Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 0.4.0 dated 2022-09-30 and 0.5.0 dated 2023-02-02
DESCRIPTION | 8 MD5 | 238 ++++----- NAMESPACE | 1 NEWS.md | 49 + R/compilation.R | 87 ++- R/geometry.R | 24 R/interface.R | 193 +++++-- R/print.R | 2 R/tree-sequences.R | 93 ++- R/utils.R | 21 R/visualization.R | 29 - R/zzz.R | 49 + README.md | 23 build/vignette.rds |binary inst/doc/vignette-00-installation.Rmd | 10 inst/doc/vignette-00-installation.html | 41 - inst/doc/vignette-01-tutorial.R | 21 inst/doc/vignette-01-tutorial.Rmd | 39 - inst/doc/vignette-01-tutorial.html | 293 ++++++----- inst/doc/vignette-02-grid-model.R | 87 +++ inst/doc/vignette-02-grid-model.Rmd | 112 ++++ inst/doc/vignette-02-grid-model.html | 397 +++++++++++----- inst/doc/vignette-03-interactions.R | 4 inst/doc/vignette-03-interactions.Rmd | 4 inst/doc/vignette-03-interactions.html | 80 +-- inst/doc/vignette-04-nonspatial-models.R | 6 inst/doc/vignette-04-nonspatial-models.Rmd | 6 inst/doc/vignette-04-nonspatial-models.html | 66 +- inst/doc/vignette-05-tree-sequences.R | 13 inst/doc/vignette-05-tree-sequences.Rmd | 22 inst/doc/vignette-05-tree-sequences.html | 524 ++++++++++----------- inst/doc/vignette-06-locations.R | 131 +++-- inst/doc/vignette-06-locations.Rmd | 151 +++--- inst/doc/vignette-06-locations.html | 544 ++++++++++------------ inst/doc/vignette-07-backends.R | 8 inst/doc/vignette-07-backends.Rmd | 8 inst/doc/vignette-07-backends.html | 18 inst/doc/vignette-08-nonslendr-tskit.R | 4 inst/doc/vignette-08-nonslendr-tskit.Rmd | 4 inst/doc/vignette-08-nonslendr-tskit.html | 42 - inst/doc/vignette-09-paper.R | 205 ++++++-- inst/doc/vignette-09-paper.Rmd | 256 +++++++--- inst/doc/vignette-09-paper.html | 321 ++++++------ inst/extdata/models/introgression.trees |binary inst/extdata/models/introgression/checksums.tsv | 8 inst/extdata/models/introgression/populations.tsv | 2 inst/extdata/models/introgression/ranges.rds |binary inst/extdata/models/introgression/script.py | 68 +- inst/extdata/models/introgression/script.slim | 24 inst/extdata/models/msprime.trees |binary inst/scripts/__pycache__/script.cpython-311.pyc |only inst/scripts/__pycache__/script.cpython-38.pyc |binary inst/scripts/script.py | 56 +- inst/scripts/script.slim | 22 man/check_env.Rd | 5 man/compile_model.Rd | 2 man/init_env.Rd |only man/msprime.Rd | 2 man/plot_model.Rd | 2 man/population.Rd | 6 man/read_model.Rd | 2 man/schedule_sampling.Rd | 2 man/slim.Rd | 2 man/ts_afs.Rd | 2 man/ts_ancestors.Rd | 2 man/ts_coalesced.Rd | 2 man/ts_descendants.Rd | 2 man/ts_divergence.Rd | 2 man/ts_diversity.Rd | 2 man/ts_draw.Rd | 2 man/ts_edges.Rd | 2 man/ts_f4ratio.Rd | 2 man/ts_fst.Rd | 2 man/ts_genotypes.Rd | 2 man/ts_load.Rd | 2 man/ts_metadata.Rd | 2 man/ts_mutate.Rd | 2 man/ts_nodes.Rd | 2 man/ts_phylo.Rd | 2 man/ts_recapitate.Rd | 2 man/ts_samples.Rd | 2 man/ts_save.Rd | 2 man/ts_segregating.Rd | 2 man/ts_simplify.Rd | 2 man/ts_tajima.Rd | 2 man/ts_tree.Rd | 2 tests/testthat/map.rds |binary tests/testthat/test-compilation.R | 51 +- tests/testthat/test-coordinate-conversions.R | 2 tests/testthat/test-geneflow.R | 12 tests/testthat/test-geometrical-operations.R | 10 tests/testthat/test-interaction-changes.R | 2 tests/testthat/test-manual-ts.R | 2 tests/testthat/test-msprime-geneflow.R | 4 tests/testthat/test-msprime-metadata.R | 2 tests/testthat/test-msprime.R | 4 tests/testthat/test-nonserialized.R | 4 tests/testthat/test-pure-msprime-vs-slendr.R | 4 tests/testthat/test-pure-slim-vs-slendr.R | 4 tests/testthat/test-resizes-locked.R | 2 tests/testthat/test-resizes.R | 2 tests/testthat/test-runners.R | 4 tests/testthat/test-sampling.R | 4 tests/testthat/test-serialization.R | 4 tests/testthat/test-simulation-runs.R | 2 tests/testthat/test-time-direction.R | 6 tests/testthat/test-trees.R | 2 tests/testthat/test-ts-ancestors-descendants.R | 2 tests/testthat/test-ts-pure-nonspatial.R | 4 tests/testthat/test-ts-pure-spatial.R | 2 tests/testthat/test-ts.R | 2 vignettes/vignette-00-installation.Rmd | 10 vignettes/vignette-01-tutorial.Rmd | 39 - vignettes/vignette-02-grid-model.Rmd | 112 ++++ vignettes/vignette-03-interactions.Rmd | 4 vignettes/vignette-04-nonspatial-models.Rmd | 6 vignettes/vignette-05-tree-sequences.Rmd | 22 vignettes/vignette-06-locations.Rmd | 151 +++--- vignettes/vignette-07-backends.Rmd | 8 vignettes/vignette-08-nonslendr-tskit.Rmd | 4 vignettes/vignette-09-paper.Rmd | 256 +++++++--- 121 files changed, 3206 insertions(+), 2026 deletions(-)
Title: R for High-Dimensional Omic Data
Description: Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. 'romic' takes advantage of these transformations to create interactive 'shiny' apps for exploratory data analysis such as an interactive heatmap.
Author: Sean Hackett [aut, cre] ,
Calico Life Sciences LLC [cph, fnd]
Maintainer: Sean Hackett <sean@calicolabs.com>
Diff between romic versions 1.0.0 dated 2021-07-20 and 1.1.1 dated 2023-02-02
romic-1.0.0/romic/R/app_scatter.R |only romic-1.0.0/romic/man/add_pca_loadings.Rd |only romic-1.0.0/romic/man/app_scatter.Rd |only romic-1.1.1/romic/DESCRIPTION | 13 romic-1.1.1/romic/MD5 | 149 romic-1.1.1/romic/NAMESPACE | 5 romic-1.1.1/romic/NEWS.md |only romic-1.1.1/romic/R/app_heatmap.R | 363 +- romic-1.1.1/romic/R/app_pcs.R |only romic-1.1.1/romic/R/data.R | 1 romic-1.1.1/romic/R/data_classes.R | 132 romic-1.1.1/romic/R/design.R | 1 romic-1.1.1/romic/R/dim_reduction.R | 201 + romic-1.1.1/romic/R/export.R | 68 romic-1.1.1/romic/R/filters.R | 14 romic-1.1.1/romic/R/module_filter.R | 1 romic-1.1.1/romic/R/module_ggbiv.R | 125 romic-1.1.1/romic/R/module_ggplot.R | 14 romic-1.1.1/romic/R/module_gguniv.R | 24 romic-1.1.1/romic/R/module_lasso.R | 7 romic-1.1.1/romic/R/module_organize.R | 22 romic-1.1.1/romic/R/module_plotsaver.R | 84 romic-1.1.1/romic/R/module_sort.R | 2 romic-1.1.1/romic/R/mutates.R | 88 romic-1.1.1/romic/R/romic.R | 4 romic-1.1.1/romic/R/utils.R | 42 romic-1.1.1/romic/README.md | 19 romic-1.1.1/romic/build/vignette.rds |binary romic-1.1.1/romic/inst/doc/romic.R | 14 romic-1.1.1/romic/inst/doc/romic.Rmd | 14 romic-1.1.1/romic/inst/doc/romic.html | 1561 +++++++++- romic-1.1.1/romic/man/add_pcs.Rd |only romic-1.1.1/romic/man/app_heatmap.Rd | 6 romic-1.1.1/romic/man/app_pcs.Rd |only romic-1.1.1/romic/man/center_tomic.Rd | 1 romic-1.1.1/romic/man/check_tidy_omic.Rd | 3 romic-1.1.1/romic/man/check_tomic.Rd | 1 romic-1.1.1/romic/man/check_triple_omic.Rd | 3 romic-1.1.1/romic/man/convert_wide_to_tidy_omic.Rd | 1 romic-1.1.1/romic/man/create_tidy_omic.Rd | 1 romic-1.1.1/romic/man/create_triple_omic.Rd | 1 romic-1.1.1/romic/man/downsample_heatmap.Rd |only romic-1.1.1/romic/man/export_tomic_as_tidy.Rd | 2 romic-1.1.1/romic/man/export_tomic_as_triple.Rd | 4 romic-1.1.1/romic/man/export_tomic_as_wide.Rd | 4 romic-1.1.1/romic/man/filter_tomic.Rd | 1 romic-1.1.1/romic/man/format_names_for_plotting.Rd | 6 romic-1.1.1/romic/man/get_design_tbl.Rd | 1 romic-1.1.1/romic/man/ggplotOutput.Rd | 10 romic-1.1.1/romic/man/hclust_order.Rd | 3 romic-1.1.1/romic/man/impute_missing_values.Rd |only romic-1.1.1/romic/man/lassoServer.Rd | 2 romic-1.1.1/romic/man/plot_bivariate.Rd | 21 romic-1.1.1/romic/man/plot_heatmap.Rd | 10 romic-1.1.1/romic/man/plot_univariate.Rd | 3 romic-1.1.1/romic/man/plotsaverInput.Rd | 8 romic-1.1.1/romic/man/plotsaverServer.Rd | 5 romic-1.1.1/romic/man/shiny_filter_test.Rd | 1 romic-1.1.1/romic/man/shiny_ggbiv_test.Rd | 3 romic-1.1.1/romic/man/shiny_ggplot_test.Rd | 3 romic-1.1.1/romic/man/shiny_gguniv_test.Rd | 3 romic-1.1.1/romic/man/shiny_lasso_test.Rd | 1 romic-1.1.1/romic/man/shiny_lasso_test_reactval.Rd | 1 romic-1.1.1/romic/man/shiny_organize_test.Rd | 1 romic-1.1.1/romic/man/shiny_plotsaver_test.Rd | 1 romic-1.1.1/romic/man/shiny_sort_test.Rd | 1 romic-1.1.1/romic/man/sort_tomic.Rd | 1 romic-1.1.1/romic/man/tidy_to_triple.Rd | 1 romic-1.1.1/romic/man/tomic_sort_status.Rd | 1 romic-1.1.1/romic/man/tomic_to.Rd | 1 romic-1.1.1/romic/man/triple_to_tidy.Rd | 1 romic-1.1.1/romic/man/update_tidy_omic.Rd | 1 romic-1.1.1/romic/man/update_tomic.Rd | 1 romic-1.1.1/romic/man/var_partial_match.Rd |only romic-1.1.1/romic/tests/testthat/test-coerce_to_classes.R |only romic-1.1.1/romic/tests/testthat/test-dim_reduction.R | 30 romic-1.1.1/romic/tests/testthat/test-downsampling.R |only romic-1.1.1/romic/tests/testthat/test-factor_pks.R |only romic-1.1.1/romic/tests/testthat/test-hclust.R | 17 romic-1.1.1/romic/tests/testthat/test-import_export.R |only romic-1.1.1/romic/tests/testthat/test-test-variable_partial_string_matching.R |only romic-1.1.1/romic/tests/testthat/test-triple_omic.R | 4 romic-1.1.1/romic/vignettes/romic.Rmd | 14 83 files changed, 2458 insertions(+), 694 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20230202.1600 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.1-1 dated 2022-05-19 and 1.2-0 dated 2023-02-02
DESCRIPTION | 12 - MD5 | 86 +++++---- NAMESPACE | 8 NEWS.md | 22 ++ R/addDictionaryEntry.R | 1 R/countAnnotations.R | 6 R/countMatchingAnnotations.R |only R/formatTranscript.R |only R/getAnnotations.R | 6 R/getFragmentAnnotations.R |only R/getFragments.R | 30 ++- R/getMatchAlignments.R | 2 R/getMatchLabels.R | 2 R/getMatches.R | 165 +++++++++++------- R/getMatchingAnnotations.R |only R/getMedia.R | 92 +++++++--- R/getMediaUrl.R |only R/getTranscriptIds.R | 6 R/getTranscriptIdsInCorpus.R | 6 R/getTranscriptIdsWithParticipant.R | 6 R/nzilbb.labbcat.R | 4 R/praatScriptIntensity.R | 4 R/praatScriptPitch.R | 5 build/partial.rdb |binary man/addDictionaryEntry.Rd | 2 man/countAnnotations.Rd | 6 man/countMatchingAnnotations.Rd |only man/formatTranscript.Rd |only man/getAnnotations.Rd | 5 man/getFragmentAnnotations.Rd |only man/getFragments.Rd | 5 man/getMatches.Rd | 118 ++++++++---- man/getMatchingAnnotations.Rd |only man/getMedia.Rd | 35 ++- man/getMediaUrl.Rd |only man/nzilbb.labbcat.Rd | 2 man/praatScriptIntensity.Rd | 4 man/praatScriptPitch.Rd | 5 man/removeDictionaryEntry.Rd | 2 tests/testthat/test-countAnnotations.R | 12 + tests/testthat/test-countMatchingAnnotations.R |only tests/testthat/test-formatTranscript.R |only tests/testthat/test-getAnnotations.R | 19 +- tests/testthat/test-getFragmentAnnotations.R |only tests/testthat/test-getMatchAlignments.R | 14 - tests/testthat/test-getMatchLabels.R | 8 tests/testthat/test-getMatches.R | 14 + tests/testthat/test-getMatchingAnnotations.R |only tests/testthat/test-getMedia.R | 23 ++ tests/testthat/test-getTranscriptIdsInCorpus.R | 8 tests/testthat/test-getTranscriptIdsWithParticipant.R | 8 51 files changed, 525 insertions(+), 228 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre],
Krisztian Sebestyen [aut],
Han Sunwoo [aut],
Jason Becker [ctb],
Bendix Carstensen [ctb],
Daryl Morris [ctb],
Josh Pasek [ctb],
Dennis Chao [ctb],
Andri Signorell [ctb],
Sue Li [ctb],
Jonathan Bartlett [ctb],
Christophe Dutang [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between kyotil versions 2022.12-20 dated 2022-12-20 and 2023.2-2 dated 2023-02-02
ChangeLog | 10 ++++++---- DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/CITATION | 4 +--- inst/doc/kyotil-vignette.pdf |binary man/predictCompetingRisk2.Rd | 4 ++-- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between imager versions 0.42.16 dated 2022-12-19 and 0.42.18 dated 2023-02-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ inst/doc/gettingstarted.html | 6 +++--- inst/doc/pixsets.R | 12 ++++++------ inst/doc/pixsets.Rmd | 12 ++++++------ inst/doc/pixsets.html | 16 ++++++++-------- vignettes/pixsets.Rmd | 12 ++++++------ 7 files changed, 40 insertions(+), 40 deletions(-)
Title: 'Shiny' Extension of 'video.js'
Description: Video interactivity within 'shiny' applications using 'video.js'. Enables
the status of the video to be sent from the UI to the server, and allows events
such as playing and pausing the video to be triggered from the server.
Author: Ashley Baldry [aut, cre],
Steve Heffernan [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Diff between video versions 0.1.0 dated 2022-07-21 and 0.1.1 dated 2023-02-02
video-0.1.0/video/R/data.R |only video-0.1.0/video/man/video_formats.Rd |only video-0.1.1/video/DESCRIPTION | 10 +- video-0.1.1/video/MD5 | 16 +-- video-0.1.1/video/NEWS.md | 6 + video-0.1.1/video/R/server-side.R | 2 video-0.1.1/video/R/sysdata.rda |binary video-0.1.1/video/build/vignette.rds |binary video-0.1.1/video/inst/doc/video.html | 124 +++++++++++++++-------------- video-0.1.1/video/man/video-server.Rd | 140 ++++++++++++++++----------------- 10 files changed, 154 insertions(+), 144 deletions(-)
Title: 'Apple App Store' and 'iTunes' Data Extraction
Description: Using 'Apple App Store' <https://www.apple.com/app-store/> web scraping and 'iTunes' API
<https://performance-partners.apple.com/search-api>
to extract content information, app ratings and reviews.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Diff between appler versions 0.1.4 dated 2022-10-06 and 0.2.0 dated 2023-02-02
DESCRIPTION | 22 ++-- MD5 | 42 +++++--- NAMESPACE | 14 +- NEWS.md | 9 + R/data.R | 128 ++++++++++++++------------ R/data_internal.R |only R/info.R | 7 + R/ratings.R | 16 ++- R/reviews.R | 103 ++++++++++++++------- R/top.R | 31 ++++-- README.md | 197 +++++++++++++---------------------------- build |only data |only inst/doc |only inst/scripts |only man/apple_apps.Rd |only man/figures |only man/get_apple_chart_postion.Rd | 27 ++++- man/get_apple_rating_split.Rd | 13 ++ man/get_apple_reviews.Rd | 53 +++++++++-- man/itunes_artists.Rd |only man/lookup_apple.Rd | 5 - man/search_apple.Rd | 2 tests/testthat/test-review.R | 49 +++++++--- vignettes |only 25 files changed, 416 insertions(+), 302 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>
Diff between gausscov versions 1.0.1 dated 2023-01-17 and 1.0.2 dated 2023-02-02
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/f1st.R | 2 +- R/f3st.R | 17 ++++++++++------- data/abcq.rda |binary data/boston.rda |binary data/leukemia.rda |binary data/mel_temp.rda |binary data/redwine.rda |binary data/snspt.rda |binary 10 files changed, 24 insertions(+), 21 deletions(-)
Title: Stable Iterative Variable Selection
Description: An iterative feature selection method (manuscript submitted) that
internally utilizes various Machine Learning methods that have embedded
feature reduction in order to shrink down the feature space into a small
and yet robust set.
Author: Mehrad Mahmoudian [aut, cre] ,
Mikko Venaelaeinen [aut, rev] ,
Riku Klen [aut, ths] ,
Laura Elo [aut, ths, fnd]
Maintainer: Mehrad Mahmoudian <mehrad.mahmoudian@utu.fi>
Diff between sivs versions 0.2.5 dated 2021-07-20 and 0.2.6 dated 2023-02-02
DESCRIPTION | 12 MD5 | 12 NEWS.md | 8 R/plot.sivs.R | 9 R/sivs.R | 97 ++++-- build/vignette.rds |binary inst/doc/vignette_simple_usage.html | 523 ++++++++++++++++++++---------------- 7 files changed, 376 insertions(+), 285 deletions(-)
Title: Setup and connect to 'OpenTripPlanner'
Description: Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>.
OTP is an open source platform for multi-modal and multi-agency
journey planning written in 'Java'. The package allows you to manage a local version or
connect to remote OTP server to find walking, cycling, driving, or transit routes.
