Title: Tools for Analyzing Time Series Data of Just Finance and
Econometrics
Description: Offers procedures to support financial-economic time series modelling and enhanced procedures for computing the investment performance indices of Bacon (2004) <DOI:10.1002/9781119206309>.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between JFE versions 2.5.7 dated 2024-06-11 and 2.5.8 dated 2025-01-24
DESCRIPTION | 14 +++++++++----- MD5 | 8 ++++---- NAMESPACE | 4 ++-- R/dataDownload.R | 47 ++++++++++++++--------------------------------- man/getFed.Rd | 12 +++++++----- 5 files changed, 36 insertions(+), 49 deletions(-)
Title: Headless Chrome Web Browser Interface
Description: An implementation of the 'Chrome DevTools Protocol', for
controlling a headless Chrome web browser.
Author: Winston Chang [aut, cre],
Barret Schloerke [aut] ,
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Winston Chang <winston@posit.co>
Diff between chromote versions 0.3.1 dated 2024-08-30 and 0.4.0 dated 2025-01-24
DESCRIPTION | 6 MD5 | 33 +- NAMESPACE | 2 NEWS.md | 8 R/browser.R | 3 R/callbacks.R | 12 R/chrome.R | 286 ++++++++++++++++++++--- R/chromote-package.R | 8 R/chromote.R | 124 +++++---- R/chromote_session.R | 135 ++++++---- R/event_manager.R | 74 ++++- R/promises.R | 11 R/protocol.R | 73 +++-- R/screenshot.R | 348 ++++++++++++++-------------- R/synchronize.R | 36 +- R/utils.R | 12 man/chromote_info.Rd |only tests/testthat/test-default_chromote_args.R | 22 + 18 files changed, 768 insertions(+), 425 deletions(-)
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound transmission experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre]
,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between baRulho versions 2.1.2 dated 2024-08-31 and 2.1.3 dated 2025-01-24
DESCRIPTION | 6 - MD5 | 58 +++++----- R/excess_attenuation.R | 2 R/internal_functions.R | 72 +++++++++---- R/master_sound_file.R | 16 ++ R/noise_profile.R | 2 R/plot_blur_ratio.R | 14 +- R/plot_degradation.R | 7 - R/set_reference_sounds.R | 5 R/signal_to_noise_ratio.R | 2 R/tail_to_signal_ratio.R | 17 ++- build/vignette.rds |binary data/master_est.rda |binary data/test_sounds_est.rda |binary inst/CITATION | 9 - inst/doc/align_test_sounds.R | 2 inst/doc/align_test_sounds.Rmd | 2 inst/doc/align_test_sounds.html | 60 +++++----- inst/doc/quantify_degradation.R | 2 inst/doc/quantify_degradation.Rmd | 2 inst/doc/quantify_degradation.html | 204 ++++++++++++++++++------------------- man/excess_attenuation.Rd | 2 man/master_sound_file.Rd | 2 man/noise_profile.Rd | 2 man/plot_blur_ratio.Rd | 4 man/set_reference_sounds.Rd | 5 man/signal_to_noise_ratio.Rd | 2 man/tail_to_signal_ratio.Rd | 2 vignettes/align_test_sounds.Rmd | 2 vignettes/quantify_degradation.Rmd | 2 30 files changed, 270 insertions(+), 235 deletions(-)
Title: Additional 'tidyverse' Functions
Description: Provides functions such as str_crush(), add_missing_column(),
coalesce_data() and drop_na_all() that complement 'tidyverse' functionality
or functions that provide alternative behaviors such as if_else2()
and str_detect2().
Author: Joe Thorley [aut] ,
Ayla Pearson [cre] ,
Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between tidyplus versions 0.0.2 dated 2022-12-16 and 0.2.0 dated 2025-01-24
DESCRIPTION | 23 +++- MD5 | 87 +++++++++++------- NAMESPACE | 6 + NEWS.md | 17 +++ R/add-missing-column.R | 39 ++++---- R/coalesce-data.R | 32 +++--- R/collapse-comments.R | 15 +-- R/drop-na-all.R | 15 +-- R/drop-uninformative-columns.R | 23 ++-- R/duplicates.R |only R/if-else2.R | 45 +++++---- R/only.R | 22 ++-- R/replace-na-if.R | 22 ++-- R/str-crush.R | 11 +- R/str-detect2.R | 13 +- R/str-replace_vec.R |only R/str-to-snake-case.R |only R/summarise2.R |only R/tidyplus-package.R | 1 R/unite-str.R | 25 ++--- README.md | 5 - build |only man/collapse_comments.Rd | 5 - man/drop_na_all.Rd | 3 man/drop_uninformative_columns.Rd | 5 - man/duplicates.Rd |only man/figures |only man/if_else2.Rd | 44 +++++---- man/replace_na_if.Rd | 16 +-- man/str_detect2.Rd | 2 man/str_replace_vec.Rd |only man/str_to_snake_case.Rd |only man/summarise2.Rd |only man/tidyplus-package.Rd | 8 + tests/testthat/_snaps/summarise2.md |only tests/testthat/test-add-missing-column.R | 26 +++-- tests/testthat/test-coalesce-data.R | 107 ++++++++++++++++++++--- tests/testthat/test-drop-na-all.R | 22 +++- tests/testthat/test-drop-uninformative-columns.R | 10 +- tests/testthat/test-duplicates.R |only tests/testthat/test-if-else2.R | 28 +++++- tests/testthat/test-replace-na-if.R | 12 +- tests/testthat/test-str-crush.R | 10 +- tests/testthat/test-str-detect2.R | 19 +++- tests/testthat/test-str-replace-vec.R |only tests/testthat/test-str-to-snake-case.R |only tests/testthat/test-summarise2.R |only tests/testthat/test-unite-str.R | 15 +-- 48 files changed, 472 insertions(+), 261 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: The quantile varying coefficient model is robust to data heterogeneity,
outliers and heavy-tailed distributions in the response variable. In addition,
it can flexibly model dynamic patterns of regression coefficients through
nonparametric varying coefficient functions. In this package, we have implemented
the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with
spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808> for efficient
Bayesian shrinkage estimation, variable selection and statistical inference. In particular,
valid Bayesian inferences on sparse quantile varying coefficient functions can be validated
on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed
and alternative models can be efficiently performed by using the package.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.3 dated 2024-12-21 and 1.0.4 dated 2025-01-24
DESCRIPTION | 19 ++--- MD5 | 22 +++-- NAMESPACE | 2 R/coverage.R |only R/estimation.R |only R/pqrBayes-package.R | 122 ++++++++++++++++---------------- R/pqrBayes.R | 171 ++++++++++++++++++++++----------------------- R/predict.pqrBayes.R | 9 +- R/select.VC.R | 8 +- README.md | 94 +++++++++++++++++++++++- man/coverage.Rd |only man/estimation.pqrBayes.Rd |only man/pqrBayes.Rd | 3 man/predict.pqrBayes.Rd | 3 14 files changed, 274 insertions(+), 179 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.4.0 dated 2024-10-26 and 1.5.0 dated 2025-01-24
DESCRIPTION | 6 ++--- MD5 | 24 +++++++++++++++++------ NEWS.md | 14 +++++++++++++ R/rd-PPGE.R | 53 ++++++++++++++++++++++++++++++++++----------------- R/rd-Russett64.R |only R/rd-china_peace.R |only R/rd-gas_demand.R |only R/rd-wb_groups.R |only build/partial.rdb |binary data/PPGE.rda |binary data/Russett64.rda |only data/china_peace.rda |only data/gas_demand.rda |only data/wb_groups.rda |only man/PPGE.Rd | 53 ++++++++++++++++++++++++++++++++++----------------- man/Russett64.Rd |only man/china_peace.Rd |only man/gas_demand.Rd |only man/wb_groups.Rd |only 19 files changed, 107 insertions(+), 43 deletions(-)
Title: Draw Samples of Truncated Multivariate Normal Distributions
Description: Draw samples from truncated multivariate normal distribution using the sequential nearest neighbor (SNN) method introduced in "Scalable Sampling of Truncated Multivariate Normals Using Sequential Nearest-Neighbor Approximation" <doi:10.48550/arXiv.2406.17307>.
