Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.6 dated 2019-12-11 and 5.5.7 dated 2022-01-12
DESCRIPTION | 18 MD5 | 137 - NAMESPACE | 5 R/CENTROIDS-dba.R | 4 R/CENTROIDS-sdtw-cent.R | 122 + R/CENTROIDS-shape-extraction.R | 2 R/CLUSTERING-cvi-evaluators.R | 6 R/CLUSTERING-ddist2.R | 573 +++--- R/CLUSTERING-tadpole.R | 3 R/DISTANCES-dtw-lb.R | 4 R/DISTANCES-lb-improved.R | 4 R/DISTANCES-sbd.R | 2 R/S4-TSClusters-methods.R | 2283 +++++++++++++-------------- R/S4-tsclustFamily.R | 12 R/SHINY-utils.R | 5 R/UTILS-compute-envelope.R | 94 - R/UTILS-nccc.R | 2 R/pkg.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/COPYRIGHTS | 2 inst/NEWS.Rd | 6 inst/doc/dtwclust.pdf |binary inst/doc/parallelization-considerations.html | 182 +- inst/doc/timing-experiments.html | 180 +- man/DBA.Rd | 38 man/Distmat-generics.Rd | 3 man/GAK.Rd | 28 man/NCCc.Rd | 2 man/SBD.Rd | 2 man/SparseDistmat-generics.Rd | 3 man/TADPole.Rd | 29 man/as.matrix.Rd | 4 man/compare_clusterings.Rd | 24 man/compare_clusterings_configs.Rd | 10 man/compute_envelope.Rd | 4 man/cvi.Rd | 15 man/cvi_evaluators.Rd | 5 man/dtw_basic.Rd | 15 man/dtw_lb.Rd | 18 man/dtwclust-package.Rd | 2 man/dtwclustTimings.Rd | 6 man/interactive_clustering.Rd | 2 man/lb_improved.Rd | 16 man/lb_keogh.Rd | 12 man/pam_cent.Rd | 12 man/pdc_configs.Rd | 12 man/reinterpolate.Rd | 2 man/sdtw_cent.Rd | 28 man/shape_extraction.Rd | 5 man/ssdtwclust.Rd | 4 man/tsclust-controls.Rd | 39 man/tsclust.Rd | 27 man/tsclustFamily-class.Rd | 10 man/tsclusters-methods.Rd | 49 man/tslist.Rd | 2 man/uciCT.Rd | 4 man/zscore.Rd | 9 tests/testthat/helper-all.R | 2 tests/testthat/integration/custom-dist.R | 150 - tests/testthat/regression/clusterings.R | 7 tests/testthat/regression/family-centroids.R | 6 tests/testthat/test-01-unit.R | 2 tests/testthat/test-02-integration.R | 2 tests/testthat/test-03-acceptance.R | 2 tests/testthat/test-04-system.R | 2 tests/testthat/test-05-regression.R | 2 tests/testthat/test-06-parallel.R | 31 tests/testthat/unit/misc.R | 2 vignettes/REFERENCES.bib | 2 70 files changed, 2303 insertions(+), 1996 deletions(-)
Title: R Interface for the C Implementation of CEC Benchmark Functions
Description: Goal of this package is to provide access to benchmark functions defined for
the Special Session and Competition on Real-Parameter Single Objective Optimization in one place.
The package contains functions from following years: 2013, 2014, 2015,
2017, 2019, 2021, 2022 (<https://github.com/P-N-Suganthan>).
Implementations of CEC-2013 (Y. Gonzalez-Fernandez & M. Zambrano-Bigiarini) and CEC2017 (D. Jagodziński) are taken from existed R packages. Also,
the original C source code has been cleaned and reorganized for better readability.
Author: Eryk Warchulski [aut, cre],
Dariusz Jagodziński [cph],
Yasser Gonzalez-Fernandez [cph],
Mauricio Zambrano-Bigiarini [cph]
Maintainer: Eryk Warchulski <ewarchul@gmail.com>
Diff between cecs versions 0.2.3 dated 2021-12-21 and 0.2.4 dated 2022-01-12
DESCRIPTION | 6 - MD5 | 19 +++--- R/cec.R | 36 +---------- R/utils.R | 148 +++++++++++++++++++++++++++++++++++------------- README.md | 6 + man/cecs_tmp_dirpath.Rd |only man/clean.Rd | 10 +-- man/destination_file.Rd |only man/download_data.Rd | 4 - man/get_cec_dirpath.Rd |only man/get_os_name.Rd |only man/unzip_data.Rd | 6 + man/win_tmp_dirpath.Rd |only 13 files changed, 149 insertions(+), 86 deletions(-)
Title: Joint Modeling of Longitudinal and Survival Data - Power
Calculation
Description: Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix, Sigma_theta, is unknown.
Author: Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between JMdesign versions 1.1 dated 2014-10-22 and 1.2 dated 2022-01-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Simultaneous Critical Values for t-Tests in Very High Dimensions
Description: Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion.
Author: Hongyuan Cao [aut],
Michael Kosorok [aut],
Shannon Holloway [aut, cre]
Maintainer: Shannon Holloway <sthollow@ncsu.edu>
Diff between highTtest versions 1.1 dated 2015-02-21 and 1.2 dated 2022-01-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Fast Symbolic Multivariate Polynomials
Description: Fast manipulation of symbolic multivariate polynomials
using the 'Map' class of the Standard Template Library. The package
uses print and coercion methods from the 'mpoly' package (Kahle 2013,
"Multivariate polynomials in R". The R Journal, 5(1):162), but offers
speed improvements. It is comparable in speed to the 'spray' package
for sparse arrays, but retains the symbolic benefits of 'mpoly'.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between mvp versions 1.0-8 dated 2019-09-05 and 1.0-12 dated 2022-01-12
mvp-1.0-12/mvp/DESCRIPTION | 13 +- mvp-1.0-12/mvp/MD5 | 59 +++++----- mvp-1.0-12/mvp/NAMESPACE | 22 +++ mvp-1.0-12/mvp/R/skimpy.R | 121 +++++++-------------- mvp-1.0-12/mvp/R/skimpy_ops.R | 18 ++- mvp-1.0-12/mvp/README.md | 8 - mvp-1.0-12/mvp/build/partial.rdb |binary mvp-1.0-12/mvp/build/vignette.rds |binary mvp-1.0-12/mvp/inst/coercion.R |only mvp-1.0-12/mvp/inst/doc/mvp.R | 57 +++++++-- mvp-1.0-12/mvp/inst/doc/mvp.Rmd | 177 ++++++++++++++++++++++--------- mvp-1.0-12/mvp/inst/doc/mvp.pdf |binary mvp-1.0-12/mvp/inst/freealg_mvp.Rmd |only mvp-1.0-12/mvp/inst/mvp_screenshot.xcf |only mvp-1.0-12/mvp/inst/timings.Rmd |only mvp-1.0-12/mvp/man/allvars.Rd | 13 ++ mvp-1.0-12/mvp/man/coeffs.Rd |only mvp-1.0-12/mvp/man/figures |only mvp-1.0-12/mvp/man/knight.Rd | 3 mvp-1.0-12/mvp/man/lowlevel.Rd | 8 - mvp-1.0-12/mvp/man/mpoly.Rd | 1 mvp-1.0-12/mvp/man/mvp.Rd | 15 ++ mvp-1.0-12/mvp/man/rmvp.Rd | 6 - mvp-1.0-12/mvp/man/series.Rd | 47 +++++++- mvp-1.0-12/mvp/man/special.Rd | 2 mvp-1.0-12/mvp/man/subs.Rd | 14 +- mvp-1.0-12/mvp/man/zero.Rd | 2 mvp-1.0-12/mvp/src/skimpy.cpp | 38 ++---- mvp-1.0-12/mvp/src/skimpy_init.c | 5 mvp-1.0-12/mvp/tests/testthat/test_aac.R | 36 ++++++ mvp-1.0-12/mvp/tests/testthat/test_aae.R |only mvp-1.0-12/mvp/tests/testthat/test_aaf.R |only mvp-1.0-12/mvp/tests/testthat/test_aag.R |only mvp-1.0-12/mvp/vignettes/mvp.Rmd | 177 ++++++++++++++++++++++--------- mvp-1.0-8/mvp/man/accessor.Rd |only mvp-1.0-8/mvp/man/spray.Rd |only 36 files changed, 554 insertions(+), 288 deletions(-)
Title: Methods for the Additive Hazard Model
Description: Methods for fitting additive hazards model.
Perform the maximum likelihood method as well as the traditional Aalen's method for estimating the additive hazards model.
For details see Chengyuan Lu(2021) <arXiv:2004.06156>.
Author: Chengyuan Lu
Maintainer: Chengyuan Lu <c.lu@lumc.nl>
Diff between ahMLE versions 1.18 dated 2021-06-24 and 1.20 dated 2022-01-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ah.R | 14 ++++++++++---- R/method_R.R | 2 +- 4 files changed, 18 insertions(+), 12 deletions(-)
Title: Specify (Pre)Registrations and Export Them Human- And
Machine-Readably
Description: Preregistrations, or more generally, registrations, enable
explicit timestamped and (often but not necessarily publicly) frozen
documentation of plans and expectations as well as decisions and
justifications. In research, preregistrations are commonly used to
clearly document plans and facilitate justifications of deviations from
those plans, as well as decreasing the effects of publication bias by
enabling identification of research that was conducted but not published.