This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Author: Malcolm Morgan [aut, cre] ,
Marcus Young [aut] ,
Robin Lovelace [aut] ,
Layik Hama [ctb]
Maintainer: Malcolm Morgan <m.morgan1@leeds.ac.uk>
Diff between opentripplanner versions 0.5 dated 2023-01-06 and 0.5.1 dated 2023-02-02
opentripplanner-0.5.1/opentripplanner/DESCRIPTION | 10 opentripplanner-0.5.1/opentripplanner/MD5 | 23 - opentripplanner-0.5.1/opentripplanner/NEWS.md | 6 opentripplanner-0.5.1/opentripplanner/R/otp-plan.R | 2 opentripplanner-0.5.1/opentripplanner/build/vignette.rds |binary opentripplanner-0.5.1/opentripplanner/inst/CITATION | 7 opentripplanner-0.5.1/opentripplanner/inst/doc/Analyst.html | 124 +++++---- opentripplanner-0.5.1/opentripplanner/inst/doc/OTPv2.html | 124 +++++---- opentripplanner-0.5.1/opentripplanner/inst/doc/advanced_features.html | 128 +++++----- opentripplanner-0.5.1/opentripplanner/inst/doc/known_issues.html | 18 - opentripplanner-0.5.1/opentripplanner/inst/doc/opentripplanner.html | 128 +++++----- opentripplanner-0.5.1/opentripplanner/inst/doc/prerequisites.html | 18 - opentripplanner-0.5/opentripplanner/vignettes/centroids.gpkg |only 13 files changed, 308 insertions(+), 280 deletions(-)
More information about opentripplanner at CRAN
Permanent link
Title: A Metabolomics Analysis Tool for Intuitive Figures and
Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>
Diff between omu versions 1.0.7 dated 2022-08-27 and 1.0.9 dated 2023-02-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/PCA_plot.R | 5 ++++- R/check_zeros.R | 3 ++- R/omu_summary.R | 2 ++ inst/CITATION | 4 +--- inst/doc/Omu_vignette.html | 22 +++++++++++----------- 7 files changed, 29 insertions(+), 25 deletions(-)
Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in 'mrgsolve', typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format. The performance of the package was described by Le Louedec et al (2021) <doi:10.1002/psp4.12689>.
Author: Felicien Le Louedec [aut, cre]
,
Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <felicienlelouedec@proton.me>
Diff between mapbayr versions 0.8.0 dated 2022-09-29 and 0.9.0 dated 2023-02-02
mapbayr-0.8.0/mapbayr/R/mrgmod.R |only mapbayr-0.8.0/mapbayr/tests/testthat/test-mbrest.R |only mapbayr-0.9.0/mapbayr/DESCRIPTION | 14 mapbayr-0.9.0/mapbayr/MD5 | 101 - mapbayr-0.9.0/mapbayr/NAMESPACE | 16 mapbayr-0.9.0/mapbayr/NEWS.md | 438 +++-- mapbayr-0.9.0/mapbayr/R/data_helpers.R |only mapbayr-0.9.0/mapbayr/R/deprecations.R |only mapbayr-0.9.0/mapbayr/R/eta.R | 48 mapbayr-0.9.0/mapbayr/R/get.R | 553 +++--- mapbayr-0.9.0/mapbayr/R/mapbayest.R | 26 mapbayr-0.9.0/mapbayr/R/mapbayest_check_and_preprocess.R | 817 +++++----- mapbayr-0.9.0/mapbayr/R/mapbayest_ofv_computation.R | 20 mapbayr-0.9.0/mapbayr/R/mapbayest_optimization.R | 13 mapbayr-0.9.0/mapbayr/R/mapbayest_postprocess.R | 185 +- mapbayr-0.9.0/mapbayr/R/mapbayests.R | 777 +++++---- mapbayr-0.9.0/mapbayr/R/use_posterior.R | 10 mapbayr-0.9.0/mapbayr/R/vs_nonmem.R | 358 ++-- mapbayr-0.9.0/mapbayr/R/zzz_utils.R | 139 - mapbayr-0.9.0/mapbayr/README.md | 207 +- mapbayr-0.9.0/mapbayr/inst/WORDLIST | 154 - mapbayr-0.9.0/mapbayr/inst/run20eta.phi |only mapbayr-0.9.0/mapbayr/man/add_covariates.Rd |only mapbayr-0.9.0/mapbayr/man/adm_rows.Rd |only mapbayr-0.9.0/mapbayr/man/compute_ofv.Rd | 7 mapbayr-0.9.0/mapbayr/man/data_helpers.Rd | 86 - mapbayr-0.9.0/mapbayr/man/deprecations.Rd |only mapbayr-0.9.0/mapbayr/man/filter.mrgmod.Rd |only mapbayr-0.9.0/mapbayr/man/get_x.Rd | 3 mapbayr-0.9.0/mapbayr/man/hist.mapbayests.Rd | 16 mapbayr-0.9.0/mapbayr/man/mapbayest.Rd | 17 mapbayr-0.9.0/mapbayr/man/obs_rows.Rd |only mapbayr-0.9.0/mapbayr/man/parse_datehour.Rd |only mapbayr-0.9.0/mapbayr/man/preprocess.ofv.Rd | 7 mapbayr-0.9.0/mapbayr/man/preprocess.optim.Rd | 3 mapbayr-0.9.0/mapbayr/man/reexports.Rd |only mapbayr-0.9.0/mapbayr/tests/testthat/test-add_covariates.R | 56 mapbayr-0.9.0/mapbayr/tests/testthat/test-adm_lines.R | 110 - mapbayr-0.9.0/mapbayr/tests/testthat/test-blq.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-check_mapbayr_data.R | 59 mapbayr-0.9.0/mapbayr/tests/testthat/test-check_mapbayr_model.R | 6 mapbayr-0.9.0/mapbayr/tests/testthat/test-check_mapbayr_modeldata.R | 112 - mapbayr-0.9.0/mapbayr/tests/testthat/test-compute_ofv.R | 24 mapbayr-0.9.0/mapbayr/tests/testthat/test-data_helpers.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-deprecations.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-eta.R | 15 mapbayr-0.9.0/mapbayr/tests/testthat/test-fill_eta.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-get_data.R | 9 mapbayr-0.9.0/mapbayr/tests/testthat/test-get_phi.R | 10 mapbayr-0.9.0/mapbayr/tests/testthat/test-hist.R | 83 - mapbayr-0.9.0/mapbayr/tests/testthat/test-newini2.R | 3 mapbayr-0.9.0/mapbayr/tests/testthat/test-obs_lines.R | 106 + mapbayr-0.9.0/mapbayr/tests/testthat/test-parse_datehour.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-preprocess.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-preprocess.optim.R | 6 mapbayr-0.9.0/mapbayr/tests/testthat/test-progress.R | 38 mapbayr-0.9.0/mapbayr/tests/testthat/test-read_mrgsolve_model.R | 3 mapbayr-0.9.0/mapbayr/tests/testthat/test-reset-conditions.R | 16 mapbayr-0.9.0/mapbayr/tests/testthat/test-select_eta.R |only mapbayr-0.9.0/mapbayr/tests/testthat/test-use_posterior.R | 10 mapbayr-0.9.0/mapbayr/tests/testthat/test-vs_nonmem.R | 21 61 files changed, 2683 insertions(+), 2019 deletions(-)
Title: Simple Tools for Examining and Cleaning Dirty Data
Description: The main janitor functions can: perfectly format data.frame column
names; provide quick counts of variable combinations (i.e., frequency
tables and crosstabs); and explore duplicate records. Other janitor functions
nicely format the tabulation results. These tabulate-and-report functions
approximate popular features of SPSS and Microsoft Excel. This package
follows the principles of the "tidyverse" and works well with the pipe function
%>%. janitor was built with beginning-to-intermediate R users in mind and is
optimized for user-friendliness.