Author: Jian Cao [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Jian Cao <jcao2416@gmail.com>
Diff between nntmvn versions 1.0.0 dated 2024-07-27 and 1.1.0 dated 2025-01-24
DESCRIPTION | 16 ++++++++-------- MD5 | 15 +++++++++++---- NAMESPACE | 3 +++ R/RcppExports.R |only R/correlation_nn_search.R |only R/nntmvn.R |only R/tmvn_sample.R | 43 ++++++++++++++++++++++++++++++------------- man/corr_nn.Rd |only man/nntmvn.Rd |only man/rtmvn_snn.Rd | 30 ++++++++++++++++++------------ src |only 11 files changed, 70 insertions(+), 37 deletions(-)
Title: Execute R in a 'Docker' Context
Description: The goal of 'jetty' is to execute R functions and code
snippets in an isolated R subprocess within a 'Docker' container
and return the evaluated results to the local R session. 'jetty'
can install necessary packages at runtime and seamlessly propagates
errors and outputs from the 'Docker' subprocess back to the main
session. 'jetty' is primarily designed for sandboxed testing and
quick execution of example code.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between jetty versions 0.1.0 dated 2025-01-09 and 0.2.0 dated 2025-01-24
DESCRIPTION | 6 - MD5 | 20 +++-- NAMESPACE | 1 NEWS.md | 15 ++++ R/script.R |only R/utils.R | 12 ++- README.md | 108 +++++++++++++++++++++++------- man/figures/README-unnamed-chunk-11-1.png |only man/run_script.Rd |only man/scaffolding |only tests/testthat/test-docker.R | 25 ++++-- tests/testthat/test-script.R |only tests/testthat/test-utils.R | 1 13 files changed, 139 insertions(+), 49 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms
of the DBSCAN family. Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and
HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering
points to identify the clustering structure), shared nearest neighbor
clustering, and the outlier detection algorithms LOF (local outlier
factor) and GLOSH (global-local outlier score from hierarchies). The
implementations use the kd-tree data structure (from library ANN) for
faster k-nearest neighbor search. An R interface to fast kNN and
fixed-radius NN search is also provided. Hahsler, Piekenbrock and
Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph]
,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph],
Claudia Malzer [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.2-0 dated 2024-06-28 and 1.2.1 dated 2025-01-24
dbscan-1.2-0/dbscan/inst/test_data |only dbscan-1.2-0/dbscan/src/buildHDBSCAN.cpp |only dbscan-1.2-0/dbscan/src/comps.cpp |only dbscan-1.2-0/dbscan/src/prims_mst.cpp |only dbscan-1.2-0/dbscan/src/union_find.cpp |only dbscan-1.2-0/dbscan/src/union_find.h |only dbscan-1.2.1/dbscan/DESCRIPTION | 63 - dbscan-1.2.1/dbscan/MD5 | 152 +-- dbscan-1.2.1/dbscan/NAMESPACE | 6 dbscan-1.2.1/dbscan/NEWS.md | 33 dbscan-1.2.1/dbscan/R/DBCV_datasets.R |only dbscan-1.2.1/dbscan/R/GLOSH.R | 2 dbscan-1.2.1/dbscan/R/LOF.R | 18 dbscan-1.2.1/dbscan/R/NN.R | 6 dbscan-1.2.1/dbscan/R/RcppExports.R | 124 +- dbscan-1.2.1/dbscan/R/broom-dbscan-tidiers.R | 2 dbscan-1.2.1/dbscan/R/comps.R | 2 dbscan-1.2.1/dbscan/R/dbcv.R |only dbscan-1.2.1/dbscan/R/dbscan.R | 33 dbscan-1.2.1/dbscan/R/dendrogram.R | 23 dbscan-1.2.1/dbscan/R/extractFOSC.R | 43 dbscan-1.2.1/dbscan/R/frNN.R | 25 dbscan-1.2.1/dbscan/R/hdbscan.R | 218 +++- dbscan-1.2.1/dbscan/R/hullplot.R | 66 + dbscan-1.2.1/dbscan/R/jpclust.R | 6 dbscan-1.2.1/dbscan/R/kNN.R | 34 dbscan-1.2.1/dbscan/R/kNNdist.R | 2 dbscan-1.2.1/dbscan/R/ncluster.R |only dbscan-1.2.1/dbscan/R/optics.R | 72 - dbscan-1.2.1/dbscan/R/pointdensity.R | 76 + dbscan-1.2.1/dbscan/R/reachability.R | 6 dbscan-1.2.1/dbscan/R/sNN.R | 6 dbscan-1.2.1/dbscan/R/sNNclust.R | 10 dbscan-1.2.1/dbscan/R/utils.R |only dbscan-1.2.1/dbscan/README.md | 53 - dbscan-1.2.1/dbscan/build/partial.rdb |binary dbscan-1.2.1/dbscan/build/vignette.rds |binary dbscan-1.2.1/dbscan/data/Dataset_1.rda |only dbscan-1.2.1/dbscan/data/Dataset_2.rda |only dbscan-1.2.1/dbscan/data/Dataset_3.rda |only dbscan-1.2.1/dbscan/data/Dataset_4.rda |only dbscan-1.2.1/dbscan/inst/README_files/OPTICS_extractDBSCAN-1.png |binary dbscan-1.2.1/dbscan/inst/README_files/dbscan-1.png |binary dbscan-1.2.1/dbscan/inst/README_files/hdbscan-1.png |binary dbscan-1.2.1/dbscan/inst/README_files/tidyverse3-1.png |binary dbscan-1.2.1/dbscan/inst/doc/dbscan.pdf |binary dbscan-1.2.1/dbscan/inst/doc/hdbscan.html | 270 +++--- dbscan-1.2.1/dbscan/man/DBCV_datasets.Rd |only dbscan-1.2.1/dbscan/man/comps.Rd | 2 dbscan-1.2.1/dbscan/man/dbcv.Rd |only dbscan-1.2.1/dbscan/man/dbscan-package.Rd | 3 dbscan-1.2.1/dbscan/man/dbscan.Rd | 3 dbscan-1.2.1/dbscan/man/dbscan_tidiers.Rd | 2 dbscan-1.2.1/dbscan/man/extractFOSC.Rd | 1 dbscan-1.2.1/dbscan/man/frNN.Rd | 4 dbscan-1.2.1/dbscan/man/hdbscan.Rd | 81 + dbscan-1.2.1/dbscan/man/hullplot.Rd | 24 dbscan-1.2.1/dbscan/man/jpclust.Rd | 5 dbscan-1.2.1/dbscan/man/kNN.Rd | 2 dbscan-1.2.1/dbscan/man/ncluster.Rd |only dbscan-1.2.1/dbscan/man/optics.Rd | 1 dbscan-1.2.1/dbscan/man/pointdensity.Rd | 17 dbscan-1.2.1/dbscan/man/reachability.Rd | 2 dbscan-1.2.1/dbscan/man/sNNclust.Rd | 3 dbscan-1.2.1/dbscan/src/Makevars | 17 dbscan-1.2.1/dbscan/src/RcppExports.cpp | 442 +++++----- dbscan-1.2.1/dbscan/src/UnionFind.cpp |only dbscan-1.2.1/dbscan/src/UnionFind.h |only dbscan-1.2.1/dbscan/src/connectedComps.cpp |only dbscan-1.2.1/dbscan/src/dbcv.cpp |only dbscan-1.2.1/dbscan/src/dendrogram.cpp | 18 dbscan-1.2.1/dbscan/src/density.cpp | 2 dbscan-1.2.1/dbscan/src/hdbscan.cpp |only dbscan-1.2.1/dbscan/src/kNN.cpp | 6 dbscan-1.2.1/dbscan/src/kNN.h |only dbscan-1.2.1/dbscan/src/lt.h |only dbscan-1.2.1/dbscan/src/mst.cpp |only dbscan-1.2.1/dbscan/src/mst.h |only dbscan-1.2.1/dbscan/src/utilities.cpp |only dbscan-1.2.1/dbscan/src/utilities.h | 92 -- dbscan-1.2.1/dbscan/tests/testthat/fixtures |only dbscan-1.2.1/dbscan/tests/testthat/test-dbcv.R |only dbscan-1.2.1/dbscan/tests/testthat/test-frNN.R | 10 dbscan-1.2.1/dbscan/tests/testthat/test-hdbscan.R | 38 dbscan-1.2.1/dbscan/tests/testthat/test-kNN.R | 10 dbscan-1.2.1/dbscan/tests/testthat/test-mst.R |only dbscan-1.2.1/dbscan/tests/testthat/test-optics.R | 6 dbscan-1.2.1/dbscan/tests/testthat/test-opticsXi.R | 8 dbscan-1.2.1/dbscan/tests/testthat/test-sNN.R | 6 dbscan-1.2.1/dbscan/vignettes/dbscan.bib | 9 90 files changed, 1262 insertions(+), 903 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Description: Functions to compute quasi variances and associated measures of approximation error.
Author: David Firth [aut, cre]
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between qvcalc versions 1.0.3 dated 2023-05-26 and 1.0.4 dated 2025-01-24
DESCRIPTION | 23 ++-- MD5 | 32 +++-- NAMESPACE | 2 NEWS.md | 5 R/qvcalc.R | 283 ++++++++++++++++++++++++++++++++++++++++++++++++++++- R/qvcalc.coxph.R | 2 R/qvcalc.itempar.R | 5 R/qvcalc.lm.R | 4 R/qvcalc.survreg.R | 4 R/worstErrors.R | 47 ++++++++ build/partial.rdb |binary man/indentPrint.Rd | 29 +++-- man/plot.qv.Rd | 126 +++++++++++++---------- man/qvcalc.Rd | 273 +++++++++++++++++++++++++-------------------------- man/worstErrors.Rd | 54 +++++----- tests |only 16 files changed, 637 insertions(+), 252 deletions(-)
Title: Tools for Create Emissions for Air Quality Models
Description: Processing tools to create emissions for use in numerical air
quality models. Emissions can be calculated both using emission factors
and activity data (Schuch et al 2018) <doi:10.21105/joss.00662> or using
pollutant inventories (Schuch et al., 2018) <doi:10.30564/jasr.v1i1.347>.
Functions to process individual point emissions, line emissions and
area emissions of pollutants are available as well as methods to
incorporate alternative data for Spatial distribution of emissions
such as satellite images (Gavidia-Calderon et. al, 2018)
<doi:10.1016/j.atmosenv.2018.09.026> or openstreetmap data
(Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.
Author: Daniel Schuch [aut, cre] ,
Sergio Ibarra-Espinosa [aut]
Maintainer: Daniel Schuch <underschuch@gmail.com>
Diff between EmissV versions 0.665.8.0 dated 2024-09-17 and 0.665.9.0 dated 2025-01-24
DESCRIPTION | 8 - MD5 | 28 ++--- NEWS.md | 4 R/read.R | 73 ++++++++++--- build/partial.rdb |binary man/EmissV-package.Rd | 60 +++++------ man/emissionFactor.Rd | 102 +++++++++---------- man/perfil.Rd | 222 +++++++++++++++++++++--------------------- man/plumeRise.Rd | 158 +++++++++++++++--------------- man/read.Rd | 31 +++-- man/speciation.Rd | 82 +++++++-------- man/species.Rd | 240 +++++++++++++++++++++++----------------------- man/totalEmission.Rd | 80 +++++++-------- man/vehicles.Rd | 172 ++++++++++++++++---------------- tests/testthat/Rplots.pdf |binary 15 files changed, 652 insertions(+), 608 deletions(-)
Title: Example Data Sets for Use with Discrete Statistical Tests
Description: Provides several data sets for use with discrete statistical tests
and discrete multiple testing procedures. Some of them are also available as a
four-column version, so that each row represents a 2x2 table.