Like reporting guidelines, (pre)registration forms often have specific
structures that facilitate systematic reporting of important items. The
'preregr' package facilitates specifying (pre)registrations in R and
exporting them to a human-readable format (using R Markdown partials or
exporting to an 'HTML' file) as well as human-readable embedded data
(using 'JSON'), as well as importing such exported (pre)registration
specifications from such embedded 'JSON'.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
Diff between preregr versions 0.1.9 dated 2021-10-13 and 0.2.0 dated 2022-01-12
preregr-0.1.9/preregr/inst/extdata/preregr-spec-generalPurpose-form.xlsx |only preregr-0.1.9/preregr/man/form_generalPurpose_v1.Rd |only preregr-0.1.9/preregr/man/form_preregQE_v0_93.Rd |only preregr-0.2.0/preregr/DESCRIPTION | 6 preregr-0.2.0/preregr/MD5 | 145 +++--- preregr-0.2.0/preregr/R/form_create.R | 7 preregr-0.2.0/preregr/R/form_fromSpreadsheet.R | 43 + preregr-0.2.0/preregr/R/form_to_rmd_template.R | 2 preregr-0.2.0/preregr/R/forms_that_are_included.R | 118 ++++- preregr-0.2.0/preregr/R/read_spreadsheet.R | 2 preregr-0.2.0/preregr/R/sanitize_identifiers.R |only preregr-0.2.0/preregr/README.md | 8 preregr-0.2.0/preregr/build/partial.rdb |binary preregr-0.2.0/preregr/build/vignette.rds |binary preregr-0.2.0/preregr/data/examplePrereg_1.rda |binary preregr-0.2.0/preregr/data/form_OSFprereg_v1.rda |binary preregr-0.2.0/preregr/data/form_almostEmptyForm.rda |only preregr-0.2.0/preregr/data/form_generalPurpose_v1.rda |binary preregr-0.2.0/preregr/data/form_generalPurpose_v1_1.rda |only preregr-0.2.0/preregr/data/form_inclSysRev_v0_92.rda |binary preregr-0.2.0/preregr/data/form_prereg2D_v1.rda |only preregr-0.2.0/preregr/data/form_preregQE_v0_94.rda |only preregr-0.2.0/preregr/data/form_prpQuant_v1.rda |binary preregr-0.2.0/preregr/inst/doc/creating_form_from_spreadsheet.Rmd | 8 preregr-0.2.0/preregr/inst/doc/creating_form_from_spreadsheet.html | 7 preregr-0.2.0/preregr/inst/doc/creating_prereg_form.R | 24 - preregr-0.2.0/preregr/inst/doc/creating_prereg_form.html | 38 - preregr-0.2.0/preregr/inst/doc/form_OSFprereg_v1.R | 12 preregr-0.2.0/preregr/inst/doc/form_OSFprereg_v1.html | 18 preregr-0.2.0/preregr/inst/doc/form_generalPurpose_v1.R | 12 preregr-0.2.0/preregr/inst/doc/form_generalPurpose_v1.Rmd | 4 preregr-0.2.0/preregr/inst/doc/form_generalPurpose_v1.html | 18 preregr-0.2.0/preregr/inst/doc/form_generalPurpose_v1_1.R |only preregr-0.2.0/preregr/inst/doc/form_generalPurpose_v1_1.Rmd |only preregr-0.2.0/preregr/inst/doc/form_generalPurpose_v1_1.html |only preregr-0.2.0/preregr/inst/doc/form_inclSysRev_v0_92.R | 12 preregr-0.2.0/preregr/inst/doc/form_inclSysRev_v0_92.html | 24 - preregr-0.2.0/preregr/inst/doc/form_prereg2D_v1.R |only preregr-0.2.0/preregr/inst/doc/form_prereg2D_v1.Rmd |only preregr-0.2.0/preregr/inst/doc/form_prereg2D_v1.html |only preregr-0.2.0/preregr/inst/doc/form_preregQE_v0_93.R | 12 preregr-0.2.0/preregr/inst/doc/form_preregQE_v0_93.Rmd | 4 preregr-0.2.0/preregr/inst/doc/form_preregQE_v0_93.html | 30 - preregr-0.2.0/preregr/inst/doc/form_preregQE_v0_94.R |only preregr-0.2.0/preregr/inst/doc/form_preregQE_v0_94.Rmd |only preregr-0.2.0/preregr/inst/doc/form_preregQE_v0_94.html |only preregr-0.2.0/preregr/inst/doc/form_prpQuant_v1.R | 12 preregr-0.2.0/preregr/inst/doc/form_prpQuant_v1.html | 18 preregr-0.2.0/preregr/inst/doc/importing_form_from_url.R | 12 preregr-0.2.0/preregr/inst/doc/importing_form_from_url.html | 16 preregr-0.2.0/preregr/inst/doc/importing_pregistration_from_url.html | 6 preregr-0.2.0/preregr/inst/doc/rmd_template_from_form.html | 12 preregr-0.2.0/preregr/inst/doc/specifying_prereg_content.html | 6 preregr-0.2.0/preregr/inst/extdata/preregr-form_OSFprereg_v1.xlsx |binary preregr-0.2.0/preregr/inst/extdata/preregr-form_almostEmptyForm_v1.xlsx |only preregr-0.2.0/preregr/inst/extdata/preregr-form_generalPurpose_v1.xlsx |binary preregr-0.2.0/preregr/inst/extdata/preregr-form_generalPurpose_v1_1.xlsx |only preregr-0.2.0/preregr/inst/extdata/preregr-form_inclSysRev_v0_92.xlsx |binary preregr-0.2.0/preregr/inst/extdata/preregr-form_prereg2D_v1.xlsx |only preregr-0.2.0/preregr/inst/extdata/preregr-form_preregQE_v0_94.xlsx |only preregr-0.2.0/preregr/inst/extdata/preregr-form_prpQuant_v1.xlsx |binary preregr-0.2.0/preregr/inst/extdata/preregr-spec-example1.yml | 86 ++- preregr-0.2.0/preregr/inst/extdata/preregr-spec-example1_1.yml |only preregr-0.2.0/preregr/inst/partials/_preregr_form_clean_partial.Rmd | 12 preregr-0.2.0/preregr/man/examplePrereg_1.Rd | 36 - preregr-0.2.0/preregr/man/export_to_yaml_or_json.Rd | 118 ++--- preregr-0.2.0/preregr/man/form_add.Rd | 226 +++++----- preregr-0.2.0/preregr/man/form_almostEmptyForm.Rd |only preregr-0.2.0/preregr/man/form_create.Rd | 7 preregr-0.2.0/preregr/man/form_fromSpreadsheet.Rd | 14 preregr-0.2.0/preregr/man/form_generalPurpose_v1_1.Rd |only preregr-0.2.0/preregr/man/form_prereg2D_v1.Rd |only preregr-0.2.0/preregr/man/form_preregQE_v0_94.Rd |only preregr-0.2.0/preregr/man/form_show.Rd | 66 +- preregr-0.2.0/preregr/man/form_to_html.Rd | 86 +-- preregr-0.2.0/preregr/man/prereg_knit_item_content.Rd | 70 +-- preregr-0.2.0/preregr/man/prereg_next_item.Rd | 100 ++-- preregr-0.2.0/preregr/man/prereg_show_item_completion.Rd | 66 +- preregr-0.2.0/preregr/man/prereg_show_item_content.Rd | 64 +- preregr-0.2.0/preregr/man/prereg_spec_to_html.Rd | 88 +-- preregr-0.2.0/preregr/man/prereg_spec_to_pdf.Rd | 104 ++-- preregr-0.2.0/preregr/man/validate_value.Rd | 174 +++---- preregr-0.2.0/preregr/vignettes/creating_form_from_spreadsheet.Rmd | 8 preregr-0.2.0/preregr/vignettes/form_generalPurpose_v1.Rmd | 4 preregr-0.2.0/preregr/vignettes/form_generalPurpose_v1_1.Rmd |only preregr-0.2.0/preregr/vignettes/form_prereg2D_v1.Rmd |only preregr-0.2.0/preregr/vignettes/form_preregQE_v0_93.Rmd | 4 preregr-0.2.0/preregr/vignettes/form_preregQE_v0_94.Rmd |only 88 files changed, 1111 insertions(+), 858 deletions(-)
Title: Toolkit Implementation of gWidgets2 for tcltk
Description: Port of the 'gWidgets2' API for the 'tcltk' package.