Author: Sam Firke [aut, cre],
Bill Denney [ctb],
Chris Haid [ctb],
Ryan Knight [ctb],
Malte Grosser [ctb],
Jonathan Zadra [ctb]
Maintainer: Sam Firke <samuel.firke@gmail.com>
Diff between janitor versions 2.1.0 dated 2021-01-04 and 2.2.0 dated 2023-02-02
janitor-2.1.0/janitor/tests/testthat/test-adorn_totals.R |only janitor-2.2.0/janitor/DESCRIPTION | 24 janitor-2.2.0/janitor/MD5 | 120 + janitor-2.2.0/janitor/NAMESPACE | 13 janitor-2.2.0/janitor/NEWS.md | 75 + janitor-2.2.0/janitor/R/adorn_ns.R | 34 janitor-2.2.0/janitor/R/adorn_pct_formatting.R | 8 janitor-2.2.0/janitor/R/adorn_percentages.R | 8 janitor-2.2.0/janitor/R/adorn_totals.R | 13 janitor-2.2.0/janitor/R/as_and_untabyl.R | 26 janitor-2.2.0/janitor/R/clean_names.R | 76 + janitor-2.2.0/janitor/R/convert_to_date.R | 2 janitor-2.2.0/janitor/R/excel_dates.R | 41 janitor-2.2.0/janitor/R/get_dupes.R | 2 janitor-2.2.0/janitor/R/get_one_to_one.R |only janitor-2.2.0/janitor/R/make_clean_names.R | 105 + janitor-2.2.0/janitor/R/remove_empties.R | 43 janitor-2.2.0/janitor/R/row_to_names.R | 115 + janitor-2.2.0/janitor/R/sas_dates.R |only janitor-2.2.0/janitor/R/single_value.R |only janitor-2.2.0/janitor/R/tabyl.R | 82 - janitor-2.2.0/janitor/README.md | 145 +- janitor-2.2.0/janitor/build/vignette.rds |binary janitor-2.2.0/janitor/inst/doc/janitor.R | 19 janitor-2.2.0/janitor/inst/doc/janitor.Rmd | 42 janitor-2.2.0/janitor/inst/doc/janitor.html | 551 +++++---- janitor-2.2.0/janitor/inst/doc/tabyls.html | 606 +++++----- janitor-2.2.0/janitor/man/adorn_ns.Rd | 30 janitor-2.2.0/janitor/man/adorn_pct_formatting.Rd | 3 janitor-2.2.0/janitor/man/clean_names.Rd | 42 janitor-2.2.0/janitor/man/convert_to_date.Rd | 9 janitor-2.2.0/janitor/man/describe_class.Rd | 6 janitor-2.2.0/janitor/man/excel_numeric_to_date.Rd | 5 janitor-2.2.0/janitor/man/find_header.Rd |only janitor-2.2.0/janitor/man/get_one_to_one.Rd |only janitor-2.2.0/janitor/man/make_clean_names.Rd | 4 janitor-2.2.0/janitor/man/mu_to_u.Rd |only janitor-2.2.0/janitor/man/remove_empty.Rd | 16 janitor-2.2.0/janitor/man/row_to_names.Rd | 27 janitor-2.2.0/janitor/man/sas_numeric_to_date.Rd |only janitor-2.2.0/janitor/man/single_value.Rd |only janitor-2.2.0/janitor/tests/testthat.R | 8 janitor-2.2.0/janitor/tests/testthat/test-adorn-ns.R | 73 - janitor-2.2.0/janitor/tests/testthat/test-adorn-pct-formatting.R | 36 janitor-2.2.0/janitor/tests/testthat/test-adorn-percentages.R | 48 janitor-2.2.0/janitor/tests/testthat/test-adorn-rounding.R | 29 janitor-2.2.0/janitor/tests/testthat/test-adorn-title.R | 34 janitor-2.2.0/janitor/tests/testthat/test-adorn-totals.R | 279 +++- janitor-2.2.0/janitor/tests/testthat/test-clean-names.R | 294 +++- janitor-2.2.0/janitor/tests/testthat/test-compare_df_cols.R | 5 janitor-2.2.0/janitor/tests/testthat/test-convert_to_date.R | 13 janitor-2.2.0/janitor/tests/testthat/test-date-conversion.R | 177 ++ janitor-2.2.0/janitor/tests/testthat/test-get-dupes.R | 90 + janitor-2.2.0/janitor/tests/testthat/test-get-level-groups.R | 4 janitor-2.2.0/janitor/tests/testthat/test-get_one_to_one.R |only janitor-2.2.0/janitor/tests/testthat/test-remove-empties.R | 147 +- janitor-2.2.0/janitor/tests/testthat/test-round_to_fraction.R | 4 janitor-2.2.0/janitor/tests/testthat/test-row-to-names.R | 159 ++ janitor-2.2.0/janitor/tests/testthat/test-sas_dates.R |only janitor-2.2.0/janitor/tests/testthat/test-signif_half_up.R | 4 janitor-2.2.0/janitor/tests/testthat/test-single_value.R |only janitor-2.2.0/janitor/tests/testthat/test-statistical-tests.R | 7 janitor-2.2.0/janitor/tests/testthat/test-tabyl-classifiers.R | 43 janitor-2.2.0/janitor/tests/testthat/test-tabyl.R | 107 + janitor-2.2.0/janitor/tests/testthat/test-top-levels.R | 22 janitor-2.2.0/janitor/tests/testthat/test-utilities.R | 7 janitor-2.2.0/janitor/vignettes/janitor.Rmd | 42 67 files changed, 2715 insertions(+), 1209 deletions(-)
Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs
Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre] ,
Henrik Singmann [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between gratia versions 0.7.3 dated 2022-05-10 and 0.8.1 dated 2023-02-02
gratia-0.7.3/gratia/R/smooth-differences.R |only gratia-0.7.3/gratia/man/seq_min_max.Rd |only gratia-0.8.1/gratia/DESCRIPTION | 21 gratia-0.8.1/gratia/LICENSE | 2 gratia-0.8.1/gratia/MD5 | 556 - gratia-0.8.1/gratia/NAMESPACE | 98 gratia-0.8.1/gratia/NEWS.md | 204 gratia-0.8.1/gratia/R/add-methods.R | 4 gratia-0.8.1/gratia/R/basis-funs.R | 278 gratia-0.8.1/gratia/R/compare-smooths.R | 2 gratia-0.8.1/gratia/R/confint-methods.R | 105 gratia-0.8.1/gratia/R/data-sim.R | 2 gratia-0.8.1/gratia/R/data-slice.R | 199 gratia-0.8.1/gratia/R/derivatives.R | 587 + gratia-0.8.1/gratia/R/diagnose.R | 64 gratia-0.8.1/gratia/R/difference-smooths.R |only gratia-0.8.1/gratia/R/draw-evaluate-smooth.R | 2 gratia-0.8.1/gratia/R/draw-gam.R | 167 gratia-0.8.1/gratia/R/draw-methods.R | 504 + gratia-0.8.1/gratia/R/edf.R | 8 gratia-0.8.1/gratia/R/evenly.R |only gratia-0.8.1/gratia/R/fitted_values.R | 9 gratia-0.8.1/gratia/R/gjrm-methods.R |only gratia-0.8.1/gratia/R/lp-matrix.R |only gratia-0.8.1/gratia/R/overview.R |only gratia-0.8.1/gratia/R/parametric-effects.R | 56 gratia-0.8.1/gratia/R/posterior-samples.R | 140 gratia-0.8.1/gratia/R/residuals.R | 2 gratia-0.8.1/gratia/R/rootogram.R | 4 gratia-0.8.1/gratia/R/simulate-methods.R | 46 gratia-0.8.1/gratia/R/smooth-coefs.R |only gratia-0.8.1/gratia/R/smooth-data.R | 26 gratia-0.8.1/gratia/R/smooth-estimates.R | 364 - gratia-0.8.1/gratia/R/smooth-type.R |only gratia-0.8.1/gratia/R/too_far.R | 3 gratia-0.8.1/gratia/R/utililties.R | 328 - gratia-0.8.1/gratia/README.md | 11 gratia-0.8.1/gratia/build/partial.rdb |binary gratia-0.8.1/gratia/build/vignette.rds |binary gratia-0.8.1/gratia/inst/doc/custom-plotting.html | 40 gratia-0.8.1/gratia/inst/doc/data-slices.R |only gratia-0.8.1/gratia/inst/doc/data-slices.Rmd |only gratia-0.8.1/gratia/inst/doc/data-slices.html |only gratia-0.8.1/gratia/inst/doc/gratia.html | 17 gratia-0.8.1/gratia/man/add_fitted.gam.Rd | 2 gratia-0.8.1/gratia/man/basis.Rd | 98 gratia-0.8.1/gratia/man/compare_smooths.Rd | 2 gratia-0.8.1/gratia/man/confint.gam.Rd | 35 gratia-0.8.1/gratia/man/data_sim.Rd | 2 gratia-0.8.1/gratia/man/data_slice.Rd | 60 gratia-0.8.1/gratia/man/derivatives.Rd | 14 gratia-0.8.1/gratia/man/difference_smooths.Rd | 28 gratia-0.8.1/gratia/man/draw.basis.Rd |only gratia-0.8.1/gratia/man/draw.compare_smooths.Rd | 5 gratia-0.8.1/gratia/man/draw.derivatives.Rd | 28 gratia-0.8.1/gratia/man/draw.difference_smooth.Rd | 10 gratia-0.8.1/gratia/man/draw.evaluated_smooth.Rd | 2 gratia-0.8.1/gratia/man/draw.gam.Rd | 28 gratia-0.8.1/gratia/man/draw.gamlss.Rd |only gratia-0.8.1/gratia/man/draw.mgcv_smooth.Rd | 6 gratia-0.8.1/gratia/man/draw.parametric_effects.Rd | 18 gratia-0.8.1/gratia/man/draw.smooth_estimates.Rd | 12 gratia-0.8.1/gratia/man/draw.smooth_samples.Rd | 16 gratia-0.8.1/gratia/man/draw_parametric_effect.Rd | 7 gratia-0.8.1/gratia/man/edf.Rd | 2 gratia-0.8.1/gratia/man/eval_smooth.Rd | 22 gratia-0.8.1/gratia/man/evenly.Rd |only gratia-0.8.1/gratia/man/figures/README-appraise-figure-1.png |binary gratia-0.8.1/gratia/man/figures/README-draw-gam-figure-1.png |binary gratia-0.8.1/gratia/man/figures/README-draw-gam-figure-2d-1.png |binary gratia-0.8.1/gratia/man/fitted_samples.Rd | 15 gratia-0.8.1/gratia/man/fitted_values.Rd | 2 gratia-0.8.1/gratia/man/is_mgcv_smooth.Rd | 14 gratia-0.8.1/gratia/man/lp_matrix.Rd |only gratia-0.8.1/gratia/man/model_vars.Rd |only gratia-0.8.1/gratia/man/nb_theta.Rd | 4 gratia-0.8.1/gratia/man/overview.Rd |only gratia-0.8.1/gratia/man/partial_derivatives.Rd |only gratia-0.8.1/gratia/man/partial_residuals.Rd | 2 gratia-0.8.1/gratia/man/posterior_samples.Rd | 17 gratia-0.8.1/gratia/man/predicted_samples.Rd | 23 gratia-0.8.1/gratia/man/ref_level.Rd |only gratia-0.8.1/gratia/man/rootogram.Rd | 2 gratia-0.8.1/gratia/man/seq_min_max_eps.Rd | 2 gratia-0.8.1/gratia/man/shift_values.Rd | 5 gratia-0.8.1/gratia/man/simulate.Rd | 38 gratia-0.8.1/gratia/man/smooth_coef_indices.Rd |only gratia-0.8.1/gratia/man/smooth_coefs.Rd | 59 gratia-0.8.1/gratia/man/smooth_data.Rd | 20 gratia-0.8.1/gratia/man/smooth_estimates.Rd | 2 gratia-0.8.1/gratia/man/smooth_samples.Rd | 27 gratia-0.8.1/gratia/man/smooth_type.Rd |only gratia-0.8.1/gratia/man/tidy_basis.Rd | 33 gratia-0.8.1/gratia/man/worm_plot.Rd | 10 gratia-0.8.1/gratia/tests/Examples/gratia-Ex.Rout.save | 1017 ++- gratia-0.8.1/gratia/tests/testthat/_snaps/bam-ar/draw-bam-ar-1-factor-by.svg | 1782 ++--- gratia-0.8.1/gratia/tests/testthat/_snaps/bam-ar/draw-bam-ar-1-single-series.svg | 885 +- gratia-0.8.1/gratia/tests/testthat/_snaps/basis |only gratia-0.8.1/gratia/tests/testthat/_snaps/by-variables/continuous-by-variable-smmoth.svg | 907 +- gratia-0.8.1/gratia/tests/testthat/_snaps/by-variables/draw-gam-user-select-and-parametric-true.svg | 464 - gratia-0.8.1/gratia/tests/testthat/_snaps/compare-smooths/compare-smooths-all-smooths.svg | 52 gratia-0.8.1/gratia/tests/testthat/_snaps/compare-smooths/compare-smooths-bottom-legened.svg | 52 gratia-0.8.1/gratia/tests/testthat/_snaps/compare-smooths/compare-smooths-set-nrow-ncol.svg | 52 gratia-0.8.1/gratia/tests/testthat/_snaps/concurvity/draw-concurvity-overall.svg | 30 gratia-0.8.1/gratia/tests/testthat/_snaps/concurvity/draw-concurvity-pairwise.svg | 150 gratia-0.8.1/gratia/tests/testthat/_snaps/confint-methods.md | 20 gratia-0.8.1/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-complex-factor-by.svg | 24 gratia-0.8.1/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-factor-by.svg | 18 gratia-0.8.1/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivatives-for-gamm-factor-by.svg | 24 gratia-0.8.1/gratia/tests/testthat/_snaps/derivatives/draw-issue-47-derivs-for-ordered-factor-by.svg | 24 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/appraise-diagnostic-plots.svg | 26 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/appraise-lm.svg | 22 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/qq-plot-glm-normal.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/qq-plot-glm-simulate.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/qq-plot-lm-normal.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/qq-plot-lm-simulate.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/worm-plot-gam-normal.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/worm-plot-gam-simulate.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/worm-plot-glm-normal.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/worm-plot-glm-simulate.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/worm-plot-lm-normal.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/diagnostic-plots/worm-plot-lm-simulate.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-bam.svg | 231 gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-bivariate-gam-contours.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-bivariate-gam.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-fixed-scales.svg | 237 gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-inc-grp-means.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam-ref-line.svg | 237 gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gam.svg | 231 gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gamm.svg | 237 gratia-0.8.1/gratia/tests/testthat/_snaps/difference-smooths/draw-difference-smooths-gamm4.svg | 231 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-dlnm-m.svg | 134 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-1-smooth-constant-fun.svg | 89 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-1-smooth-constant.svg | 107 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-1-smooth-fun.svg | 83 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-1-smooth-hotpink-residuals.svg | 897 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-1-smooth-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-1-smooth.svg | 501 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-2-fac-parametric.svg | 1625 ----- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-2-fac.svg | 1483 ---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-ar1-by.svg | 1782 ++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-ar1.svg | 885 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-bam.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gam-constant-fun.svg | 382 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gam-constant.svg | 374 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gam-fun.svg | 378 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gam-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gam.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gamgcv.svg | 364 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gamm.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gamm4.