity.Rd | 1 sfdep-0.2.0/sfdep/man/st_nb_apply.Rd | 1 sfdep-0.2.0/sfdep/man/st_weights.Rd | 1 sfdep-0.2.0/sfdep/man/std_dev_ellipse.Rd |only sfdep-0.2.0/sfdep/man/std_distance.Rd |only sfdep-0.2.0/sfdep/man/szero.Rd |only sfdep-0.2.0/sfdep/man/tidyverse.Rd |only sfdep-0.2.0/sfdep/man/wt_as_matrix.Rd |only sfdep-0.2.0/sfdep/vignettes/conditional-permutation.Rmd | 55 + sfdep-0.2.0/sfdep/vignettes/spacetime-s3.Rmd |only 120 files changed, 1408 insertions(+), 372 deletions(-)
Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages
for fitting Bayesian models or working with output from Bayesian models.
The primary goals of the package are to:
(a) Efficiently convert between many different useful formats of
draws (samples) from posterior or prior distributions.
(b) Provide consistent methods for operations commonly performed on draws,
for example, subsetting, binding, or mutating draws.
(c) Provide various summaries of draws in convenient formats.
(d) Provide lightweight implementations of state of the art posterior
inference diagnostics. References: Vehtari et al. (2021)
<doi:10.1214/20-BA1221>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [aut],
Matthew Kay [aut],
Aki Vehtari [aut],
Måns Magnusson [ctb],
Rok Česnovar [ctb],
Ben Lambert [ctb],
Ozan Adıguezel [ctb],
Jacob Socolar [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between posterior versions 1.2.2 dated 2022-06-09 and 1.3.0 dated 2022-08-15
DESCRIPTION | 15 ++-- MD5 | 82 ++++++++++++++------------ NAMESPACE | 12 +++ NEWS.md | 23 +++++++ R/as_draws.R | 2 R/as_draws_array.R | 1 R/as_draws_matrix.R | 1 R/as_draws_rvars.R | 16 +++-- R/for_each_draw.R |only R/resample_draws.R | 14 +++- R/rvar-.R | 39 +++++++----- R/rvar-cast.R | 2 R/rvar-dim.R | 49 +++++++++++++++ R/rvar-math.R | 64 ++++++++++++++++++++ R/rvar-print.R | 12 ++- R/rvar-rfun.R | 11 --- R/rvar-slice.R | 14 ---- R/subset_draws.R | 13 +++- R/thin_draws.R | 6 + inst/doc/posterior.html | 96 +++++++++++++++---------------- inst/doc/rvar.R | 21 ++++++ inst/doc/rvar.Rmd | 44 +++++++++++++- inst/doc/rvar.html | 57 ++++++++++++++++-- man/diag-rvar-method.Rd |only man/drop-rvar-method.Rd |only man/figures/logo.svg |only man/for_each_draw.Rd |only man/resample_draws.Rd | 8 +- man/sub-.draws_array.Rd | 1 man/sub-.draws_matrix.Rd | 1 man/subset_draws.Rd | 3 man/thin_draws.Rd | 3 tests/testthat/test-as_draws.R | 108 +++++++++++++++++++++++++++++++++++ tests/testthat/test-for_each_draw.R |only tests/testthat/test-resample_draws.R | 24 ++++++- tests/testthat/test-rvar-.R | 10 +++ tests/testthat/test-rvar-bind.R | 4 + tests/testthat/test-rvar-dim.R | 39 +++++++++++- tests/testthat/test-rvar-math.R | 26 ++++++++ tests/testthat/test-rvar-print.R | 4 - tests/testthat/test-rvar-rfun.R | 19 ++++++ tests/testthat/test-rvar-slice.R | 48 ++++++++++----- tests/testthat/test-subset_draws.R | 16 +++++ tests/testthat/test-thin_draws.R | 6 + vignettes/rvar.Rmd | 44 +++++++++++++- 45 files changed, 777 insertions(+), 181 deletions(-)
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Description: Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: [...truncated...]
Author: Ege Ulgen [aut, cre, cph]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between driveR versions 0.3.0 dated 2022-01-18 and 0.4.0 dated 2022-08-15
driveR-0.3.0/driveR/man/KEGG_cancer_pathways.Rd |only driveR-0.3.0/driveR/man/MCR_table.Rd |only driveR-0.3.0/driveR/man/TCGA_MTL_fit.Rd |only driveR-0.3.0/driveR/man/metapredictor_model.Rd |only driveR-0.4.0/driveR/DESCRIPTION | 13 driveR-0.4.0/driveR/MD5 | 42 -- driveR-0.4.0/driveR/NEWS.md | 7 driveR-0.4.0/driveR/R/core_functions.R | 4 driveR-0.4.0/driveR/R/data.R | 55 -- driveR-0.4.0/driveR/R/sysdata.rda |binary driveR-0.4.0/driveR/R/utility.R | 21 - driveR-0.4.0/driveR/README.md | 3 driveR-0.4.0/driveR/build/vignette.rds |binary driveR-0.4.0/driveR/inst/doc/how_to_use.R | 6 driveR-0.4.0/driveR/inst/doc/how_to_use.Rmd | 10 driveR-0.4.0/driveR/inst/doc/how_to_use.html | 377 ++++++++++++++++--- driveR-0.4.0/driveR/man/MTL_submodel_descriptions.Rd | 3 driveR-0.4.0/driveR/man/create_SCNA_score_df.Rd | 3 driveR-0.4.0/driveR/man/create_features_df.Rd | 3 driveR-0.4.0/driveR/man/create_gene_level_scna_df.Rd | 8 driveR-0.4.0/driveR/man/prioritize_driver_genes.Rd | 1 driveR-0.4.0/driveR/man/specific_thresholds.Rd | 3 driveR-0.4.0/driveR/tests/testthat/test-utility.R | 18 driveR-0.4.0/driveR/vignettes/how_to_use.Rmd | 10 24 files changed, 435 insertions(+), 152 deletions(-)
Title: A Generator of Multidimensional Noise
Description: Generation of natural looking noise has many application within
simulation, procedural generation, and art, to name a few. The 'ambient'
package provides an interface to the 'FastNoise' C++ library and allows for
efficient generation of perlin, simplex, worley, cubic, value, and white
noise with optional perturbation in either 2, 3, or 4 (in case of simplex and
white noise) dimensions.
Author: Thomas Lin Pedersen [cre, aut]
,
Jordan Peck [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ambient versions 1.0.0 dated 2020-03-21 and 1.0.1 dated 2022-08-15
ambient-1.0.0/ambient/R/RcppExports.R |only ambient-1.0.0/ambient/src/RcppExports.cpp |only ambient-1.0.1/ambient/DESCRIPTION | 17 +-- ambient-1.0.1/ambient/MD5 | 54 +++++----- ambient-1.0.1/ambient/NAMESPACE | 5 ambient-1.0.1/ambient/NEWS.md | 8 + ambient-1.0.1/ambient/R/aaa.R | 11 +- ambient-1.0.1/ambient/R/ambient-package.R | 13 +- ambient-1.0.1/ambient/R/cpp11.R |only ambient-1.0.1/ambient/R/modify.R | 2 ambient-1.0.1/ambient/R/noise-blue.R |only ambient-1.0.1/ambient/R/noise-cubic.R | 6 - ambient-1.0.1/ambient/R/noise-perlin.R | 8 - ambient-1.0.1/ambient/R/noise-simplex.R | 6 - ambient-1.0.1/ambient/R/noise-value.R | 8 - ambient-1.0.1/ambient/R/noise-white.R | 4 ambient-1.0.1/ambient/R/noise-worley.R | 18 +-- ambient-1.0.1/ambient/README.md | 34 +++--- ambient-1.0.1/ambient/man/ambient-package.Rd | 11 -- ambient-1.0.1/ambient/man/figures/README-unnamed-chunk-3-1.png |binary ambient-1.0.1/ambient/man/figures/README-unnamed-chunk-4-1.png |binary ambient-1.0.1/ambient/man/modifications.Rd | 2 ambient-1.0.1/ambient/man/noise_blue.Rd |only ambient-1.0.1/ambient/src/FastNoise.cpp | 6 - ambient-1.0.1/ambient/src/cpp11.cpp |only ambient-1.0.1/ambient/src/cubic.cpp | 32 ++--- ambient-1.0.1/ambient/src/perlin.cpp | 30 ++--- ambient-1.0.1/ambient/src/simplex.cpp | 41 +++---- ambient-1.0.1/ambient/src/value.cpp | 29 ++--- ambient-1.0.1/ambient/src/white.cpp | 41 +++---- ambient-1.0.1/ambient/src/worley.cpp | 34 +++--- 31 files changed, 222 insertions(+), 198 deletions(-)
Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.23.6 dated 2021-11-23 and 0.27.1 dated 2022-08-15
rayrender-0.23.6/rayrender/src/Makevars |only rayrender-0.27.1/rayrender/DESCRIPTION | 15 rayrender-0.27.1/rayrender/MD5 | 302 - rayrender-0.27.1/rayrender/NAMESPACE | 3 rayrender-0.27.1/rayrender/R/RcppExports.R | 8 rayrender-0.27.1/rayrender/R/add_object.R | 7 rayrender-0.27.1/rayrender/R/animate_objects.R | 34 rayrender-0.27.1/rayrender/R/csg_construct.R | 193 rayrender-0.27.1/rayrender/R/generate_camera_motion.R | 108 rayrender-0.27.1/rayrender/R/generate_cornell.R | 23 rayrender-0.27.1/rayrender/R/generate_ground.R | 4 rayrender-0.27.1/rayrender/R/generate_studio.R | 10 rayrender-0.27.1/rayrender/R/group_objects.R | 51 rayrender-0.27.1/rayrender/R/materials.R | 126 rayrender-0.27.1/rayrender/R/objects.R | 1098 +++ rayrender-0.27.1/rayrender/R/pig.R | 19 rayrender-0.27.1/rayrender/R/post_process_scene.R |only rayrender-0.27.1/rayrender/R/prepare_scene_list.R |only rayrender-0.27.1/rayrender/R/r_obj.R | 2 rayrender-0.27.1/rayrender/R/render_animation.R | 506 - rayrender-0.27.1/rayrender/R/render_ao.R |only rayrender-0.27.1/rayrender/R/render_preview.R | 10 rayrender-0.27.1/rayrender/R/render_scene.R | 732 -- rayrender-0.27.1/rayrender/R/save_png.R | 2 rayrender-0.27.1/rayrender/R/util-functions.R | 118 rayrender-0.27.1/rayrender/R/zzz.R |only rayrender-0.27.1/rayrender/cleanup |only rayrender-0.27.1/rayrender/cleanup.win |only rayrender-0.27.1/rayrender/configure |only rayrender-0.27.1/rayrender/configure.ac |only rayrender-0.27.1/rayrender/configure.win |only rayrender-0.27.1/rayrender/inst/extdata/dgauss.50mm.txt |only rayrender-0.27.1/rayrender/inst/extdata/fisheye.10mm.txt |only rayrender-0.27.1/rayrender/inst/extdata/telephoto.250mm.txt |only rayrender-0.27.1/rayrender/inst/extdata/wide.22mm.txt |only rayrender-0.27.1/rayrender/man/add_object.Rd | 4 rayrender-0.27.1/rayrender/man/add_points_polygon.Rd |only rayrender-0.27.1/rayrender/man/animate_objects.Rd | 34 rayrender-0.27.1/rayrender/man/arrow.Rd | 12 rayrender-0.27.1/rayrender/man/bezier_curve.Rd | 10 rayrender-0.27.1/rayrender/man/calculate_final_twist.Rd |only rayrender-0.27.1/rayrender/man/cone.Rd | 12 rayrender-0.27.1/rayrender/man/csg_box.Rd | 8 rayrender-0.27.1/rayrender/man/csg_capsule.Rd | 11 rayrender-0.27.1/rayrender/man/csg_combine.Rd | 23 rayrender-0.27.1/rayrender/man/csg_cone.Rd | 11 rayrender-0.27.1/rayrender/man/csg_cylinder.Rd | 11 rayrender-0.27.1/rayrender/man/csg_ellipsoid.Rd | 11 rayrender-0.27.1/rayrender/man/csg_elongate.Rd | 14 rayrender-0.27.1/rayrender/man/csg_group.Rd | 2 rayrender-0.27.1/rayrender/man/csg_object.Rd | 14 rayrender-0.27.1/rayrender/man/csg_onion.Rd | 11 rayrender-0.27.1/rayrender/man/csg_plane.Rd | 8 rayrender-0.27.1/rayrender/man/csg_pyramid.Rd | 8 rayrender-0.27.1/rayrender/man/csg_rotate.Rd | 5 rayrender-0.27.1/rayrender/man/csg_round.Rd | 5 rayrender-0.27.1/rayrender/man/csg_rounded_cone.Rd | 11 rayrender-0.27.1/rayrender/man/csg_scale.Rd | 2 rayrender-0.27.1/rayrender/man/csg_sphere.Rd | 14 rayrender-0.27.1/rayrender/man/csg_torus.Rd | 11 rayrender-0.27.1/rayrender/man/csg_translate.Rd | 5 rayrender-0.27.1/rayrender/man/csg_triangle.Rd | 8 rayrender-0.27.1/rayrender/man/cube.Rd | 12 rayrender-0.27.1/rayrender/man/cylinder.Rd | 12 rayrender-0.27.1/rayrender/man/dielectric.Rd | 22 rayrender-0.27.1/rayrender/man/diffuse.Rd | 20 rayrender-0.27.1/rayrender/man/disk.Rd | 12 rayrender-0.27.1/rayrender/man/ellipsoid.Rd | 12 rayrender-0.27.1/rayrender/man/extruded_path.Rd |only rayrender-0.27.1/rayrender/man/extruded_polygon.Rd | 40 rayrender-0.27.1/rayrender/man/generate_camera_motion.Rd | 23 rayrender-0.27.1/rayrender/man/generate_cornell.Rd | 23 rayrender-0.27.1/rayrender/man/generate_ground.Rd | 4 rayrender-0.27.1/rayrender/man/generate_studio.Rd | 8 rayrender-0.27.1/rayrender/man/get_saved_keyframes.Rd |only rayrender-0.27.1/rayrender/man/glossy.Rd | 24 rayrender-0.27.1/rayrender/man/group_objects.Rd | 25 rayrender-0.27.1/rayrender/man/hair.Rd | 5 rayrender-0.27.1/rayrender/man/lambertian.Rd | 2 rayrender-0.27.1/rayrender/man/light.Rd | 14 rayrender-0.27.1/rayrender/man/mesh3d_model.Rd | 2 rayrender-0.27.1/rayrender/man/metal.Rd | 14 rayrender-0.27.1/rayrender/man/microfacet.Rd | 25 rayrender-0.27.1/rayrender/man/obj_model.Rd | 8 rayrender-0.27.1/rayrender/man/path.Rd | 28 rayrender-0.27.1/rayrender/man/pig.Rd | 19 rayrender-0.27.1/rayrender/man/post_process_scene.Rd |only rayrender-0.27.1/rayrender/man/prepare_scene_list.Rd |only rayrender-0.27.1/rayrender/man/r_obj.Rd | 2 rayrender-0.27.1/rayrender/man/render_animation.Rd | 53 rayrender-0.27.1/rayrender/man/render_ao.Rd |only rayrender-0.27.1/rayrender/man/render_preview.Rd | 8 rayrender-0.27.1/rayrender/man/render_scene.Rd | 115 rayrender-0.27.1/rayrender/man/run_documentation.Rd |only rayrender-0.27.1/rayrender/man/segment.Rd | 16 rayrender-0.27.1/rayrender/man/slerp.Rd |only rayrender-0.27.1/rayrender/man/sphere.Rd | 8 rayrender-0.27.1/rayrender/man/text3d.Rd | 10 rayrender-0.27.1/rayrender/man/triangle.Rd | 8 rayrender-0.27.1/rayrender/man/tween.Rd | 4 rayrender-0.27.1/rayrender/man/xy_rect.Rd | 8 rayrender-0.27.1/rayrender/man/xz_rect.Rd | 8 rayrender-0.27.1/rayrender/man/yz_rect.Rd | 8 rayrender-0.27.1/rayrender/src/Makevars.in |only rayrender-0.27.1/rayrender/src/Makevars.win |only rayrender-0.27.1/rayrender/src/PreviewDisplay.cpp |only rayrender-0.27.1/rayrender/src/PreviewDisplay.h |only rayrender-0.27.1/rayrender/src/RayMatrix.cpp |only rayrender-0.27.1/rayrender/src/RayMatrix.h |only rayrender-0.27.1/rayrender/src/RcppExports.cpp | 22 rayrender-0.27.1/rayrender/src/aabb.cpp | 16 rayrender-0.27.1/rayrender/src/aabb.h | 22 rayrender-0.27.1/rayrender/src/adaptivesampler.h | 52 rayrender-0.27.1/rayrender/src/animatedtransform.cpp | 16 rayrender-0.27.1/rayrender/src/animatedtransform.h | 7 rayrender-0.27.1/rayrender/src/bounds.h |only rayrender-0.27.1/rayrender/src/buildscene.cpp | 20 rayrender-0.27.1/rayrender/src/bvh_node.cpp | 6 rayrender-0.27.1/rayrender/src/camera.cpp | 919 +++ rayrender-0.27.1/rayrender/src/camera.h | 273 rayrender-0.27.1/rayrender/src/color.cpp | 7 rayrender-0.27.1/rayrender/src/cone.cpp | 190 rayrender-0.27.1/rayrender/src/csg.h | 42 rayrender-0.27.1/rayrender/src/curve.cpp | 6 rayrender-0.27.1/rayrender/src/cylinder.cpp | 47 rayrender-0.27.1/rayrender/src/debug.cpp | 383 - rayrender-0.27.1/rayrender/src/debug.h | 53 rayrender-0.27.1/rayrender/src/define_functions.cpp |only rayrender-0.27.1/rayrender/src/disk.cpp | 4 rayrender-0.27.1/rayrender/src/distributions.h | 12 rayrender-0.27.1/rayrender/src/ellipsoid.cpp | 8 rayrender-0.27.1/rayrender/src/float.h |only rayrender-0.27.1/rayrender/src/hitable.h | 6 rayrender-0.27.1/rayrender/src/integrator.cpp | 257 rayrender-0.27.1/rayrender/src/integrator.h | 23 rayrender-0.27.1/rayrender/src/material.cpp | 54 rayrender-0.27.1/rayrender/src/mathinline.h | 48 rayrender-0.27.1/rayrender/src/matrix.cpp | 11 rayrender-0.27.1/rayrender/src/matrix.h | 17 rayrender-0.27.1/rayrender/src/mesh3d.cpp | 171 rayrender-0.27.1/rayrender/src/mesh3d.h | 8 rayrender-0.27.1/rayrender/src/normal.h | 15 rayrender-0.27.1/rayrender/src/pcg/pcg_extras.hpp | 27 rayrender-0.27.1/rayrender/src/plymesh.cpp | 30 rayrender-0.27.1/rayrender/src/point2.h | 31 rayrender-0.27.1/rayrender/src/point3.h | 10 rayrender-0.27.1/rayrender/src/ray.h | 20 rayrender-0.27.1/rayrender/src/rectangle.cpp | 103 rayrender-0.27.1/rayrender/src/render_animation_rcpp.cpp | 266 rayrender-0.27.1/rayrender/src/render_scene_rcpp.cpp | 244 rayrender-0.27.1/rayrender/src/rng.h | 1 rayrender-0.27.1/rayrender/src/sampler.cpp | 4 rayrender-0.27.1/rayrender/src/sampler.h | 4 rayrender-0.27.1/rayrender/src/singletriangle.cpp |only rayrender-0.27.1/rayrender/src/singletriangle.h |only rayrender-0.27.1/rayrender/src/sphere.cpp | 8 rayrender-0.27.1/rayrender/src/stb_image.h | 3342 ++++++++---- rayrender-0.27.1/rayrender/src/stb_image_resize.h |only rayrender-0.27.1/rayrender/src/test_windows.cpp |only rayrender-0.27.1/rayrender/src/texture.cpp | 68 rayrender-0.27.1/rayrender/src/texture.h | 45 rayrender-0.27.1/rayrender/src/transform.cpp | 24 rayrender-0.27.1/rayrender/src/transform.h | 3 rayrender-0.27.1/rayrender/src/transformcache.h | 2 rayrender-0.27.1/rayrender/src/triangle.cpp | 442 + rayrender-0.27.1/rayrender/src/triangle.h | 39 rayrender-0.27.1/rayrender/src/trianglemesh.cpp |only rayrender-0.27.1/rayrender/src/trianglemesh.h |only rayrender-0.27.1/rayrender/src/trimesh.cpp | 146 rayrender-0.27.1/rayrender/src/vec2.h | 11 rayrender-0.27.1/rayrender/src/vec3.h | 17 171 files changed, 7942 insertions(+), 3898 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-5 dated 2022-06-21 and 1.1-6 dated 2022-08-15
mlt.docreg-1.1-5/mlt.docreg/tests/udist-Ex.R |only mlt.docreg-1.1-5/mlt.docreg/tests/udist-Ex.Rout.save |only mlt.docreg-1.1-6/mlt.docreg/DESCRIPTION | 10 +++++----- mlt.docreg-1.1-6/mlt.docreg/MD5 | 16 +++++++--------- mlt.docreg-1.1-6/mlt.docreg/NAMESPACE | 1 - mlt.docreg-1.1-6/mlt.docreg/build/vignette.rds |binary mlt.docreg-1.1-6/mlt.docreg/inst/NEWS.Rd | 8 ++++++++ mlt.docreg-1.1-6/mlt.docreg/inst/doc/mlt.Rnw | 4 ++-- mlt.docreg-1.1-6/mlt.docreg/inst/doc/mlt.pdf |binary mlt.docreg-1.1-6/mlt.docreg/vignettes/mlt.Rnw | 4 ++-- 10 files changed, 24 insertions(+), 19 deletions(-)
Title: Outlier Robust Two-Stage Least Squares Inference and Testing
Description: An implementation of easy tools for outlier robust inference in
two-stage least squares (2SLS) models. The user specifies a reference
distribution against which observations are classified as outliers or not.