Author: Christina Kihn [aut],
Sebastian Doehler [aut],
Florian Junge [cre, aut],
Lukas Klein [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between DiscreteDatasets versions 0.1.1 dated 2024-05-28 and 0.1.2 dated 2025-01-24
DESCRIPTION | 18 ++++++++++-------- MD5 | 11 +++++++---- NEWS.md | 5 +++++ R/federalist.R |only build/partial.rdb |binary data/federalist.rda |only man/DiscreteDatasets-package.Rd | 5 +++++ man/federalist.Rd |only 8 files changed, 27 insertions(+), 12 deletions(-)
More information about DiscreteDatasets at CRAN
Permanent link
Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It
is designed to be simple, fast and customizable. Error messages
follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [aut] ,
Ayla Pearson [aut] ,
Florencia D'Andrea [ctb],
Nadine Hussein [ctb] ,
Evan Amies-Galonski [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between chk versions 0.9.2 dated 2024-07-09 and 0.10.0 dated 2025-01-24
chk-0.10.0/chk/DESCRIPTION | 15 chk-0.10.0/chk/MD5 | 348 ++-- chk-0.10.0/chk/NAMESPACE | 8 chk-0.10.0/chk/NEWS.md | 8 chk-0.10.0/chk/R/check-length.R |only chk-0.10.0/chk/R/chk-all-equal.R | 8 chk-0.10.0/chk/R/chk-all-equivalent.R | 9 chk-0.10.0/chk/R/chk-all-identical.R | 9 chk-0.10.0/chk/R/chk-all.R | 7 chk-0.10.0/chk/R/chk-array.R | 7 chk-0.10.0/chk/R/chk-atomic.R | 7 chk-0.10.0/chk/R/chk-character-or-factor.R | 9 chk-0.10.0/chk/R/chk-character.R | 7 chk-0.10.0/chk/R/chk-compatible-lengths.R | 6 chk-0.10.0/chk/R/chk-complex-number.R |only chk-0.10.0/chk/R/chk-complex.R |only chk-0.10.0/chk/R/chk-count.R | 9 chk-0.10.0/chk/R/chk-data.R | 11 chk-0.10.0/chk/R/chk-date.R | 9 chk-0.10.0/chk/R/chk-datetime.R | 9 chk-0.10.0/chk/R/chk-dir.R | 8 chk-0.10.0/chk/R/chk-double.R | 7 chk-0.10.0/chk/R/chk-environment.R | 8 chk-0.10.0/chk/R/chk-equal.R | 8 chk-0.10.0/chk/R/chk-equivalent.R | 8 chk-0.10.0/chk/R/chk-ext.R | 8 chk-0.10.0/chk/R/chk-factor.R | 8 chk-0.10.0/chk/R/chk-false.R | 9 chk-0.10.0/chk/R/chk-file.R | 9 chk-0.10.0/chk/R/chk-flag.R | 12 chk-0.10.0/chk/R/chk-function.R | 9 chk-0.10.0/chk/R/chk-gt.R | 7 chk-0.10.0/chk/R/chk-gte.R | 7 chk-0.10.0/chk/R/chk-identical.R | 7 chk-0.10.0/chk/R/chk-integer.R | 7 chk-0.10.0/chk/R/chk-is.R | 7 chk-0.10.0/chk/R/chk-join.R | 10 chk-0.10.0/chk/R/chk-length.R | 9 chk-0.10.0/chk/R/chk-lgl.R | 22 chk-0.10.0/chk/R/chk-list.R | 7 chk-0.10.0/chk/R/chk-logical.R | 12 chk-0.10.0/chk/R/chk-lt.R | 8 chk-0.10.0/chk/R/chk-lte.R | 7 chk-0.10.0/chk/R/chk-match.R | 8 chk-0.10.0/chk/R/chk-matrix.R | 7 chk-0.10.0/chk/R/chk-missing.R | 7 chk-0.10.0/chk/R/chk-named.R | 8 chk-0.10.0/chk/R/chk-not-any-na.R | 6 chk-0.10.0/chk/R/chk-not-empty.R | 7 chk-0.10.0/chk/R/chk-not-missing.R | 8 chk-0.10.0/chk/R/chk-not-null.R | 8 chk-0.10.0/chk/R/chk-not-subset.R | 8 chk-0.10.0/chk/R/chk-null.R | 8 chk-0.10.0/chk/R/chk-number.R | 8 chk-0.10.0/chk/R/chk-numeric.R | 7 chk-0.10.0/chk/R/chk-orderset.R | 9 chk-0.10.0/chk/R/chk-package.R | 4 chk-0.10.0/chk/R/chk-range.R | 8 chk-0.10.0/chk/R/chk-raw.R |only chk-0.10.0/chk/R/chk-s3-class.R | 7 chk-0.10.0/chk/R/chk-s4-class.R | 7 chk-0.10.0/chk/R/chk-scalar.R | 7 chk-0.10.0/chk/R/chk-setequal.R | 8 chk-0.10.0/chk/R/chk-sorted.R | 7 chk-0.10.0/chk/R/chk-string.R | 7 chk-0.10.0/chk/R/chk-subset.R | 11 chk-0.10.0/chk/R/chk-superset.R | 11 chk-0.10.0/chk/R/chk-true.R | 9 chk-0.10.0/chk/R/chk-tz.R | 12 chk-0.10.0/chk/R/chk-unique.R | 8 chk-0.10.0/chk/R/chk-unused.R | 8 chk-0.10.0/chk/R/chk-used.R | 7 chk-0.10.0/chk/R/chk-valid-name.R | 8 chk-0.10.0/chk/R/chk-vector.R | 8 chk-0.10.0/chk/R/chk-whole-number.R | 11 chk-0.10.0/chk/R/chk-whole-numeric.R | 11 chk-0.10.0/chk/R/params.R |only chk-0.10.0/chk/R/utils.R | 2 chk-0.10.0/chk/README.md | 61 chk-0.10.0/chk/build/vignette.rds |binary chk-0.10.0/chk/inst/doc/chk-families.R | 219 ++ chk-0.10.0/chk/inst/doc/chk-families.Rmd | 609 ++++++- chk-0.10.0/chk/inst/doc/chk-families.html | 1336 +++++++++++++--- chk-0.10.0/chk/inst/doc/chk.R | 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chk-0.10.0/chk/vignettes/chk_diagram_II.png |only chk-0.9.2/chk/R/namespace.R |only chk-0.9.2/chk/R/template.R |only 184 files changed, 4260 insertions(+), 1064 deletions(-)
Title: Next Eigenvalue Sufficiency Test
Description: Determine the number of dimensions to retain in exploratory factor analysis. The main function, nest(), returns the solution and the plot(nest()) returns a plot.
Author: P.-O. Caron [aut, cre, cph]
Maintainer: P.-O. Caron <pocaron19@gmail.com>
Diff between Rnest versions 0.0.0.2 dated 2024-11-07 and 1.0 dated 2025-01-24
Rnest-0.0.0.2/Rnest/R/ex.mqr.R |only Rnest-0.0.0.2/Rnest/data/ex.mqr.rda |only Rnest-0.0.0.2/Rnest/man/ex.mqr.Rd |only Rnest-1.0/Rnest/DESCRIPTION | 10 +- Rnest-1.0/Rnest/MD5 | 109 ++++++++++++++---------- Rnest-1.0/Rnest/NAMESPACE | 20 ++++ Rnest-1.0/Rnest/R/BartlettSphericity.R |only Rnest-1.0/Rnest/R/EKC.R |only Rnest-1.0/Rnest/R/Ledermann.R |only Rnest-1.0/Rnest/R/MAP.R |only Rnest-1.0/Rnest/R/achim.R | 5 - Rnest-1.0/Rnest/R/achim24.R |only Rnest-1.0/Rnest/R/briggs_maccallum2003.R | 7 - Rnest-1.0/Rnest/R/caron2016.R | 7 - Rnest-1.0/Rnest/R/caron2019.R |only Rnest-1.0/Rnest/R/cor_nest.R |only Rnest-1.0/Rnest/R/cormat.R | 7 + Rnest-1.0/Rnest/R/cormat.l.R | 7 + Rnest-1.0/Rnest/R/covFIML.R |only Rnest-1.0/Rnest/R/ex_2factors.R | 5 - Rnest-1.0/Rnest/R/ex_3factors_doub_unique.R | 10 +- Rnest-1.0/Rnest/R/ex_4factors_corr.R | 7 + Rnest-1.0/Rnest/R/ex_mqr.R |only Rnest-1.0/Rnest/R/genr8.R | 10 +- Rnest-1.0/Rnest/R/loadings.R | 8 - Rnest-1.0/Rnest/R/meek_bouchard.R | 9 + Rnest-1.0/Rnest/R/nest.R | 65 ++++++++------ Rnest-1.0/Rnest/R/pa.R | 66 +++++++++----- Rnest-1.0/Rnest/R/plot.nest.R | 34 +------ Rnest-1.0/Rnest/R/print.nest.R | 7 + Rnest-1.0/Rnest/R/remove_unique.R |only Rnest-1.0/Rnest/R/shem.R | 4 Rnest-1.0/Rnest/R/summary.nest.R | 5 - Rnest-1.0/Rnest/R/tabachnick_fidell2019.R |only Rnest-1.0/Rnest/R/unique_variable.R |only Rnest-1.0/Rnest/README.md | 113 +++++++++++++++++++------ Rnest-1.0/Rnest/build/partial.rdb |binary Rnest-1.0/Rnest/data/achim24.rda |only Rnest-1.0/Rnest/data/caron2019.rda |only Rnest-1.0/Rnest/data/ex_mqr.rda |only Rnest-1.0/Rnest/data/tabachnick_fidell2019.rda |only Rnest-1.0/Rnest/inst/ma.bib | 18 +++ Rnest-1.0/Rnest/man/BartlettSphericity.Rd |only Rnest-1.0/Rnest/man/EKC.Rd |only Rnest-1.0/Rnest/man/Ledermann.Rd |only Rnest-1.0/Rnest/man/MAP.Rd |only Rnest-1.0/Rnest/man/achim.Rd | 7 + Rnest-1.0/Rnest/man/achim24.Rd |only Rnest-1.0/Rnest/man/briggs_maccallum2003.Rd | 9 + Rnest-1.0/Rnest/man/caron2016.Rd | 9 + Rnest-1.0/Rnest/man/caron2019.Rd |only Rnest-1.0/Rnest/man/cormat.Rd | 7 + Rnest-1.0/Rnest/man/cormat.l.Rd | 7 + Rnest-1.0/Rnest/man/covFIML.Rd |only Rnest-1.0/Rnest/man/cov_nest.Rd |only Rnest-1.0/Rnest/man/ex_2factors.Rd | 5 - Rnest-1.0/Rnest/man/ex_3factors_doub_unique.Rd | 10 +- Rnest-1.0/Rnest/man/ex_4factors_corr.Rd | 7 + Rnest-1.0/Rnest/man/ex_mqr.Rd |only Rnest-1.0/Rnest/man/genr8.Rd | 8 - Rnest-1.0/Rnest/man/loadings.Rd | 8 - Rnest-1.0/Rnest/man/meek_bouchard.Rd | 9 + Rnest-1.0/Rnest/man/nest.Rd | 39 ++++---- Rnest-1.0/Rnest/man/pa.Rd | 22 ++-- Rnest-1.0/Rnest/man/plot.nest.Rd | 8 - Rnest-1.0/Rnest/man/print.nest.Rd | 4 Rnest-1.0/Rnest/man/remove_unique.Rd |only Rnest-1.0/Rnest/man/shem.Rd | 4 Rnest-1.0/Rnest/man/summary.nest.Rd | 4 Rnest-1.0/Rnest/man/tabachnick_fidell2019.Rd |only Rnest-1.0/Rnest/man/unique_variable.Rd |only 71 files changed, 444 insertions(+), 256 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.1.3-1 dated 2024-12-08 and 1.1.3-2 dated 2025-01-24
DESCRIPTION | 6 MD5 | 45 - NEWS.md | 22 R/cpp11.R | 25 R/cpp12.R |only R/relational.R | 20 R/rethrow-gen.R | 55 + cleanup | 2 src/Makevars | 3 src/Makevars.win | 3 src/cpp11.cpp | 53 + src/duckdb.tar.xz |binary src/include/from-tar.mk | 1 src/include/to-tar-win.mk | 1 src/include/to-tar.mk | 1 src/include/typesr.hpp | 2 src/relational.cpp | 16 src/reltoaltrep.cpp | 87 ++ src/scan.cpp | 30 src/statement.cpp | 4 tests/testthat/_snaps/relational.md | 40 + tests/testthat/test-DBItest.R | 5 tests/testthat/test-rel_api.R | 1224 +++++++++++++++--------------------- tests/testthat/test-relational.R | 66 + 24 files changed, 940 insertions(+), 771 deletions(-)
Title: Reporting Tools for 'shiny' Modules
Description: Prebuilt 'shiny' modules containing tools for the generation
of 'rmarkdown' reports, supporting reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre] ,
Kartikeya Kirar [aut] ,
Marcin Kosinski [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Mahmoud Hallal [aut],
Chendi Liao [rev],
Dony Unardi [rev],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.reporter versions 0.3.1 dated 2024-03-15 and 0.4.0 dated 2025-01-24
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Title: Time to Event Outcome in Experimental Designs of Pre-Clinical
Studies
Description: Conduct simulation-based customized power calculation
for clustered time to event data in a mixed crossed/nested design,
where a number of cell lines and a number of mice within each cell line are considered to achieve a desired statistical power,
motivated by Eckel-Passow and colleagues (2021) <doi:10.1093/neuonc/noab137> and Li and colleagues (2024) <doi:10.48550/arXiv.2404.08927>.
This package provides two commonly used models for powering a design, linear mixed effects and Cox frailty model. Both models account for
within-subject (cell line) correlation while holding different distributional assumptions about the outcome.
Alternatively, the counterparts of fixed effects model are also available, which produces similar estimates of statistical power.