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-gaulss.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-para-sm-parametric.svg | 1633 ----- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-para-sm.svg | 1786 ++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-m-scat.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-parametric-only-model-rotated-labels.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-parametric-only-model.svg | 1637 ----- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-quadvar-te.svg | 814 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-rm1.svg | 1257 --- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-rm2.svg | 1880 +---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-gam/draw-gam-trivar-te.svg | 822 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-1d-smooth-for-selected-smooth.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-2d-smooth-with-spectral-palette.svg | 171 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-am-with-2d-smooth.svg | 2171 ------ gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-am-with-factor-by-variable-smooth.svg | 2010 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-basic-tprs-basis-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-basic-tprs-basis.svg | 104 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-by-factor-basis.svg | 380 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-derivatives-for-a-gam-rotated-labels.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-derivatives-for-a-gam-with-fixed-scales-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-derivatives-for-a-gam-with-fixed-scales.svg | 24 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-derivatives-for-a-gam.svg | 24 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-factor-by-variable-smooth-with-fixed-scales.svg | 1998 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-fs-smooth-with-discrete-plasma-palette.svg | 301 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-model-with-fs-smooth.svg | 301 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-model-with-non-standard-names.svg | 199 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-model-with-ranef-smooth-factor-by.svg | 1880 +---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-model-with-ranef-smooth.svg | 1257 --- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-smooth-for-selected-smooth-character.svg | 489 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-smooth-for-selected-smooth-logical.svg | 491 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-smooth-for-selected-smooth-numeric.svg | 489 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-smooth-for-two-selected-smooths-character.svg | 980 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-smooth-for-two-selected-smooths-logical.svg | 980 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-smooth-for-two-selected-smooths-numeric.svg | 980 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-factor-parametric-term.svg | 1461 ++-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-linear-parametric-term.svg | 1461 ++-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-overall-uncertainty-false.svg | 358 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-partial-match-true.svg | 1081 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-select-and-parametric-is-false.svg | 1081 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-select-and-parametric-is-null.svg | 1081 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-with-select-and-parametric-is-true.svg | 1172 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-without-select-and-parametric-is-false.svg | 1210 --- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-gam-without-select-and-parametric-is-true.svg | 1309 ---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-issue-39-empty-plots.svg | 1483 ---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-model-with-fs-smooth-fixed-scales.svg | 315 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-model-with-ranef-smooth-fixed-scales.svg | 1327 ---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-selected-factor-by-smooth-samples-for-gam-m3.svg | 570 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-selected-smooth-samples-for-gam-m3.svg | 180 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-simple-multi-smooth-am-with-fixed-scales.svg | 1988 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-simple-multi-smooth-am.svg | 1962 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-simple-partial-residuals-with-fixed-scales.svg | 1940 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-simple-partial-residuals.svg | 1940 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-bivariate-gam-contours.svg | 393 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m1-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m1.svg | 774 -- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m2-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m2.svg | 406 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m3-fixed-scales-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m3-fixed-scales.svg | 656 -- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m3-rotated.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-m3.svg | 605 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-gam-n-samples.svg | 702 -- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-m1-n-samples.svg | 714 -- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-smooth-samples-for-m2-n-samples.svg | 188 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-with-continuous-by-var-fixed-scale.svg | 907 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-with-continuous-by-variable-smooth.svg | 907 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-with-linear-parametric-term.svg | 406 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-with-ranef-smooth-factor-by-fixed-scales.svg | 1920 +---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/draw-ziplss-parametric-terms-issue-45.svg | 1198 --- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/issue-22-draw-with-mixed-random-effects.svg | 717 +- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-methods/issue-73-draw-uses-fixed-scales-if-asked-for-them.svg | 369 - gratia-0.8.1/gratia/tests/testthat/_snaps/draw-parametric-effects/draw-parametric-effects-m-2-fac-with-term.svg | 69 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-parametric-effects/draw-parametric-effects-m-2-fac.svg | 154 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-parametric-effects/draw-parametric-effects-m-only-para.svg | 2837 ++++---- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-parametric-effects/draw-parametric-effects-m-para-sm-with-term.svg | 69 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-parametric-effects/draw-parametric-effects-m-para-sm.svg | 1047 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-1-smooth.svg | 101 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-bam.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gam.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gamgcv.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gamm.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gamm4.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-gaulss.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-m-scat.svg | 91 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-bivar-t2.svg | 153 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-bivar-te.svg | 151 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-bivar.svg | 171 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-t2.svg | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-te.svg | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar.svg | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-trivar-t2.svg | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-trivar-te.svg | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-su-m-trivar.svg | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-sz-factor-smooth.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/draw-smooth-estimates/draw-smooth-estimates-sz-two-factor-smooth.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/evaluate-smooth-methods.md | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/fderiv.md | 2 gratia-0.8.1/gratia/tests/testthat/_snaps/gjrm |only gratia-0.8.1/gratia/tests/testthat/_snaps/gjrm-methods |only gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-bird-move-model-1.svg | 163 gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-bird-move-model-2.svg | 582 + gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-bird-move-model-3.svg | 1127 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-bird-move-model-4.svg |only gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-bird-move-model-5.svg | 1016 +-- gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-1.svg | 394 - gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-2.svg | 536 - gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-3.svg | 2240 +++--- gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-4.svg | 281 gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-co2-model-5.svg | 1863 ++--- gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-zoop-model-4.svg | 2490 +++---- gratia-0.8.1/gratia/tests/testthat/_snaps/hgam-paper/hgam-paper-zoop-model-5.svg | 3226 +++++----- gratia-0.8.1/gratia/tests/testthat/_snaps/lp-matrix.md |only gratia-0.8.1/gratia/tests/testthat/_snaps/overview.md |only gratia-0.8.1/gratia/tests/testthat/_snaps/posterior-samples.md | 26 gratia-0.8.1/gratia/tests/testthat/_snaps/qq-plot/qq-plot-data-simulation-pearson-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/qq-plot/qq-plot-data-simulation-response-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/qq-plot/qq-plot-data-simulation.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/qq-plot/qq-plot-normality-assumption-pearson-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/qq-plot/qq-plot-normality-assumption-response-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/qq-plot/qq-plot-normality-assumption.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/rootograms/draw-gaussian-rootogram.svg | 26 gratia-0.8.1/gratia/tests/testthat/_snaps/rootograms/draw-neg-bin-rootogram.svg | 94 gratia-0.8.1/gratia/tests/testthat/_snaps/rootograms/draw-poisson-rootogram.svg | 94 gratia-0.8.1/gratia/tests/testthat/_snaps/smooth-coefs.md |only gratia-0.8.1/gratia/tests/testthat/_snaps/worm-plot/worm-plot-data-simulation-pearson-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/worm-plot/worm-plot-data-simulation-response-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/worm-plot/worm-plot-data-simulation.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/worm-plot/worm-plot-normality-assumption-pearson-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/worm-plot/worm-plot-normality-assumption-response-residuals.svg | 6 gratia-0.8.1/gratia/tests/testthat/_snaps/worm-plot/worm-plot-normality-assumption.svg | 6 gratia-0.8.1/gratia/tests/testthat/setup.R | 109 gratia-0.8.1/gratia/tests/testthat/test-basis.R | 35 gratia-0.8.1/gratia/tests/testthat/test-confint-methods.R | 32 gratia-0.8.1/gratia/tests/testthat/test-data-slice.R | 77 gratia-0.8.1/gratia/tests/testthat/test-derivatives.R | 199 gratia-0.8.1/gratia/tests/testthat/test-difference-smooths.R | 40 gratia-0.8.1/gratia/tests/testthat/test-draw-gam.R | 47 gratia-0.8.1/gratia/tests/testthat/test-draw-methods.R | 90 gratia-0.8.1/gratia/tests/testthat/test-draw-smooth-estimates.R | 17 gratia-0.8.1/gratia/tests/testthat/test-evenly.R |only gratia-0.8.1/gratia/tests/testthat/test-gjrm-methods.R |only gratia-0.8.1/gratia/tests/testthat/test-gjrm.R |only gratia-0.8.1/gratia/tests/testthat/test-hgam-paper.R | 21 gratia-0.8.1/gratia/tests/testthat/test-lp-matrix.R |only gratia-0.8.1/gratia/tests/testthat/test-other-scam-methods.R | 8 gratia-0.8.1/gratia/tests/testthat/test-overview.R |only gratia-0.8.1/gratia/tests/testthat/test-partial-derivatives.R |only gratia-0.8.1/gratia/tests/testthat/test-posterior-samples.R | 16 gratia-0.8.1/gratia/tests/testthat/test-simulate-methods.R | 7 gratia-0.8.1/gratia/tests/testthat/test-smooth-coefs.R |only gratia-0.8.1/gratia/tests/testthat/test-smooth-estimates.R | 18 gratia-0.8.1/gratia/tests/testthat/test-subsetting.R | 13 gratia-0.8.1/gratia/tests/testthat/test-utilities.R | 2 gratia-0.8.1/gratia/vignettes/data-slices.Rmd |only 304 files changed, 43214 insertions(+), 57763 deletions(-)
Title: Load 'CDRC' Data
Description: A wrapper for the 'CDRC' 'API' that returns data frames or 'sf' of 'CDRC' data. The 'API' web reference is:<https://api.cdrc.ac.uk/swagger/index.html>.