After removing the outliers, adjusted standard errors are automatically
provided. Furthermore, several statistical tests for the false outlier
detection rate can be calculated. The outlier removing algorithm can be
iterated a fixed number of times or until the procedure converges. The
algorithms and robust inference are described in more detail in Jiao (2019)
<https://drive.google.com/file/d/1qPxDJnLlzLqdk94X9wwVASptf1MPpI2w/view>.
Author: Jonas Kurle [aut, cre]
Maintainer: Jonas Kurle <mail@jonaskurle.com>
Diff between robust2sls versions 0.2.0 dated 2022-02-14 and 0.2.1 dated 2022-08-15
DESCRIPTION | 14 MD5 | 120 - NAMESPACE | 5 NEWS.md | 15 R/beta_inf_test.R | 19 R/bootstrap.R | 62 R/class.R | 5 R/gauge.R | 209 +- R/initial_estimators.R | 119 + R/iterative_estimators.R | 72 R/monte_carlo.R | 6 R/outlier_tests.R | 98 - R/parameter_estimators.R | 2 R/utility.R | 137 + README.md | 5 build/robust2sls.pdf |binary build/vignette.rds |binary inst/doc/monte-carlo.Rmd | 2 inst/doc/monte-carlo.html | 319 +++ inst/doc/outlier-testing.Rmd | 2 inst/doc/outlier-testing.html | 369 +++- inst/doc/overview.R | 2 inst/doc/overview.Rmd | 4 inst/doc/overview.html | 1047 ++++++++---- man/constants.Rd | 2 man/count_indices.Rd | 6 man/counttest.Rd | 33 man/estimate_param.Rd | 4 man/extract_formula.Rd | 62 man/gauge_avar.Rd | 19 man/gauge_covar.Rd | 13 man/iis_init.Rd |only man/nonmissing.Rd | 62 man/outlier.Rd | 48 man/outlier_detection.Rd | 34 man/robustified_init.Rd | 80 man/saturated_init.Rd | 116 - man/selection.Rd | 112 - man/selection_iis.Rd |only man/sumtest.Rd | 2 man/suptest.Rd | 2 man/update_list.Rd | 58 man/user_init.Rd | 100 - tests/testthat/_snaps/beta_inf_test.md | 518 +++--- tests/testthat/_snaps/bootstrap.md |only tests/testthat/_snaps/class.md | 2122 +++++++++++++++++++++++++ tests/testthat/_snaps/initial_estimators.md | 594 ++++++ tests/testthat/_snaps/iterative_estimators2.md |only tests/testthat/_snaps/monte_carlo |only tests/testthat/_snaps/monte_carlo.md | 165 + tests/testthat/_snaps/outlier_tests.md | 152 + tests/testthat/test-beta_inf_test.R | 88 + tests/testthat/test-bootstrap.R |only tests/testthat/test-class.R | 25 tests/testthat/test-gauge.R | 19 tests/testthat/test-initial_estimators.R | 267 +++ tests/testthat/test-iterative_estimators.R | 80 tests/testthat/test-iterative_estimators2.R |only tests/testthat/test-monte_carlo.R | 203 ++ tests/testthat/test-outlier_tests.R | 156 + tests/testthat/test-utility.R | 505 +++++ vignettes/monte-carlo.Rmd | 2 vignettes/outlier-testing.Rmd | 2 vignettes/overview.Rmd | 4 64 files changed, 6899 insertions(+), 1389 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Gruen <dominic.gruen@gmail.com>
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.2.4 dated 2022-07-19 and 0.2.5 dated 2022-08-15
DESCRIPTION | 17 MD5 | 77 + NAMESPACE | 43 R/VarID_functions.R | 2136 ++++++++++++++++++++++++++++++++++++++++------- inst/doc/RaceID.R | 322 ++++--- inst/doc/RaceID.Rmd | 568 +++++++++--- inst/doc/RaceID.html | 528 +++++++---- man/calcAlphaG.Rd |only man/calcVar.Rd |only man/calcVarFit.Rd |only man/cleanNN.Rd |only man/compMean.Rd | 23 man/compNoise.Rd | 23 man/compTBNoise.Rd |only man/corrVar.Rd |only man/createKnnMatrix.Rd | 2 man/diffNoisyGenes.Rd | 6 man/diffNoisyGenesTB.Rd |only man/extractCounts.Rd |only man/fitBackVar.Rd | 2 man/fitGammaRt.Rd |only man/fitLogVarLogMean.Rd |only man/fitNBtb.Rd |only man/fitNBtbCl.Rd |only man/getExpData.Rd | 2 man/getFilteredCounts.Rd |only man/getNode.Rd |only man/graphCluster.Rd | 29 man/inspectKNN.Rd |only man/maxNoisyGenes.Rd | 4 man/maxNoisyGenesTB.Rd |only man/plotB.Rd |only man/plotBackVar.Rd | 6 man/plotDiffNoise.Rd |only man/plotExpNoise.Rd |only man/plotMV.Rd |only man/plotPC.Rd |only man/plotPP.Rd |only man/plotPT.Rd |only man/plotPearsonRes.Rd | 13 man/plotQQ.Rd |only man/plotQuantMap.Rd |only man/plotRegNB.Rd | 19 man/plotTrProbs.Rd | 10 man/plotUMINoise.Rd |only man/plotfeatmap.Rd |only man/postfntb.Rd |only man/priorfn.Rd |only man/pruneKnn.Rd | 59 - man/pseudoTime.Rd |only man/quantKnn.Rd |only man/testPrior.Rd |only man/transitionProbs.Rd | 4 man/updateSC.Rd | 6 man/violinMarkerPlot.Rd |only vignettes/RaceID.Rmd | 568 +++++++++--- 56 files changed, 3496 insertions(+), 971 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-03 0.3.2
2022-03-11 0.3.0
2022-03-09 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-01 0.2.1
Title: Download and Load Various Text Datasets
Description: Provides a framework to download, parse, and store text
datasets on the disk and load them when needed. Includes various
sentiment lexicons and labeled text data sets for classification and
analysis.
Author: Emil Hvitfeldt [aut, cre] ,
Julia Silge [ctb]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between textdata versions 0.4.2 dated 2022-05-02 and 0.4.3 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/download_functions.R | 5 ++++- R/process_functions.R | 5 ++++- README.md | 6 +++--- build/vignette.rds |binary man/textdata-package.Rd | 2 +- 8 files changed, 27 insertions(+), 17 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible combinatorial iterators
implemented in C++ for solving problems in combinatorics and
computational mathematics. Utilizes the RMatrix class from 'RcppParallel'
for thread safety. There are combination/permutation functions with
constraint parameters that allow for generation of all results of a vector
meeting specific criteria (e.g. generating integer partitions/compositions
or finding all combinations such that the sum is between two bounds).
Capable of generating specific combinations/permutations (e.g. retrieve
only the nth lexicographical result) which sets up nicely for
parallelization as well as random sampling. Gmp support permits exploration
where the total number of results is large (e.g. comboSample(10000, 500,
n = 4)). Additionally, there are several high performance number theoretic
functions that are useful for problems common in computational mathematics.
Some of these functions make use of the fast integer division library
'libdiv [...truncated...]
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.5.3 dated 2022-03-31 and 2.6.0 dated 2022-08-15
RcppAlgos-2.5.3/RcppAlgos/R/Threads.R |only RcppAlgos-2.5.3/RcppAlgos/tests/testthat/testPartitionsSample.R |only RcppAlgos-2.6.0/RcppAlgos/DESCRIPTION | 8 RcppAlgos-2.6.0/RcppAlgos/MD5 | 272 ++- RcppAlgos-2.6.0/RcppAlgos/NAMESPACE | 8 RcppAlgos-2.6.0/RcppAlgos/NEWS.md | 38 RcppAlgos-2.6.0/RcppAlgos/R/Combinations.R | 12 RcppAlgos-2.6.0/RcppAlgos/R/ComboGrid.R | 33 RcppAlgos-2.6.0/RcppAlgos/R/Compositions.R |only RcppAlgos-2.6.0/RcppAlgos/R/Partitions.R | 42 RcppAlgos-2.6.0/RcppAlgos/R/Permutations.R | 14 RcppAlgos-2.6.0/RcppAlgos/R/Utility.R |only RcppAlgos-2.6.0/RcppAlgos/README.md | 17 RcppAlgos-2.6.0/RcppAlgos/build/vignette.rds |binary RcppAlgos-2.6.0/RcppAlgos/inst/NEWS.Rd | 50 RcppAlgos-2.6.0/RcppAlgos/inst/doc/CombPermConstraints.Rmd | 354 ++++- RcppAlgos-2.6.0/RcppAlgos/inst/doc/CombPermConstraints.html | 642 ++++++--- RcppAlgos-2.6.0/RcppAlgos/inst/doc/CombinatorialSampling.Rmd | 238 +++ RcppAlgos-2.6.0/RcppAlgos/inst/doc/CombinatorialSampling.html | 367 ++++- RcppAlgos-2.6.0/RcppAlgos/inst/doc/CombinatoricsIterators.Rmd | 72 - RcppAlgos-2.6.0/RcppAlgos/inst/doc/CombinatoricsIterators.html | 344 ++--- RcppAlgos-2.6.0/RcppAlgos/inst/doc/ComputationalMathematics.html | 1 RcppAlgos-2.6.0/RcppAlgos/inst/doc/GeneralCombinatorics.Rmd | 4 RcppAlgos-2.6.0/RcppAlgos/inst/doc/GeneralCombinatorics.html | 9 RcppAlgos-2.6.0/RcppAlgos/inst/doc/HighPerformanceBenchmarks.Rmd | 305 ++-- RcppAlgos-2.6.0/RcppAlgos/inst/doc/HighPerformanceBenchmarks.html | 688 +++++----- RcppAlgos-2.6.0/RcppAlgos/inst/doc/OtherCombinatorics.Rmd | 6 RcppAlgos-2.6.0/RcppAlgos/inst/doc/OtherCombinatorics.html | 20 RcppAlgos-2.6.0/RcppAlgos/inst/doc/SubsetSum.html | 1 RcppAlgos-2.6.0/RcppAlgos/inst/include/CleanConvert.h | 7 RcppAlgos-2.6.0/RcppAlgos/inst/include/Combinations/BigComboCount.h | 6 RcppAlgos-2.6.0/RcppAlgos/inst/include/Combinations/ComboCount.h | 8 RcppAlgos-2.6.0/RcppAlgos/inst/include/Combinations/NthCombination.h | 6 RcppAlgos-2.6.0/RcppAlgos/inst/include/Combinations/RankCombination.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/Constraints/ConstraintsTypes.h | 2 RcppAlgos-2.6.0/RcppAlgos/inst/include/Constraints/ConstraintsUtils.h | 3 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/BigPartsCountRep.h | 2 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/CompositionsRep.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/NextComposition.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/NextPartition.h | 3 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/NthPartition.h | 2 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsClass.h | 6 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsCount.h | 19 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsCountDistinct.h | 2 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsCountRep.h | 3 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsManager.h | 10 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsTypes.h | 18 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/PartitionsUtils.h | 6 RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/RankPartition.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/Partitions/ThreadSafeParts.h | 4 RcppAlgos-2.6.0/RcppAlgos/inst/include/Permutations/BigPermuteCount.h | 4 RcppAlgos-2.6.0/RcppAlgos/inst/include/Permutations/NthPermutation.h | 2 RcppAlgos-2.6.0/RcppAlgos/inst/include/Permutations/PermuteCount.h | 5 RcppAlgos-2.6.0/RcppAlgos/inst/include/Permutations/RankPermutation.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/RankResult.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/RankUtils.h |only RcppAlgos-2.6.0/RcppAlgos/inst/include/SetUpUtils.h | 9 RcppAlgos-2.6.0/RcppAlgos/man/combinatoricsGeneral.Rd | 34 RcppAlgos-2.6.0/RcppAlgos/man/combinatoricsIterator.Rd | 2 RcppAlgos-2.6.0/RcppAlgos/man/combinatoricsRank.Rd |only RcppAlgos-2.6.0/RcppAlgos/man/combinatoricsSample.Rd | 13 RcppAlgos-2.6.0/RcppAlgos/man/comboGrid.Rd | 2 RcppAlgos-2.6.0/RcppAlgos/man/comboGroups.Rd | 2 RcppAlgos-2.6.0/RcppAlgos/man/comboGroupsSample.Rd | 10 RcppAlgos-2.6.0/RcppAlgos/man/divisorsSieve.Rd | 2 RcppAlgos-2.6.0/RcppAlgos/man/partitionsCount.Rd | 22 RcppAlgos-2.6.0/RcppAlgos/man/partitionsGeneral.Rd | 26 RcppAlgos-2.6.0/RcppAlgos/man/partitionsIterator.Rd | 25 RcppAlgos-2.6.0/RcppAlgos/man/partitionsRank.Rd |only RcppAlgos-2.6.0/RcppAlgos/man/partitionsSample.Rd | 20 RcppAlgos-2.6.0/RcppAlgos/man/primeFactorizeSieve.Rd | 2 RcppAlgos-2.6.0/RcppAlgos/man/primeSieve.Rd | 2 RcppAlgos-2.6.0/RcppAlgos/src/BigComboCount.cpp | 56 RcppAlgos-2.6.0/RcppAlgos/src/BigPartsCountRep.cpp | 23 RcppAlgos-2.6.0/RcppAlgos/src/BigPermuteCount.cpp | 24 RcppAlgos-2.6.0/RcppAlgos/src/CartesianContainer.cpp | 320 +--- RcppAlgos-2.6.0/RcppAlgos/src/CheckReturn.cpp | 9 RcppAlgos-2.6.0/RcppAlgos/src/ClassUtils.cpp | 23 RcppAlgos-2.6.0/RcppAlgos/src/CleanConvert.cpp | 179 +- RcppAlgos-2.6.0/RcppAlgos/src/CnstrntsSpecialClass.cpp | 19 RcppAlgos-2.6.0/RcppAlgos/src/CnstrntsToRClass.cpp | 13 RcppAlgos-2.6.0/RcppAlgos/src/CombinatoricsCount.cpp | 30 RcppAlgos-2.6.0/RcppAlgos/src/ComboApplyClass.cpp | 17 RcppAlgos-2.6.0/RcppAlgos/src/ComboClass.cpp | 21 RcppAlgos-2.6.0/RcppAlgos/src/ComboCount.cpp | 82 - RcppAlgos-2.6.0/RcppAlgos/src/ComboGroups.cpp | 47 RcppAlgos-2.6.0/RcppAlgos/src/ComboResClass.cpp | 42 RcppAlgos-2.6.0/RcppAlgos/src/CompositionsRep.