Author: John Verzani
Maintainer: John Verzani <jverzani@gmail.com>
Diff between gWidgets2tcltk versions 1.0-6 dated 2018-09-25 and 1.0-7 dated 2022-01-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/gnotebook.R | 23 +++++++++++++---------- R/gtoolbar.R | 5 ++--- R/gwindow.R | 37 ++++++++++++++++++------------------- 6 files changed, 43 insertions(+), 41 deletions(-)
More information about gWidgets2tcltk at CRAN
Permanent link
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Mike FC [aut] (Code/docs adapted from ggpattern),
Trevor L Davis [aut, cre],
Thomas Lin Pedersen [ctb] (new_data_frame() copied from ggplot2)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 0.3.1 dated 2021-12-02 and 0.4.0 dated 2022-01-12
DESCRIPTION | 6 MD5 | 54 NAMESPACE | 2 NEWS.md | 21 R/pattern-geometry-circle.R | 1 R/pattern-geometry-regular_polygon.R | 40 R/pattern-geometry-tiling.R | 28 R/utils-params.R | 35 R/zzz.R | 2 README.md | 24 inst/doc/developing-patterns.html | 197 ++ inst/doc/tiling.R | 29 inst/doc/tiling.Rmd | 36 inst/doc/tiling.html | 1270 ++++++++++-------- man/figures/README-hex_ggpattern-1.png |binary man/grid.pattern_circle.Rd | 3 man/grid.pattern_crosshatch.Rd | 3 man/grid.pattern_pch.Rd | 3 man/grid.pattern_polygon_tiling.Rd | 3 man/grid.pattern_regular_polygon.Rd | 3 man/grid.pattern_rose.Rd | 3 man/grid.pattern_stripe.Rd | 3 man/grid.pattern_text.Rd | 3 man/grid.pattern_wave.Rd | 3 man/grid.pattern_weave.Rd | 3 man/guess_has_R4.1_features.Rd |only tests/testthat/_snaps/tiling/elongated-triangular.svg |only tests/testthat/test_tiling.R | 2 vignettes/tiling.Rmd | 36 29 files changed, 1225 insertions(+), 588 deletions(-)
Title: Doubly Truncated Data Analysis
Description: Implementation of different algorithms for analyzing
randomly truncated data, one-sided and two-sided (i.e. doubly)
truncated data. It serves to compute empirical cumulative
distributions and also kernel density and hazard functions
using different bandwidth selectors.
Several real data sets are included.
Author: Carla Moreira, Jacobo de Uña-Álvarez and Rosa Crujeiras
Maintainer: Carla Moreira <carlamgmm@gmail.com>
Diff between DTDA versions 3.0 dated 2021-04-11 and 3.0.1 dated 2022-01-12
DTDA-3.0.1/DTDA/DESCRIPTION | 11 DTDA-3.0.1/DTDA/MD5 | 39 +- DTDA-3.0.1/DTDA/R/densityDT.R | 30 +- DTDA-3.0.1/DTDA/R/efron.petrosian.R | 176 +++++++---- DTDA-3.0.1/DTDA/R/hazardDT.R | 128 ++++---- DTDA-3.0.1/DTDA/R/lynden.R | 495 +++++++++++++++++++++++++-------- DTDA-3.0.1/DTDA/R/rsim.DT.R | 8 DTDA-3.0.1/DTDA/R/shen.R | 340 +++++++++++++--------- DTDA-3.0.1/DTDA/man/ACSred.Rd | 16 - DTDA-3.0.1/DTDA/man/AIDS.DT.Rd | 10 DTDA-3.0.1/DTDA/man/AIDS.Rd | 13 DTDA-3.0.1/DTDA/man/ChildCancer.Rd | 7 DTDA-3.0.1/DTDA/man/EqSRounded.Rd | 2 DTDA-3.0.1/DTDA/man/PDlate.Rd | 2 DTDA-3.0.1/DTDA/man/densityDT.Rd | 20 - DTDA-3.0.1/DTDA/man/efron.petrosian.Rd | 23 - DTDA-3.0.1/DTDA/man/hazardDT.Rd | 38 +- DTDA-3.0.1/DTDA/man/lynden.Rd | 28 + DTDA-3.0.1/DTDA/man/rsim.DT.Rd | 5 DTDA-3.0.1/DTDA/man/shen.Rd | 21 - DTDA-3.0/DTDA/man/DTDA-package.Rd |only 21 files changed, 917 insertions(+), 495 deletions(-)
Title: A Collection of Tools and Helpers Extending the Tidyverse
Description: A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages.
This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of
'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count,
various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks,
saving to PDF and PNG from a pipe and various small utilities.
Author: Marcel Wiesweg [aut, cre]
Maintainer: Marcel Wiesweg <marcel.wiesweg@uk-essen.de>
Diff between tidytidbits versions 0.2.3 dated 2021-03-08 and 0.3.0 dated 2022-01-12
tidytidbits-0.2.3/tidytidbits/man/add_summary.Rd |only tidytidbits-0.2.3/tidytidbits/man/add_summary_by.Rd |only tidytidbits-0.2.3/tidytidbits/man/cross_tabulate.Rd |only tidytidbits-0.2.3/tidytidbits/man/execute_if.Rd |only tidytidbits-0.2.3/tidytidbits/man/execute_in_pipeline.Rd |only tidytidbits-0.3.0/tidytidbits/DESCRIPTION | 11 tidytidbits-0.3.0/tidytidbits/MD5 | 24 tidytidbits-0.3.0/tidytidbits/NAMESPACE | 12 tidytidbits-0.3.0/tidytidbits/NEWS.md | 11 tidytidbits-0.3.0/tidytidbits/R/dplyr-like.R | 393 +++------- tidytidbits-0.3.0/tidytidbits/R/tidytidbits.R | 5 tidytidbits-0.3.0/tidytidbits/man/add_prop_test.Rd | 9 tidytidbits-0.3.0/tidytidbits/man/categorical_test_by.Rd |only tidytidbits-0.3.0/tidytidbits/man/contingency_table_as_matrix.Rd |only tidytidbits-0.3.0/tidytidbits/man/contingency_table_by.Rd |only tidytidbits-0.3.0/tidytidbits/man/count_at.Rd | 2 tidytidbits-0.3.0/tidytidbits/man/count_by.Rd | 2 17 files changed, 198 insertions(+), 271 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 1.1.0 dated 2021-10-18 and 1.1.1 dated 2022-01-12
DESCRIPTION | 17 LICENSE | 4 MD5 | 456 +- NAMESPACE | 666 +-- NEWS.md | 790 +-- R/00_global_variables.R | 30 R/data.R | 218 - R/dev-constructor.R | 178 R/dev-model_descriptions.R | 588 +- R/dev-parse_index.R | 216 - R/dev-xregs.R | 664 +-- R/dials-adam_params.R | 250 - R/dials-arima_params.R | 206 R/dials-ets_params.R | 282 - R/dials-nnetar_params.R | 74 R/dials-prophet_params.R | 318 - R/dials-temporal_hierarchy_params.R | 80 R/dials-ts_params.R | 114 R/helpers-modeltime_residuals.R | 86 R/helpers-modeltime_table.R | 580 +- R/modeltime-accuracy-table.R | 314 - R/modeltime-accuracy.R | 344 - R/modeltime-calibrate.R | 724 +-- R/modeltime-fit-workflowset.R | 646 +-- R/modeltime-forecast-plot.R | 464 +- R/modeltime-forecast.R | 2076 +++++----- R/modeltime-recursive.R | 1430 +++--- R/modeltime-refit.R | 992 ++-- R/modeltime-residuals-plot.R | 298 - R/modeltime-residuals-tests.R | 396 - R/modeltime-residuals.R | 206 R/modeltime-table.R | 220 - R/nested-modeltime-forecast.R | 828 +-- R/nested-modeltime_data_prep.R | 640 +-- R/nested-modeltime_extractors.R | 256 - R/nested-modeltime_fit.R | 1198 ++--- R/nested-modeltime_refit.R | 844 ++-- R/nested-modeltime_select_best.R | 410 - R/parsnip-adam.R | 1456 +++---- R/parsnip-adam_data.R | 868 ++-- R/parsnip-arima_boost.R | 1614 +++---- R/parsnip-arima_boost_data.R | 742 +-- R/parsnip-arima_reg.R | 1070 ++--- R/parsnip-arima_reg_data.R | 494 +- R/parsnip-exp_smoothing.R | 1786 ++++---- R/parsnip-exp_smoothing_data.R | 754 +-- R/parsnip-naive_reg.R | 1002 ++-- R/parsnip-naive_reg_data.R | 308 - R/parsnip-nnetar_reg.R | 774 +-- R/parsnip-nnetar_reg_data.R | 266 - R/parsnip-prophet_boost.R | 1370 +++--- R/parsnip-prophet_boost_data.R | 496 +- R/parsnip-prophet_reg.R | 1154 ++--- R/parsnip-prophet_reg_data.R | 356 - R/parsnip-seasonal_reg.R | 1336 +++--- R/parsnip-seasonal_reg_data.R | 510 +- R/parsnip-temporal_hierarchy.R | 748 +-- R/parsnip-temporal_hierarchy_data.R | 192 R/parsnip-window_reg.R | 1220 ++--- R/parsnip-window_reg_data.R | 344 - R/tibble-type_sum.R | 64 R/utils-checks-validations.R | 804 +-- R/utils-control-par.R | 1092 ++--- R/utils-is_modeltime.R | 124 R/utils-make_grouped_predictions.R | 112 R/utils-parsnip-helpers.R | 346 - R/utils-pipe.R | 22 R/utils-tidy-eval.R | 94 R/utils-xgboost.R | 162 R/yardstick-metric-sets.R | 574 +- R/zzz.R | 86 README.md | 392 - build/vignette.rds |binary inst/doc/getting-started-with-modeltime.R | 282 - inst/doc/getting-started-with-modeltime.Rmd | 818 +-- inst/doc/getting-started-with-modeltime.html | 1852 ++++---- man/Adam_predict_impl.Rd | 36 man/Arima_fit_impl.Rd | 88 man/Arima_predict_impl.Rd | 36 man/Auto_adam_predict_impl.Rd | 36 man/adam_fit_impl.Rd | 158 man/adam_params.Rd | 166 man/adam_reg.Rd | 580 +- man/add_modeltime_model.Rd | 80 man/arima_boost.Rd | 608 +- man/arima_params.Rd | 112 man/arima_reg.Rd | 498 +- man/arima_xgboost_fit_impl.Rd | 248 - man/arima_xgboost_predict_impl.Rd | 36 man/auto_adam_fit_impl.Rd | 158 man/auto_arima_fit_impl.Rd | 88 man/auto_arima_xgboost_fit_impl.Rd | 368 - man/combine_modeltime_tables.Rd | 144 man/control_modeltime.Rd | 200 man/create_model_grid.Rd | 150 man/create_xreg_recipe.Rd | 136 man/croston_fit_impl.Rd | 40 man/croston_predict_impl.Rd | 36 man/dot_prepare_transform.Rd | 40 man/ets_fit_impl.Rd | 96 man/ets_predict_impl.Rd | 36 man/exp_smoothing.Rd | 672 +-- man/exp_smoothing_params.Rd | 144 man/get_arima_description.Rd | 60 man/get_model_description.Rd | 84 man/get_tbats_description.Rd | 38 man/is_calibrated.Rd | 30 man/is_modeltime_model.Rd | 30 man/is_modeltime_table.Rd | 28 man/is_residuals.Rd | 28 man/load_namespace.Rd | 38 man/log_extractors.Rd | 98 man/m750.Rd | 60 man/m750_models.Rd | 68 man/m750_splits.Rd | 60 man/m750_training_resamples.Rd | 72 man/maape.Rd | 34 man/maape.data.frame.Rd | 44 man/maape_vec.Rd | 40 man/make_ts_splits.Rd | 44 man/mdl_time_forecast.Rd | 106 man/mdl_time_refit.Rd | 64 man/modeltime_accuracy.Rd | 182 man/modeltime_calibrate.Rd | 218 - man/modeltime_fit_workflowset.Rd | 138 man/modeltime_forecast.Rd | 458 +- man/modeltime_nested_fit.Rd | 130 man/modeltime_nested_forecast.Rd | 142 man/modeltime_nested_refit.Rd | 46 man/modeltime_nested_select_best.Rd | 80 man/modeltime_refit.Rd | 198 man/modeltime_residuals.Rd | 134 man/modeltime_residuals_test.Rd | 222 - man/modeltime_table.Rd | 174 man/naive_fit_impl.Rd | 44 man/naive_predict_impl.Rd | 32 man/naive_reg.Rd | 306 - man/new_modeltime_bridge.Rd | 102 man/nnetar_fit_impl.Rd | 100 man/nnetar_params.Rd | 80 man/nnetar_predict_impl.Rd | 36 man/nnetar_reg.Rd | 388 - man/panel_tail.Rd | 68 man/parallel_start.Rd | 106 man/parse_index.Rd | 88 man/pipe.Rd | 24 man/plot_modeltime_forecast.Rd | 200 man/plot_modeltime_residuals.Rd | 204 man/pluck_modeltime_model.Rd | 74 man/predict.recursive.Rd | 98 man/predict.recursive_panel.Rd | 98 man/prep_nested.Rd | 254 - man/prophet_boost.Rd | 648 +-- man/prophet_fit_impl.Rd | 176 man/prophet_params.Rd | 172 man/prophet_predict_impl.Rd | 36 man/prophet_reg.Rd | 502 +- man/prophet_xgboost_fit_impl.Rd | 304 - man/prophet_xgboost_predict_impl.Rd | 36 man/pull_modeltime_residuals.Rd | 36 man/pull_parsnip_preprocessor.Rd | 34 man/recipe_helpers.Rd | 108 man/recursive.Rd | 442 +- man/seasonal_reg.Rd | 390 - man/smooth_fit_impl.Rd | 96 man/smooth_predict_impl.Rd | 36 man/snaive_fit_impl.Rd | 44 man/snaive_predict_impl.Rd | 32 man/stlm_arima_fit_impl.Rd | 68 man/stlm_arima_predict_impl.Rd | 36 man/stlm_ets_fit_impl.Rd | 68 man/stlm_ets_predict_impl.Rd | 36 man/summarize_accuracy_metrics.Rd | 84 man/table_modeltime_accuracy.Rd | 242 - man/tbats_fit_impl.Rd | 74 man/tbats_predict_impl.Rd | 36 man/temporal_hier_fit_impl.Rd | 64 man/temporal_hier_predict_impl.Rd | 36 man/temporal_hierarchy.Rd | 296 - man/temporal_hierarchy_params.Rd | 56 man/theta_fit_impl.Rd | 36 man/theta_predict_impl.Rd | 36 man/tidyeval.Rd | 102 man/time_series_params.Rd | 82 man/type_sum.mdl_time_tbl.Rd | 36 man/update_model_description.Rd | 74 man/update_modeltime_model.Rd | 80 man/window_function_fit_impl.Rd | 64 man/window_function_predict_impl.Rd | 32 man/window_reg.Rd | 420 +- man/xgboost_impl.Rd | 158 man/xgboost_predict.Rd | 36 tests/testthat.R | 62 tests/testthat/test-algo-adam_reg-Adam.R | 418 -- tests/testthat/test-algo-adam_reg-auto_adam.R | 421 +- tests/testthat/test-algo-arima_boost-Arima.R | 578 +- tests/testthat/test-algo-arima_boost-auto_arima.R | 548 +- tests/testthat/test-algo-arima_reg-Arima.R | 416 +- tests/testthat/test-algo-arima_reg-auto_arima.R | 384 - tests/testthat/test-algo-exp_smoothing-ets.R | 830 ++- tests/testthat/test-algo-nnetar_reg.R | 453 +- tests/testthat/test-algo-prophet_boost.R | 770 +-- tests/testthat/test-algo-prophet_reg.R | 658 +-- tests/testthat/test-algo-seasonal_decomp_arima.R | 309 - tests/testthat/test-algo-seasonal_decomp_ets.R | 297 - tests/testthat/test-algo-seasonal_reg_tbats.R | 308 - tests/testthat/test-algo-temporal_hierarchy.R | 276 - tests/testthat/test-algo-window_reg.R | 865 ++-- tests/testthat/test-conf_by_id.R | 175 tests/testthat/test-default_accuracy_metric_sets.R | 116 tests/testthat/test-developer-tools-constructor.R | 292 - tests/testthat/test-developer-tools-xregs.R | 124 tests/testthat/test-extended_accuracy_metric_set.R | 114 tests/testthat/test-fit_workflowsets.R | 439 +- tests/testthat/test-helpers-combine-modeltime-tables.R | 172 tests/testthat/test-helpers-pull_parsnip_preprocessor.R | 132 tests/testthat/test-helpers-update-modeltime-tables.R | 248 - tests/testthat/test-modeltime_residuals.R |only tests/testthat/test-modeltime_table-forecast-accuracy-refitting.R | 970 ++-- tests/testthat/test-modeltime_table-no-calib-refit.R | 243 - tests/testthat/test-nested-modeltime.R | 546 +- tests/testthat/test-panel-data.R | 238 - tests/testthat/test-recursive.R | 670 +-- tests/testthat/test-refit-parallel.R | 106 tests/testthat/test-results-accuracy-tables.R | 361 - tests/testthat/test-results-forecast-plots.R | 268 - tests/testthat/test-results-residuals-tests.R | 205 tests/testthat/test-tune_workflows.R | 146 vignettes/getting-started-with-modeltime.Rmd | 818 +-- vignettes/time_series_course.jpg |only 230 files changed, 36775 insertions(+), 36772 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.11.0 dated 2021-05-07 and 2.12.0 dated 2022-01-12