Author: Shanpeng Li [aut, cre],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between PDXpower versions 1.0.3 dated 2024-07-31 and 1.0.4 dated 2025-01-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/plotpower.R | 22 ++++++++++++++-------- 3 files changed, 20 insertions(+), 14 deletions(-)
Title: Simulation of Parameterized Stochastic Boolean Networks
Description: A Boolean network is a particular kind of discrete dynamical system where the variables are simple binary switches. Despite its simplicity, Boolean network modeling has been a successful method to describe the behavioral pattern of various phenomena. Applying stochastic noise to Boolean networks is a useful approach for representing the effects of various perturbing stimuli on complex systems. A number of methods have been developed to control noise effects on Boolean networks using parameters integrated into the update rules. This package provides functions to examine three such methods: Boolean network with perturbations (BNp), described by Trairatphisan et al. (2013) <doi:10.1186/1478-811X-11-46>, stochastic discrete dynamical systems (SDDS), proposed by Murrugarra et al. (2012) <doi:10.1186/1687-4153-2012-5>, and Boolean network with probabilistic edge weights (PEW), presented by Deritei et al. (2022) <doi:10.1371/journal.pcbi.1010536>. This package includes sourc [...truncated...]
Author: Mohammad Taheri-Ledari [aut, cre, cph]
,
Kaveh Kavousi [ctb] ,
Sayed-Amir Marashi [ctb] ,
Authors of BoolNet [ctb] ,
Troy D. Hanson [ctb]
Maintainer: Mohammad Taheri-Ledari <mo.taheri@ut.ac.ir>
Diff between pastboon versions 0.1.3 dated 2025-01-08 and 0.1.4 dated 2025-01-24
pastboon-0.1.3/pastboon/data/myeloid_differentiation_net.rda |only pastboon-0.1.3/pastboon/man/myeloid_differentiation_net.Rd |only pastboon-0.1.4/pastboon/DESCRIPTION | 6 +++--- pastboon-0.1.4/pastboon/MD5 | 6 +++--- pastboon-0.1.4/pastboon/data/myeloid_diff_net.rda |only pastboon-0.1.4/pastboon/man/myeloid_diff_net.Rd |only 6 files changed, 6 insertions(+), 6 deletions(-)
Title: Tidy Presentation of Clinical Reporting
Description: Streamlined statistical reporting in 'Rmarkdown' environments.
Facilitates the automated reporting of descriptive statistics, multiple
univariate models, multivariable models and tables combining these outputs.
Plotting functions include customisable survival curves, forest plots from
logistic and ordinal regression and bivariate comparison plots.
Author: Lisa Avery [cre, aut] ,
Ryan Del Bel [aut],
Osvaldo Espin-Garcia [aut],
Katherine Lajkosz [aut] ,
Clarina Ong [aut],
Tyler Pittman [aut] ,
Anna Santiago [aut] ,
Yanning Wang [ctr],
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Lisa Avery <lisa.avery@uhn.ca>
Diff between reportRmd versions 0.1.0 dated 2023-11-16 and 0.1.1 dated 2025-01-24
reportRmd-0.1.0/reportRmd/data/testData.rda |only reportRmd-0.1.0/reportRmd/man/testData.Rd |only reportRmd-0.1.1/reportRmd/DESCRIPTION | 26 reportRmd-0.1.1/reportRmd/MD5 | 113 reportRmd-0.1.1/reportRmd/NAMESPACE | 8 reportRmd-0.1.1/reportRmd/NEWS.md | 103 reportRmd-0.1.1/reportRmd/R/autoreg.R |only reportRmd-0.1.1/reportRmd/R/autosum.R |only reportRmd-0.1.1/reportRmd/R/data.R | 116 reportRmd-0.1.1/reportRmd/R/getVarLevels.R |only reportRmd-0.1.1/reportRmd/R/helper.R | 1370 - reportRmd-0.1.1/reportRmd/R/lblCode.R | 408 reportRmd-0.1.1/reportRmd/R/main.R | 7435 +++--- reportRmd-0.1.1/reportRmd/R/rm_compactsum.R |only reportRmd-0.1.1/reportRmd/R/rm_mvsum2.R |only reportRmd-0.1.1/reportRmd/R/rm_uvsum2.R |only reportRmd-0.1.1/reportRmd/R/sysdata.rda |only reportRmd-0.1.1/reportRmd/README.md | 2677 +- reportRmd-0.1.1/reportRmd/build/partial.rdb |binary reportRmd-0.1.1/reportRmd/build/vignette.rds |binary reportRmd-0.1.1/reportRmd/data/ctDNA.rda |binary reportRmd-0.1.1/reportRmd/data/pembrolizumab.rda |binary reportRmd-0.1.1/reportRmd/data/uvmodels.rda |only reportRmd-0.1.1/reportRmd/inst/doc/reportRmd.R | 608 reportRmd-0.1.1/reportRmd/inst/doc/reportRmd.Rmd | 1280 - reportRmd-0.1.1/reportRmd/inst/doc/reportRmd.html |10979 +++++----- reportRmd-0.1.1/reportRmd/man/clear_labels.Rd | 1 reportRmd-0.1.1/reportRmd/man/covsum.Rd | 11 reportRmd-0.1.1/reportRmd/man/crrRx.Rd | 2 reportRmd-0.1.1/reportRmd/man/ctDNA.Rd | 4 reportRmd-0.1.1/reportRmd/man/extract_labels.Rd | 1 reportRmd-0.1.1/reportRmd/man/figures/README-unnamed-chunk-10-1.png |binary reportRmd-0.1.1/reportRmd/man/figures/README-unnamed-chunk-11-1.png |only reportRmd-0.1.1/reportRmd/man/figures/README-unnamed-chunk-8-1.png |binary reportRmd-0.1.1/reportRmd/man/figures/README-unnamed-chunk-9-1.png |binary reportRmd-0.1.1/reportRmd/man/ggkmcif.Rd | 2 reportRmd-0.1.1/reportRmd/man/ggkmcif2.Rd | 14 reportRmd-0.1.1/reportRmd/man/ggkmcif2Parameters.Rd | 59 reportRmd-0.1.1/reportRmd/man/m_summary.Rd |only reportRmd-0.1.1/reportRmd/man/mvsum.Rd | 146 reportRmd-0.1.1/reportRmd/man/pembrolizumab.Rd | 8 reportRmd-0.1.1/reportRmd/man/plotuv.Rd | 31 reportRmd-0.1.1/reportRmd/man/replace_plot_labels.Rd |only reportRmd-0.1.1/reportRmd/man/rm_compactsum.Rd |only reportRmd-0.1.1/reportRmd/man/rm_covsum.Rd | 348 reportRmd-0.1.1/reportRmd/man/rm_mvsum.Rd | 77 reportRmd-0.1.1/reportRmd/man/rm_survdiff.Rd | 16 reportRmd-0.1.1/reportRmd/man/rm_survsum.Rd | 4 reportRmd-0.1.1/reportRmd/man/rm_survtime.Rd | 4 reportRmd-0.1.1/reportRmd/man/rm_uvsum.Rd | 136 reportRmd-0.1.1/reportRmd/man/sanitizestr.Rd | 4 reportRmd-0.1.1/reportRmd/man/scrolling_table.Rd |only reportRmd-0.1.1/reportRmd/man/set_labels.Rd | 6 reportRmd-0.1.1/reportRmd/man/set_var_labels.Rd | 6 reportRmd-0.1.1/reportRmd/man/uvmodels.Rd |only reportRmd-0.1.1/reportRmd/man/uvsum.Rd | 238 reportRmd-0.1.1/reportRmd/man/xvar_function.Rd |only reportRmd-0.1.1/reportRmd/man/xvar_function.default.Rd |only reportRmd-0.1.1/reportRmd/tests/testthat/mytests.R |only reportRmd-0.1.1/reportRmd/tests/testthat/test_calculations.R | 562 reportRmd-0.1.1/reportRmd/vignettes/images |only reportRmd-0.1.1/reportRmd/vignettes/reportRmd.Rmd | 1280 - reportRmd-0.1.1/reportRmd/vignettes/usingLabels.qmd | 8 63 files changed, 15452 insertions(+), 12639 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.2.0 dated 2024-12-16 and 0.2.1 dated 2025-01-24
DESCRIPTION | 6 +- MD5 | 40 +++++++------ NAMESPACE | 4 + NEWS.md | 8 ++ R/RcppExports.R | 8 ++ R/filter-decimate.R | 1 R/image-resample3d.R |only R/imaging-fill-surface.R | 29 ++++++++++ R/reexports.R | 3 + R/vcg.R | 113 +++++++++++++++++++++++++++++++++++++++ man/reexports.Rd | 3 - man/resample_3d_volume.Rd |only man/vcg_kdtree_nearest.Rd |only src/RcppExports.cpp | 34 +++++++++++ src/glVector3.cpp | 3 - src/resample3D.cpp |only src/vcgCommon.cpp | 63 +++++++++++++++++++++ src/vcgCommon.h | 22 +++++++ tests/testthat.R | 1 tests/testthat/test-convolve.R | 14 ++++ tests/testthat/test-pwelch.R | 2 tests/testthat/test-resample3D.R |only tests/testthat/test-vcg.R |only tests/testthat/test-vector3.R | 20 ++++-- 24 files changed, 339 insertions(+), 35 deletions(-)
Title: Convert R Models to PMML
Description: R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>,
which converts R models to Predictive Model Markup Language (PMML).
Author: Villu Ruusmann [aut, cre]
Maintainer: Villu Ruusmann <villu.ruusmann@gmail.com>
Diff between r2pmml versions 0.29.0 dated 2024-11-10 and 0.30.0 dated 2025-01-24
r2pmml-0.29.0/r2pmml/inst/java/pmml-converter-1.5.8.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-lightgbm-1.5.5.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-model-1.6.6.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-model-metro-1.6.6.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-rexp-1.6.1.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-rexp-evaluator-1.6.1.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-rexp-lightgbm-1.6.1.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-rexp-xgboost-1.6.1.jar |only r2pmml-0.29.0/r2pmml/inst/java/pmml-xgboost-1.8.6.jar |only r2pmml-0.29.0/r2pmml/java/pmml-converter-1.5.8-sources.jar |only r2pmml-0.29.0/r2pmml/java/pmml-lightgbm-1.5.5-sources.jar |only r2pmml-0.29.0/r2pmml/java/pmml-rexp-1.6.1-sources.jar |only r2pmml-0.29.0/r2pmml/java/pmml-rexp-evaluator-1.6.1-sources.jar |only r2pmml-0.29.0/r2pmml/java/pmml-rexp-lightgbm-1.6.1-sources.jar |only r2pmml-0.29.0/r2pmml/java/pmml-rexp-xgboost-1.6.1-sources.jar |only r2pmml-0.29.0/r2pmml/java/pmml-xgboost-1.8.6-sources.jar |only r2pmml-0.30.0/r2pmml/DESCRIPTION | 8 - r2pmml-0.30.0/r2pmml/MD5 | 42 +++++----- r2pmml-0.30.0/r2pmml/NEWS.md | 25 +++++ r2pmml-0.30.0/r2pmml/README.md | 4 r2pmml-0.30.0/r2pmml/inst/java/classpath.txt | 18 ++-- r2pmml-0.30.0/r2pmml/inst/java/pmml-converter-1.5.12.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-lightgbm-1.5.6.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-model-1.6.11.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-model-metro-1.6.11.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-rexp-1.6.6.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-rexp-evaluator-1.6.6.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-rexp-lightgbm-1.6.6.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-rexp-xgboost-1.6.6.jar |only r2pmml-0.30.0/r2pmml/inst/java/pmml-xgboost-1.8.8.jar |only r2pmml-0.30.0/r2pmml/inst/java/r2pmml-1.0-SNAPSHOT.jar |binary r2pmml-0.30.0/r2pmml/java/pmml-converter-1.5.12-sources.jar |only r2pmml-0.30.0/r2pmml/java/pmml-lightgbm-1.5.6-sources.jar |only r2pmml-0.30.0/r2pmml/java/pmml-rexp-1.6.6-sources.jar |only r2pmml-0.30.0/r2pmml/java/pmml-rexp-evaluator-1.6.6-sources.jar |only r2pmml-0.30.0/r2pmml/java/pmml-rexp-lightgbm-1.6.6-sources.jar |only r2pmml-0.30.0/r2pmml/java/pmml-rexp-xgboost-1.6.6-sources.jar |only r2pmml-0.30.0/r2pmml/java/pmml-xgboost-1.8.8-sources.jar |only 38 files changed, 61 insertions(+), 36 deletions(-)
Title: Genetic Algorithm Optimization
Description: Genetic algorithm are a class of optimization
algorithms inspired by the process of natural selection and genetics.