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/ConstraintsClass.cpp | 13 RcppAlgos-2.6.0/RcppAlgos/src/ConstraintsMain.cpp | 42 RcppAlgos-2.6.0/RcppAlgos/src/ConstraintsRep.cpp | 3 RcppAlgos-2.6.0/RcppAlgos/src/ConstraintsUtils.cpp | 17 RcppAlgos-2.6.0/RcppAlgos/src/DivNumSieve.cpp | 24 RcppAlgos-2.6.0/RcppAlgos/src/ExposeClass.cpp | 42 RcppAlgos-2.6.0/RcppAlgos/src/FunAssign.cpp | 7 RcppAlgos-2.6.0/RcppAlgos/src/GetClassVals.cpp | 30 RcppAlgos-2.6.0/RcppAlgos/src/GetCombPerm.cpp | 25 RcppAlgos-2.6.0/RcppAlgos/src/GetCombPermApply.cpp | 127 - RcppAlgos-2.6.0/RcppAlgos/src/GetConstraints.cpp | 165 +- RcppAlgos-2.6.0/RcppAlgos/src/GetPrevCombPerm.cpp | 20 RcppAlgos-2.6.0/RcppAlgos/src/GetPrevCombPermApply.cpp | 118 - RcppAlgos-2.6.0/RcppAlgos/src/ImportExportMPZ.cpp | 1 RcppAlgos-2.6.0/RcppAlgos/src/MotleyPrimes.cpp | 18 RcppAlgos-2.6.0/RcppAlgos/src/NextComposition.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/NextPartition.cpp | 49 RcppAlgos-2.6.0/RcppAlgos/src/NthCombination.cpp | 48 RcppAlgos-2.6.0/RcppAlgos/src/NthPartition.cpp | 249 ++- RcppAlgos-2.6.0/RcppAlgos/src/NthPermutation.cpp | 58 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsClass.cpp | 59 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsCount.cpp | 93 + RcppAlgos-2.6.0/RcppAlgos/src/PartitionsCountRep.cpp | 22 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsDesign.cpp | 7 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsEsqueDistinct.cpp | 1 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsEsqueMultiset.cpp | 2 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsEsqueRep.cpp | 1 RcppAlgos-2.6.0/RcppAlgos/src/PartitionsManager.cpp | 71 - RcppAlgos-2.6.0/RcppAlgos/src/PartitionsUtils.cpp | 99 - RcppAlgos-2.6.0/RcppAlgos/src/PermuteCount.cpp | 38 RcppAlgos-2.6.0/RcppAlgos/src/PollardRho.cpp | 18 RcppAlgos-2.6.0/RcppAlgos/src/PrimeSieve.cpp | 12 RcppAlgos-2.6.0/RcppAlgos/src/RankCombPermMain.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/RankCombination.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/RankPartition.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/RankPartitionMain.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/RankPermutation.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/RankResult.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/RankUtils.cpp |only RcppAlgos-2.6.0/RcppAlgos/src/SampCombPermStd.cpp | 39 RcppAlgos-2.6.0/RcppAlgos/src/SampleApply.cpp | 223 +-- RcppAlgos-2.6.0/RcppAlgos/src/SamplePartitions.cpp | 58 RcppAlgos-2.6.0/RcppAlgos/src/SetUpUtils.cpp | 138 +- RcppAlgos-2.6.0/RcppAlgos/src/ThreadSafeParts.cpp | 59 RcppAlgos-2.6.0/RcppAlgos/src/cpp11.cpp | 54 RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testCombPermRank.R |only RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testCombPermSample.R | 8 RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testConstraintsClass.R | 70 - RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testErrors.R | 274 ++- RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testPartitionsClass.R | 271 +++ RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testPartitionsDesign.R | 8 RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testPartitionsGmp.R | 218 +++ RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testPartitionsParallel.R | 307 +++- RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testPartitionsSampleRank.R |only RcppAlgos-2.6.0/RcppAlgos/tests/testthat/testPermuteGeneral.R | 13 RcppAlgos-2.6.0/RcppAlgos/vignettes/CombPermConstraints.Rmd | 354 ++++- RcppAlgos-2.6.0/RcppAlgos/vignettes/CombinatorialSampling.Rmd | 238 +++ RcppAlgos-2.6.0/RcppAlgos/vignettes/CombinatoricsIterators.Rmd | 72 - RcppAlgos-2.6.0/RcppAlgos/vignettes/GeneralCombinatorics.Rmd | 4 RcppAlgos-2.6.0/RcppAlgos/vignettes/HighPerformanceBenchmarks.Rmd | 305 ++-- RcppAlgos-2.6.0/RcppAlgos/vignettes/OtherCombinatorics.Rmd | 6 149 files changed, 5961 insertions(+), 2976 deletions(-)
Title: Tools for qPCR
Description: RT-qPCR is a widely used method to detect the expression level of genes in
biological research. A crucial step in processing qPCR data is to calculate
the amplification efficiency of genes to determine which method should be used
to calculate expression level of genes. This Package can do it easily.
In addition to that, this package can calculate the expression level of genes
based on three methods.
Author: Xiang LI [cre, aut]
Maintainer: Xiang LI <lixiang117423@gmail.com>
Diff between qPCRtools versions 0.2.0 dated 2022-08-07 and 0.2.1 dated 2022-08-15
DESCRIPTION | 12 +++++++----- MD5 | 29 ++++++++++++++++++----------- NAMESPACE | 2 ++ R/CalCurve.R | 1 + R/CalExp2ddCt.R | 2 +- R/CalExpCurve.R | 2 +- R/CalExpRqPCR.R | 2 +- R/CalRTable.R | 2 +- build |only inst/doc |only man/CalExp2ddCt.Rd | 2 +- man/CalExpCurve.Rd | 2 +- man/CalExpRqPCR.Rd | 2 +- man/CalRTable.Rd | 2 +- vignettes |only 15 files changed, 36 insertions(+), 24 deletions(-)
Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks,
predictions, resample results or benchmark results via the autoplot()
generic of 'ggplot2'. The returned 'ggplot' objects are intended to
provide sensible defaults, yet can easily be customized to create
camera-ready figures. Visualizations include barplots, boxplots,
histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.5.9 dated 2022-05-25 and 0.5.10 dated 2022-08-15
DESCRIPTION | 19 ++-- MD5 | 109 ++++++++++++------------- NEWS.md | 5 + R/BenchmarkResult.R | 22 ++--- R/Filter.R | 18 ++-- R/LearnerClassifRpart.R | 26 +++-- R/LearnerClustHierarchical.R | 38 ++++---- R/OptimInstanceSingleCrit.R | 2 R/PredictionClassif.R | 29 +++--- R/PredictionClust.R | 18 ++-- R/PredictionRegr.R | 20 ++-- R/ResampleResult.R | 62 +++++++------- R/TaskClassif.R | 18 ++-- R/TaskClust.R | 14 +-- R/TaskRegr.R | 16 ++- R/plot_learner_prediction.R | 14 +-- R/theme-mlr3.R | 6 - README.md | 10 +- build/partial.rdb |binary man/autoplot.BenchmarkResult.Rd | 22 ++--- man/autoplot.Filter.Rd | 18 ++-- man/autoplot.LearnerClassifRpart.Rd | 26 +++-- man/autoplot.LearnerClustHierarchical.Rd | 38 ++++---- man/autoplot.OptimInstanceSingleCrit.Rd | 2 man/autoplot.PredictionClassif.Rd | 23 ++--- man/autoplot.PredictionClust.Rd | 18 ++-- man/autoplot.PredictionRegr.Rd | 20 ++-- man/autoplot.ResampleResult.Rd | 46 +++++----- man/autoplot.TaskClassif.Rd | 18 ++-- man/autoplot.TaskClust.Rd | 14 +-- man/autoplot.TaskRegr.Rd | 16 ++- man/figures/README-demo-1.png |binary man/figures/README-demo-2.png |binary man/plot_learner_prediction.Rd | 14 +-- tests/testthat/helper.R |only tests/testthat/setup.R | 8 + tests/testthat/test_BenchmarkResult.R | 10 +- tests/testthat/test_Filter.R | 6 - tests/testthat/test_LearnerClassifCVGlmnet.R | 3 tests/testthat/test_LearnerClassifRpart.R | 3 tests/testthat/test_LearnerClasssifGlmnet.R | 3 tests/testthat/test_LearnerClustHierarchical.R | 5 - tests/testthat/test_LearnerRegrCVGlmnet.R | 3 tests/testthat/test_LearnerRegrGlmnet.R | 3 tests/testthat/test_LearnerRegrRpart.R | 3 tests/testthat/test_OptimInstanceSingleCrit.R | 4 tests/testthat/test_PredictionClassif.R | 10 +- tests/testthat/test_PredictionClust.R | 7 - tests/testthat/test_PredictionRegr.R | 8 + tests/testthat/test_ResampleResult.R | 10 +- tests/testthat/test_Task.R | 2 tests/testthat/test_TaskClassif.R | 8 + tests/testthat/test_TaskClust.R | 5 - tests/testthat/test_TaskRegr.R | 6 - tests/testthat/test_TuningInstanceSingleCrit.R | 4 tests/testthat/test_plot_learner_prediction.R | 18 ++-- 56 files changed, 466 insertions(+), 384 deletions(-)
More information about WrensBookshelf at CRAN
Permanent link
Title: Graphical Elements of the University of Konstanz's Corporate
Design
Description: Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other institutions and purposes.
Author: Hansjoerg Neth [aut, cre] ,
Nico Gradwohl [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between unikn versions 0.4.0 dated 2021-03-27 and 0.5.0 dated 2022-08-15
DESCRIPTION | 10 MD5 | 99 ++-- NAMESPACE | 3 NEWS.md | 82 ++- R/color_def_1.R | 55 ++ R/color_def_2.R | 20 R/color_fun.R | 726 +++++++++++++++++++++++++++++----- R/color_util.R | 191 ++++++++ R/plot_box.R | 10 R/plot_box_calls.R | 8 R/plot_kn.R | 38 - R/plot_text.R | 268 +++++++++--- R/plot_text_calls.R | 162 +++++-- R/plot_themes.R | 4 R/plot_util.R | 42 - R/start_unikn.R | 12 README.md | 263 ++++++------ build/vignette.rds |binary inst/CITATION | 8 inst/WORDLIST | 62 +- inst/doc/color_inst.R | 10 inst/doc/color_inst.Rmd | 19 inst/doc/color_inst.html | 378 ++++------------- inst/doc/color_recipes.R | 57 +- inst/doc/color_recipes.Rmd | 104 +++- inst/doc/color_recipes.html | 480 ++++++++-------------- inst/doc/colors.R | 71 ++- inst/doc/colors.Rmd | 233 +++++++--- inst/doc/colors.html | 582 ++++++++++----------------- inst/doc/text.R | 261 ++++++++++++ inst/doc/text.Rmd | 371 +++++++++++++++-- inst/doc/text.html | 521 ++++++++---------------- inst/pix/README-others-google-1.png |binary inst/pix/README-others-txt-demo-1.png |binary inst/pix/README-uline-demo-1.png |binary man/ac.Rd |only man/grepal.Rd | 47 +- man/heading.Rd | 26 + man/mark.Rd | 30 + man/newpal.Rd | 12 man/pal_unikn.Rd | 6 man/post.Rd | 32 + man/seecol.Rd | 32 + man/shades_of.Rd |only man/simcol.Rd |only man/slide.Rd | 3 man/uline.Rd | 28 + man/usecol.Rd | 26 - vignettes/color_inst.Rmd | 19 vignettes/color_recipes.Rmd | 104 +++- vignettes/colors.Rmd | 233 +++++++--- vignettes/text.Rmd | 371 +++++++++++++++-- 52 files changed, 3965 insertions(+), 2154 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.5.5 dated 2022-05-31 and 4.5.6 dated 2022-08-15
secr-4.5.5/secr/README.md |only secr-4.5.6/secr/DESCRIPTION | 36 +++++--- secr-4.5.6/secr/MD5 | 52 ++++++------ secr-4.5.6/secr/NAMESPACE | 4 secr-4.5.6/secr/NEWS | 13 +++ secr-4.5.6/secr/R/clone.R | 15 ++- secr-4.5.6/secr/R/makeStart.R | 2 secr-4.5.6/secr/R/methods.R | 3 secr-4.5.6/secr/R/plot.mask.r | 28 +++--- secr-4.5.6/secr/R/sim.popn.R | 37 +++------ secr-4.5.6/secr/R/utility.R | 4 secr-4.5.6/secr/build/partial.rdb |binary secr-4.5.6/secr/build/vignette.rds |binary secr-4.5.6/secr/inst/doc/index.html | 115 +++++++++++++++++++++++++++- secr-4.5.6/secr/inst/doc/secr-datainput.pdf |binary secr-4.5.6/secr/inst/doc/secr-overview.Rmd | 18 ++-- secr-4.5.6/secr/inst/doc/secr-overview.pdf |binary secr-4.5.6/secr/man/RSE.Rd | 2 secr-4.5.6/secr/man/Rsurface.Rd | 22 ++--- secr-4.5.6/secr/man/capthist.Rd | 19 ++-- secr-4.5.6/secr/man/clone.Rd | 11 ++ secr-4.5.6/secr/man/detectfn.Rd | 2 secr-4.5.6/secr/man/deviance.secr.Rd | 6 - secr-4.5.6/secr/man/nontarget.Rd |only secr-4.5.6/secr/man/secr-package.Rd | 18 ++-- secr-4.5.6/secr/man/sim.popn.Rd | 2 secr-4.5.6/secr/man/utility.Rd | 2 secr-4.5.6/secr/vignettes/secr-overview.Rmd | 18 ++-- 28 files changed, 302 insertions(+), 127 deletions(-)
Title: Access the 'Public Transport Victoria' Timetable API
Description: Access the 'Public Transport Victoria' Timetable API
<https://www.ptv.vic.gov.au/footer/data-and-reporting/datasets/ptv-timetable-api/>,
with results returned as familiar R data structures. Retrieve information on
stops, routes, disruptions, departures, and more.
Author: David Neuzerling [aut, cre, cph]
Maintainer: David Neuzerling <david@neuzerling.com>
Diff between ptvapi versions 2.0.1 dated 2021-05-02 and 2.0.3 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ R/outlets.R | 2 +- R/ptvapi.R | 2 +- README.md | 2 +- man/outlets.Rd | 4 ++-- man/ptvapi.Rd | 8 +++++--- tests/testthat/test-outlets.R | 12 ++++++------ 9 files changed, 36 insertions(+), 26 deletions(-)
Title: Empirical Extrapolation of Time Feature Patterns
Description: An application for the empirical extrapolation of time features selecting and summarizing the most relevant patterns in time sequences.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between naive versions 1.0.0 dated 2022-05-18 and 1.1.0 dated 2022-08-15
DESCRIPTION | 10 + MD5 | 10 - NAMESPACE | 3 NEWS.md | 6 + R/main.R | 345 ++++++++++++++++++++++++++++++++++++++++------------------- man/naive.Rd | 10 - 6 files changed, 262 insertions(+), 122 deletions(-)
Title: Interface with Live Bikeshare Data
Description: Supplies a set of functions to interface with bikeshare data
following the General Bikeshare Feed Specification, allowing users to query
and accumulate tidy datasets for specified cities/bikeshare programs.