DESCRIPTION | 14 ++--- MD5 | 17 ++++-- NAMESPACE | 6 ++ NEWS.md | 6 ++ R/global_search.R |only R/object.R | 83 ++++++++++++++++++++++++++++++++- R/solvebio.R | 12 +++- man/GlobalSearch.request.Rd |only man/GlobalSearch.search.Rd |only man/GlobalSearch.subjects.Rd |only man/Object.disable_global_beacon.Rd |only man/Object.enable_global_beacon.Rd |only man/Object.get_global_beacon_status.Rd |only 13 files changed, 122 insertions(+), 16 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.5.1 dated 2021-10-06 and 1.6.0 dated 2022-01-12
DESCRIPTION | 19 ++- MD5 | 110 ++++++++++++--------- NAMESPACE | 16 ++- NEWS.md | 30 +++++ R/Consensus.R | 12 +- R/ImposeConstraint.R | 16 ++- R/Information.R | 18 ++- R/RoguePlot.R |only R/Support.R | 11 +- R/parse_files.R | 167 +++++++++++++++++++++++++-------- R/tree_display.R | 18 +++ R/tree_generation.R | 161 +++++++++++++++++++++++++++++-- R/tree_numbering.R | 5 R/tree_properties.R | 2 R/tree_rearrangement.R | 156 +++++++++++++++++++++++------- R/tree_shape.R | 4 R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/REFERENCES.bib | 35 ++++++ inst/WORDLIST | 3 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.R | 6 - inst/doc/load-data.Rmd | 10 - inst/doc/load-data.html | 17 +-- inst/doc/load-trees.html | 4 man/CharacterInformation.Rd | 10 + man/CompatibleSplits.Rd | 104 ++++++++++---------- man/Consensus.Rd | 14 ++ man/ConsensusWithout.Rd | 3 man/ConstrainedNJ.Rd | 10 + man/DropTip.Rd | 21 +++- man/GenerateTree.Rd | 6 - man/Hamming.Rd |only man/MatrixToPhyDat.Rd | 23 +++- man/NJTree.Rd | 7 - man/PhyToString.Rd | 9 - man/ReadCharacters.Rd | 3 man/Reorder.Rd | 2 man/RoguePlot.Rd |only man/RootNode.Rd | 2 man/SplitInformation.Rd | 8 - man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only tests/figs |only tests/spelling.R |only tests/testthat/_snaps/RoguePlot |only tests/testthat/test-ImposeConstraint.R | 2 tests/testthat/test-RoguePlot.R |only tests/testthat/test-parsers.R | 57 +++++++---- tests/testthat/test-tree_comparison.R | 1 tests/testthat/test-tree_generation.R | 53 ++++++++++ tests/testthat/test-tree_numbering.R | 10 - tests/testthat/test-tree_rearrange.R | 33 +++++- vignettes/load-data.Rmd | 10 - 62 files changed, 897 insertions(+), 321 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Søren Højsgaard [aut],
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik),
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-1995-6531>,
@vincentab),
Jeffrey Girard [ctb] (<https://orcid.org/0000-0002-7359-3746>,
@jeffreymgirard),
Christina Maimone [rev],
Niels Ohlsen [rev] (@Niels_Bremen)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between parameters versions 0.15.0 dated 2021-10-18 and 0.16.0 dated 2022-01-12
DESCRIPTION | 26 MD5 | 238 +++--- NAMESPACE | 14 NEWS.md | 482 +------------ R/1_model_parameters.R | 309 ++++---- R/2_ci.R | 23 R/3_p_value.R | 30 R/bootstrap_model.R | 6 R/check_clusterstructure.R | 7 R/check_factorstructure.R | 18 R/check_heterogeneity.R | 8 R/ci_betwithin.R | 6 R/ci_generic.R | 9 R/ci_ml1.R | 6 R/ci_profile_boot.R | 4 R/ci_satterthwaite.R | 6 R/cluster_analysis.R | 511 +++++++++----- R/cluster_discrimination.R | 38 - R/compare_parameters.R | 59 + R/dof.R | 45 - R/dof_betwithin.R | 4 R/dof_ml1.R | 4 R/extract_parameters.R | 32 R/extract_random_variances.R | 686 +++++++++++++++++-- R/format.R | 59 + R/format_p_adjust.R | 2 R/format_parameters.R | 13 R/methods_BayesFactor.R | 73 +- R/methods_aov.R | 58 + R/methods_bamlss.R | 2 R/methods_betareg.R | 1 R/methods_bfsl.R |only R/methods_brms.R | 4 R/methods_cplm.R | 6 R/methods_dbscan.R | 1 R/methods_gee.R | 3 R/methods_glmmTMB.R | 21 R/methods_htest.R | 19 R/methods_lavaan.R | 7 R/methods_lme4.R | 59 - R/methods_mediate.R | 4 R/methods_metafor.R | 2 R/methods_mixmod.R | 64 - R/methods_mixor.R | 2 R/methods_panelr.R | 4 R/methods_psych.R | 31 R/methods_rstanarm.R | 2 R/methods_survival.R | 2 R/n_clusters_easystats.R | 10 R/p_value_betwithin.R | 4 R/p_value_ml1.R | 22 R/p_value_satterthwaite.R | 17 R/parameters_type.R | 19 R/plot.R | 9 R/print.compare_parameters.R | 4 R/print.parameters_model.R | 38 - R/random_parameters.R | 10 R/reduce_parameters.R | 8 R/robust_estimation.R | 35 R/utils_clustering.R | 29 R/utils_format.R | 70 + R/utils_model_parameters.R | 84 +- README.md | 16 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 28 inst/doc/overview_of_vignettes.Rmd | 1 inst/doc/overview_of_vignettes.html | 1 man/check_clusterstructure.Rd | 1 man/check_heterogeneity.Rd | 7 man/check_kmo.Rd | 3 man/check_sphericity_bartlett.Rd | 1 man/ci.default.Rd | 176 ++-- man/cluster_analysis.Rd | 181 +++-- man/cluster_discrimination.Rd | 12 man/compare_parameters.Rd | 9 man/degrees_of_freedom.Rd | 16 man/display.parameters_model.Rd | 6 man/equivalence_test.lm.Rd | 3 man/model_parameters.BFBayesFactor.Rd | 30 man/model_parameters.Rd | 313 ++++---- man/model_parameters.aov.Rd | 4 man/model_parameters.averaging.Rd | 2 man/model_parameters.cgam.Rd | 6 man/model_parameters.default.Rd | 160 ++-- man/model_parameters.kmeans.Rd | 1 man/model_parameters.lavaan.Rd | 5 man/model_parameters.merMod.Rd | 220 +++++- man/model_parameters.mlm.Rd | 2 man/model_parameters.principal.Rd | 13 man/model_parameters.rma.Rd | 2 man/model_parameters.stanreg.Rd | 172 ++++ man/model_parameters.t1way.Rd | 2 man/model_parameters.zcpglm.Rd | 6 man/n_clusters.Rd | 10 man/p_value.BFBayesFactor.Rd | 8 man/p_value.DirichletRegModel.Rd | 4 man/p_value.Rd | 22 man/p_value.zcpglm.Rd | 8 man/p_value_betwithin.Rd | 11 man/p_value_ml1.Rd | 24 man/p_value_satterthwaite.Rd | 11 man/pool_parameters.Rd | 3 man/print.parameters_model.Rd | 12 man/standard_error.Rd | 4 man/standard_error_robust.Rd | 5 tests/testthat.R | 7 tests/testthat/test-GLMMadaptive.R | 34 tests/testthat/test-emmGrid-df_colname.R | 10 tests/testthat/test-glmmTMB.R | 221 +++--- tests/testthat/test-ivreg.R | 3 tests/testthat/test-model_parameters.BFBayesFactor.R | 88 ++ tests/testthat/test-model_parameters.anova.R | 2 tests/testthat/test-model_parameters.aov.R | 10 tests/testthat/test-model_parameters.aov_es_ci.R | 90 -- tests/testthat/test-model_parameters.cgam.R | 62 - tests/testthat/test-model_parameters.glm.R | 24 tests/testthat/test-model_parameters.mixed.R | 6 tests/testthat/test-model_parameters_df.R | 40 - tests/testthat/test-model_parameters_ordinal.R |only vignettes/overview_of_vignettes.Rmd | 1 121 files changed, 3404 insertions(+), 2084 deletions(-)
Title: Exhaustive Chemical Enumeration for Ultimate Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using a exhaustive chemical enumeration-based approach.