This package is for learning purposes and allows users to optimize
various functions or parameters by mimicking biological evolution
processes such as selection, crossover, and mutation. Ideal for tasks
like machine learning parameter tuning, mathematical function
optimization, and solving an optimization problem that involves finding
the best solution in a discrete space.
Author: Dany Mukesha [aut, cre]
Maintainer: Dany Mukesha <danymukesha@gmail.com>
Diff between genetic.algo.optimizeR versions 0.3.2 dated 2024-10-10 and 0.3.3 dated 2025-01-24
DESCRIPTION | 7 ++- MD5 | 10 ++--- NEWS.md | 48 +++++++++++++------------- R/mutation.R | 2 - inst/doc/intro_to_genetic.algo.optimizeR.html | 6 +-- tests/testthat/test-test_mutation.R | 4 +- 6 files changed, 40 insertions(+), 37 deletions(-)
More information about genetic.algo.optimizeR at CRAN
Permanent link
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and evaluation,
ensemble of models, ensemble forecasting and visualization. The package permits to run
consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences)
dataset and to combine them in ensemble models and ensemble projections. Some bench of other
evaluation and visualization tools are also available within the package.
Author: Wilfried Thuiller [aut],
Damien Georges [aut],
Maya Gueguen [aut, cre],
Robin Engler [aut],
Frank Breiner [aut],
Bruno Lafourcade [aut],
Remi Patin [aut],
Helene Blancheteau [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.2-5-2 dated 2024-06-14 and 4.2-6-2 dated 2025-01-24
DESCRIPTION | 12 MD5 | 201 +++++------ NAMESPACE | 3 R/BIOMOD_EnsembleForecasting.R | 8 R/BIOMOD_EnsembleModeling.R | 6 R/BIOMOD_FormatingData.R | 23 - R/BIOMOD_Modeling.R | 21 - R/BIOMOD_Projection.R | 13 R/DEPRECATED.R | 17 R/biomod2-package.R | 3 R/biomod2_classes_0.R | 27 + R/biomod2_classes_1.R | 57 +-- R/biomod2_classes_3.R | 37 +- R/biomod2_classes_4.R | 80 ++++ R/biomod2_classes_5.R | 13 R/biomod2_data.R | 44 +- R/biomod2_globalVariables.R | 2 R/biomod2_internal.R | 9 R/bm_BinaryTransformation.R | 2 R/bm_CrossValidation.R | 4 R/bm_FindOptimStat.R | 6 R/bm_MakeFormula.R | 2 R/bm_ModelingOptions.R | 18 R/bm_PlotEvalBoxplot.R | 39 +- R/bm_PlotEvalMean.R | 147 ++++---- R/bm_PlotRangeSize.R | 2 R/bm_PlotResponseCurves.R | 9 R/bm_PlotVarImpBoxplot.R | 37 +- R/bm_PseudoAbsences.R | 65 ++- R/bm_RunModelsLoop.R | 50 ++ R/bm_SRE.R | 4 R/bm_SampleBinaryVector.R | 2 R/bm_SampleFactorLevels.R | 4 R/bm_Tuning.R | 54 +- R/bm_VariablesImportance.R | 4 R/sysdata.rda |binary README.md | 52 ++ build/vignette.rds |binary data/ModelsTable.rda |binary data/OptionsBigboss.rda |binary inst/doc/examples_1_mainFunctions.Rmd | 9 inst/doc/examples_1_mainFunctions.html | 8 inst/doc/examples_2_secundaryFunctions.Rmd | 13 inst/doc/examples_2_secundaryFunctions.html | 12 inst/doc/news.Rmd | 30 + inst/doc/news.html | 43 +- inst/doc/vignette_Abundance.Rmd |only inst/doc/vignette_Abundance.html |only inst/doc/vignette_crossValidation.Rmd | 4 inst/doc/vignette_crossValidation.html | 2 inst/doc/vignette_dataPreparation.Rmd | 6 inst/doc/vignette_dataPreparation.html | 6 inst/doc/vignette_modelingOptions.Rmd | 2 inst/doc/vignette_modelingOptions.html | 2 inst/doc/vignette_presentation.Rmd | 4 inst/doc/vignette_presentation.html | 4 inst/doc/vignette_pseudoAbsences.Rmd | 4 inst/doc/vignette_pseudoAbsences.html | 4 inst/doc/vignette_variability.Rmd | 4 inst/doc/vignette_variability.html | 4 inst/doc/vignette_videos.Rmd | 39 ++ inst/doc/vignette_videos.html | 97 +++++ man/BIOMOD.formated.data.PA.Rd | 18 man/BIOMOD.projection.out.Rd | 2 man/BIOMOD_FormatingData.Rd | 21 - man/BIOMOD_Modeling.Rd | 14 man/BIOMOD_ModelingOptions-deprecated.Rd |only man/DataSpecies.Rd | 2 man/ModelsTable.Rd | 2 man/OptionsBigboss.Rd | 17 man/biomod2-deprecated.Rd | 8 man/biomod2_model.Rd | 3 man/bm_BinaryTransformation.Rd | 4 man/bm_CrossValidation.Rd | 4 man/bm_FindOptimStat.Rd | 8 man/bm_MakeFormula.Rd | 4 man/bm_ModelingOptions.Rd | 13 man/bm_PlotEvalBoxplot.Rd | 4 man/bm_PlotEvalMean.Rd | 4 man/bm_PlotRangeSize.Rd | 4 man/bm_PlotResponseCurves.Rd | 4 man/bm_PlotVarImpBoxplot.Rd | 4 man/bm_PseudoAbsences.Rd | 31 + man/bm_RunModelsLoop.Rd | 8 man/bm_SRE.Rd | 6 man/bm_SampleBinaryVector.Rd | 4 man/bm_SampleFactorLevels.Rd | 6 man/bm_Tuning.Rd | 36 + man/bm_VariablesImportance.Rd | 6 man/predict2.bm.Rd | 8 vignettes/examples_1_mainFunctions.Rmd | 9 vignettes/examples_2_secundaryFunctions.Rmd | 13 vignettes/news.Rmd | 30 + vignettes/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.pdf |binary vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf |binary vignettes/pictures/biomod2_v4.2.6_TOC.png |only vignettes/vignette_Abundance.Rmd |only vignettes/vignette_crossValidation.Rmd | 4 vignettes/vignette_dataPreparation.Rmd | 6 vignettes/vignette_modelingOptions.Rmd | 2 vignettes/vignette_presentation.Rmd | 4 vignettes/vignette_pseudoAbsences.Rmd | 4 vignettes/vignette_variability.Rmd | 4 vignettes/vignette_videos.Rmd | 39 ++ 104 files changed, 1180 insertions(+), 554 deletions(-)
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.12.0 dated 2024-11-20 and 0.12.1 dated 2025-01-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 ++++- R/encoding.R | 5 ++++- inst/doc/cfda.html | 6 +++--- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: Store and Retrieve Data.frames in a Git Repository
Description: The git2rdata package is an R package for writing and reading
dataframes as plain text files. A metadata file stores important
information. 1) Storing metadata allows to maintain the classes of
variables. By default, git2rdata optimizes the data for file storage.
The optimization is most effective on data containing factors. The
optimization makes the data less human readable. The user can turn
this off when they prefer a human readable format over smaller files.
Details on the implementation are available in vignette("plain_text",
package = "git2rdata"). 2) Storing metadata also allows smaller row
based diffs between two consecutive commits. This is a useful feature
when storing data as plain text files under version control. Details
on this part of the implementation are available in
vignette("version_control", package = "git2rdata"). Although we
envisioned git2rdata with a git workflow in mind, you can use it in
combination with other version control systems like subversion [...truncated...]
Author: Thierry Onkelinx [aut, cre] ),
Floris Vanderhaeghe [ctb] ),
Peter Desmet [ctb] ),
Els Lommelen [ctb] ),
Research Institute for Nature and Forest [cph, fnd]
Maintainer: Thierry Onkelinx <thierry.onkelinx@inbo.be>
Diff between git2rdata versions 0.4.1 dated 2024-09-06 and 0.5.0 dated 2025-01-24
DESCRIPTION | 22 +-- MD5 | 100 +++++++------- NAMESPACE | 2 NEWS.md | 7 + R/data_package.R |only R/meta.R | 53 ++++++- R/read_vc.R | 55 ++++---- R/recent_commit.R | 12 + R/update_metadata.R | 23 ++- R/upgrade_data.R | 11 + R/write_vc.R | 36 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/doc/efficiency.R | 150 ++++++++++----------- inst/doc/efficiency.html | 34 ++-- inst/doc/metadata.html | 60 ++++---- inst/doc/plain_text.R | 2 inst/doc/plain_text.html | 112 ++++++++-------- inst/doc/split_by.R | 70 +++++----- inst/doc/split_by.html | 6 inst/doc/version_control.R | 4 inst/doc/version_control.html | 76 +++++------ inst/doc/workflow.R | 104 +++++++-------- inst/doc/workflow.html | 61 ++++---- man/data_package.Rd |only man/display_metadata.Rd | 1 man/list_data.Rd | 1 man/meta.Rd | 15 +- man/prune_meta.Rd | 1 man/read_vc.Rd | 6 man/recent_commit.Rd | 12 + man/relabel.Rd | 1 man/rename_variable.Rd | 1 man/rm_data.Rd | 1 man/update_metadata.Rd | 13 + man/upgrade_data.Rd | 11 + man/verify_vc.Rd | 1 man/write_vc.Rd | 22 ++- tests/testthat/setup_test_data.R | 12 + tests/testthat/test_a_basics.R | 205 +++++++++++++++++------------- tests/testthat/test_a_coalesce.R |only tests/testthat/test_b_is_git2rmeta.R | 12 + tests/testthat/test_b_prune.R | 15 +- tests/testthat/test_b_update.R | 29 ++-- tests/testthat/test_b_verify_vc.R | 3 tests/testthat/test_c_git.R | 78 +++-------- tests/testthat/test_d_description.R | 38 ++++- tests/testthat/test_d_recent_commit.R | 6 tests/testthat/test_e_data_package.R |only tests/testthat/test_e_validate_metadata.R | 12 + tests/testthat/test_f_split_by.R | 11 + tests/testthat/test_g_rename_variable.R | 11 + 53 files changed, 893 insertions(+), 631 deletions(-)
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.3.8 dated 2024-12-19 and 0.4.0 dated 2025-01-24
FuzzyImputationTest-0.3.8/FuzzyImputationTest/R/ValueAmbiguityArea.R |only FuzzyImputationTest-0.4.0/FuzzyImputationTest/DESCRIPTION | 6 - FuzzyImputationTest-0.4.0/FuzzyImputationTest/MD5 | 19 ++- FuzzyImputationTest-0.4.0/FuzzyImputationTest/R/CalculateFuzzyMeasures.R | 3 FuzzyImputationTest-0.4.0/FuzzyImputationTest/R/CalculateFuzzyMeasuresSingleVar.R | 8 + FuzzyImputationTest-0.4.0/FuzzyImputationTest/R/MeasureCharacteristic.R |only FuzzyImputationTest-0.4.0/FuzzyImputationTest/R/ValueAmbiguityAreaWidth.R |only FuzzyImputationTest-0.4.0/FuzzyImputationTest/R/utils.R | 2 FuzzyImputationTest-0.4.0/FuzzyImputationTest/man/CalculateFuzzyMeasures.Rd | 3 FuzzyImputationTest-0.4.0/FuzzyImputationTest/tests/testthat/_snaps/CalculateFuzzyMeasures.md | 16 +++ FuzzyImputationTest-0.4.0/FuzzyImputationTest/tests/testthat/_snaps/ImputationTests.md | 16 +++ FuzzyImputationTest-0.4.0/FuzzyImputationTest/tests/testthat/_snaps/MethodsComparison.md | 48 ++++++++++ 12 files changed, 106 insertions(+), 15 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
Title: Detection and Attribution Analysis of Climate Change
Description: Conduct detection and attribution of climate change using methods including optimal fingerprinting via
generalized total least squares or estimating equation approach from Ma et al. (2023) <doi:10.1175/JCLI-D-22-0681.1>.