Author: Simon P. Couch [aut, cre],
Kaelyn Rosenberg [aut],
Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between gbfs versions 1.3.7 dated 2021-04-03 and 1.3.8 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/gbfs_description.R | 2 -- man/gbfs.Rd | 2 -- tests/testthat/test-wrapper.R | 7 ++++++- 6 files changed, 20 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-04 0.0.1
Title: Target Controlled Infusion (TCI)
Description: Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.
Author: Ryan Jarrett [aut, cre]
Maintainer: Ryan Jarrett <ryantjarrett@gmail.com>
Diff between tci versions 0.1.2 dated 2021-11-04 and 0.2.0 dated 2022-08-15
tci-0.1.2/tci/R/misc_functions.R |only tci-0.1.2/tci/R/simulations.R |only tci-0.1.2/tci/inst/doc/open-closed-loop-control.R |only tci-0.1.2/tci/inst/doc/open-closed-loop-control.Rmd |only tci-0.1.2/tci/inst/doc/open-closed-loop-control.html |only tci-0.1.2/tci/inst/doc/user-defined-ode-pkmod.R |only tci-0.1.2/tci/inst/doc/user-defined-ode-pkmod.Rmd |only tci-0.1.2/tci/inst/doc/user-defined-ode-pkmod.html |only tci-0.1.2/tci/man/apply_poppk.Rd |only tci-0.1.2/tci/man/apply_targetfn.Rd |only tci-0.1.2/tci/man/bayes_control.Rd |only tci-0.1.2/tci/man/cl_targets.Rd |only tci-0.1.2/tci/man/cl_updates.Rd |only tci-0.1.2/tci/man/combine_sim.Rd |only tci-0.1.2/tci/man/create_intvl.Rd |only tci-0.1.2/tci/man/eleveld_poppk.Rd |only tci-0.1.2/tci/man/eleveld_vcov.Rd |only tci-0.1.2/tci/man/gen_data.Rd |only tci-0.1.2/tci/man/gen_eleveld_pd_pars.Rd |only tci-0.1.2/tci/man/gen_eleveld_pk_pars.Rd |only tci-0.1.2/tci/man/gen_eleveld_pk_pars_nonmem.Rd |only tci-0.1.2/tci/man/inv_emax.Rd |only tci-0.1.2/tci/man/inv_emax_eleveld.Rd |only tci-0.1.2/tci/man/marsh_poppk.Rd |only tci-0.1.2/tci/man/pal.Rd |only tci-0.1.2/tci/man/pk_basic_solution_3cpt_metab.Rd |only tci-0.1.2/tci/man/pk_solution_3cpt_metab.Rd |only tci-0.1.2/tci/man/pk_solution_3cpt_metab_singleinf.Rd |only tci-0.1.2/tci/man/plot.Rd |only tci-0.1.2/tci/man/predict_pkmod.Rd |only tci-0.1.2/tci/man/predict_pkmod_Rcpp.Rd |only tci-0.1.2/tci/man/restrict_sigmoid.Rd |only tci-0.1.2/tci/man/schnider_poppk.Rd |only tci-0.1.2/tci/man/seqby.Rd |only tci-0.1.2/tci/man/sigmoid_targetfn.Rd |only tci-0.1.2/tci/man/tail_vec.Rd |only tci-0.1.2/tci/man/tci.Rd |only tci-0.1.2/tci/man/tci_comb.Rd |only tci-0.1.2/tci/man/tci_pd.Rd |only tci-0.1.2/tci/vignettes/open-closed-loop-control.Rmd |only tci-0.1.2/tci/vignettes/open-closed-loop-control_cache |only tci-0.1.2/tci/vignettes/three_compartment_diagram.pdf |only tci-0.1.2/tci/vignettes/user-defined-ode-pkmod.Rmd |only tci-0.2.0/tci/DESCRIPTION | 14 tci-0.2.0/tci/MD5 | 158 +- tci-0.2.0/tci/NAMESPACE | 82 - tci-0.2.0/tci/R/RcppExports.R | 12 tci-0.2.0/tci/R/documentation.R | 7 tci-0.2.0/tci/R/methods.R | 1248 ++++++++++++----- tci-0.2.0/tci/R/pd_mods.R | 153 -- tci-0.2.0/tci/R/pk_mods.R | 986 ------------- tci-0.2.0/tci/R/pkpd_assist.R | 224 +-- tci-0.2.0/tci/R/poppk_mods.R | 641 ++++++-- tci-0.2.0/tci/R/simulate.R |only tci-0.2.0/tci/R/tci_algorithms.R | 383 +++-- tci-0.2.0/tci/README.md | 393 +++-- tci-0.2.0/tci/build/vignette.rds |binary tci-0.2.0/tci/inst/doc/custom.R |only tci-0.2.0/tci/inst/doc/custom.Rmd |only tci-0.2.0/tci/inst/doc/custom.html |only tci-0.2.0/tci/inst/doc/overview.R | 230 +-- tci-0.2.0/tci/inst/doc/overview.Rmd | 283 ++- tci-0.2.0/tci/inst/doc/overview.html | 758 +++++++--- tci-0.2.0/tci/inst/doc/poppk.R |only tci-0.2.0/tci/inst/doc/poppk.Rmd |only tci-0.2.0/tci/inst/doc/poppk.html |only tci-0.2.0/tci/man/apply_tci.Rd |only tci-0.2.0/tci/man/bayes_update.Rd |only tci-0.2.0/tci/man/clc.Rd |only tci-0.2.0/tci/man/emax_eleveld.Rd | 2 tci-0.2.0/tci/man/emax_inv.Rd |only tci-0.2.0/tci/man/emax_inv_eleveld.Rd |only tci-0.2.0/tci/man/emax_inv_remi.Rd |only tci-0.2.0/tci/man/emax_remi.Rd |only tci-0.2.0/tci/man/format_pars.Rd | 4 tci-0.2.0/tci/man/inf_manual.Rd |only tci-0.2.0/tci/man/inf_tci.Rd |only tci-0.2.0/tci/man/infer_pkfn.Rd |only tci-0.2.0/tci/man/init_pkmod.Rd |only tci-0.2.0/tci/man/init_poppkmod.Rd |only tci-0.2.0/tci/man/list_parnms.Rd |only tci-0.2.0/tci/man/list_pkmods.Rd |only tci-0.2.0/tci/man/log_likelihood.Rd | 50 tci-0.2.0/tci/man/log_posterior_neg.Rd | 52 tci-0.2.0/tci/man/log_prior.Rd | 36 tci-0.2.0/tci/man/olc.Rd |only tci-0.2.0/tci/man/pkmod.Rd |only tci-0.2.0/tci/man/pkmod1cpt.Rd | 6 tci-0.2.0/tci/man/pkmod2cpt.Rd | 10 tci-0.2.0/tci/man/pkmod3cpt.Rd | 11 tci-0.2.0/tci/man/pkmod3cptm.Rd | 14 tci-0.2.0/tci/man/pkmod_eleveld_ppf.Rd |only tci-0.2.0/tci/man/pkmod_eleveld_remi.Rd |only tci-0.2.0/tci/man/pkmod_kim.Rd |only tci-0.2.0/tci/man/pkmod_marsh.Rd |only tci-0.2.0/tci/man/pkmod_minto.Rd |only tci-0.2.0/tci/man/pkmod_schnider.Rd |only tci-0.2.0/tci/man/plot.sim_tci.Rd |only tci-0.2.0/tci/man/poppkmod.Rd |only tci-0.2.0/tci/man/predict.pkmod.Rd |only tci-0.2.0/tci/man/predict.poppkmod.Rd |only tci-0.2.0/tci/man/print.pkmod.Rd |only tci-0.2.0/tci/man/print.poppkmod.Rd |only tci-0.2.0/tci/man/print.sim_tci.Rd |only tci-0.2.0/tci/man/sample_iiv.Rd |only tci-0.2.0/tci/man/sample_pkmod.Rd |only tci-0.2.0/tci/man/simulate.pkmod.Rd |only tci-0.2.0/tci/man/simulate.poppkmod.Rd |only tci-0.2.0/tci/man/simulate_clc.Rd |only tci-0.2.0/tci/man/simulate_olc.Rd |only tci-0.2.0/tci/man/simulate_tci.Rd |only tci-0.2.0/tci/man/tci_documentation.Rd | 7 tci-0.2.0/tci/man/tci_effect.Rd | 48 tci-0.2.0/tci/man/tci_effect_only.Rd |only tci-0.2.0/tci/man/tci_plasma.Rd | 14 tci-0.2.0/tci/man/update.pkmod.Rd |only tci-0.2.0/tci/man/validate_pkmod.Rd |only tci-0.2.0/tci/man/validate_poppkmod.Rd |only tci-0.2.0/tci/src/RcppExports.cpp | 29 tci-0.2.0/tci/src/pk_cpp_functions.cpp | 62 tci-0.2.0/tci/vignettes/bibfile.bib | 14 tci-0.2.0/tci/vignettes/custom.Rmd |only tci-0.2.0/tci/vignettes/figures/Cascone_fig2.png |only tci-0.2.0/tci/vignettes/overview.Rmd | 283 ++- tci-0.2.0/tci/vignettes/poppk.Rmd |only 125 files changed, 3574 insertions(+), 2640 deletions(-)
Title: Color Manipulation Tools
Description: Manipulate and visualize colors in a intuitive,
low-dependency and functional way.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between prismatic versions 1.1.0 dated 2021-10-17 and 1.1.1 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ README.md | 7 ++++--- man/clr_extract.Rd | 4 ++-- man/figures/README-unnamed-chunk-3-7.png |binary man/prismatic-package.Rd | 2 +- 7 files changed, 21 insertions(+), 16 deletions(-)
Title: Functions for Optimal Matching
Description: Distance based bipartite matching using minimum cost flow, oriented
to matching of treatment and control groups in observational studies (Hansen
and Klopfer 2006 <doi:10.1198/106186006X137047>). Routines are provided to
generate distances from generalised linear models (propensity score
matching), formulas giving variables on which to limit matched distances,
stratified or exact matching directives, or calipers, alone or in
combination.
Author: Ben Hansen [aut],
Mark Fredrickson [aut],
Josh Errickson [cre, aut],
Josh Buckner [aut],
Adam Rauh [ctb]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between optmatch versions 0.10.4 dated 2022-08-09 and 0.10.5 dated 2022-08-15
DESCRIPTION | 9 ++-- MD5 | 18 ++++----- NEWS.md | 6 ++- inst/doc/fullmatch-vignette.R | 9 ++-- inst/doc/fullmatch-vignette.Rmd | 9 ++-- inst/doc/fullmatch-vignette.html | 49 +++++++++++++++++++++++---- inst/doc/matching-from-foreign-software.html | 4 +- inst/doc/matching-within-subgroups.html | 4 +- tests/testthat/test.utilities.R | 2 - vignettes/fullmatch-vignette.Rmd | 9 ++-- 10 files changed, 78 insertions(+), 41 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3'
with interfaces to essential machine learning packages on
CRAN. This includes, but is not limited to: (penalized) linear and
logistic regression, linear and quadratic discriminant analysis,
k-nearest neighbors, naive Bayes, support vector machines, and
gradient boosting.
Author: Michel Lang [cre, aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3learners versions 0.5.3 dated 2022-05-25 and 0.5.4 dated 2022-08-15
mlr3learners-0.5.3/mlr3learners/tests/testthat/test-test_construction.R |only mlr3learners-0.5.4/mlr3learners/DESCRIPTION | 16 - mlr3learners-0.5.4/mlr3learners/MD5 | 79 ++++---- mlr3learners-0.5.4/mlr3learners/NAMESPACE | 5 mlr3learners-0.5.4/mlr3learners/NEWS.md | 7 mlr3learners-0.5.4/mlr3learners/R/LearnerClassifLogReg.R | 9 mlr3learners-0.5.4/mlr3learners/R/LearnerClassifRanger.R | 23 +- mlr3learners-0.5.4/mlr3learners/R/LearnerClassifSVM.R | 11 + mlr3learners-0.5.4/mlr3learners/R/LearnerClassifXgboost.R | 2 mlr3learners-0.5.4/mlr3learners/R/LearnerRegrNnet.R |only mlr3learners-0.5.4/mlr3learners/R/LearnerRegrRanger.R | 12 + mlr3learners-0.5.4/mlr3learners/R/LearnerRegrSVM.R | 11 + mlr3learners-0.5.4/mlr3learners/R/LearnerRegrXgboost.R | 2 mlr3learners-0.5.4/mlr3learners/R/zzz.R | 1 mlr3learners-0.5.4/mlr3learners/README.md | 1 mlr3learners-0.5.4/mlr3learners/build/partial.rdb |binary mlr3learners-0.5.4/mlr3learners/inst/paramtest/test_paramtest_regr.nnet.R |only mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.cv_glmnet.Rd | 71 ++++++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.glmnet.Rd | 65 +++++-- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.kknn.Rd | 35 ++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.lda.Rd | 36 ++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.log_reg.Rd | 47 +++-- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.multinom.Rd | 47 +++-- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.naive_bayes.Rd | 32 ++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.nnet.Rd | 45 +++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.qda.Rd | 34 ++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.ranger.Rd | 76 ++++++-- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.svm.Rd | 45 +++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_classif.xgboost.Rd | 91 ++++++++-- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.cv_glmnet.Rd | 72 ++++++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.glmnet.Rd | 70 ++++++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.kknn.Rd | 35 ++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.km.Rd | 57 +++++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.lm.Rd | 40 +++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.nnet.Rd |only mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.ranger.Rd | 74 ++++++-- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.svm.Rd | 43 +++- mlr3learners-0.5.4/mlr3learners/man/mlr_learners_regr.xgboost.Rd | 91 ++++++++-- mlr3learners-0.5.4/mlr3learners/tests/testthat/test_classif_ranger.R | 14 + mlr3learners-0.5.4/mlr3learners/tests/testthat/test_classif_svm.R | 12 + mlr3learners-0.5.4/mlr3learners/tests/testthat/test_regr_nnet.R |only mlr3learners-0.5.4/mlr3learners/tests/testthat/test_regr_ranger.R | 14 + mlr3learners-0.5.4/mlr3learners/tests/testthat/test_regr_svm.R | 12 + 43 files changed, 1045 insertions(+), 292 deletions(-)
Title: Multiple Imputation with Automated Machine Learning
Description: Using automated machine learning, the package fine-tunes an Elastic
Net or Gradient Boosting Machine model for imputing the missing
observations of each variable. This procedure has been implemented for the
first time by this package and is expected to outperform other packages for
imputing missing data that do not fine-tune their models.
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>
Diff between mlim versions 0.0.1 dated 2022-08-13 and 0.0.2 dated 2022-08-15
DESCRIPTION | 10 MD5 | 34 +- NAMESPACE | 3 R/algoSelector.R |only R/getDigits.R |only R/init.R | 1 R/iterate.R |only R/iteration_loop.R |only R/mlim.R | 805 ++++++++++++++++++++------------------------------- R/mlim.error.R | 132 ++++---- R/mlim.mids.R |only R/mlim.na.R | 10 R/mlim.preimpute.R | 31 - R/stoppingCriteria.R | 127 +++++--- R/syntaxProcessing.R | 54 +++ R/zzz.R | 2 README.md | 31 + man/mlim.Rd | 177 +++++------ man/mlim.error.Rd | 9 man/mlim.mids.Rd |only man/mlim.na.Rd | 10 21 files changed, 702 insertions(+), 734 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, simulation, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
and recoding variables.
Author: Frank E Harrell Jr [aut, cre] ,
Charles Dupont [ctb]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between Hmisc versions 4.7-0 dated 2022-04-18 and 4.7-1 dated 2022-08-15
DESCRIPTION | 10 ++--- MD5 | 82 ++++++++++++++++++++++----------------------- NAMESPACE | 4 +- NEWS | 22 +++++++++++- R/Cs.s | 8 ++++ R/Merge.r | 25 +++++++------ R/Misc.s | 87 +++++++++++++++++++++++++++++------------------- R/combplotp.r | 6 ++- R/curveRep.s | 12 +++++- R/describe.s | 10 ++++- R/dotchart3.s | 8 ++-- R/dotchartpl.s | 7 ++- R/fit.mult.impute.s | 4 +- R/na.pattern.s | 25 +++++-------- R/panel.bpplot.s | 2 - R/plot.describe.s | 20 ++++++----- R/plotCorrM.r | 3 + R/plotlyM.r | 2 + R/scat1d.s | 8 +++- R/simMarkovOrd.r | 1 R/summary.formula.s | 2 - R/summaryM.s | 9 +++- R/upData.s | 8 ++-- man/Cs.Rd | 14 +++++-- man/Merge.Rd | 6 +-- man/abs.error.pred.Rd | 8 ++-- man/curveRep.Rd | 17 +++++++-- man/describe.Rd | 5 ++ man/getHdata.Rd | 3 + man/getRs.Rd | 12 ++++-- man/intMarkovOrd.Rd | 5 ++ man/rcorr.cens.Rd | 8 ++-- man/rcorrp.cens.Rd | 4 +- man/rcspline.plot.Rd | 6 +-- man/rcspline.restate.Rd | 4 +- man/rm.boot.Rd | 13 +++---- man/scat1d.Rd | 32 ++++++++--------- man/spower.Rd | 6 +-- man/transace.Rd | 22 ++++++------ man/transcan.Rd | 54 ++++++++++++++--------------- man/upData.Rd | 3 + man/varclus.Rd | 7 +-- 42 files changed, 355 insertions(+), 239 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic,
and programmer friendly through a flexible and parsimonious syntax.