Author: Sadjad Fakouri-Baygi [cre, aut]
(<https://orcid.org/0000-0002-6864-6911>),
Dinesh Barupal [aut] (<https://orcid.org/0000-0002-9954-8628>)
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFAx versions 1.0 dated 2022-01-06 and 1.0.1 dated 2022-01-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/UFAx_workflow.R | 4 ++-- data/UFAx_null.rda |binary man/UFAx_workflow.Rd | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Periodically Correlated and Periodically Integrated Time Series
Description: Classes and methods for modelling and simulation of
periodically correlated (PC) and periodically integrated time
series. Compute theoretical periodic autocovariances and related
properties of PC autoregressive moving average models. Some original
methods including Boshnakov & Iqelan (2009)
<doi:10.1111/j.1467-9892.2009.00617.x>, Boshnakov (1996)
<doi:10.1111/j.1467-9892.1996.tb00281.x>.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between pcts versions 0.15 dated 2020-10-31 and 0.15.2 dated 2022-01-12
DESCRIPTION | 8 +- MD5 | 57 ++++++++++---------- NAMESPACE | 1 NEWS.md | 35 +++++++----- README.md | 4 - build/partial.rdb |binary inst/REFERENCES.bib | 36 ++++++------ inst/doc/pcts_data.R | 5 - inst/doc/pcts_data.Rmd | 12 ++-- inst/doc/pcts_data.html | 86 ++++++++++++++---------------- man/Fraser2017.Rd | 2 man/PeriodicAutocorrelations-class.Rd | 2 man/PeriodicMTS-class.Rd | 10 +++ man/availStart.Rd | 2 man/fitPM.Rd | 29 +++------- man/mC.ss.Rd | 10 --- man/pc.acf2model.Rd | 9 --- man/pc.hat.h.Rd | 8 -- man/pcAR2acf.Rd | 16 +---- man/pcalg1.Rd | 23 +------- man/pcarma_solve.Rd | 8 -- man/pclspiar.Rd | 25 +------- man/pcts-package.Rd | 96 +--------------------------------- man/pcts_reexports.Rd | 5 - man/permodelmf.Rd | 8 -- man/sim_parAcvf.Rd | 8 -- man/sim_parCoef.Rd | 9 --- man/sl_utils.Rd | 8 -- man/window.Rd |only vignettes/pcts_data.Rmd | 12 ++-- 30 files changed, 179 insertions(+), 355 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.8.3 dated 2021-11-23 and 0.8.4 dated 2022-01-12
DESCRIPTION | 8 +- MD5 | 38 ++++++------- R/ARMA_optim.R | 45 +++++++--------- R/FSD.R | 10 +-- R/NNS_meboot.R | 10 +-- R/Normalization.R | 2 R/SD_Efficient_Set.R | 95 +++++++++++++++++----------------- R/SSD.R | 9 +-- R/TSD.R | 15 ++--- R/Uni_SD_Routines.R | 24 ++------ README.md | 6 +- inst/doc/NNSvignette_Forecasting.R | 4 - inst/doc/NNSvignette_Forecasting.Rmd | 6 +- inst/doc/NNSvignette_Forecasting.html | 26 ++++----- man/NNS.ARMA.optim.Rd | 4 - man/NNS.FSD.Rd | 4 + man/NNS.SSD.Rd | 4 + man/NNS.TSD.Rd | 4 + man/NNS.meboot.Rd | 3 + vignettes/NNSvignette_Forecasting.Rmd | 6 +- 20 files changed, 157 insertions(+), 166 deletions(-)
Title: Produce Forest Plots to Visualize Covariate Effects
Description: Produce forest plots to visualize covariate effects using either
the command line or an interactive 'Shiny' application.
Author: Samer Mouksassi [aut, cre] (<https://orcid.org/0000-0002-7152-6654>),
Dean Attali [ctb]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between coveffectsplot versions 0.0.9.1 dated 2020-12-10 and 1.0.0 dated 2022-01-12
coveffectsplot-0.0.9.1/coveffectsplot/inst/doc/Introduction_to_coveffectsplot.R |only coveffectsplot-0.0.9.1/coveffectsplot/inst/doc/Introduction_to_coveffectsplot.Rmd |only coveffectsplot-0.0.9.1/coveffectsplot/inst/doc/Introduction_to_coveffectsplot.html |only coveffectsplot-0.0.9.1/coveffectsplot/vignettes/Introduction_to_coveffectsplot.Rmd |only coveffectsplot-1.0.0/coveffectsplot/DESCRIPTION | 16 coveffectsplot-1.0.0/coveffectsplot/MD5 | 61 coveffectsplot-1.0.0/coveffectsplot/NAMESPACE | 2 coveffectsplot-1.0.0/coveffectsplot/NEWS.md | 12 coveffectsplot-1.0.0/coveffectsplot/R/forest_plot.R | 89 coveffectsplot-1.0.0/coveffectsplot/README.md | 4 coveffectsplot-1.0.0/coveffectsplot/build/vignette.rds |binary coveffectsplot-1.0.0/coveffectsplot/inst/doc/Exposure_Response_Example.R | 11 coveffectsplot-1.0.0/coveffectsplot/inst/doc/Exposure_Response_Example.Rmd | 15 coveffectsplot-1.0.0/coveffectsplot/inst/doc/Exposure_Response_Example.html | 869 ++--- coveffectsplot-1.0.0/coveffectsplot/inst/doc/PKPD_Example.R | 4 coveffectsplot-1.0.0/coveffectsplot/inst/doc/PKPD_Example.Rmd | 17 coveffectsplot-1.0.0/coveffectsplot/inst/doc/PKPD_Example.html | 804 +---- coveffectsplot-1.0.0/coveffectsplot/inst/doc/PK_Example.R | 10 coveffectsplot-1.0.0/coveffectsplot/inst/doc/PK_Example.Rmd | 27 coveffectsplot-1.0.0/coveffectsplot/inst/doc/PK_Example.html | 1543 ++++------ coveffectsplot-1.0.0/coveffectsplot/inst/doc/Pediatric_Cov_Sim.Rmd | 8 coveffectsplot-1.0.0/coveffectsplot/inst/doc/Pediatric_Cov_Sim.html | 960 ++---- coveffectsplot-1.0.0/coveffectsplot/inst/doc/introduction_to_coveffectsplot.R |only coveffectsplot-1.0.0/coveffectsplot/inst/doc/introduction_to_coveffectsplot.Rmd |only coveffectsplot-1.0.0/coveffectsplot/inst/doc/introduction_to_coveffectsplot.html |only coveffectsplot-1.0.0/coveffectsplot/inst/shiny/global.r | 13 coveffectsplot-1.0.0/coveffectsplot/inst/shiny/server.R | 277 + coveffectsplot-1.0.0/coveffectsplot/inst/shiny/ui.R | 21 coveffectsplot-1.0.0/coveffectsplot/man/draw_key.Rd |only coveffectsplot-1.0.0/coveffectsplot/man/forest_plot.Rd | 20 coveffectsplot-1.0.0/coveffectsplot/vignettes/Exposure_Response_Example.Rmd | 15 coveffectsplot-1.0.0/coveffectsplot/vignettes/PKPD_Example.Rmd | 17 coveffectsplot-1.0.0/coveffectsplot/vignettes/PK_Example.Rmd | 27 coveffectsplot-1.0.0/coveffectsplot/vignettes/Pediatric_Cov_Sim.Rmd | 8 coveffectsplot-1.0.0/coveffectsplot/vignettes/introduction_to_coveffectsplot.Rmd |only coveffectsplot-1.0.0/coveffectsplot/vignettes/tutfigs |only 36 files changed, 2061 insertions(+), 2789 deletions(-)
More information about coveffectsplot at CRAN
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Title: Tool for Stability Indices Calculation
Description: Tools to calculate stability indices with parametric,
non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values,
genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype.
Function "table_stability" offers the summary table of all stability indices in this package.
Sample dataset in this package is from:
Casadebaig P, Zheng B, Chapman S et al. (2016) <doi: 10.1371/journal.pone.0146385>.
Indices used in this package are from:
Döring TF, Reckling M (2018) <doi: 10.1016/j.eja.2018.06.007>.
Eberhart SA, Russell WA (1966) <doi: 10.2135/cropsci1966.0011183X000600010011x>.
Eskridge KM (1990) <doi: 10.2135/cropsci1990.0011183X003000020025x>.
Finlay KW, Wilkinson GN (1963) <doi: 10.1071/AR9630742>.
Hanson WD (1970) Genotypic stability. <doi: 10.1007/BF00285245>.
Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>.
Nassar R, Hühn M (1987).
Pinthus MJ (1973) <doi: 10.1007/BF00021563>.
Römer T (1917).
Shukla GK (1972).
Wricke G (1962).
Author: Tien-Cheng Wang [aut, cre],
Tsu-Wei Chen [com]
Maintainer: Tien-Cheng Wang <wangtien@student.hu-berlin.de>
Diff between toolStability versions 0.1.0 dated 2021-12-22 and 0.1.1 dated 2022-01-12
toolStability-0.1.0/toolStability/inst/doc/REFERENCES.bib |only toolStability-0.1.1/toolStability/DESCRIPTION | 17 toolStability-0.1.1/toolStability/MD5 | 39 toolStability-0.1.1/toolStability/NEWS.md |only toolStability-0.1.1/toolStability/R/ecovalence.R | 2 toolStability-0.1.1/toolStability/R/environmental_variance.R | 2 toolStability-0.1.1/toolStability/R/genotypic_stability.R | 2 toolStability-0.1.1/toolStability/R/genotypic_superiority_measure.R | 2 toolStability-0.1.1/toolStability/README.md | 460 +++++----- toolStability-0.1.1/toolStability/build/partial.rdb |binary toolStability-0.1.1/toolStability/build/vignette.rds |binary toolStability-0.1.1/toolStability/inst/REFERENCES.bib | 10 toolStability-0.1.1/toolStability/inst/doc/toolStability.R |only toolStability-0.1.1/toolStability/inst/doc/toolStability.Rmd | 12 toolStability-0.1.1/toolStability/inst/doc/toolStability.pdf |binary toolStability-0.1.1/toolStability/man/ecovalence.Rd | 2 toolStability-0.1.1/toolStability/man/environmental_variance.Rd | 2 toolStability-0.1.1/toolStability/man/genotypic_stability.Rd | 2 toolStability-0.1.1/toolStability/man/genotypic_superiority_measure.Rd | 2 toolStability-0.1.1/toolStability/man/toolStability-package.Rd | 22 toolStability-0.1.1/toolStability/vignettes/REFERENCES.bib | 10 toolStability-0.1.1/toolStability/vignettes/toolStability.Rmd | 12 22 files changed, 312 insertions(+), 286 deletions(-)
Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Lai J.,Zou Y., Zhang J.,Peres-Neto P.(2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package.Methods in Ecology and Evolution,<DOI:10.1111/2041-210X.13800>.