Author: Alessia Calafiore [aut, cre]
Maintainer: Alessia Calafiore <aelissa3388@gmail.com>
Diff between cdrcR versions 0.0.1 dated 2021-11-19 and 0.1.0 dated 2023-02-02
DESCRIPTION | 13 +++++++------ MD5 | 7 ++++--- NEWS.md |only R/getCDRC.R | 6 +++--- README.md | 10 ++++++++-- 5 files changed, 22 insertions(+), 14 deletions(-)
Title: Empirical Mode Decomposition for Cyclostratigraphy
Description: Tools to apply Ensemble Empirical Mode
Decomposition (EEMD) for cyclostratigraphy purposes. Mainly: a new
algorithm, extricate, that performs EEMD in seconds, a linear interpolation
algorithm using the greatest rational common divisor of depth or time,
different algorithms to compute instantaneous amplitude, frequency and
ratios of frequencies, and functions to verify and visualise the outputs.
The functions were developed during the CRASH project (Checking the
Reproducibility of Astrochronology in the Hauterivian). When using for
publication please cite Wouters, S., Crucifix, M., Sinnesael, M., Da Silva,
A.C., Zeeden, C., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2022,
"A decomposition approach to cyclostratigraphic signal processing".
Earth-Science Reviews 225 (103894).
<doi:10.1016/j.earscirev.2021.103894>.
Author: Sebastien Wouters [aut, cre]
Maintainer: Sebastien Wouters <wouterseb@gmail.com>
Diff between DecomposeR versions 1.0.5 dated 2022-12-02 and 1.0.6 dated 2023-02-02
DESCRIPTION | 19 +++++++++---------- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/DecomposeR.R | 15 +++++++-------- R/check.emd.R | 4 ++-- R/extremist.R | 4 ++-- R/extricate.R | 2 +- inst/CITATION | 47 ++++++++++++++++------------------------------- man/DecomposeR.Rd | 15 +++++++-------- 9 files changed, 58 insertions(+), 70 deletions(-)
Title: Interface to 'ChatGPT' from R
Description: 'OpenAI's 'ChatGPT' <https://chat.openai.com/> coding assistant for 'RStudio'. A set
of functions and 'RStudio' addins that aim to help the R developer in tedious coding tasks.
Author: Juan Cruz Rodriguez [aut, cre]
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>
Diff between chatgpt versions 0.1.4 dated 2023-01-16 and 0.1.5 dated 2023-02-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++++---- NAMESPACE | 2 ++ R/addins.R | 2 ++ R/ask_chatgpt.R |only R/create_unit_tests.R |only inst/rstudio/addins.dcf | 5 +++++ man/ask_chatgpt.Rd |only man/create_unit_tests.Rd |only 9 files changed, 22 insertions(+), 9 deletions(-)
Title: Present Data with Style
Description: Consists of custom wrapper functions using packages
'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames.
These viewer friendly outputs are intended to match expectations of professional looking presentations
in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data
frame to have certain properties in order to take advantage of the automated formatting.
Author: Harrison Tietze [aut, cre]
Maintainer: Harrison Tietze <Harrison4192@gmail.com>
Diff between presenter versions 0.1.1 dated 2021-11-18 and 0.1.2 dated 2023-02-02
DESCRIPTION | 12 LICENSE | 4 MD5 | 112 +- NAMESPACE | 36 NEWS.md | 2 R/flextable_helpers.R | 270 +++--- R/formatters.R | 275 +++---- R/get_piped_name.R | 304 +++---- R/globals.R | 6 R/make_excel.R | 822 ++++++++++----------- R/make_flextable.R | 462 +++++------ R/make_pivot_table.R | 702 +++++++++--------- R/make_powerpoint.R | 142 +-- R/make_simple_excel.R | 88 +- R/pivot_summary.R | 106 +- R/utils-pipe.R | 22 README.md | 148 +-- build/vignette.rds |binary inst/doc/exportToExcel.R | 68 - inst/doc/exportToExcel.Rmd | 180 ++-- inst/doc/exportToExcel.html | 676 +++++++++++------ inst/doc/flextableAndPowerpoint.R | 88 +- inst/doc/flextableAndPowerpoint.Rmd | 128 +-- inst/doc/flextableAndPowerpoint.html | 954 +++++++++++++++--------- inst/doc/flextableThemes.R | 98 +- inst/doc/flextableThemes.Rmd | 166 ++-- inst/doc/flextableThemes.html | 1358 ++++++++++++++++++++--------------- inst/doc/formattedFlextable.R | 92 +- inst/doc/formattedFlextable.Rmd | 140 +-- inst/doc/formattedFlextable.html | 970 +++++++++++++++---------- inst/doc/pivotSummary.R | 94 +- inst/doc/pivotSummary.Rmd | 192 ++-- inst/doc/pivotSummary.html | 712 +++++++++++------- man/charvec_to_formula.Rd | 36 man/finish_excel_wb.Rd | 38 man/flex_create_headers.Rd | 40 - man/flex_mergev1.Rd | 40 - man/flex_mergev1_formula.Rd | 36 man/flex_set_headers.Rd | 44 - man/format_number.Rd | 130 +-- man/format_red.Rd | 44 - man/get_piped_name.Rd | 98 +- man/is_percentage.Rd | 47 - man/make_excel.Rd | 62 - man/make_excel_wb.Rd | 68 - man/make_flextable.Rd | 70 - man/make_pivot_table.Rd | 85 +- man/make_powerpoint.Rd | 66 - man/make_simple_excel.Rd | 38 man/pipe.Rd | 24 man/pivot_summary.Rd | 50 - man/style_header_sequence.Rd | 52 - vignettes/exportToExcel.Rmd | 180 ++-- vignettes/flextableAndPowerpoint.Rmd | 128 +-- vignettes/flextableThemes.Rmd | 166 ++-- vignettes/formattedFlextable.Rmd | 140 +-- vignettes/pivotSummary.Rmd | 192 ++-- 57 files changed, 6211 insertions(+), 5092 deletions(-)
More information about SampleSizeMeans at CRAN
Permanent link
Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7].