It is well integrated with base R, 'dplyr' / (grouped) 'tibble',
'data.table', 'sf', 'plm' (panel-series and data frames), and
non-destructively handles other matrix or data frame based classes (like
'ts', 'xts' / 'zoo', 'tsibble', ...)
--- Key Features: ---
(1) Advanced statistical programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast and programmable grouping, ordering, unique values/rows,
factor generation and interactions. Fast and flexible functions for data
manipulation, data object conversions, and memory efficient R programming.
(2) Advanced aggregation: Fast and easy multi-data-type, multi-function, weighted
and parallelized data aggregation.
(3) Advanced transformations: Fast row/column arithmetic, [...truncated...]
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [ [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.8.6 dated 2022-06-14 and 1.8.8 dated 2022-08-15
collapse-1.8.6/collapse/R/fsubset_ftransform.R |only collapse-1.8.8/collapse/DESCRIPTION | 13 collapse-1.8.8/collapse/MD5 | 120 ++-- collapse-1.8.8/collapse/NAMESPACE | 5 collapse-1.8.8/collapse/NEWS.md | 37 + collapse-1.8.8/collapse/R/BY.R | 1 collapse-1.8.8/collapse/R/GRP.R | 6 collapse-1.8.8/collapse/R/collap.R | 1 collapse-1.8.8/collapse/R/fFtest.R | 23 collapse-1.8.8/collapse/R/ffirst.R | 1 collapse-1.8.8/collapse/R/flast.R | 1 collapse-1.8.8/collapse/R/flm.R | 16 collapse-1.8.8/collapse/R/fmean.R | 1 collapse-1.8.8/collapse/R/fmin_fmax.R | 2 collapse-1.8.8/collapse/R/fmode.R | 1 collapse-1.8.8/collapse/R/fndistinct.R | 1 collapse-1.8.8/collapse/R/fnobs.R | 1 collapse-1.8.8/collapse/R/fnth_fmedian.R | 2 collapse-1.8.8/collapse/R/fprod.R | 1 collapse-1.8.8/collapse/R/fscale.R | 2 collapse-1.8.8/collapse/R/fsubset_ftransform_fmutate.R |only collapse-1.8.8/collapse/R/fsum.R | 75 +- collapse-1.8.8/collapse/R/fsummarise.R | 17 collapse-1.8.8/collapse/R/fvar_fsd.R | 2 collapse-1.8.8/collapse/R/global_macros.R | 4 collapse-1.8.8/collapse/R/my_RcppExports.R | 4 collapse-1.8.8/collapse/R/qsu.R | 53 + collapse-1.8.8/collapse/R/small_helper.R | 10 collapse-1.8.8/collapse/R/varying.R | 1 collapse-1.8.8/collapse/R/zzz.R | 19 collapse-1.8.8/collapse/inst/doc/collapse_documentation.Rmd | 24 collapse-1.8.8/collapse/inst/doc/collapse_documentation.html | 60 +- collapse-1.8.8/collapse/man/GRP.Rd | 12 collapse-1.8.8/collapse/man/collapse-documentation.Rd | 4 collapse-1.8.8/collapse/man/collapse-options.Rd | 7 collapse-1.8.8/collapse/man/collapse-package.Rd | 4 collapse-1.8.8/collapse/man/efficient-programming.Rd | 70 +- collapse-1.8.8/collapse/man/fFtest.Rd | 34 - collapse-1.8.8/collapse/man/flag.Rd | 4 collapse-1.8.8/collapse/man/flm.Rd | 44 + collapse-1.8.8/collapse/man/fmode.Rd | 2 collapse-1.8.8/collapse/man/fsum.Rd | 10 collapse-1.8.8/collapse/man/indexing.Rd | 7 collapse-1.8.8/collapse/man/psacf.Rd | 2 collapse-1.8.8/collapse/man/qF.Rd | 8 collapse-1.8.8/collapse/man/qsu.Rd | 33 - collapse-1.8.8/collapse/man/quick-conversion.Rd | 2 collapse-1.8.8/collapse/man/small-helpers.Rd | 14 collapse-1.8.8/collapse/man/summary-statistics.Rd | 2 collapse-1.8.8/collapse/src/ExportSymbols.c | 7 collapse-1.8.8/collapse/src/collapse_c.h | 7 collapse-1.8.8/collapse/src/data.table_subset.c | 2 collapse-1.8.8/collapse/src/fmean.c | 102 +-- collapse-1.8.8/collapse/src/fsum.c | 121 ++-- collapse-1.8.8/collapse/src/programming.c | 281 ++++++---- collapse-1.8.8/collapse/src/small_helper.c | 60 ++ collapse-1.8.8/collapse/tests/testthat/test-fsum.R | 82 ++ collapse-1.8.8/collapse/tests/testthat/test-misc.R | 15 collapse-1.8.8/collapse/tests/testthat/test-miscellaneous-issues.R | 174 +++--- collapse-1.8.8/collapse/tests/testthat/test-sf.R | 4 collapse-1.8.8/collapse/tests/testthat/test-whichv.R | 14 collapse-1.8.8/collapse/vignettes/collapse_documentation.Rmd | 24 62 files changed, 1071 insertions(+), 585 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through
matching, weighting or subclassification, for example, using propensity scores. Includes
integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt',
'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing
functions. Users can also specify data for balance assessment not generated through
the above packages. Also included are methods for assessing balance in clustered or
multiply imputed data sets or data sets with longitudinal treatments.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 4.3.2 dated 2022-01-19 and 4.4.0 dated 2022-08-15
DESCRIPTION | 22 MD5 | 111 NEWS.md | 26 R/bal.plot.R | 29 R/bal.tab.R | 93 R/base.bal.tab.R | 24 R/functions_for_processing.R | 5854 ++++++++++++++--------------- R/get.w.R | 42 R/love.plot.R | 2 R/x2base.R | 124 README.md | 20 build/cobalt.pdf |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/cobalt.R | 28 inst/doc/cobalt.Rmd | 30 inst/doc/cobalt.html | 1777 +++++++- inst/doc/cobalt_A1_other_packages.R | 115 inst/doc/cobalt_A1_other_packages.Rmd | 113 inst/doc/cobalt_A1_other_packages.html | 810 ++-- inst/doc/cobalt_A2_segmented_data.R | 26 inst/doc/cobalt_A2_segmented_data.Rmd | 26 inst/doc/cobalt_A2_segmented_data.html | 655 ++- inst/doc/cobalt_A3_longitudinal_treat.R | 12 inst/doc/cobalt_A3_longitudinal_treat.Rmd | 12 inst/doc/cobalt_A3_longitudinal_treat.html | 214 - inst/doc/cobalt_A4_love.plot.R | 11 inst/doc/cobalt_A4_love.plot.Rmd | 11 inst/doc/cobalt_A4_love.plot.html | 234 - man/bal.tab.CBPS.Rd | 123 man/bal.tab.Match.Rd | 132 man/bal.tab.Rd | 132 man/bal.tab.cem.match.Rd | 88 man/bal.tab.default.Rd | 32 man/bal.tab.df.formula.Rd | 161 man/bal.tab.df.formula.list.Rd | 132 man/bal.tab.matchit.Rd | 113 man/bal.tab.mimids.Rd | 116 man/bal.tab.ps.Rd | 181 man/bal.tab.sbw.Rd | 107 man/bal.tab.weightit.Rd | 117 man/balance.summary.Rd | 4 man/cobalt-package.Rd | 34 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/logo.png |binary man/get.w.Rd | 7 man/love.plot.Rd | 4 man/macros/macros.Rd | 4 man/print.bal.tab.Rd | 4 vignettes/cobalt.Rmd | 30 vignettes/cobalt_A1_other_packages.Rmd | 113 vignettes/cobalt_A2_segmented_data.Rmd | 26 vignettes/cobalt_A3_longitudinal_treat.Rmd | 12 vignettes/cobalt_A4_love.plot.Rmd | 11 vignettes/references.bib | 26 57 files changed, 6936 insertions(+), 5194 deletions(-)
Title: A Tidy Data Model for Natural Language Processing
Description: Provides a set of fast tools for converting a textual corpus into
a set of normalized tables. Users may make use of the 'udpipe' back end with
no external dependencies, or two Python back ends with 'spaCy'
<https://spacy.io> or 'CoreNLP' <https://stanfordnlp.github.io/CoreNLP/>.
Exposed annotation tasks include tokenization, part of speech tagging, named
entity recognition, and dependency parsing.
Author: Taylor B. Arnold [aut, cre]
Maintainer: Taylor B. Arnold <tarnold2@richmond.edu>
Diff between cleanNLP versions 3.0.3 dated 2020-10-13 and 3.0.4 dated 2022-08-15
DESCRIPTION | 10 MD5 | 8 build/vignette.rds |binary inst/doc/state-of-union.html | 1006 +++++++++++++++++++++---------------------- inst/doc/wikipedia.html | 587 +++++++++++++++---------- 5 files changed, 860 insertions(+), 751 deletions(-)
Title: Regression Spline Functions and Classes
Description: Constructs basis matrix of B-splines, M-splines,
I-splines, convex splines (C-splines), periodic M-splines,
natural cubic splines, generalized Bernstein polynomials,
and their integrals (except C-splines) and derivatives
of given order by close-form recursive formulas.
It also contains a C++ head-only library integrated with Rcpp.
See Wang and Yan (2021) <doi:10.6339/21-JDS1020> for details.
Author: Wenjie Wang [aut, cre] ,
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between splines2 versions 0.4.5 dated 2021-09-19 and 0.4.6 dated 2022-08-15
DESCRIPTION | 8 MD5 | 90 ++-- NAMESPACE | 27 - NEWS.md | 13 R/bSpline.R | 4 R/bernsteinPoly.R | 4 R/cSpline.R | 8 R/dbs.R | 4 R/deriv.R | 2 R/iSpline.R | 4 R/ibs.R | 4 R/knots.R | 41 -- R/mSpline.R | 6 R/makepredictcall.R | 2 R/misc.R | 16 R/naturalSpline.R | 4 R/predict.R | 121 +++--- R/print.R | 46 -- R/splines2-package.R | 2 R/update.R |only README.md | 74 +--- build/vignette.rds |binary inst/CITATION | 4 inst/doc/splines2-intro.html | 415 ++++++++++++++++++++--- inst/doc/splines2-wi-rcpp.html | 336 ++++++++++++++++-- inst/examples/ex-update.R |only inst/include/splines2Armadillo.h | 2 inst/include/splines2Armadillo/BSpline.h | 2 inst/include/splines2Armadillo/BernsteinPoly.h | 2 inst/include/splines2Armadillo/CSpline.h | 2 inst/include/splines2Armadillo/ISpline.h | 2 inst/include/splines2Armadillo/MSpline.h | 2 inst/include/splines2Armadillo/NaturalSpline.h | 2 inst/include/splines2Armadillo/PeriodicMSpline.h | 2 inst/include/splines2Armadillo/SplineBase.h | 2 inst/include/splines2Armadillo/common.h | 2 inst/include/splines2Armadillo/utils.h | 2 inst/tinytest/test-update.R |only man/knots.Rd | 25 - man/mSpline.Rd | 2 man/predict.Rd | 5 man/update.Rd |only src/BSpline_export.cpp | 2 src/BernsteinPoly_export.cpp | 2 src/CSpline_export.cpp | 2 src/ISpline_export.cpp | 2 src/MSpline_export.cpp | 2 src/NaturalSpline_export.cpp | 2 48 files changed, 920 insertions(+), 381 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: Implementation of stability selection for graphical modelling and variable selection in regression and dimensionality reduction. These models use on resampling approaches to estimate selection probabilities (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>). Calibration of the hyper-parameters is done via maximisation of a stability score measuring the likelihood of informative (non-uniform) selection (B Bodinier, S Filippi, TH Nost, J Chiquet, M Chadeau-Hyam (2021) <arXiv:2106.02521>).
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <b.bodinier@imperial.ac.uk>
Diff between sharp versions 1.1.0 dated 2022-06-17 and 1.2.0 dated 2022-08-15
sharp-1.1.0/sharp/R/simulations.R |only sharp-1.1.0/sharp/man/BlockDiagonal.Rd |only sharp-1.1.0/sharp/man/BlockMatrix.Rd |only sharp-1.1.0/sharp/man/BlockStructure.Rd |only sharp-1.1.0/sharp/man/Contrast.Rd |only sharp-1.1.0/sharp/man/Heatmap.Rd |only sharp-1.1.0/sharp/man/HugeAdjacency.Rd |only sharp-1.1.0/sharp/man/MakePositiveDefinite.Rd |only sharp-1.1.0/sharp/man/MatchingArguments.Rd |only sharp-1.1.0/sharp/man/MaxContrast.Rd |only sharp-1.1.0/sharp/man/Recalibrate.Rd |only sharp-1.1.0/sharp/man/SamplePredictors.Rd |only sharp-1.1.0/sharp/man/SimulateAdjacency.Rd |only sharp-1.1.0/sharp/man/SimulateComponents.Rd |only sharp-1.1.0/sharp/man/SimulateGraphical.Rd |only sharp-1.1.0/sharp/man/SimulatePrecision.Rd |only sharp-1.1.0/sharp/man/SimulateRegression.Rd |only sharp-1.1.0/sharp/man/SimulateSymmetricMatrix.Rd |only sharp-1.1.0/sharp/man/TuneExplainedVarianceCor.Rd |only sharp-1.1.0/sharp/man/TuneExplainedVarianceCov.Rd |only sharp-1.1.0/sharp/man/TuneExplainedVarianceReg.Rd |only sharp-1.2.0/sharp/DESCRIPTION | 12 sharp-1.2.0/sharp/MD5 | 93 ++--- sharp-1.2.0/sharp/NAMESPACE | 30 - sharp-1.2.0/sharp/NEWS.md | 9 sharp-1.2.0/sharp/R/calibration.R | 162 ---------- sharp-1.2.0/sharp/R/dimensionality_reduction.R | 2 sharp-1.2.0/sharp/R/ensemble.R |only sharp-1.2.0/sharp/R/explanatory_performance.R | 194 ++++++------ sharp-1.2.0/sharp/R/graphical_model.R | 2 sharp-1.2.0/sharp/R/multi_block.R | 97 ------ sharp-1.2.0/sharp/R/s3_classes.R | 171 +++------- sharp-1.2.0/sharp/R/sharp-package.R | 4 sharp-1.2.0/sharp/R/utils.R | 30 - sharp-1.2.0/sharp/R/variable_selection.R | 4 sharp-1.2.0/sharp/README.md | 139 ++++---- sharp-1.2.0/sharp/build/partial.rdb |binary sharp-1.2.0/sharp/inst/WORDLIST | 9 sharp-1.2.0/sharp/man/AggregatedEffects.Rd | 10 sharp-1.2.0/sharp/man/BlockLambdaGrid.Rd | 4 sharp-1.2.0/sharp/man/Ensemble.Rd |only sharp-1.2.0/sharp/man/EnsemblePredictions.Rd |only sharp-1.2.0/sharp/man/ExplanatoryPerformance.Rd | 26 - sharp-1.2.0/sharp/man/Incremental.Rd | 14 sharp-1.2.0/sharp/man/PLS.Rd | 2 sharp-1.2.0/sharp/man/PlotIncremental.Rd | 2 sharp-1.2.0/sharp/man/PlotROC.Rd | 6 sharp-1.2.0/sharp/man/ROC.Rd | 16 sharp-1.2.0/sharp/man/Refit.Rd |only sharp-1.2.0/sharp/man/SelectedVariables.Rd | 2 sharp-1.2.0/sharp/man/VariableSelection.Rd | 2 sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-10-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-16-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-18-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-20-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-21-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-24-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-27-1.png |binary sharp-1.2.0/sharp/man/figures/README-unnamed-chunk-7-1.png |binary sharp-1.2.0/sharp/man/sharp-package.Rd | 4 60 files changed, 354 insertions(+), 692 deletions(-)
Title: Rendering Risk Literacy more Transparent
Description: Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, 'riskyr' computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent.