Author: Jiangshan Lai,Pedro Peres-Neto,Kim Nimon
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>
Diff between rdacca.hp versions 1.0-4 dated 2021-12-06 and 1.0-5 dated 2022-01-12
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/rdacca.hp.r | 2 +- inst/CITATION | 16 ++++++++-------- man/rdacca.hp.Rd | 2 +- 5 files changed, 19 insertions(+), 19 deletions(-)
Title: Visualization using Graph Traversal
Description: Improving graphics by ameliorating order effects, using Eulerian tours
and Hamiltonian decompositions of graphs. References for the methods presented
here are C.B. Hurley and R.W. Oldford (2010) <doi:10.1198/jcgs.2010.09136> and
C.B. Hurley and R.W. Oldford (2011) <doi:10.1007/s00180-011-0229-5>.
Author: C.B. Hurley and R.W. Oldford
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between PairViz versions 1.3.4 dated 2020-10-05 and 1.3.5 dated 2022-01-12
DESCRIPTION | 17 MD5 | 17 README.md |only build/vignette.rds |binary inst/doc/MultipleComparisons.R | 2 inst/doc/MultipleComparisons.Rmd | 2 inst/doc/MultipleComparisons.html | 789 ++++++++++++++------------------------ inst/doc/PairVizIntroduction.html | 574 +++++++++------------------ inst/doc/pcp.html | 554 ++++++++------------------ vignettes/MultipleComparisons.Rmd | 2 10 files changed, 710 insertions(+), 1247 deletions(-)
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] (<https://orcid.org/0000-0003-1866-860X>),
Jonathan M. Mang [aut] (<https://orcid.org/0000-0003-0518-4710>),
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitätsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@uk-erlangen.de>
Diff between DQAstats versions 0.2.1 dated 2022-01-11 and 0.2.2 dated 2022-01-12
DQAstats-0.2.1/DQAstats/tests/testthat/output |only DQAstats-0.2.1/DQAstats/tests/testthat/test-lints.R |only DQAstats-0.2.2/DQAstats/DESCRIPTION | 8 DQAstats-0.2.2/DQAstats/MD5 | 24 DQAstats-0.2.2/DQAstats/tests/testthat/test-DQA.R | 13 DQAstats-0.2.2/DQAstats/tests/testthat/test-MDR.R | 192 +-- DQAstats-0.2.2/DQAstats/tests/testthat/test-dataloading.R | 328 ++--- DQAstats-0.2.2/DQAstats/tests/testthat/test-descriptive_results.R | 631 ++++------ DQAstats-0.2.2/DQAstats/tests/testthat/test-helper_vars.R | 294 ++-- DQAstats-0.2.2/DQAstats/tests/testthat/test-import.R | 212 +-- 10 files changed, 819 insertions(+), 883 deletions(-)
Title: R Bindings to 'hiredis'
Description: A 'hiredis' wrapper that includes support for
transactions, pipelining, blocking subscription, serialisation of
all keys and values, 'Redis' error handling with R errors.
Includes an automatically generated 'R6' interface to the full
'hiredis' API. Generated functions are faithful to the
'hiredis' documentation while attempting to match R's argument
semantics. Serialisation must be explicitly done by the user, but
both binary and text-mode serialisation is supported.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between redux versions 1.1.0 dated 2018-05-31 and 1.1.3 dated 2022-01-12
DESCRIPTION | 11 MD5 | 84 ++- NEWS.md | 4 R/config.R | 8 R/redis.R | 12 R/redis_api.R | 35 + README.md | 13 build/vignette.rds |binary configure | 31 - inst/doc/low_level.Rmd |only inst/doc/low_level.html |only inst/doc/redux.Rmd | 79 +-- inst/doc/redux.html | 628 ++++++++++++++++++++--------- man/from_redis_hash.Rd | 9 man/redis.Rd | 4 man/redis_config.Rd | 3 man/scan_apply.Rd | 11 man/storr_redis_api.Rd | 8 src/Makevars.ucrt |only src/Makevars.win | 4 src/connection.c | 30 + src/connection.c.gcov |only src/connection.gcda |only src/connection.gcno |only src/connection.h | 4 src/conversions.c | 1 src/conversions.c.gcov |only src/conversions.gcda |only src/conversions.gcno |only src/registration.c | 7 src/registration.c.gcov |only src/registration.gcda |only src/registration.gcno |only src/subscribe.c.gcov |only src/subscribe.gcda |only src/subscribe.gcno |only tests/testthat/helper-common.R | 6 tests/testthat/helper-publisher.R | 2 tests/testthat/test-config.R | 5 tests/testthat/test-connection-redux.R | 28 + tests/testthat/test-conversions.R | 2 tests/testthat/test-interface.R | 8 tests/testthat/test-redis-socket.R | 15 tests/testthat/test-zzz-commands-generic.R | 2 tests/testthat/test-zzz-commands-hash.R | 4 tests/testthat/test-zzz-commands-server.R | 6 tests/testthat/test-zzz-commands-string.R | 4 tests/testthat/test-zzz-subscribe.R | 15 tools/winlibs.R | 4 vignettes/low_level.Rmd |only vignettes/redux.Rmd | 79 +-- 51 files changed, 783 insertions(+), 383 deletions(-)
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapproj versions 1.2.7 dated 2020-02-03 and 1.2.8 dated 2022-01-12
DESCRIPTION | 8 +++---- MD5 | 8 +++---- R/mapproj.r | 59 +++++++++++++++++++++++++++--------------------------- man/mapproject.Rd | 4 +-- src/mapproject.c | 6 ++--- 5 files changed, 43 insertions(+), 42 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.0.7 dated 2021-10-25 and 0.0.8 dated 2022-01-12
DESCRIPTION | 8 - MD5 | 30 +++--- NAMESPACE | 1 NEWS.md | 4 R/grid-draw-utilities.R | 50 +++++++++- R/method-grid-draw.R | 14 +- R/scales.R | 30 +++--- R/utilities.R | 3 build/vignette.rds |binary inst/CITATION | 2 inst/doc/ggbreak.R | 3 inst/doc/ggbreak.Rmd | 19 +++ inst/doc/ggbreak.html | 235 +++++++++++++++++++++++++++++------------------- man/scale_break.Rd | 18 +++ man/scale_cut.Rd | 6 - vignettes/ggbreak.Rmd | 19 +++ 16 files changed, 303 insertions(+), 139 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression
model 'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel D. Sjoberg [aut] (<https://orcid.org/0000-0003-0862-2018>)
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.5.0 dated 2021-12-07 and 1.6.0 dated 2022-01-12
DESCRIPTION | 8 MD5 | 36 ++-- NAMESPACE | 2 NEWS.md | 20 ++ R/model_get_model_matrix.R | 7 R/model_get_xlevels.R | 4 R/select_utilities.R | 85 +++++++--- README.md | 189 +++++++++++----------- build/vignette.rds |binary inst/doc/tidy.R | 3 inst/doc/tidy.Rmd | 3 inst/doc/tidy.html | 257 +++++++++++++++---------------- man/dot-formula_list_to_named_list.Rd | 6 man/model_get_model_matrix.Rd | 5 man/model_get_xlevels.Rd | 3 tests/testthat/test-identify_variables.R | 29 +++ tests/testthat/test-select_helpers.R | 52 ++++++ tests/testthat/test-tidy_plus_plus.R | 19 ++ vignettes/tidy.Rmd | 3 19 files changed, 464 insertions(+), 267 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.2.4 dated 2021-12-14 and 1.2.5 dated 2022-01-12
DESCRIPTION | 10 +++--- MD5 | 22 +++++++------- NEWS.md | 4 ++ R/HCRs.R | 58 +++++++++++++++++++++++++++++---------- R/assess_SCA.R | 74 +++++++++++++++++++++++++++++++++----------------- R/assess_SCA_RWM.R | 15 ++++++++-- R/interim_MP.R | 22 +++----------- build/partial.rdb |binary inst/doc/SAMtool.html | 5 ++- man/HCR_ramp.Rd | 55 ++++++++++++++++++++++++++++++------- man/HCR_segment.Rd | 41 ++++++++++++++++++++++++--- man/SCA_RWM.Rd | 15 ++++++++-- 12 files changed, 228 insertions(+), 93 deletions(-)
Title: Inference and Prediction of ToxicoKinetic (TK) Models
Description: The MOSAICbioacc application is a turnkey package providing bioaccumulation
factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to
accumulation-depuration data. It is designed to fulfil the requirements
of regulators when examining applications for market authorization of active
substances. See Ratier et al. (2021) <doi:10.1101/2021.09.08.459421>.