Provide shrinkage estimators for covariance matrix from Ledoit and Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4>,
and Ledoit and Wolf (2017) <doi:10.2139/ssrn.2383361>.
Author: Yan Li [aut, cre],
Kun Chen [aut],
Jun Yan [aut]
Maintainer: Yan Li <yan.4.li@uconn.edu>
Diff between dacc versions 0.0-5 dated 2024-09-20 and 0.0-6 dated 2025-01-24
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/fingerprint.R | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: 'AWS Python SDK' ('boto3') for R
Description: Fork-safe, raw access to the 'Amazon Web Services' ('AWS') 'SDK' via the 'boto3' 'Python' module, and convenient helper functions to query the 'Simple Storage Service' ('S3') and 'Key Management Service' ('KMS'), partial support for 'IAM', the 'Systems Manager Parameter Store' and 'Secrets Manager'.
Author: Gergely Daroczi [aut, cre] ,
System1 [fnd]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between botor versions 0.4.0 dated 2023-03-12 and 0.4.1 dated 2025-01-24
DESCRIPTION | 10 +++--- MD5 | 47 ++++++++++++++++---------------- NEWS.md | 23 +++++++++++---- R/botor.R | 47 ++++++++++++++++++++++---------- R/kinesis.R | 46 +++++++++++++++++++------------ R/kms.R | 20 ++++++++++--- R/s3.R | 48 ++++++++++++++++++++++----------- R/sm.R | 40 +++++++++++++-------------- R/utils.R | 7 +++- R/zzz.R | 2 - README.md | 6 ++-- inst/tests/testthat/test-load.R | 15 ++++++++-- man/botor_client.Rd | 20 ++++++++++--- man/coerce_bytes_literals_to_string.Rd | 5 ++- man/figures |only man/kinesis_get_records.Rd | 7 +++- man/kinesis_get_shard_iterator.Rd | 9 ++++-- man/kinesis_put_record.Rd | 13 ++++++-- man/kms_encrypt.Rd | 9 ++++-- man/kms_encrypt_file.Rd | 9 ++++-- man/kms_generate_data_key.Rd | 14 +++++++-- man/s3.Rd | 5 ++- man/s3_ls.Rd | 8 ++++- man/s3_put_object_tagging.Rd | 13 ++++++-- man/s3_write.Rd | 12 ++++++-- 25 files changed, 287 insertions(+), 148 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Eric Anderson [ctb],
Matthew Fidler [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.1.8 dated 2024-10-31 and 0.1.9 dated 2025-01-24
NMdata-0.1.8/NMdata/R/addOmegaCorr.R |only NMdata-0.1.8/NMdata/inst/examples/nonmem/xgxr132.msf |only NMdata-0.1.8/NMdata/inst/examples/nonmem/xgxr132.xml |only NMdata-0.1.8/NMdata/inst/examples/nonmem/xgxr132_ETAS.msf |only NMdata-0.1.9/NMdata/DESCRIPTION | 18 NMdata-0.1.9/NMdata/MD5 | 130 +++-- NMdata-0.1.9/NMdata/NAMESPACE | 2 NMdata-0.1.9/NMdata/NEWS.md | 77 +++ NMdata-0.1.9/NMdata/R/NMcheckData.R | 41 + NMdata-0.1.9/NMdata/R/NMgenText.R | 27 - NMdata-0.1.9/NMdata/R/NMorderColumns.R | 13 NMdata-0.1.9/NMdata/R/NMreadExt.R | 14 NMdata-0.1.9/NMdata/R/NMreadInits.R |only NMdata-0.1.9/NMdata/R/NMreadParsText.R | 237 +++++++--- NMdata-0.1.9/NMdata/R/NMrelate.R | 3 NMdata-0.1.9/NMdata/R/NMrelateOne.R | 26 - NMdata-0.1.9/NMdata/R/NMscanInput.R | 2 NMdata-0.1.9/NMdata/R/NMwriteData.R | 21 NMdata-0.1.9/NMdata/R/NMwriteSection.R | 4 NMdata-0.1.9/NMdata/R/NMwriteSectionOne.R | 30 - NMdata-0.1.9/NMdata/R/addCor.R |only NMdata-0.1.9/NMdata/R/addParType.R | 2 NMdata-0.1.9/NMdata/R/addTAPD.R | 28 + NMdata-0.1.9/NMdata/R/addTableStep.R | 4 NMdata-0.1.9/NMdata/R/compareCols.R | 6 NMdata-0.1.9/NMdata/R/dt2mat.R | 8 NMdata-0.1.9/NMdata/R/flagsCount.R | 7 NMdata-0.1.9/NMdata/R/fnAppend.R | 40 + NMdata-0.1.9/NMdata/R/getLines.R | 11 NMdata-0.1.9/NMdata/R/mat2dt.R | 4 NMdata-0.1.9/NMdata/R/searchColRow.R | 2 NMdata-0.1.9/NMdata/R/zzz.R | 2 NMdata-0.1.9/NMdata/man/NMgenText.Rd | 16 NMdata-0.1.9/NMdata/man/NMreadInits.Rd |only NMdata-0.1.9/NMdata/man/NMreadParsText.Rd | 61 ++ NMdata-0.1.9/NMdata/man/NMwriteData.Rd | 6 NMdata-0.1.9/NMdata/man/NMwriteSection.Rd | 2 NMdata-0.1.9/NMdata/man/addCor.Rd |only NMdata-0.1.9/NMdata/man/addOmegaCorr.Rd | 23 NMdata-0.1.9/NMdata/man/addTAPD.Rd | 15 NMdata-0.1.9/NMdata/man/count_ij.Rd |only NMdata-0.1.9/NMdata/man/flagsCount.Rd | 3 NMdata-0.1.9/NMdata/man/fnAppend.Rd | 13 NMdata-0.1.9/NMdata/man/getLines.Rd |only NMdata-0.1.9/NMdata/man/initsToExt.Rd |only NMdata-0.1.9/NMdata/man/itriag.Rd |only NMdata-0.1.9/NMdata/man/jtriag.Rd |only NMdata-0.1.9/NMdata/man/triagSize.Rd |only NMdata-0.1.9/NMdata/tests/testthat/testData/nonmem/xgxr032.mod | 2 NMdata-0.1.9/NMdata/tests/testthat/testData/nonmem/xgxr032_spaces.mod |only NMdata-0.1.9/NMdata/tests/testthat/testData/nonmem/xgxr133.mod |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMcheckDataFile_01.rds |binary NMdata-0.1.9/NMdata/tests/testthat/testReference/NMcheckData_22.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_01_elems.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_01_lines.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_01_pars.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_02_elems.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_02_lines.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_02_pars.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_03_elems.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_03_lines.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMreadInits_03_pars.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/NMwriteSection_08.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/addOmegaCorr_01.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/compareCols_06.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/fnAppend_03.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/getLines_01.rds |only NMdata-0.1.9/NMdata/tests/testthat/testReference/searchColRow_01.rds |only NMdata-0.1.9/NMdata/tests/testthat/test_NMcheckData.R | 66 +- NMdata-0.1.9/NMdata/tests/testthat/test_NMgenText.R | 8 NMdata-0.1.9/NMdata/tests/testthat/test_NMorderColumns.R | 14 NMdata-0.1.9/NMdata/tests/testthat/test_NMreadInits.R |only NMdata-0.1.9/NMdata/tests/testthat/test_NMreadParText.R | 34 + NMdata-0.1.9/NMdata/tests/testthat/test_NMrelate.R | 1 NMdata-0.1.9/NMdata/tests/testthat/test_NMwriteData.R | 36 + NMdata-0.1.9/NMdata/tests/testthat/test_NMwriteSection.R | 24 + NMdata-0.1.9/NMdata/tests/testthat/test_addCor.R |only NMdata-0.1.9/NMdata/tests/testthat/test_compareCols.R | 17 NMdata-0.1.9/NMdata/tests/testthat/test_flags.R | 2 NMdata-0.1.9/NMdata/tests/testthat/test_fnAppend.R | 39 + NMdata-0.1.9/NMdata/tests/testthat/test_getLines.R |only NMdata-0.1.9/NMdata/tests/testthat/test_listMissings.R | 2 NMdata-0.1.9/NMdata/tests/testthat/test_mat2dt.R | 2 NMdata-0.1.9/NMdata/tests/testthat/test_searchColRow.R |only 84 files changed, 820 insertions(+), 325 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 5.1.0 dated 2024-11-04 and 5.2.0 dated 2025-01-24
DESCRIPTION | 8 MD5 | 94 ++++---- NAMESPACE | 4 NEWS | 22 + R/AIC.R | 11 R/Dsurface.R | 36 +-- R/addCovariates.R | 6 R/confint.secr.R | 45 ++- R/derivedDsurface.R |only R/derivedMS.R | 31 +- R/esa.R | 29 +- R/fastsecrloglik.R | 20 + R/generalsecrloglik.R | 20 + R/loglikhelperfn.R | 3 R/mask.check.R | 2 R/methods.R | 20 - R/modelAverage.R | 19 - R/predict.secr.R | 468 ++++++++++++++++++++-------------------- R/preparedata.R | 12 + R/pxi.R |only R/regionN.R | 76 ++++-- R/score.test.R | 35 +- R/secr.fit.R | 42 ++- R/split.capthist.R | 5 R/split.mask.R | 6 R/split.traps.R | 5 R/summary.secr.R | 5 R/utility.R | 82 ++++++- data/blackbear.RData |binary data/ovenbird.RData |binary data/ovensong.RData |binary data/possum.RData |binary data/secrdemo.RData |binary data/stoatDNA.RData |binary inst/doc/secr-datainput.pdf |binary inst/doc/secr-overview.Rmd | 22 + inst/doc/secr-overview.pdf |binary man/MCgof.Rd | 2 man/OVpossum.Rd | 13 - man/blackbear.Rd | 4 man/derivedDsurface.Rd |only man/derivedMS.Rd | 7 man/details.Rd | 70 ++++- man/predictDsurface.Rd | 16 + man/secr-package.Rd | 4 man/secr.fit.Rd | 13 - man/subset.mask.Rd | 2 src/trapping.cpp | 17 - tests/testthat/test-relativeD.R |only vignettes/secr-overview.Rmd | 22 + 50 files changed, 772 insertions(+), 526 deletions(-)
Title: Graph Community Detection Methods into Systematic Conservation
Planning
Description: An innovative tool-set that incorporates graph community detection
methods into systematic conservation planning. It is designed to
enhance spatial prioritization by focusing on the protection of
areas with high ecological connectivity. Unlike traditional
approaches that prioritize individual planning units, 'priorCON'
focuses on clusters of features that exhibit strong ecological
linkages. The 'priorCON' package is built upon the 'prioritizr'
package <doi:10.32614/CRAN.package.prioritizr>, using commercial
and open-source exact algorithm solvers that ensure optimal
solutions to prioritization problems.