Author: Hansjoerg Neth [aut, cre] ,
Felix Gaisbauer [aut] ,
Nico Gradwohl [aut] ,
Wolfgang Gaissmaier [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between riskyr versions 0.3.0 dated 2021-03-23 and 0.4.0 dated 2022-08-15
DESCRIPTION | 17 - MD5 | 214 +++++++++------- NAMESPACE | 11 NEWS.md | 125 +++++++-- R/FFTrees_riskyr.R |only R/comp_popu.R | 137 +++++----- R/comp_prob_prob.R | 9 R/comp_util.R | 226 +++++++++++++++-- R/comp_xxxx_prob.R | 243 +++++++++--------- R/data.R | 243 ++++++++++++++++++ R/init_freq.R | 2 R/init_freq_num.R | 261 +++++++++++--------- R/init_pal.R | 125 ++++++++- R/init_prob_num.R | 66 ++--- R/init_txt.R | 27 -- R/plot_area.R | 158 +++++++----- R/plot_bar.R | 200 +++++++++------ R/plot_crisk.R |only R/plot_curve.R | 87 ++++-- R/plot_fnet.R | 93 +++++-- R/plot_icons.R | 135 +++++++--- R/plot_plane.R | 109 +++++--- R/plot_prism.R | 145 +++++++---- R/plot_tab.R | 100 +++++-- R/plot_tree.R | 2 R/plot_util.R | 194 +++++++------- R/riskyr_class.R | 335 ++++++++++--------------- R/riskyr_sims.R |only README.md | 327 +++++++++++-------------- build/partial.rdb |only data/BRCA1.rda |only data/BRCA1_mam.rda |only data/BRCA1_ova.rda |only data/BRCA2.rda |only data/BRCA2_mam.rda |only data/BRCA2_ova.rda |only data/t_A.rda |only data/t_B.rda |only data/t_I.rda |only inst/CITATION | 14 - inst/WORDLIST | 151 ++++++----- inst/doc/A_user_guide.R | 2 inst/doc/A_user_guide.Rmd | 14 - inst/doc/A_user_guide.html | 415 ++++++++++++++++---------------- inst/doc/B_data_formats.R | 2 inst/doc/B_data_formats.Rmd | 6 inst/doc/B_data_formats.html | 122 +++++---- inst/doc/C_confusion_matrix.R | 2 inst/doc/C_confusion_matrix.Rmd | 10 inst/doc/C_confusion_matrix.html | 98 ++++--- inst/doc/D_functional_perspectives.R | 2 inst/doc/D_functional_perspectives.Rmd | 6 inst/doc/D_functional_perspectives.html | 108 ++++---- inst/doc/E_riskyr_primer.R | 2 inst/doc/E_riskyr_primer.Rmd | 6 inst/doc/E_riskyr_primer.html | 395 +++++++++++++++--------------- man/BRCA1.Rd |only man/BRCA1_mam.Rd |only man/BRCA1_ova.Rd |only man/BRCA2.Rd |only man/BRCA2_mam.Rd |only man/BRCA2_ova.Rd |only man/FFTrees_riskyr.Rd |only man/comp_PPV.Rd | 1 man/comp_complement.Rd | 1 man/comp_freq.Rd | 74 +++-- man/comp_freq_freq.Rd | 1 man/comp_freq_prob.Rd | 79 +++--- man/comp_min_N.Rd | 1 man/comp_popu.Rd | 38 +- man/comp_prob.Rd | 7 man/comp_prob_prob.Rd | 47 +-- man/df_scenarios.Rd | 12 man/freq.Rd | 10 man/init_pal.Rd | 8 man/is_complement.Rd | 2 man/is_extreme_prob_set.Rd | 2 man/is_freq.Rd | 2 man/is_integer.Rd |only man/is_matrix.Rd |only man/is_perc.Rd | 2 man/is_prob.Rd | 2 man/is_suff_prob_set.Rd | 2 man/is_valid_prob_pair.Rd | 2 man/is_valid_prob_set.Rd | 2 man/is_valid_prob_triple.Rd | 2 man/pal_bw.Rd | 12 man/pal_bwp.Rd | 12 man/pal_crisk.Rd |only man/pal_kn.Rd | 12 man/pal_mbw.Rd | 12 man/pal_mod.Rd | 12 man/pal_org.Rd | 12 man/pal_rgb.Rd | 12 man/pal_unikn.Rd | 12 man/pal_vir.Rd | 12 man/plot.riskyr.Rd | 12 man/plot_area.Rd | 36 ++ man/plot_bar.Rd | 54 ++-- man/plot_crisk.Rd |only man/plot_curve.Rd | 21 + man/plot_fnet.Rd | 27 +- man/plot_icons.Rd | 41 ++- man/plot_mosaic.Rd | 1 man/plot_plane.Rd | 33 +- man/plot_prism.Rd | 49 ++- man/plot_tab.Rd | 33 ++ man/plot_tree.Rd | 1 man/popu.Rd | 18 - man/prob.Rd | 9 man/read_popu.Rd | 60 ++-- man/riskyr.Rd | 28 +- man/summary.riskyr.Rd | 1 man/t_A.Rd |only man/t_B.Rd |only man/t_I.Rd |only man/write_popu.Rd |only vignettes/A_user_guide.Rmd | 14 - vignettes/B_data_formats.Rmd | 6 vignettes/C_confusion_matrix.Rmd | 10 vignettes/D_functional_perspectives.Rmd | 6 vignettes/E_riskyr_primer.Rmd | 6 122 files changed, 3560 insertions(+), 2257 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] ),
Chris Putman [aut] ,
Richard Mathar [ctb] ,
Johannes Wilm [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2.8 dated 2022-04-11 and 2.2.9 dated 2022-08-15
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- NEWS.md | 10 ++++++++-- TODO | 6 ++++++ build/partial.rdb |binary 5 files changed, 22 insertions(+), 11 deletions(-)
Title: Binary Exponentiation
Description: Fast exponentiation when the exponent is an integer.
Author: Jonathan Debove [aut, cre]
Maintainer: Jonathan Debove <jondebove@gmail.com>
Diff between pow.int versions 1.0 dated 2022-08-12 and 1.1 dated 2022-08-15
DESCRIPTION | 12 +++++------- MD5 | 6 +++--- man/pow.int.Rd | 9 +++++++++ src/pow_int.c | 3 ++- 4 files changed, 19 insertions(+), 11 deletions(-)
Title: Single-Cell Immune Repertoire and Gene Expression Analysis
Description: We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology (Yermanos A, et al (2021) <doi:10.1093/nargab/lqab023>).
Author: Alexander Yermanos [aut, cre],
Andreas Agrafiotis [ctb],
Raphael Kuhn [ctb],
Danielle Shlesinger [ctb],
Jiami Han [ctb],
Tudor-Stefan Cotet [ctb],
Victor Kreiner [ctb]
Maintainer: Alexander Yermanos <ayermanos@gmail.com>
Diff between Platypus versions 3.3.5 dated 2022-04-11 and 3.4.1 dated 2022-08-15
Platypus-3.3.5/Platypus/R/VDJ_clonotype_v3.R |only Platypus-3.3.5/Platypus/man/VDJ_call_recon.Rd |only Platypus-3.3.5/Platypus/man/VDJ_clonotype_clusters_circos.Rd |only Platypus-3.3.5/Platypus/man/VDJ_clonotype_v3.Rd |only Platypus-3.4.1/Platypus/DESCRIPTION | 37 Platypus-3.4.1/Platypus/MD5 | 241 Platypus-3.4.1/Platypus/NAMESPACE | 55 Platypus-3.4.1/Platypus/R/AlphaFold_prediction.R |only Platypus-3.4.1/Platypus/R/AntibodyForests.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_communities.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_dynamics.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_embeddings.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_expand_intermediates.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_heterogeneous.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_infer_ancestral.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_join_trees.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_kernels.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_label_propagation.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_metrics.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_node_transitions.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_overlap.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_paths.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_phylo.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_plot.R |only Platypus-3.4.1/Platypus/R/AntibodyForests_plot_metrics.R |only Platypus-3.4.1/Platypus/R/CellPhoneDB_analyse.R |only Platypus-3.4.1/Platypus/R/Echidna_data.R | 9 Platypus-3.4.1/Platypus/R/GEX_DEgenes.R | 14 Platypus-3.4.1/Platypus/R/GEX_GSEA.R | 9 Platypus-3.4.1/Platypus/R/GEX_coexpression_coefficient.R | 3 Platypus-3.4.1/Platypus/R/GEX_gene_visualization.R |only Platypus-3.4.1/Platypus/R/GEX_lineage_trajectories.R |only Platypus-3.4.1/Platypus/R/GEX_projecTILS.R |only Platypus-3.4.1/Platypus/R/GEX_pseudobulk.R |only Platypus-3.4.1/Platypus/R/GEX_pseudotime_trajectory_plot.R |only Platypus-3.4.1/Platypus/R/GEX_trajectories.R |only Platypus-3.4.1/Platypus/R/GEX_volcano.R | 21 Platypus-3.4.1/Platypus/R/PlatypusDB_find_CDR3s.R | 2 Platypus-3.4.1/Platypus/R/PlatypusDB_load_from_disk.R | 23 Platypus-3.4.1/Platypus/R/PlatypusML_balance.R |only Platypus-3.4.1/Platypus/R/PlatypusML_classification.R |only Platypus-3.4.1/Platypus/R/PlatypusML_feature_extraction_GEX.R |only Platypus-3.4.1/Platypus/R/PlatypusML_feature_extraction_VDJ.R |only Platypus-3.4.1/Platypus/R/Spatial_VDJ_assignment.R |only Platypus-3.4.1/Platypus/R/Spatial_VDJ_plot.R |only Platypus-3.4.1/Platypus/R/Spatial_celltype_plot.R |only Platypus-3.4.1/Platypus/R/Spatial_cluster.R |only Platypus-3.4.1/Platypus/R/Spatial_density_plot.R |only Platypus-3.4.1/Platypus/R/Spatial_evolution_of_clonotype_plot.R |only Platypus-3.4.1/Platypus/R/Spatial_marker_expression.R |only Platypus-3.4.1/Platypus/R/Spatial_module_expression.R |only Platypus-3.4.1/Platypus/R/Spatial_nb_SHM_compare_to_germline_plot.R |only Platypus-3.4.1/Platypus/R/Spatial_scaling_parameters.R |only Platypus-3.4.1/Platypus/R/Spatial_selection_expanded_clonotypes.R |only Platypus-3.4.1/Platypus/R/Spatial_selection_of_cells_on_image.R |only Platypus-3.4.1/Platypus/R/Spatial_vgm_formation.R |only Platypus-3.4.1/Platypus/R/VDJ_GEX_clonotyme.R |only Platypus-3.4.1/Platypus/R/VDJ_GEX_clonotype_clusters_circos.R | 131 Platypus-3.4.1/Platypus/R/VDJ_GEX_matrix.R | 1884 ++--- Platypus-3.4.1/Platypus/R/VDJ_VJ_usage_circos.R | 166 Platypus-3.4.1/Platypus/R/VDJ_Vgene_usage_barplot.R | 8 Platypus-3.4.1/Platypus/R/VDJ_Vgene_usage_stacked_barplot.R | 4 Platypus-3.4.1/Platypus/R/VDJ_abundances.R | 130 Platypus-3.4.1/Platypus/R/VDJ_alpha_beta_Vgene_circos.R | 145 Platypus-3.4.1/Platypus/R/VDJ_antigen_integrate.R | 57 Platypus-3.4.1/Platypus/R/VDJ_bulk_to_vgm.R | 544 + Platypus-3.4.1/Platypus/R/VDJ_call_MIXCR.R | 4 Platypus-3.4.1/Platypus/R/VDJ_call_MIXCR_full.R |only Platypus-3.4.1/Platypus/R/VDJ_call_enclone.R |only Platypus-3.4.1/Platypus/R/VDJ_call_recon.R | 298 Platypus-3.4.1/Platypus/R/VDJ_circos.R | 369 - Platypus-3.4.1/Platypus/R/VDJ_clonal_donut.R | 2 Platypus-3.4.1/Platypus/R/VDJ_clonotype.R | 3457 +--------- Platypus-3.4.1/Platypus/R/VDJ_contigs_to_vgm.R | 177 Platypus-3.4.1/Platypus/R/VDJ_db_annotate.R | 20 Platypus-3.4.1/Platypus/R/VDJ_db_load.R | 24 Platypus-3.4.1/Platypus/R/VDJ_diversity.R | 738 +- Platypus-3.4.1/Platypus/R/VDJ_dynamics.R | 48 Platypus-3.4.1/Platypus/R/VDJ_enclone.R |only Platypus-3.4.1/Platypus/R/VDJ_get_public.R | 2 Platypus-3.4.1/Platypus/R/VDJ_kmers.R |only Platypus-3.4.1/Platypus/R/VDJ_ordination.R |only Platypus-3.4.1/Platypus/R/VDJ_phylogenetic_trees.R | 119 Platypus-3.4.1/Platypus/R/VDJ_phylogenetic_trees_plot.R | 73 Platypus-3.4.1/Platypus/R/VDJ_public.R |only Platypus-3.4.1/Platypus/R/VDJ_rarefaction.R |only Platypus-3.4.1/Platypus/R/VDJ_select_clonotypes.R |only Platypus-3.4.1/Platypus/R/VDJ_structure_analysis.R |only Platypus-3.4.1/Platypus/R/VGM_expanded_clones.R | 4 Platypus-3.4.1/Platypus/R/VGM_integrate.R | 29 Platypus-3.4.1/Platypus/R/dot_plot.R |only Platypus-3.4.1/Platypus/README.md | 23 Platypus-3.4.1/Platypus/build/vignette.rds |binary Platypus-3.4.1/Platypus/inst/doc/PlatypusV3_agedCNS.html | 24 Platypus-3.4.1/Platypus/man/AlphaFold_prediction.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_communities.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_dynamics.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_embeddings.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_expand_intermediates.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_heterogeneous.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_infer_ancestral.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_join_trees.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_kernels.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_label_propagation.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_metrics.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_node_transitions.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_overlap.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_paths.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_phylo.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_plot.Rd |only Platypus-3.4.1/Platypus/man/AntibodyForests_plot_metrics.Rd |only Platypus-3.4.1/Platypus/man/CellPhoneDB_analyse.Rd |only Platypus-3.4.1/Platypus/man/GEX_DEgenes.Rd | 4 Platypus-3.4.1/Platypus/man/GEX_gene_visualization.Rd |only Platypus-3.4.1/Platypus/man/GEX_lineage_trajectories.Rd |only Platypus-3.4.1/Platypus/man/GEX_projecTILS.Rd |only Platypus-3.4.1/Platypus/man/GEX_pseudobulk.Rd |only Platypus-3.4.1/Platypus/man/GEX_pseudotime_trajectory_plot.Rd |only Platypus-3.4.1/Platypus/man/GEX_trajectories.Rd |only Platypus-3.4.1/Platypus/man/PlatypusML_balance.Rd |only Platypus-3.4.1/Platypus/man/PlatypusML_classification.Rd |only Platypus-3.4.1/Platypus/man/PlatypusML_feature_extraction_GEX.Rd |only Platypus-3.4.1/Platypus/man/PlatypusML_feature_extraction_VDJ.Rd |only Platypus-3.4.1/Platypus/man/Spatial_VDJ_assignment.Rd |only Platypus-3.4.1/Platypus/man/Spatial_VDJ_plot.Rd |only Platypus-3.4.1/Platypus/man/Spatial_celltype_plot.Rd |only Platypus-3.4.1/Platypus/man/Spatial_cluster.Rd |only Platypus-3.4.1/Platypus/man/Spatial_density_plot.Rd |only Platypus-3.4.1/Platypus/man/Spatial_evolution_of_clonotype_plot.Rd |only Platypus-3.4.1/Platypus/man/Spatial_marker_expression.Rd |only Platypus-3.4.1/Platypus/man/Spatial_module_expression.Rd |only Platypus-3.4.1/Platypus/man/Spatial_nb_SHM_compare_to_germline_plot.Rd |only Platypus-3.4.1/Platypus/man/Spatial_scaling_parameters.Rd |only Platypus-3.4.1/Platypus/man/Spatial_selection_expanded_clonotypes.Rd |only Platypus-3.4.1/Platypus/man/Spatial_selection_of_cells_on_image.Rd |only Platypus-3.4.1/Platypus/man/Spatial_vgm_formation.Rd |only Platypus-3.4.1/Platypus/man/VDJ_GEX_clonotyme.Rd |only Platypus-3.4.1/Platypus/man/VDJ_GEX_clonotype_clusters_circos.Rd |only Platypus-3.4.1/Platypus/man/VDJ_GEX_matrix.Rd | 37 Platypus-3.4.1/Platypus/man/VDJ_VJ_usage_circos.Rd | 50 Platypus-3.4.1/Platypus/man/VDJ_abundances.Rd | 145 Platypus-3.4.1/Platypus/man/VDJ_alpha_beta_Vgene_circos.Rd | 51 Platypus-3.4.1/Platypus/man/VDJ_antigen_integrate.Rd | 117 Platypus-3.4.1/Platypus/man/VDJ_bulk_to_vgm.Rd | 144 Platypus-3.4.1/Platypus/man/VDJ_call_MIXCR_full.Rd |only Platypus-3.4.1/Platypus/man/VDJ_call_RECON.Rd |only Platypus-3.4.1/Platypus/man/VDJ_call_enclone.Rd |only Platypus-3.4.1/Platypus/man/VDJ_circos.Rd | 43 Platypus-3.4.1/Platypus/man/VDJ_clonal_expansion_abundances.Rd | 84 Platypus-3.4.1/Platypus/man/VDJ_clonotype.Rd | 41 Platypus-3.4.1/Platypus/man/VDJ_contigs_to_vgm.Rd | 11 Platypus-3.4.1/Platypus/man/VDJ_db_annotate.Rd | 64 Platypus-3.4.1/Platypus/man/VDJ_db_load.Rd | 108 Platypus-3.4.1/Platypus/man/VDJ_diversity.Rd | 34 Platypus-3.4.1/Platypus/man/VDJ_dynamics.Rd | 128 Platypus-3.4.1/Platypus/man/VDJ_enclone.Rd |only Platypus-3.4.1/Platypus/man/VDJ_expand_aberrants.Rd | 92 Platypus-3.4.1/Platypus/man/VDJ_get_public.Rd | 92 Platypus-3.4.1/Platypus/man/VDJ_kmers.Rd |only Platypus-3.4.1/Platypus/man/VDJ_ordination.Rd |only Platypus-3.4.1/Platypus/man/VDJ_phylogenetic_trees.Rd | 156 Platypus-3.4.1/Platypus/man/VDJ_phylogenetic_trees_plot.Rd | 79 Platypus-3.4.1/Platypus/man/VDJ_public.Rd |only Platypus-3.4.1/Platypus/man/VDJ_rarefaction.Rd |only Platypus-3.4.1/Platypus/man/VDJ_select_clonotypes.Rd |only Platypus-3.4.1/Platypus/man/VDJ_structure_analysis.Rd |only Platypus-3.4.1/Platypus/man/VGM_expand_featurebarcodes.Rd | 142 Platypus-3.4.1/Platypus/man/VGM_expanded_clones.Rd | 62 Platypus-3.4.1/Platypus/man/VGM_integrate.Rd | 92 Platypus-3.4.1/Platypus/man/dot_plot.Rd |only Platypus-3.4.1/Platypus/man/mus_b_trans.Rd | 21 Platypus-3.4.1/Platypus/man/select.top.clone.Rd | 38 Platypus-3.4.1/Platypus/man/vdj_length_prob.Rd | 16 Platypus-3.4.1/Platypus/vignettes/out |only 175 files changed, 5072 insertions(+), 5673 deletions(-)
Title: Plackett-Luce Models for Rankings
Description: Functions to prepare rankings data and fit the Plackett-Luce model
jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce
(1959, ISBN:0486441369). The standard Plackett-Luce model is generalized
to accommodate ties of any order in the ranking. Partial rankings, in which
only a subset of items are ranked in each ranking, are also accommodated in
the implementation. Disconnected/weakly connected networks implied by the
rankings may be handled by adding pseudo-rankings with a hypothetical item.