Main references:
[1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>,
[2] Mualem (1976) <doi:10.1029/WR012i003p00513>,
[3] Peters (2013) <doi:10.1002/wrcr.20548>,
[4] Iden and Durner (2013) <doi:10.1002/2014WR015937>,
[5] Peters (2014) <doi:10.1002/2014WR015937>,
[6] Wind G. P. (1966),
[7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and
[8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre],
Felix Andrews [ctb] which is not on r-cran
. The SCEoptim function is
adapted, and substantially revised from Brecht Donckels MATLAB code
which is in turn adopted from Qingyun Duans MATLAB code),
Brecht Donckels [ctb] ,
[...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>
Diff between SoilHyP versions 0.1.6 dated 2022-05-25 and 0.1.7 dated 2023-02-02
DESCRIPTION | 8 - MD5 | 6 - R/Ku.R | 328 ++++++++++++++++++++++++++++++------------------------------ R/SWC.R | 287 ++++++++++++++++++++++++++-------------------------- 4 files changed, 315 insertions(+), 314 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
and 'lbfgsb_cpp' is a 'C++' wrapper by Colin Fang around 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Pascal Have [aut],
Yann Richet [aut, cre] ,
Yves Deville [aut],
Conrad Sanderson [ctb],
Colin Fang [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between rlibkriging versions 0.7-4.1 dated 2023-01-17 and 0.7-4.2 dated 2023-02-02
rlibkriging-0.7-4.1/rlibkriging/tools/libKriging_CMakeLists.txt |only rlibkriging-0.7-4.2/rlibkriging/DESCRIPTION | 8 - rlibkriging-0.7-4.2/rlibkriging/MD5 | 9 - rlibkriging-0.7-4.2/rlibkriging/src/libK/CMakeLists.txt | 48 +++++----- rlibkriging-0.7-4.2/rlibkriging/src/libK/src/lib/CMakeLists.txt | 4 rlibkriging-0.7-4.2/rlibkriging/tools/setup.sh | 16 +++ 6 files changed, 49 insertions(+), 36 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 0.5.1 dated 2022-12-15 and 0.6.0 dated 2023-02-02
DESCRIPTION | 7 +- MD5 | 64 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 20 +++++++ R/OCN_to_SSN.R | 40 +++++++++++++-- R/aggregate_OCN.R | 100 +++++++++++++++++++++++++------------- R/create_OCN.R | 32 ++++++------ R/create_general_contour_OCN.R |only R/draw_contour_OCN.R | 8 +-- R/draw_elev2D_OCN.R | 30 +++++++++-- R/draw_elev3D_OCN.R | 27 +++++++--- R/draw_elev3Drgl_OCN.R | 67 ++++++++++++++++++------- R/draw_simple_OCN.R | 6 +- R/draw_subcatchments_OCN.R | 45 ++++++++++++++--- R/draw_thematic_OCN.R | 89 ++++++++++++++++++++------------- R/landscape_OCN.R | 2 R/paths_OCN.R | 3 + data/flowDir.rda |only inst/CITATION | 28 ++++------ inst/doc/OCNet.html | 3 - man/OCN_to_SSN.Rd | 39 +++++++++++--- man/OCNet-package.Rd | 4 + man/aggregate_OCN.Rd | 19 ++++++- man/continue_OCN.Rd | 6 +- man/create_OCN.Rd | 25 ++++----- man/create_general_contour_OCN.Rd |only man/draw_contour_OCN.Rd | 2 man/draw_elev3D_OCN.Rd | 2 man/draw_elev3Drgl_OCN.Rd | 2 man/draw_simple_OCN.Rd | 2 man/draw_subcatchments_OCN.Rd | 7 ++ man/draw_thematic_OCN.Rd | 26 ++++++--- man/flowDir.Rd |only man/landscape_OCN.Rd | 3 - man/paths_OCN.Rd | 10 +-- 35 files changed, 489 insertions(+), 230 deletions(-)
Title: Steve's R Markdown Templates
Description: These are my collection of 'R Markdown' templates, mostly for compilation to PDF.
These are useful for all things academic and professional, if you are using 'R Markdown'
for things like your CV or your articles and manuscripts.
Author: Steven V. Miller
Maintainer: Steven V. Miller <steven.v.miller@gmail.com>
Diff between stevetemplates versions 0.8.0 dated 2022-09-29 and 0.9.0 dated 2023-02-02
DESCRIPTION | 6 +-- MD5 | 24 ++++++------ NEWS.md | 7 +++ R/beamer.R | 1 inst/rmarkdown/templates/anonms/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/article/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/article2/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/beamer/resources/template.tex | 9 +++- inst/rmarkdown/templates/cover_letter/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/cv/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/html_article/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/statement/skeleton/skeleton.Rmd | 4 +- inst/rmarkdown/templates/syllabus/skeleton/skeleton.Rmd | 4 +- 13 files changed, 39 insertions(+), 28 deletions(-)
More information about stevetemplates at CRAN
Permanent link
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.5.4 dated 2023-01-11 and 0.5.5 dated 2023-02-02
DESCRIPTION | 6 - MD5 | 9 +- NEWS.md | 3 R/credential_providers.R | 160 +++++++++++++++++++++++++++----------- tests/testthat/data_sso_ini |only tests/testthat/test_config.R | 179 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 304 insertions(+), 53 deletions(-)
Title: Convert Images to Usable Color Schemes
Description: A fast and adaptable tool to convert photos and images into usable colour schemes for data visualisation. Contains functionality to extract colour palettes from images, as well for the conversion of images between colour spaces.
Author: Stuart Morrison [aut, cre]
Maintainer: Stuart Morrison <smorrison@ucdavis.edu>
Diff between schemr versions 0.1.0 dated 2021-03-10 and 0.2.0 dated 2023-02-02
DESCRIPTION | 17 ++++++++--------- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++-- R/color-spaces.R | 6 ++++-- R/extract-colours.R | 50 +++++++++++++++++++++++++------------------------- README.md | 17 +++++++++++------ 7 files changed, 57 insertions(+), 50 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data
structures and functions that facilitate the plotting of missing values and
examination of imputations. This allows missing data dependencies to be
explored with minimal deviation from the common work patterns of 'ggplot2'
and tidy data. The work is fully discussed at Tierney & Cook (2023)
<doi:10.18637/jss.v105.i07>.
Author: Nicholas Tierney [aut, cre] ,
Di Cook [aut] ,
Miles McBain [aut] ,
Colin Fay [aut] ,
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb],
Andrew Heiss [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.6.1 dated 2021-05-14 and 1.0.0 dated 2023-02-02
naniar-0.6.1/naniar/man/group_by_fun.Rd |only naniar-0.6.1/naniar/man/label_shadow.Rd |only naniar-0.6.1/naniar/man/new_shade.Rd |only naniar-0.6.1/naniar/man/shadow_expand_relevel.Rd |only naniar-0.6.1/naniar/man/test_if_dataframe.Rd |only naniar-0.6.1/naniar/man/test_if_missing.Rd |only naniar-0.6.1/naniar/man/test_if_null.Rd |only naniar-0.6.1/naniar/man/update_shadow.Rd |only naniar-0.6.1/naniar/man/what_levels.Rd |only naniar-0.6.1/naniar/tests/testthat/fontconfig-helper.R |only naniar-1.0.0/naniar/DESCRIPTION | 33 naniar-1.0.0/naniar/MD5 | 273 ++-- naniar-1.0.0/naniar/NAMESPACE | 5 naniar-1.0.0/naniar/NEWS.md | 30 naniar-1.0.0/naniar/R/add-cols.R | 2 naniar-1.0.0/naniar/R/add-n-prop-miss.R | 2 naniar-1.0.0/naniar/R/data-common-na-strings.R | 1 naniar-1.0.0/naniar/R/data-pedestrian.R | 4 naniar-1.0.0/naniar/R/geom2plotly.R | 2 naniar-1.0.0/naniar/R/gg-miss-case-cumsum.R | 2 naniar-1.0.0/naniar/R/gg-miss-case.R | 4 naniar-1.0.0/naniar/R/gg-miss-fct.R | 8 naniar-1.0.0/naniar/R/gg-miss-span.R | 12 naniar-1.0.0/naniar/R/gg-miss-var-cumsum.R | 2 naniar-1.0.0/naniar/R/gg-miss-var.R | 9 naniar-1.0.0/naniar/R/mcar-test.R | 4 naniar-1.0.0/naniar/R/miss-scan-count.R | 10 naniar-1.0.0/naniar/R/miss-x-cumsum.R | 5 naniar-1.0.0/naniar/R/naniar-package.R | 3 naniar-1.0.0/naniar/R/set-n-prop-miss.R |only naniar-1.0.0/naniar/R/shade.R | 16 naniar-1.0.0/naniar/R/shadow-recode.R | 18 naniar-1.0.0/naniar/R/shadows.R | 45 naniar-1.0.0/naniar/R/utils.R | 45 naniar-1.0.0/naniar/README.md | 134 + naniar-1.0.0/naniar/build/partial.rdb |binary naniar-1.0.0/naniar/build/vignette.rds |binary naniar-1.0.0/naniar/data/common_na_strings.rda |binary naniar-1.0.0/naniar/inst/CITATION |only naniar-1.0.0/naniar/inst/WORDLIST | 5 naniar-1.0.0/naniar/inst/doc/exploring-imputed-values.R | 7 naniar-1.0.0/naniar/inst/doc/exploring-imputed-values.Rmd | 7 naniar-1.0.0/naniar/inst/doc/exploring-imputed-values.html | 437 ++++-- naniar-1.0.0/naniar/inst/doc/getting-started-w-naniar.Rmd | 2 naniar-1.0.0/naniar/inst/doc/getting-started-w-naniar.html | 681 +++++++--- naniar-1.0.0/naniar/inst/doc/naniar-visualisation.html | 465 +++++- naniar-1.0.0/naniar/inst/doc/replace-with-na.R | 5 naniar-1.0.0/naniar/inst/doc/replace-with-na.Rmd | 7 naniar-1.0.0/naniar/inst/doc/replace-with-na.html | 526 +++++-- naniar-1.0.0/naniar/inst/doc/special-missing-values.Rmd | 2 naniar-1.0.0/naniar/inst/doc/special-missing-values.html | 495 +++++-- naniar-1.0.0/naniar/man/add_prop_miss.Rd | 2 naniar-1.0.0/naniar/man/common_na_strings.Rd | 3 naniar-1.0.0/naniar/man/figures/README-facet-by-month-1.png |binary naniar-1.0.0/naniar/man/figures/README-geom-miss-point-1.png |binary naniar-1.0.0/naniar/man/figures/README-gg-miss-span-1.png |binary naniar-1.0.0/naniar/man/figures/README-gg-miss-upset-1.png |binary naniar-1.0.0/naniar/man/figures/README-gg-miss-var-1.png |binary naniar-1.0.0/naniar/man/figures/README-regular-geom-point-1.png |binary naniar-1.0.0/naniar/man/figures/README-shadow-impute-1.png |binary naniar-1.0.0/naniar/man/figures/README-shadow-w-ggplot-1.png |binary naniar-1.0.0/naniar/man/mcar_test.Rd | 4 naniar-1.0.0/naniar/man/naniar.Rd | 3 naniar-1.0.0/naniar/man/pedestrian.Rd | 4 naniar-1.0.0/naniar/man/plotly_helpers.Rd | 1 naniar-1.0.0/naniar/man/recode_shadow.Rd | 6 naniar-1.0.0/naniar/man/set-prop-n-miss.Rd |only naniar-1.0.0/naniar/tests/testthat.R | 8 naniar-1.0.0/naniar/tests/testthat/_snaps |only naniar-1.0.0/naniar/tests/testthat/test-add-any-miss.R | 4 naniar-1.0.0/naniar/tests/testthat/test-add-label-missings.R | 4 naniar-1.0.0/naniar/tests/testthat/test-add-label-shadow.R | 5 naniar-1.0.0/naniar/tests/testthat/test-add-n-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-add-prop-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-add-shadow-shift.R | 4 naniar-1.0.0/naniar/tests/testthat/test-add-shadow.R | 4 naniar-1.0.0/naniar/tests/testthat/test-all-na.R | 2 naniar-1.0.0/naniar/tests/testthat/test-as-shadow.R | 18 naniar-1.0.0/naniar/tests/testthat/test-as_shadow_upset.R | 2 naniar-1.0.0/naniar/tests/testthat/test-cast-shadow-shift-label.R | 5 naniar-1.0.0/naniar/tests/testthat/test-cast-shadow-shift.R | 4 naniar-1.0.0/naniar/tests/testthat/test-cast-shadow.R | 4 naniar-1.0.0/naniar/tests/testthat/test-defunct.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gather-shadow.R | 6 naniar-1.0.0/naniar/tests/testthat/test-geom-miss-point.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-case-cumsum.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-case.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-fct.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-span.R | 3 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-var-cumsum.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-var-plot.R | 2 naniar-1.0.0/naniar/tests/testthat/test-gg-miss-which.R | 2 naniar-1.0.0/naniar/tests/testthat/test-impute-below-at.R | 4 naniar-1.0.0/naniar/tests/testthat/test-impute-below.R | 11 naniar-1.0.0/naniar/tests/testthat/test-impute-median.R | 2 naniar-1.0.0/naniar/tests/testthat/test-impute_mean.R | 2 naniar-1.0.0/naniar/tests/testthat/test-label-miss-1d.R | 2 naniar-1.0.0/naniar/tests/testthat/test-label-miss-2d.R | 2 naniar-1.0.0/naniar/tests/testthat/test-label-shadow.R | 4 naniar-1.0.0/naniar/tests/testthat/test-mcar-test.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-case-summary.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-case-table.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-prop-summary.R | 4 naniar-1.0.0/naniar/tests/testthat/test-miss-scan-count.R | 5 naniar-1.0.0/naniar/tests/testthat/test-miss-summary.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-var-run.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-var-span.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-var-summary.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-var-table.R | 6 naniar-1.0.0/naniar/tests/testthat/test-miss-var-which.R | 2 naniar-1.0.0/naniar/tests/testthat/test-miss-x-pct.R | 2 naniar-1.0.0/naniar/tests/testthat/test-n-complete.R | 2 naniar-1.0.0/naniar/tests/testthat/test-n-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-nabular.R | 6 naniar-1.0.0/naniar/tests/testthat/test-prop-complete.R | 2 naniar-1.0.0/naniar/tests/testthat/test-prop-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-prop_row.R | 2 naniar-1.0.0/naniar/tests/testthat/test-replace-with-na-scoped-var.R | 2 naniar-1.0.0/naniar/tests/testthat/test-replace-with-na.R | 2 naniar-1.0.0/naniar/tests/testthat/test-set-n-prop-miss.R |only naniar-1.0.0/naniar/tests/testthat/test-shade-verifiers.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shade.R | 21 naniar-1.0.0/naniar/tests/testthat/test-shadow-expand-relevel.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shadow-identifiers.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shadow-long.R | 8 naniar-1.0.0/naniar/tests/testthat/test-shadow-shift-inf.R | 2 naniar-1.0.0/naniar/tests/testthat/test-shadow-shift.R | 2 naniar-1.0.0/naniar/tests/testthat/test-special-missing-values.R | 28 naniar-1.0.0/naniar/tests/testthat/test-test-any-miss.R | 2 naniar-1.0.0/naniar/tests/testthat/test-unbind.R | 4 naniar-1.0.0/naniar/vignettes/exploring-imputed-values.Rmd | 7 naniar-1.0.0/naniar/vignettes/getting-started-w-naniar.Rmd | 2 naniar-1.0.0/naniar/vignettes/replace-with-na.Rmd | 7 naniar-1.0.0/naniar/vignettes/special-missing-values.Rmd | 2 134 files changed, 2550 insertions(+), 1057 deletions(-)
Title: Filter Methods for Parameter Estimation in Linear and Non Linear
Regression Models
Description: We present a method based on filtering algorithms to estimate the parameters of linear, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods. Parameters of logistic regression models are also estimated using an evolutionary particle filter method.
Author: Christian Llano Robayo [aut, cre],
Nazrul Shaikh [aut],
Pegu Nilutpal [aut]
Maintainer: Christian Llano Robayo <info@cecareus.com>
Diff between LMfilteR versions 0.1.3 dated 2020-10-12 and 0.1.3.1 dated 2023-02-02
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/EPF_L_compl.R | 2 +- R/EPF_logist_compl.R | 2 +- 5 files changed, 20 insertions(+), 15 deletions(-)
Title: Exponential Multivariate Hawkes Model
Description: Simulate and fitting exponential multivariate Hawkes model.
This package simulates a multivariate Hawkes model, introduced by Hawkes (1971) <doi:10.2307/2334319>, with an exponential kernel and fits the parameters from the data.
Models with the constant parameters, as well as complex dependent structures, can also be simulated and estimated.
The estimation is based on the maximum likelihood method, introduced by introduced by Ozaki (1979) <doi:10.1007/BF02480272>, with 'maxLik' package.
Author: Kyungsub Lee [aut, cre]
Maintainer: Kyungsub Lee <kyungsub@gmail.com>
Diff between emhawkes versions 0.9.5 dated 2021-02-16 and 0.9.7 dated 2023-02-02
emhawkes-0.9.5/emhawkes/man/logLik-hspec-method.Rd |only emhawkes-0.9.7/emhawkes/DESCRIPTION | 13 emhawkes-0.9.7/emhawkes/MD5 | 48 emhawkes-0.9.7/emhawkes/NAMESPACE | 2 emhawkes-0.9.7/emhawkes/NEWS.md |only emhawkes-0.9.7/emhawkes/R/harrival.R | 2 emhawkes-0.9.7/emhawkes/R/hfit.R | 131 - emhawkes-0.9.7/emhawkes/R/hgfit.R | 179 - emhawkes-0.9.7/emhawkes/R/hllf.R | 129 - emhawkes-0.9.7/emhawkes/R/hmoment.R | 251 ++ emhawkes-0.9.7/emhawkes/R/hreal.R | 63 emhawkes-0.9.7/emhawkes/R/hsim.R | 128 - emhawkes-0.9.7/emhawkes/R/hspec.R | 244 +- emhawkes-0.9.7/emhawkes/R/utilities.R | 9 emhawkes-0.9.7/emhawkes/build/vignette.rds |binary emhawkes-0.9.7/emhawkes/inst/doc/example.R | 357 +++ emhawkes-0.9.7/emhawkes/inst/doc/example.Rmd | 793 ++++++- emhawkes-0.9.7/emhawkes/inst/doc/example.html | 2306 ++++++++++++++++----- emhawkes-0.9.7/emhawkes/man/hfit.Rd | 47 emhawkes-0.9.7/emhawkes/man/hreal.Rd | 34 emhawkes-0.9.7/emhawkes/man/hsim.Rd | 93 emhawkes-0.9.7/emhawkes/man/hspec-class.Rd | 33 emhawkes-0.9.7/emhawkes/man/hvol.Rd |only emhawkes-0.9.7/emhawkes/man/infer_lambda.Rd | 24 emhawkes-0.9.7/emhawkes/man/logLik.Rd |only emhawkes-0.9.7/emhawkes/man/residual_process.Rd | 39 emhawkes-0.9.7/emhawkes/vignettes/example.Rmd | 793 ++++++- 27 files changed, 4567 insertions(+), 1151 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2022) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.1 dated 2022-10-19 and 1.1.1 dated 2023-02-02
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NEWS.md | 8 +++++- R/CheckDiemFormat.r | 2 - R/diem.r | 5 +--- inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 +-- man/CheckDiemFormat.Rd | 2 - 7 files changed, 22 insertions(+), 17 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-03 0.1.3.3
2019-03-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-02 0.10.2
2019-12-14 0.10.1
2017-02-17 0.10
2015-07-01 0.8
2014-11-04 0.3
2013-03-21 0.2
2013-02-21 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-23 0.2.7
2021-01-07 0.2.6
2020-01-27 0.2.3
2019-03-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-04 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-14 2.1.34
2021-06-02 2.1.33
2021-01-06 2.1.31
2020-12-15 2.1.30
2020-11-18 2.1.26
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-06 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-04 1.1-11
2022-10-31 1.1-10
2022-06-17 1.1-8
2022-06-01 1.1-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-09 0.1-1
2014-11-18 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-21 0.1.9
2017-12-18 0.1.8
2017-06-30 0.1.7
2017-06-01 0.1.6
2017-05-20 0.1.5
2017-03-15 0.1.3
2017-03-05 0.1.2
2017-02-12 0.1.1
2016-12-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-29 2.0.1
2019-07-28 2.0.0
2018-12-25 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-23 1.0.0