Author: Virgile Baudrot [aut],
Sandrine Charles [aut],
Ophélia Gestin [ctb],
Mélina Kaag [aut],
Christelle Lopes [ctb],
Gauthier Multari [ctb],
Alain Pavé [ctb],
Aude Ratier [aut],
Aurélie Siberchicot [aut, cre]
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between rbioacc versions 1.0.2 dated 2021-09-15 and 1.1-0 dated 2022-01-12
rbioacc-1.0.2/rbioacc/man/plot.predictTK.Rd |only rbioacc-1.1-0/rbioacc/DESCRIPTION | 25 +-- rbioacc-1.1-0/rbioacc/MD5 | 64 ++++--- rbioacc-1.1-0/rbioacc/NAMESPACE | 5 rbioacc-1.1-0/rbioacc/R/fitTK.R | 2 rbioacc-1.1-0/rbioacc/R/plot_PP.R | 38 ++++ rbioacc-1.1-0/rbioacc/R/plot_fit.R | 52 +++--- rbioacc-1.1-0/rbioacc/R/plot_predict.R | 84 ++++++++++ rbioacc-1.1-0/rbioacc/R/predict_fit.R | 149 +++++++++++++++++- rbioacc-1.1-0/rbioacc/R/predict_manual.R | 1 rbioacc-1.1-0/rbioacc/R/rbioacc-package.R | 1 rbioacc-1.1-0/rbioacc/R/stanmodels.R | 3 rbioacc-1.1-0/rbioacc/R/zzz_internals.R | 85 ++++++++++ rbioacc-1.1-0/rbioacc/build/vignette.rds |binary rbioacc-1.1-0/rbioacc/inst/doc/MWE.Rmd | 2 rbioacc-1.1-0/rbioacc/inst/doc/MWE.html | 2 rbioacc-1.1-0/rbioacc/inst/doc/Tutorial.R | 5 rbioacc-1.1-0/rbioacc/inst/doc/Tutorial.Rmd | 5 rbioacc-1.1-0/rbioacc/inst/doc/Tutorial.html | 27 +-- rbioacc-1.1-0/rbioacc/inst/stan/TK.stan | 5 rbioacc-1.1-0/rbioacc/inst/stan/TK_predict.stan |only rbioacc-1.1-0/rbioacc/man/plot.fitTK.Rd | 5 rbioacc-1.1-0/rbioacc/man/plot_PP.Rd | 11 - rbioacc-1.1-0/rbioacc/man/plot_predict.Rd |only rbioacc-1.1-0/rbioacc/man/predict.Rd | 19 ++ rbioacc-1.1-0/rbioacc/man/replace_.Rd |only rbioacc-1.1-0/rbioacc/src/RcppExports.cpp | 2 rbioacc-1.1-0/rbioacc/src/stanExports_TK.h | 2 rbioacc-1.1-0/rbioacc/src/stanExports_TK_predict.cc |only rbioacc-1.1-0/rbioacc/src/stanExports_TK_predict.h |only rbioacc-1.1-0/rbioacc/tests/testthat/test-PP.R | 34 +++- rbioacc-1.1-0/rbioacc/tests/testthat/test-internal.R | 4 rbioacc-1.1-0/rbioacc/tests/testthat/test-modelData.R | 6 rbioacc-1.1-0/rbioacc/tests/testthat/test-predict.R | 62 +++++++ rbioacc-1.1-0/rbioacc/vignettes/MWE.Rmd | 2 rbioacc-1.1-0/rbioacc/vignettes/Tutorial.Rmd | 5 36 files changed, 599 insertions(+), 108 deletions(-)
More information about jab.adverse.reactions at CRAN
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More information about BASiNETEntropy at CRAN
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Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.9.6 dated 2020-02-05 and 1.15.0 dated 2022-01-12
DESCRIPTION | 11 MD5 | 98 +- NAMESPACE | 38 + NEWS | 22 R/AuxMethodforPPR.R | 35 R/IC.R | 626 +++++++++++++++-- R/NewClasses.R | 427 ++++++----- R/RcppExports.R | 80 +- R/adaBayes.R | 1400 +++++++++++++++++++++++---------------- R/ae.R |only R/changeFixedToConstant.R |only R/llag.R | 2 R/lm.jumptest.R |only R/ntv.R |only R/pz.test.R |only R/qmle.R | 920 +++++++++++++------------ R/qmleLevy.R | 587 ++++++++++++++++ R/sim.euler.R | 6 R/simBmllag.r |only R/simCP.R | 24 R/simulateForPpr.R | 8 R/spectralcov.R | 4 R/wllag.r |only build |only inst/CITATION | 2 man/IC.Rd | 165 ++-- man/LogSPX.Rd | 2 man/MWK151.Rd | 50 - man/adaBayes.Rd | 180 ++--- man/ae.Rd |only man/aeCharacteristic.Rd |only man/aeDensity.Rd |only man/aeExpectation.Rd |only man/aeKurtosis.Rd |only man/aeMarginal.Rd |only man/aeMean.Rd |only man/aeMoment.Rd |only man/aeSd.Rd |only man/aeSkewness.Rd |only man/asymptotic_term.Rd | 3 man/bns.test.Rd | 5 man/cce.factor.Rd | 12 man/lasso.Rd | 2 man/llag.Rd | 2 man/llag.test.Rd | 5 man/lm.jumptest.Rd |only man/mpv.Rd | 8 man/ntv.Rd |only man/pz.test.Rd |only man/qmle.Rd | 897 ++++++++++++------------ man/qmleLevy.Rd | 268 +++---- man/rng.Rd | 530 +++++++------- man/setPoisson.Rd | 3 man/simBmllag.Rd |only man/snr.Rd | 4 man/wllag.Rd |only man/yuima.ae-class.Rd |only man/yuima.qmleLevy.incr-class.Rd |only src/RcppExports.cpp | 228 +++++- src/ae.cpp |only src/euler.c | 22 src/rng.c | 48 - src/yuima_init.c | 122 ++- 63 files changed, 4374 insertions(+), 2472 deletions(-)
Title: Random-Effect Multiple QTL Mapping in Autopolyploids
Description: Performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. (2020) <doi:10.1534/genetics.120.303080>.
Author: Guilherme da Silva Pereira [aut]
(<https://orcid.org/0000-0002-7106-8630>),
Marcelo Mollinari [ctb] (<https://orcid.org/0000-0002-7001-8498>),
Gabriel de Siqueira Gesteira [ctb, cre]
(<https://orcid.org/0000-0002-4106-7346>),
Zhao-Bang Zeng [ctb] (<https://orcid.org/0000-0002-3115-1149>),
Long Qu [ctb] (R code for variance component tests using score
statistics in R/varComp.R),
Giovanny Covarrubias-Pazaran [ctb] (C code for fitting mixed models
with REML estimation in src/MNR.cpp)
Maintainer: Gabriel de Siqueira Gesteira <gdesiqu@ncsu.edu>
Diff between qtlpoly versions 0.2.2 dated 2021-11-10 and 0.2.3 dated 2022-01-12
DESCRIPTION | 14 ++++----- MD5 | 20 +++++++------- R/breeding_values.R | 2 - R/data.R | 2 - R/read_data.R | 4 +- README.md | 74 ++++++++++++++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary data/B2721.rda |binary data/maps4x.rda |binary man/B2721.Rd | 2 - man/read_data.Rd | 2 - 11 files changed, 87 insertions(+), 33 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-08 1.0.2
2019-05-21 1.0.1
2018-12-16 1.0.0
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2021,
<doi:10.31234/osf.io/kvsp7>; Maier, Bartoš & Wagenmakers, in press,
<doi:10.31234/osf.io/u4cns>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: František Bartoš [aut, cre] (<https://orcid.org/0000-0002-0018-5573>),
Maximilian Maier [aut] (<https://orcid.org/0000-0002-9873-6096>),
Eric-Jan Wagenmakers [ths] (<https://orcid.org/0000-0003-1596-1034>),
Joris Goosen [ctb],
Matthew Denwood [cph] (Original copyright holder of some modified code
where indicated.),
Martyn Plummer [cph] (Original copyright holder of some modified code
where indicated.)
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between RoBMA versions 2.1.1 dated 2021-11-03 and 2.1.2 dated 2022-01-12
DESCRIPTION | 6 ++--- MD5 | 33 +++++++++++++++--------------- NEWS.md | 5 ++++ R/RoBMA-package.R | 2 - R/utilities.R | 45 ++++++++++++++++++++++++++++++++++++++++++ R/zzz.R | 4 ++- README.md | 35 +++++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/CustomEnsembles.Rmd | 4 +-- inst/doc/CustomEnsembles.html | 35 +++++++++++++++----------------- inst/doc/MedicineBMA.Rmd | 4 +-- inst/doc/MedicineBMA.html | 8 +++---- inst/doc/ReproducingBMA.html | 4 +-- man/RoBMA-package.Rd | 2 - src/Makevars.ucrt |only vignettes/CustomEnsembles.Rmd | 4 +-- vignettes/MedicineBMA.Rmd | 4 +-- 18 files changed, 125 insertions(+), 70 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-07 1.1.2
2017-01-03 1.1.1
2016-12-12 1.1.0