Optionally, a multivariate normal prior may be set on the log-worth
parameters and ranker reliabilities may be incorporated as proposed by
Raman and Joachims (2014) <doi:10.1145/2623330.2623654>. Maximum a
posteriori estimation is used when priors are set. Methods are provided to
estimate standard errors or quasi-standard errors for inference as well as
to fit Plackett-Luce trees. See the package website or vignette for further
details.
Author: Heather Turner [aut, cre] ,
Ioannis Kosmidis [aut] ,
David Firth [aut] ,
Jacob van Etten [ctb]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between PlackettLuce versions 0.4.1 dated 2021-08-16 and 0.4.2 dated 2022-08-15
PlackettLuce-0.4.1/PlackettLuce/tests/testthat/Rplots.pdf |only PlackettLuce-0.4.2/PlackettLuce/DESCRIPTION | 7 PlackettLuce-0.4.2/PlackettLuce/MD5 | 110 PlackettLuce-0.4.2/PlackettLuce/NAMESPACE | 280 PlackettLuce-0.4.2/PlackettLuce/NEWS.md | 4 PlackettLuce-0.4.2/PlackettLuce/R/admm_log.R | 332 PlackettLuce-0.4.2/PlackettLuce/R/anova.R | 140 PlackettLuce-0.4.2/PlackettLuce/R/pladmm.R | 560 - PlackettLuce-0.4.2/PlackettLuce/R/pladmm_mob_fit.R | 162 PlackettLuce-0.4.2/PlackettLuce/R/pltree-summaries.R | 486 - PlackettLuce-0.4.2/PlackettLuce/R/pltree.R | 402 - PlackettLuce-0.4.2/PlackettLuce/R/predict.R | 82 PlackettLuce-0.4.2/PlackettLuce/R/rankings.R | 994 +- PlackettLuce-0.4.2/PlackettLuce/R/utils.R | 634 - PlackettLuce-0.4.2/PlackettLuce/R/vcov.PLADMM.R | 56 PlackettLuce-0.4.2/PlackettLuce/README.md | 504 - PlackettLuce-0.4.2/PlackettLuce/build/partial.rdb |binary PlackettLuce-0.4.2/PlackettLuce/build/vignette.rds |binary PlackettLuce-0.4.2/PlackettLuce/inst/WORDLIST | 1 PlackettLuce-0.4.2/PlackettLuce/inst/doc/Overview.R | 894 +- PlackettLuce-0.4.2/PlackettLuce/inst/doc/Overview.html | 3765 ++++++---- PlackettLuce-0.4.2/PlackettLuce/inst/doc/PLADMM.R | 168 PlackettLuce-0.4.2/PlackettLuce/inst/doc/PLADMM.html | 1701 ++-- PlackettLuce-0.4.2/PlackettLuce/man/pladmm.Rd | 218 PlackettLuce-0.4.2/PlackettLuce/man/pltree.Rd | 208 PlackettLuce-0.4.2/PlackettLuce/man/preflib.Rd | 230 PlackettLuce-0.4.2/PlackettLuce/man/rankings.Rd | 382 - PlackettLuce-0.4.2/PlackettLuce/tests/testthat/_snaps |only PlackettLuce-0.4.2/PlackettLuce/tests/testthat/helper.R | 52 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/outputs/print_summary_PLADMM.txt | 2 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-S3-methods-PLADMM.R | 10 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-S3-methods.R | 31 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-adherence.R | 380 - PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-admm.R | 48 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-aggregated_rankings.R | 2 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-agrank.R | 118 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-algorithms.R | 80 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-anova.R | 13 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-estfun-PLADMM.R | 13 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-estfun.R | 125 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-itempar-PLADMM.R | 20 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-log-likelihood.R | 398 - PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-networks.R | 2 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-pltree-PLADMM.R | 213 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-pltree.R | 33 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-predict-PLADMM.R | 28 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-preflib.R | 22 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-pseudo.R | 388 - PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-rankings.R | 2 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-reference.R | 6 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-simulate.R | 167 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-start.R | 11 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-ties.R | 282 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-vcov.R | 34 PlackettLuce-0.4.2/PlackettLuce/tests/testthat/test-weights.R | 12 55 files changed, 8043 insertions(+), 6769 deletions(-)
Title: Waveband Definitions for UV, VIS, and IR Radiation
Description: Constructors of waveband objects for commonly used biological
spectral weighting functions (BSWFs) and for different wavebands describing
named ranges of wavelengths in the ultraviolet (UV), visible (VIS)
and infrared (IR) regions of the electromagnetic spectrum. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyWavebands versions 0.4.5 dated 2022-01-07 and 0.5.0 dated 2022-08-15
DESCRIPTION | 10 MD5 | 166 +++++++-------- NEWS.md | 9 R/blue.r | 2 R/far.red.r | 45 ++-- R/green.r | 2 R/ir.r | 16 - R/landsat.bands.r | 8 R/orange.r | 2 R/par.r | 2 R/purple.r | 2 R/red.r | 2 R/uv.r | 2 R/uva.r | 38 ++- R/uvb.r | 2 R/uvc.r | 2 R/uvi.r | 4 R/vis.r | 8 R/yellow.r | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/r4p-introduction.html | 290 +++++++++++++++++++++++++-- inst/doc/user-guide.R | 2 inst/doc/user-guide.Rmd | 40 +-- inst/doc/user-guide.html | 368 ++++++++++++++++++++++++++++++----- man/Blue.Rd | 86 ++++---- man/CH4.Rd | 86 ++++---- man/CH4_e_fun.Rd | 90 ++++---- man/CH4_q_fun.Rd | 78 +++---- man/CIE.Rd | 92 ++++---- man/CIE1924_lef.spct.Rd | 58 ++--- man/CIE1951_scotopic_lef.spct.Rd | 50 ++-- man/CIE2008_lef2deg.spct.Rd | 50 ++-- man/CIE_e_fun.Rd | 80 +++---- man/CIE_q_fun.Rd | 80 +++---- man/DNA.GM.Rd | 30 +- man/DNA.N.Rd | 30 +- man/DNA.P.Rd | 30 +- man/DNA_GM.Rd | 86 ++++---- man/DNA_GM_q_fun.Rd | 80 +++---- man/DNA_N.Rd | 86 ++++---- man/DNA_N_q_fun.Rd | 56 ++--- man/DNA_P.Rd | 86 ++++---- man/DNA_P_q_fun.Rd | 80 +++---- man/FLAV.Rd | 86 ++++---- man/FLAV_q_fun.Rd | 80 +++---- man/Far_red.Rd | 128 ++++++------ man/GEN.G.Rd | 30 +- man/GEN.M.Rd | 30 +- man/GEN.T.Rd | 30 +- man/GEN_G.Rd | 128 ++++++------ man/GEN_G_q_fun.Rd | 124 +++++------ man/GEN_M.Rd | 122 +++++------ man/GEN_M_q_fun.Rd | 126 +++++------ man/GEN_T.Rd | 108 +++++----- man/GEN_T_q_fun.Rd | 92 ++++---- man/Green.Rd | 92 ++++---- man/ICNIRP.Rd | 104 ++++----- man/ICNIRP_e_fun.Rd | 82 +++---- man/IR.Rd | 176 ++++++++-------- man/IR_bands.Rd | 66 +++--- man/Landsat_bands.Rd | 114 +++++----- man/Orange.Rd | 78 +++---- man/PAR.Rd | 60 ++--- man/PG.Rd | 146 ++++++------- man/PG_q_fun.Rd | 90 ++++---- man/Plant_bands.Rd | 76 +++---- man/Purple.Rd | 82 +++---- man/Red.Rd | 140 ++++++------- man/SetlowTUV.spct.Rd | 50 ++-- man/UV.Rd | 86 ++++---- man/UVA.Rd | 157 ++++++++------ man/UVB.Rd | 104 ++++----- man/UVC.Rd | 90 ++++---- man/UVI.Rd | 98 ++++----- man/UVI_wb.Rd | 88 ++++---- man/UV_bands.Rd | 72 +++--- man/VIS.Rd | 88 ++++---- man/VIS_bands.Rd | 60 ++--- man/Yellow.Rd | 80 +++---- man/photobiologyWavebands-package.Rd | 298 ++++++++++++++-------------- man/photopic_sensitivity.Rd | 40 +-- man/scotopic_sensitivity.Rd | 40 +-- vignettes/user-guide.Rmd | 40 +-- 84 files changed, 3346 insertions(+), 2773 deletions(-)
More information about photobiologyWavebands at CRAN
Permanent link
Title: Spectral Data for Light-Emitting-Diodes
Description: Spectral emission data for some frequently used light emitting
diodes available as electronic components. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Shafiuddin Ahmed [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyLEDs versions 0.5.0 dated 2022-05-14 and 0.5.1 dated 2022-08-15
DESCRIPTION | 15 ++-- MD5 | 26 ++++---- NEWS.md | 5 + build/partial.rdb |binary build/vignette.rds |binary data/COB-dimming-mspct.rda |binary data/COB-reflectors-mspct.rda |binary data/leds-mspct.rda |binary inst/doc/r4p-introduction.html | 12 +-- inst/doc/user-guide.html | 129 ++++++++++++++++++++++------------------ man/led_brands.Rd | 2 man/led_colors.Rd | 4 - man/led_uses.Rd | 2 man/photobiologyLEDs-package.Rd | 4 - 14 files changed, 110 insertions(+), 89 deletions(-)
More information about photobiologyLEDs at CRAN
Permanent link
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.24 dated 2022-05-14 and 0.4.25 dated 2022-08-15
photobiologyInOut-0.4.24/photobiologyInOut/man/as.generic_mspct.Rd |only photobiologyInOut-0.4.24/photobiologyInOut/man/as.generic_spct.Rd |only photobiologyInOut-0.4.25/photobiologyInOut/DESCRIPTION | 14 photobiologyInOut-0.4.25/photobiologyInOut/MD5 | 32 photobiologyInOut-0.4.25/photobiologyInOut/NAMESPACE | 4 photobiologyInOut-0.4.25/photobiologyInOut/NEWS.md | 17 photobiologyInOut-0.4.25/photobiologyInOut/R/foreign-conversion.r | 156 ++-- photobiologyInOut-0.4.25/photobiologyInOut/R/on-load.r | 9 photobiologyInOut-0.4.25/photobiologyInOut/R/read-cid-spectravue-csv.r | 14 photobiologyInOut-0.4.25/photobiologyInOut/R/read-yoctopuce-csv.r | 2 photobiologyInOut-0.4.25/photobiologyInOut/build/partial.rdb |binary photobiologyInOut-0.4.25/photobiologyInOut/build/vignette.rds |binary photobiologyInOut-0.4.25/photobiologyInOut/inst/doc/user-guide.html | 246 ++++--- photobiologyInOut-0.4.25/photobiologyInOut/man/as.colorSpec.Rd | 23 photobiologyInOut-0.4.25/photobiologyInOut/man/colorSpec2mspct.Rd | 56 - photobiologyInOut-0.4.25/photobiologyInOut/man/photobiologyInOut-package.Rd | 4 photobiologyInOut-0.4.25/photobiologyInOut/man/read_cid_spectravue_csv.Rd | 334 ++++------ photobiologyInOut-0.4.25/photobiologyInOut/man/read_yoctopuce_csv.Rd | 1 18 files changed, 500 insertions(+), 412 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Palmer Archipelago (Antarctica) Penguin Data
Description: Size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data were collected and made available by Dr. Kristen Gorman and the Palmer Station Long Term Ecological Research (LTER) Program.
Author: Allison Horst [aut, cre] ,
Alison Hill [aut] ,
Kristen Gorman [aut]
Maintainer: Allison Horst <ahorst@ucsb.edu>
Diff between palmerpenguins versions 0.1.0 dated 2020-07-23 and 0.1.1 dated 2022-08-15
DESCRIPTION | 10 ++-- MD5 | 23 +++++----- R/penguins.R | 6 +- R/penguins_raw.R | 6 +- README.md | 75 ++++++++++++++++++---------------- build |only inst/CITATION | 3 - man/figures/README-flipper-bill-1.png |binary man/figures/README-flipper-hist-1.png |binary man/figures/README-mass-flipper-1.png |binary man/palmerpenguins-package.Rd | 2 man/penguins.Rd | 6 +- man/penguins_raw.Rd | 6 +- 13 files changed, 72 insertions(+), 65 deletions(-)
More information about palmerpenguins at CRAN
Permanent link
Title: Collection of Machine Learning Data Sets for 'mlr3'
Description: A small collection of interesting and educational machine
learning data sets which are used as examples in the 'mlr3' book
(<https://mlr3book.mlr-org.com>), the use case gallery
(<https://mlr3gallery.mlr-org.com>), or in other examples. All data
sets are properly preprocessed and ready to be analyzed by most
machine learning algorithms. Data sets are automatically added to the
dictionary of tasks if 'mlr3' is loaded.
Author: Michel Lang [cre, aut] ,
Marc Becker [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3data versions 0.6.0 dated 2022-03-18 and 0.6.1 dated 2022-08-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/penguins_simple.R | 2 +- build/partial.rdb |binary man/mlr3data-package.Rd | 2 +- man/penguins_simple.Rd | 2 +- 7 files changed, 20 insertions(+), 13 deletions(-)
Title: The Knockoff Filter for Controlled Variable Selection
Description: The knockoff filter is a general procedure for controlling the false discovery rate (FDR)
when performing variable selection.