Author: Christos Adam [aut, cre] ,
Aggeliki Doxa [aut] ,
Nikolaos Nagkoulis [aut] ,
Maria Papazekou [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between priorCON versions 0.1.3 dated 2024-11-28 and 0.1.4 dated 2025-01-24
DESCRIPTION | 7 +-- MD5 | 18 ++++---- NAMESPACE | 7 +-- NEWS.md | 7 +++ R/functions_connect.R | 26 +++++++++-- README.md | 2 man/basic_scenario.Rd | 15 +++++- man/connectivity_scenario.Rd | 14 +++++- tests/testthat/test-basic_scenario.r | 51 ++++++++++++++++++----- tests/testthat/test-connectivity_scenario.r | 62 ++++++++++++++++++++-------- 10 files changed, 158 insertions(+), 51 deletions(-)
Title: Read, Plot and Analyse Output from the DEPONS Model
Description: Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Author: Jacob Nabe-Nielsen [aut, cre],
Caitlin K. Frankish [aut],
Axelle Cordier [aut],
Florian G. Weller [aut]
Maintainer: Jacob Nabe-Nielsen <jnn@ecos.au.dk>
Diff between DEPONS2R versions 1.2.5 dated 2025-01-10 and 1.2.6 dated 2025-01-24
DESCRIPTION | 6 - MD5 | 30 +++--- NAMESPACE | 3 R/a-misc.R | 34 ++++--- R/blockdyn-methods.R | 19 ++-- R/dyn-methods.R | 11 +- R/parameter-methods.R | 4 R/ships_methods.R | 190 ++++++++++++++++++++++++++++++------------- R/track-methods.R | 1 man/check.DeponsShips.Rd | 55 +++++++++--- man/make.stationary.ships.Rd | 100 ++++++++++++++++------ man/read.DeponsBlockdyn.Rd | 12 ++ man/read.DeponsDyn.Rd | 9 -- man/read.DeponsParam.Rd | 3 man/shipdata.Rd | 38 +------- man/tick.to.time.Rd | 2 16 files changed, 337 insertions(+), 180 deletions(-)
Title: Spike-and-Slab Variational Bayes for Linear and Logistic
Regression
Description: Implements variational Bayesian algorithms to perform scalable variable selection for sparse, high-dimensional linear and logistic regression models. Features include a novel prioritized updating scheme, which uses a preliminary estimator of the variational means during initialization to generate an updating order prioritizing large, more relevant, coefficients. Sparsity is induced via spike-and-slab priors with either Laplace or Gaussian slabs. By default, the heavier-tailed Laplace density is used. Formal derivations of the algorithms and asymptotic consistency results may be found in Kolyan Ray and Botond Szabo (JASA 2020) and Kolyan Ray, Botond Szabo, and Gabriel Clara (NeurIPS 2020).
Author: Gabriel Clara [aut, cre],
Botond Szabo [aut],
Kolyan Ray [aut]
Maintainer: Gabriel Clara <gabriel.j.clara@gmail.com>
Diff between sparsevb versions 0.1.0 dated 2021-01-15 and 0.1.1 dated 2025-01-24
DESCRIPTION | 17 ++++++++--------- MD5 | 8 ++++---- src/Makevars | 2 +- src/Makevars.win | 6 +++--- src/RcppExports.cpp | 5 +++++ 5 files changed, 21 insertions(+), 17 deletions(-)
Title: Logistic Mapping
Description: Set of tools for mapping of categorical response variables based on principal component analysis (pca) and multidimensional unfolding (mdu).
Author: Mark de Rooij [aut, cre, cph],
Frank Busing [aut, cph],
Juan Claramunt Gonzalez [aut]
Maintainer: Mark de Rooij <rooijm@fsw.leidenuniv.nl>
Diff between lmap versions 0.1.3 dated 2024-12-11 and 0.2.4 dated 2025-01-24
lmap-0.1.3/lmap/R/esm.R |only lmap-0.1.3/lmap/R/summary.esm.R |only lmap-0.1.3/lmap/man/esm.Rd |only lmap-0.1.3/lmap/man/summary.esm.Rd |only lmap-0.2.4/lmap/DESCRIPTION | 10 lmap-0.2.4/lmap/MD5 | 153 ++- lmap-0.2.4/lmap/NAMESPACE | 43 lmap-0.2.4/lmap/R/bootstrap.clmdu.R |only lmap-0.2.4/lmap/R/bootstrap.clpca.R |only lmap-0.2.4/lmap/R/bootstrap.lmdu.R |only lmap-0.2.4/lmap/R/bootstrap.lpca.R |only lmap-0.2.4/lmap/R/bootstrap.mcd.R |only lmap-0.2.4/lmap/R/bootstrap.mrrr.R |only lmap-0.2.4/lmap/R/bootstrap.mru.R |only lmap-0.2.4/lmap/R/clmdu.R | 622 ++++++------ lmap-0.2.4/lmap/R/clpca.R | 523 +++++----- lmap-0.2.4/lmap/R/diabetes.R |only lmap-0.2.4/lmap/R/dpes.R |only lmap-0.2.4/lmap/R/fastmbu.R | 1 lmap-0.2.4/lmap/R/fastmru.R | 17 lmap-0.2.4/lmap/R/kieskompas.R |only lmap-0.2.4/lmap/R/liver.R |only lmap-0.2.4/lmap/R/lmdu.R | 4 lmap-0.2.4/lmap/R/lpca.R | 455 ++++----- lmap-0.2.4/lmap/R/make.df.for.varlabels.R |only lmap-0.2.4/lmap/R/make.dfs.for.X.R |only lmap-0.2.4/lmap/R/mcd1.R |only lmap-0.2.4/lmap/R/mcd2.R |only lmap-0.2.4/lmap/R/mlr.R |only lmap-0.2.4/lmap/R/mrrr.R |only lmap-0.2.4/lmap/R/mru.R | 74 + lmap-0.2.4/lmap/R/nesda.R |only lmap-0.2.4/lmap/R/oos.comparison.R |only lmap-0.2.4/lmap/R/plot.bootstrap.R |only lmap-0.2.4/lmap/R/plot.clmdu.R | 128 -- lmap-0.2.4/lmap/R/plot.clpca.R | 120 -- lmap-0.2.4/lmap/R/plot.lmdu.R | 118 -- lmap-0.2.4/lmap/R/plot.lpca.R | 9 lmap-0.2.4/lmap/R/plot.mrrr.R |only lmap-0.2.4/lmap/R/plot.mru.R | 154 +-- lmap-0.2.4/lmap/R/plot.trioscale.R |only lmap-0.2.4/lmap/R/predict.lpca.R | 130 +- lmap-0.2.4/lmap/R/predict.mlr.R |only lmap-0.2.4/lmap/R/predict.mrrr.R |only lmap-0.2.4/lmap/R/predict.mru.R | 102 +- lmap-0.2.4/lmap/R/procrustes.R |only lmap-0.2.4/lmap/R/procx.R | 84 + lmap-0.2.4/lmap/R/read_drugdata.R |only lmap-0.2.4/lmap/R/read_isspdata_peb.R |only lmap-0.2.4/lmap/R/summary.mcd.R |only lmap-0.2.4/lmap/R/summary.mlr.R |only lmap-0.2.4/lmap/R/summary.mrrr.R |only lmap-0.2.4/lmap/R/summary.mru.R | 62 - lmap-0.2.4/lmap/R/summary.trioscale.R |only lmap-0.2.4/lmap/R/supportPlotlpca.R | 1042 +++++++++------------ lmap-0.2.4/lmap/R/theme_lmda.R |only lmap-0.2.4/lmap/R/trioscale.R |only lmap-0.2.4/lmap/data/diabetes.rda |only lmap-0.2.4/lmap/data/dpes.rda |only lmap-0.2.4/lmap/data/kieskompas.rda |only lmap-0.2.4/lmap/data/liver.rda |only lmap-0.2.4/lmap/data/nesda.rda |only lmap-0.2.4/lmap/man/bootstrap.clmdu.Rd |only lmap-0.2.4/lmap/man/bootstrap.clpca.Rd |only lmap-0.2.4/lmap/man/bootstrap.lmdu.Rd |only lmap-0.2.4/lmap/man/bootstrap.lpca.Rd |only lmap-0.2.4/lmap/man/bootstrap.mcd.Rd |only lmap-0.2.4/lmap/man/bootstrap.mrrr.Rd |only lmap-0.2.4/lmap/man/bootstrap.mru.Rd |only lmap-0.2.4/lmap/man/clpca.Rd | 7 lmap-0.2.4/lmap/man/diabetes.Rd |only lmap-0.2.4/lmap/man/dpes.Rd |only lmap-0.2.4/lmap/man/fastmru.Rd | 3 lmap-0.2.4/lmap/man/ggplot2-ggproto.Rd |only lmap-0.2.4/lmap/man/kieskompas.Rd |only lmap-0.2.4/lmap/man/liver.Rd |only lmap-0.2.4/lmap/man/lpca.Rd | 3 lmap-0.2.4/lmap/man/make.df.for.varlabels.Rd |only lmap-0.2.4/lmap/man/make.dfs.for.X.Rd |only lmap-0.2.4/lmap/man/mcd1.Rd |only lmap-0.2.4/lmap/man/mcd2.Rd |only lmap-0.2.4/lmap/man/mlr.Rd |only lmap-0.2.4/lmap/man/mrrr.Rd |only lmap-0.2.4/lmap/man/mru.Rd | 14 lmap-0.2.4/lmap/man/nesda.Rd |only lmap-0.2.4/lmap/man/oos.comparison.Rd |only lmap-0.2.4/lmap/man/plot.clmdu.Rd | 8 lmap-0.2.4/lmap/man/plot.clpca.Rd | 8 lmap-0.2.4/lmap/man/plot.lmdu.Rd | 8 lmap-0.2.4/lmap/man/plot.lpca.Rd | 5 lmap-0.2.4/lmap/man/plot.mrrr.Rd |only lmap-0.2.4/lmap/man/plot.mru.Rd | 8 lmap-0.2.4/lmap/man/plot.trioscale.Rd |only lmap-0.2.4/lmap/man/predict.lpca.Rd | 1 lmap-0.2.4/lmap/man/predict.mlr.Rd |only lmap-0.2.4/lmap/man/predict.mrrr.Rd |only lmap-0.2.4/lmap/man/predict.mru.Rd | 2 lmap-0.2.4/lmap/man/procrustes1.Rd |only lmap-0.2.4/lmap/man/procx.Rd |only lmap-0.2.4/lmap/man/read_drugdata.Rd |only lmap-0.2.4/lmap/man/read_isspdata_peb.Rd |only lmap-0.2.4/lmap/man/summary.mcd.Rd |only lmap-0.2.4/lmap/man/summary.mlr.Rd |only lmap-0.2.4/lmap/man/summary.mrrr.Rd |only lmap-0.2.4/lmap/man/summary.mru.Rd | 4 lmap-0.2.4/lmap/man/summary.trioscale.Rd |only lmap-0.2.4/lmap/man/theme_lmda.Rd |only lmap-0.2.4/lmap/man/trioscale.Rd |only lmap-0.2.4/lmap/src/bigmdu.c |only lmap-0.2.4/lmap/src/flib.c | 1314 +++++++++++++++++++++++++-- lmap-0.2.4/lmap/src/flib.h | 47 lmap-0.2.4/lmap/src/fmdu.h | 8 lmap-0.2.4/lmap/src/init.c | 4 lmap-0.2.4/lmap/src/lmap.h | 6 lmap-0.2.4/lmap/src/mulnomresmduneg.c | 4 lmap-0.2.4/lmap/src/resmduneg.c | 46 116 files changed, 3264 insertions(+), 2087 deletions(-)
Title: Spatially Explicit Capture-Recapture by Inverse Prediction
Description: Estimates the density of a spatially distributed animal population
sampled with an array of passive detectors, such as traps. Models incorporating
distance-dependent detection are fitted by simulation and inverse prediction
as proposed by Efford (2004) <doi:10.1111/j.0030-1299.2004.13043.x>.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between ipsecr versions 1.4.1 dated 2024-01-15 and 1.4.2 dated 2025-01-24
DESCRIPTION | 8 ++-- MD5 | 28 +++++++------- NEWS | 8 ++++ R/ipsecr.fit.R | 4 +- R/plot.ipsecr.R | 4 +- R/simCH.R | 5 +- R/utility.R | 82 ++----------------------------------------- inst/doc/ipsecr-vignette.pdf |binary man/ipsecr-internal.Rd | 12 +++--- man/ipsecr-package.Rd | 14 +++---- man/ipsecr.fit.Rd | 8 ++-- man/ipsecrdemo.Rd | 2 - man/plot.ipsecr.Rd | 2 - man/plotProxy.Rd | 2 - man/predict.ipsecr.Rd | 4 +- 15 files changed, 58 insertions(+), 125 deletions(-)