For more information, see the website below and the accompanying paper: Candes et al.,
"Panning for gold: model-X knockoffs for high-dimensional controlled variable selection",
J. R. Statist. Soc. B (2018) 80, 3, pp. 551-577.
Author: Rina Foygel Barber [ctb] ,
Emmanuel Candes [ctb] ,
Lucas Janson [ctb] ,
Evan Patterson [aut] ,
Matteo Sesia [aut, cre]
Maintainer: Matteo Sesia <sesia@marshall.usc.edu>
Diff between knockoff versions 0.3.5 dated 2022-02-02 and 0.3.6 dated 2022-08-15
knockoff-0.3.5/knockoff/build/partial.rdb |only knockoff-0.3.5/knockoff/inst/doc/hiv.R |only knockoff-0.3.5/knockoff/inst/doc/hiv.Rmd |only knockoff-0.3.5/knockoff/inst/doc/hiv.html |only knockoff-0.3.5/knockoff/vignettes/hiv.Rmd |only knockoff-0.3.6/knockoff/DESCRIPTION | 8 +- knockoff-0.3.6/knockoff/MD5 | 51 +++++++--------- knockoff-0.3.6/knockoff/NEWS | 49 ++++++++------- knockoff-0.3.6/knockoff/R/create_fixed.R | 3 knockoff-0.3.6/knockoff/R/create_gaussian.R | 2 knockoff-0.3.6/knockoff/R/create_second_order.R | 2 knockoff-0.3.6/knockoff/R/knockoff_filter.R | 3 knockoff-0.3.6/knockoff/build/vignette.rds |binary knockoff-0.3.6/knockoff/inst/doc/advanced.R | 4 - knockoff-0.3.6/knockoff/inst/doc/advanced.Rmd | 4 - knockoff-0.3.6/knockoff/inst/doc/advanced.html | 10 +-- knockoff-0.3.6/knockoff/inst/doc/fixed.R | 4 - knockoff-0.3.6/knockoff/inst/doc/fixed.Rmd | 4 - knockoff-0.3.6/knockoff/inst/doc/fixed.html | 13 ++-- knockoff-0.3.6/knockoff/inst/doc/knockoff.R | 4 - knockoff-0.3.6/knockoff/inst/doc/knockoff.Rmd | 4 - knockoff-0.3.6/knockoff/inst/doc/knockoff.html | 65 +++++++++------------ knockoff-0.3.6/knockoff/man/create.fixed.Rd | 3 knockoff-0.3.6/knockoff/man/create.gaussian.Rd | 2 knockoff-0.3.6/knockoff/man/create.second_order.Rd | 2 knockoff-0.3.6/knockoff/man/knockoff.filter.Rd | 3 knockoff-0.3.6/knockoff/vignettes/advanced.Rmd | 4 - knockoff-0.3.6/knockoff/vignettes/fixed.Rmd | 4 - knockoff-0.3.6/knockoff/vignettes/knockoff.Rmd | 4 - 29 files changed, 122 insertions(+), 130 deletions(-)
Title: Collection of Practical Institutional Research Examples and
Tutorials
Description: Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Diff between IRexamples versions 0.0.1 dated 2021-09-06 and 0.0.2 dated 2022-08-15
DESCRIPTION | 11 - MD5 | 43 ++- NAMESPACE | 6 R/00_document_and_pack.R | 2 R/data_ccc_list.R |only R/uc_list.R |only README.md | 1 build/vignette.rds |binary data/ccc_list.rda |only data/uc_list.rda |only inst/doc/Ex-01-Propensity-Score-Weights-Using-GBM.Rmd | 12 - inst/doc/Ex-01-Propensity-Score-Weights-Using-GBM.html | 8 inst/doc/Ex-02-Adjusting-For-Survey-Non-Response-Using-Weights.Rmd | 5 inst/doc/Ex-02-Adjusting-For-Survey-Non-Response-Using-Weights.html | 9 inst/doc/Ex-03-Instructor-Level-Effects-With-Bayesian-Multilevel-Models.Rmd | 5 inst/doc/Ex-03-Instructor-Level-Effects-With-Bayesian-Multilevel-Models.html | 7 inst/doc/Ex-04-Webscraping-Online-Data-Files.Rmd | 109 +++++----- inst/doc/Ex-04-Webscraping-Online-Data-Files.html | 71 ++++-- inst/doc/Ex-05-Geocoding-Addresses.Rmd |only inst/doc/Ex-05-Geocoding-Addresses.html |only man/ccc_list.Rd |only man/uc_list.Rd |only vignettes/Ex-01-Propensity-Score-Weights-Using-GBM.Rmd | 12 - vignettes/Ex-02-Adjusting-For-Survey-Non-Response-Using-Weights.Rmd | 5 vignettes/Ex-03-Instructor-Level-Effects-With-Bayesian-Multilevel-Models.Rmd | 5 vignettes/Ex-04-Webscraping-Online-Data-Files.Rmd | 109 +++++----- vignettes/Ex-05-Geocoding-Addresses.Rmd |only 27 files changed, 259 insertions(+), 161 deletions(-)
Title: Infinite Mixtures of Infinite Factor Analysers and Related
Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2020) <doi:10.1214/19-BA1179>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
Author: Keefe Murphy [aut, cre] ,
Cinzia Viroli [ctb] ,
Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between IMIFA versions 2.1.8 dated 2021-12-19 and 2.1.9 dated 2022-08-15
DESCRIPTION | 10 MD5 | 54 - R/Diagnostics.R | 36 R/FullConditionals.R | 37 R/Gibbs_FA.R | 14 R/Gibbs_IFA.R | 12 R/Gibbs_IMFA.R | 3 R/Gibbs_IMIFA.R | 3 R/IMIFA.R | 4 R/MainFunction.R | 27 R/PlottingFunctions.R | 22 R/data.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.md | 10 inst/doc/IMIFA.html | 592 ++++++++++-- man/IMIFA-package.Rd | 4 man/Procrustes.Rd | 2 man/USPSdigits.Rd | 2 man/coffee.Rd | 2 man/gumbel_max.Rd | 3 man/heat_legend.Rd | 4 man/olive.Rd | 2 man/pareto_scale.Rd | 2 man/post_conf_mat.Rd | 2 man/rDirichlet.Rd | 2 man/storeControl.Rd | 5 vignettes/res_olive_IMIFA__Edited-Vignette-only-Version.rda |binary 28 files changed, 679 insertions(+), 181 deletions(-)
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Description: Analysis of plant pathogen pathotype survey data. Functions
provided calculate distribution of susceptibilities, distribution of
complexities with statistics, pathotype frequency distribution, as well as
diversity indices for pathotypes. This package is meant to be a direct
replacement for Herrmann, Löwer and Schachtel's (1999)
<doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS',
previously used for pathotype analysis.
Author: Austin G. McCoy [aut, ccp] ,
Zachary Noel [aut, ccp] ,
Adam H. Sparks [aut, cre] ,
Martin Chilvers [aut, ths] ,
Zhian N. Kamvar [ctb, rev] ,
Michigan Soybean Promotion Committee [fnd],
Project GREEEN [fnd],
North Central Soybean Research Program [fnd [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between hagis versions 3.1.3 dated 2021-10-14 and 3.1.4 dated 2022-08-15
hagis-3.1.3/hagis/tests/figs |only hagis-3.1.3/hagis/tests/testthat/helper_functions.R |only hagis-3.1.4/hagis/DESCRIPTION | 8 hagis-3.1.4/hagis/LICENSE | 4 hagis-3.1.4/hagis/MD5 | 48 hagis-3.1.4/hagis/NEWS.md | 11 hagis-3.1.4/hagis/README.md | 12 hagis-3.1.4/hagis/build/partial.rdb |only hagis-3.1.4/hagis/build/vignette.rds |binary hagis-3.1.4/hagis/inst/doc/betadiversity.html | 1551 +++++++++- hagis-3.1.4/hagis/inst/doc/hagis.html | 541 ++- hagis-3.1.4/hagis/inst/vector |only hagis-3.1.4/hagis/man/hagis-package.Rd | 2 hagis-3.1.4/hagis/tests/testthat.R | 1 hagis-3.1.4/hagis/tests/testthat/test-autoplot_hagis_complexities.R | 1 hagis-3.1.4/hagis/tests/testthat/test-autoplot_rps_summary.R | 1 hagis-3.1.4/hagis/tests/testthat/test-calculate_complexities.R | 4 hagis-3.1.4/hagis/tests/testthat/test-calculate_diversities.R | 3 hagis-3.1.4/hagis/tests/testthat/test-create_binary_matrix.R | 1 hagis-3.1.4/hagis/tests/testthat/test-diversities_table.R | 1 hagis-3.1.4/hagis/tests/testthat/test-individual_pathotypes.R | 1 21 files changed, 1929 insertions(+), 261 deletions(-)
Title: 'Rstudio' Addin for Version Control and Assignment Management
using Git
Description: An 'Rstudio' addin for version control that allows users to clone
repositories, create and delete branches, and sync forks on GitHub, GitLab, etc.
Furthermore, the addin uses the GitLab API to allow instructors to create
forks and merge requests for all students/teams with one click of a button.
Author: Vincent Nijs [aut, cre],
Sanjiv Erat [aut]
Maintainer: Vincent Nijs <vnijs@ucsd.edu>
Diff between gitgadget versions 0.7.0 dated 2022-06-13 and 0.7.5 dated 2022-08-15
DESCRIPTION | 8 - MD5 | 44 ++++---- NEWS.md | 2 R/gadget.R | 6 - R/git.R | 217 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/app/app.R | 7 - inst/app/components/create.R | 39 ++++--- inst/app/components/intro.R | 47 ++++++--- inst/app/components/sync.R | 51 ++++++---- inst/app/gitgadget_ui.R | 133 +++++++++++++++++--------- inst/app/init.R | 13 +- inst/doc/gitgadget.html | 4 man/add_users_repo.Rd | 2 man/assign_work.Rd | 4 man/check_tokens.Rd | 2 man/collect_work.Rd | 2 man/create_group.Rd | 8 - man/create_repo.Rd | 4 man/fetch_work.Rd | 2 man/projID.Rd | 2 man/remove_project.Rd | 2 man/remove_users_repo.Rd | 2 23 files changed, 345 insertions(+), 256 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.8 dated 2022-04-15 and 0.3.8-1 dated 2022-08-15
DESCRIPTION | 10 - MD5 | 22 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/r4p-introduction.html | 12 - inst/doc/userguide1-grammar.html | 133 ++++++++++---------- inst/doc/userguide2-autoplot-methods.html | 48 +++---- inst/doc/userguide3-data-manip.html | 14 +- man/ggspectra-package.Rd | 194 +++++++++++++++--------------- man/scale_y_A_continuous.Rd | 13 -- man/scale_y_counts_continuous.Rd | 4 man/scale_y_s.e.response_continuous.Rd | 8 - 12 files changed, 232 insertions(+), 226 deletions(-)
Title: Reliable Comparison of Floating Point Numbers
Description: Comparisons of floating point numbers are problematic due to errors
associated with the binary representation of decimal numbers.
Despite being aware of these problems, people still use numerical methods
that fail to account for these and other rounding errors (this pitfall is
the first to be highlighted in Circle 1 of Burns (2012)
'The R Inferno' <https://www.burns-stat.com/pages/Tutor/R_inferno.pdf>).
This package provides new relational operators useful for performing
floating point number comparisons with a set tolerance.
Author: Alex M Chubaty [aut, cre] ,
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between fpCompare versions 0.2.3 dated 2019-09-10 and 0.2.4 dated 2022-08-15
fpCompare-0.2.3/fpCompare/inst/doc/fpCompare.pdf |only fpCompare-0.2.4/fpCompare/DESCRIPTION | 31 +++++++++--------- fpCompare-0.2.4/fpCompare/MD5 | 21 ++++++------ fpCompare-0.2.4/fpCompare/NEWS.md | 6 ++- fpCompare-0.2.4/fpCompare/R/fpCompare.R | 4 +- fpCompare-0.2.4/fpCompare/README.md | 6 ++- fpCompare-0.2.4/fpCompare/build/vignette.rds |binary fpCompare-0.2.4/fpCompare/inst/WORDLIST |only fpCompare-0.2.4/fpCompare/inst/doc/fpCompare.Rmd | 11 +----- fpCompare-0.2.4/fpCompare/inst/doc/fpCompare.html |only fpCompare-0.2.4/fpCompare/man/relational-operators.Rd | 4 +- fpCompare-0.2.4/fpCompare/vignettes/bibliography.bib | 4 +- fpCompare-0.2.4/fpCompare/vignettes/fpCompare.Rmd | 11 +----- 13 files changed, 47 insertions(+), 51 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), ivreg() (from package 'AER'), ivreg() (from package 'ivreg' when
estimated by ordinary least squares), plm() (from package 'plm'), gls() a [...truncated...]
Author: James Pustejovsky [aut, cre]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.7 dated 2022-06-15 and 0.5.8 dated 2022-08-15
clubSandwich-0.5.7/clubSandwich/tests/testthat/test_ivreg.R |only clubSandwich-0.5.8/clubSandwich/DESCRIPTION | 15 +- clubSandwich-0.5.8/clubSandwich/MD5 | 21 +- clubSandwich-0.5.8/clubSandwich/NEWS.md | 9 - clubSandwich-0.5.8/clubSandwich/R/ivreg.R | 35 ++++ clubSandwich-0.5.8/clubSandwich/build/partial.rdb |binary clubSandwich-0.5.8/clubSandwich/inst/doc/Wald-tests-in-clubSandwich.html | 23 +-- clubSandwich-0.5.8/clubSandwich/inst/doc/meta-analysis-with-CRVE.html | 4 clubSandwich-0.5.8/clubSandwich/inst/doc/panel-data-CRVE.html | 75 ++++------ clubSandwich-0.5.8/clubSandwich/man/vcovCR.ivreg.Rd | 35 ++++ clubSandwich-0.5.8/clubSandwich/tests/testthat/test_AER_ivreg.R |only clubSandwich-0.5.8/clubSandwich/tests/testthat/test_ivreg_ivreg.R |only clubSandwich-0.5.8/clubSandwich/tests/testthat/test_plm-first-differences.R | 15 ++ 13 files changed, 151 insertions(+), 81 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph]
,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 0.2.2 dated 2022-04-08 and 0.2.3 dated 2022-08-15
DESCRIPTION | 8 MD5 | 52 NEWS.md | 150 - README.md | 63 build/partial.rdb |binary build/vignette.rds |binary data/cran_to_spdx.rda |binary inst/CITATION | 31 inst/doc/cffr.html | 4 inst/doc/crosswalk.html | 419 +-- man/cffr-package.Rd | 4 tests/testthat/_snaps/bibtex2cff.md | 816 +++--- tests/testthat/_snaps/cff.md | 3400 ++++++++++++++-------------- tests/testthat/_snaps/cff_create.md | 306 +- tests/testthat/_snaps/cff_description.md | 1270 +++++----- tests/testthat/_snaps/cff_parse_citation.md | 662 ++--- tests/testthat/_snaps/cff_parse_person.md | 96 tests/testthat/_snaps/cff_to_bibtex.md | 986 ++++---- tests/testthat/_snaps/cff_write.md | 242 - tests/testthat/_snaps/encoding.md | 276 +- tests/testthat/_snaps/merge_desc_cit.md | 1788 +++++++------- tests/testthat/_snaps/mock-package.md | 120 tests/testthat/_snaps/parse_citation.md | 356 +- tests/testthat/_snaps/utils-persons.md | 450 +-- tests/testthat/_snaps/utils-schema.md | 26 tests/testthat/_snaps/write_bib.md | 28 tests/testthat/test-cff_description.R | 720 ++--- 27 files changed, 6180 insertions(+), 6093 deletions(-)
Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Robert Krause [aut]
Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo@tudublin.ie>
Diff between Bergm versions 5.0.3 dated 2021-06-15 and 5.0.4 dated 2022-08-15
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 1 + R/Bergm-package.R | 1 + 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Handle Data with Messy Header Rows and Broken Values
Description: Verb-like functions to work with messy data, often derived from
spreadsheets or parsed PDF tables. Includes functions for unwrapping
values broken up across rows, relocating embedded grouping values,
and to annotate meaningful formatting in spreadsheet files.
Author: Luis D. Verde Arregoitia [aut, cre]
Maintainer: Luis D. Verde Arregoitia <luis@liomys.mx>
Diff between unheadr versions 0.3.2 dated 2021-04-09 and 0.3.3 dated 2022-08-15
DESCRIPTION | 8 MD5 | 12 NEWS.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/unheadr-vignette.html | 623 +++++++++++++++++++++++------------------ man/unheadr-package.Rd | 7 7 files changed, 370 insertions(+), 284 deletions(-)
Title: Symbols for 'Markdown' and 'Shiny' Application
Description: Direct insertion of symbols (e.g. currencies, letters, arrows, mathematical symbols and so on) into 'Rmarkdown' documents and 'Shiny' applications by incorporating 'HTML' hex codes.
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2symbols versions 0.1 dated 2020-09-09 and 1.1 dated 2022-08-15
r2symbols-0.1/r2symbols/R/zzz.R |only r2symbols-1.1/r2symbols/DESCRIPTION | 14 r2symbols-1.1/r2symbols/MD5 | 33 r2symbols-1.1/r2symbols/NAMESPACE | 4 r2symbols-1.1/r2symbols/NEWS.md |only r2symbols-1.1/r2symbols/R/includeScripts.R |only r2symbols-1.1/r2symbols/R/r2symbols-package.R |only r2symbols-1.1/r2symbols/R/symbolSetting.R | 2 r2symbols-1.1/r2symbols/README.md |only r2symbols-1.1/r2symbols/build/vignette.rds |binary r2symbols-1.1/r2symbols/inst/data_pack.ob |binary r2symbols-1.1/r2symbols/inst/doc/introduction_r_symbols.R | 10 r2symbols-1.1/r2symbols/inst/doc/introduction_r_symbols.Rmd | 2 r2symbols-1.1/r2symbols/inst/doc/introduction_r_symbols.html | 461 ++++++++--- r2symbols-1.1/r2symbols/inst/doc/newversion_r_symbols.R |only r2symbols-1.1/r2symbols/inst/doc/newversion_r_symbols.Rmd |only r2symbols-1.1/r2symbols/inst/doc/newversion_r_symbols.html |only r2symbols-1.1/r2symbols/inst/includes |only r2symbols-1.1/r2symbols/man/sym.setting.Rd | 2 r2symbols-1.1/r2symbols/man/symbol.setting.Rd | 2 r2symbols-1.1/r2symbols/man/trans.r2symbols.Rd |only r2symbols-1.1/r2symbols/vignettes/introduction_r_symbols.Rmd | 2 r2symbols-1.1/r2symbols/vignettes/newversion_r_symbols.Rmd |only 23 files changed, 405 insertions(+), 127 deletions(-)