Title: Group Elastic Net Regularized GLMs and GAMs
Description: Efficient algorithms for fitting generalized linear and additive models with group elastic net penalties as described in Helwig (2024) <doi:10.1080/10618600.2024.2362232>. Implements group LASSO, group MCP, and group SCAD with an optional group ridge penalty. Computes the regularization path for linear regression (gaussian), multivariate regression (multigaussian), logistic regression (binomial), multinomial logistic regression (multinomial), log-linear count regression (poisson and negative.binomial), and log-linear continuous regression (gamma and inverse gaussian). Supports default and formula methods for model specification, k-fold cross-validation for tuning the regularization parameters, and nonparametric regression via tensor product reproducing kernel (smoothing spline) basis function expansion.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between grpnet versions 0.6 dated 2024-10-11 and 0.7 dated 2025-01-24
ChangeLog | 35 +++++++ DESCRIPTION | 10 +- MD5 | 58 ++++++------ NAMESPACE | 4 R/R_grpnet_binomial.R | 4 R/R_grpnet_gamma.R | 4 R/R_grpnet_gaussian.R | 4 R/R_grpnet_invgaus.R | 4 R/R_grpnet_multigaus.R |only R/R_grpnet_multinom.R | 4 R/R_grpnet_negbin.R | 4 R/R_grpnet_poisson.R | 4 R/coef.grpnet.R | 6 - R/cv.grpnet.default.R | 210 ++++++++++++++++++++++++++++++++++++++++++++--- R/family.grpnet.R | 6 - R/grpnet.R | 4 R/grpnet.default.R | 159 +++++++++++++++++++++++++++++++++-- R/grpnet.formula.R | 12 +- R/predict.grpnet.R | 47 +++++----- R/rk.R | 25 ++--- build/partial.rdb |binary man/coef.Rd | 2 man/cv.grpnet.Rd | 19 ++++ man/family.grpnet.Rd | 5 - man/grpnet.Rd | 37 +++++++- man/internals-grpnet.Rd | 7 + man/plot.grpnet.Rd | 2 man/predict.cv.grpnet.Rd | 23 +++++ man/predict.grpnet.Rd | 6 - src/grpnet_init.c | 2 src/grpnet_multigaus.f90 |only 31 files changed, 577 insertions(+), 130 deletions(-)
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C for speed.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 2.0.10 dated 2025-01-19 and 2.0.13 dated 2025-01-24
DESCRIPTION | 23 - MD5 | 66 ++-- NAMESPACE | 11 R/bdiv_table.r | 74 ++--- R/boxplot_stats.r | 34 +- R/clustering.r | 12 R/convert.r | 164 +++++------ R/documentation.r | 3 R/rarefy.r | 16 - R/read_biom.r | 14 - R/stats_emmeans.r | 62 ++++ R/stats_table.r | 1 R/utils.r | 12 R/validate.r | 9 R/write_biom.r | 70 ++--- R/zzz.r | 29 +- README.md | 4 man/bdiv_clusters.Rd | 10 man/bdiv_stats.Rd | 1 man/bdiv_table.Rd | 6 man/convert_to_SE.Rd |only man/documentation_default.Rd | 3 man/taxa_clusters.Rd | 4 src/beta_div.c | 154 +++++------ src/get.c |only src/get.h |only src/init.c | 8 src/pair.h |only src/rarefy.c | 139 ++++++--- src/unifrac.c | 532 +++++++++++++++++++++----------------- tests/testthat/test-bdiv_table.r | 41 ++ tests/testthat/test-boxplot.r | 9 tests/testthat/test-convert.r | 55 ++- tests/testthat/test-read_biom.r | 14 - tests/testthat/test-stats_table.r | 2 tests/testthat/test-write_biom.r | 9 36 files changed, 934 insertions(+), 657 deletions(-)
Title: R Interface to 'IGN' Web Services
Description: Automatic open data acquisition from resources of IGN
('Institut National de Information Geographique et forestiere')
(<https://www.ign.fr/>). Available datasets include various types of
raster and vector data, such as digital elevation models, state
borders, spatial databases, cadastral parcels, and more. There also
access to point clouds data ('LIDAR') and specifics API
(<https://apicarto.ign.fr/api/doc/>).
Author: Paul Carteron [aut, cre]
Maintainer: Paul Carteron <carteronpaul@gmail.com>
Diff between happign versions 0.3.1 dated 2024-09-03 and 0.3.2 dated 2025-01-24
happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-156949.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-1b1baa.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-24b05a.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-2fd566.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-349fc2.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-3cdc11.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-56b8d1.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-ec5c6a.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v1-c0ba08.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-5df1f9.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-83136d.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-a9a80f.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-bedfcd.R |only happign-0.3.1/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-fbf477.R |only happign-0.3.1/happign/vignettes/unnamed-chunk-8-1.png |only happign-0.3.2/happign/DESCRIPTION | 8 happign-0.3.2/happign/MD5 | 69 +-- happign-0.3.2/happign/NAMESPACE | 3 happign-0.3.2/happign/NEWS.md | 16 happign-0.3.2/happign/R/data.R | 15 happign-0.3.2/happign/R/get_apicarto_cadastre.R | 20 happign-0.3.2/happign/R/get_apicarto_rpg.R | 168 ++++++- happign-0.3.2/happign/R/get_iso.R | 5 happign-0.3.2/happign/R/get_wms_raster.R | 2 happign-0.3.2/happign/data/com_2024.rda |only happign-0.3.2/happign/inst/doc/Getting_started.Rmd | 114 ++--- happign-0.3.2/happign/inst/doc/Getting_started.html | 165 ++++--- happign-0.3.2/happign/man/com_2024.Rd |only happign-0.3.2/happign/man/get_apicarto_cadastre.Rd | 14 happign-0.3.2/happign/man/get_apicarto_rpg.Rd | 26 - happign-0.3.2/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-454d5f.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-762292.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-820ece.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_cadastre/apicarto.ign.fr/api/cadastre/parcelle-f46f07.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v1-2cbf34.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-21bee7.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-24fbfb.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-8d6e67.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-90cdf6.R |only happign-0.3.2/happign/tests/testthat/get_apicarto_rpg/apicarto.ign.fr/api/rpg/v2-fe16a6.R |only happign-0.3.2/happign/tests/testthat/test-get_apicarto_cadastre.R | 15 happign-0.3.2/happign/tests/testthat/test-get_iso.R | 4 happign-0.3.2/happign/tests/testthat/test-get_wms_raster.R | 75 +++ happign-0.3.2/happign/vignettes/Getting_started.Rmd | 114 ++--- happign-0.3.2/happign/vignettes/Getting_started.Rmd.orig | 2 happign-0.3.2/happign/vignettes/unnamed-chunk-5-1.png |binary happign-0.3.2/happign/vignettes/unnamed-chunk-6-1.png |binary happign-0.3.2/happign/vignettes/unnamed-chunk-7-1.png |binary happign-0.3.2/happign/vignettes/web_only/happign_for_foresters.Rmd | 219 +++++----- 49 files changed, 672 insertions(+), 382 deletions(-)
Title: Dynamic Model Averaging and Dynamic Model Selection for
Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre]
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between fDMA versions 2.2.7 dated 2023-07-16 and 2.2.8 dated 2025-01-24
DESCRIPTION | 8 +- MD5 | 122 +++++++++++++++++++++---------------------- NEWS | 8 ++ R/altf.R | 4 - R/altf2.R | 4 - R/altf3.R | 4 - R/altf4.R | 4 - R/summary.altf2.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/crudeoil.RData |binary data/trends.RData |binary man/altf.Rd | 5 + man/altf2.Rd | 5 + man/altf3.Rd | 5 + man/altf4.Rd | 5 + man/coef.dma.Rd | 5 + man/crudeoil.Rd | 55 ++++++++++++++----- man/dmtest.Rd | 11 ++- man/fDMA.Rd | 5 + man/fitted.dma.Rd | 5 + man/grid.DMA.Rd | 5 + man/grid.roll.reg.Rd | 5 + man/grid.tvp.Rd | 5 + man/hit.ratio.Rd | 7 +- man/hmdmtest.Rd | 11 ++- man/mdmtest.Rd | 11 ++- man/onevar.Rd | 5 + man/plot.altf.Rd | 2 man/plot.altf2.Rd | 4 - man/plot.altf3.Rd | 2 man/plot.altf4.Rd | 2 man/plot.dma.Rd | 11 ++- man/plot.grid.dma.Rd | 9 ++- man/plot.grid.roll.reg.Rd | 7 +- man/plot.grid.tvp.Rd | 7 +- man/plot.reg.Rd | 9 ++- man/plot.tvp.Rd | 7 +- man/predict.dma.Rd | 5 + man/print.altf2.Rd | 2 man/print.dma.Rd | 5 + man/print.grid.dma.Rd | 5 + man/print.grid.roll.reg.Rd | 5 + man/print.grid.tvp.Rd | 5 + man/print.reg.Rd | 5 + man/print.tvp.Rd | 5 + man/rec.reg.Rd | 5 + man/reduce.size.Rd | 5 + man/residuals.dma.Rd | 5 + man/roll.reg.Rd | 5 + man/rvi.Rd | 5 + man/stest.Rd | 5 + man/summary.altf2.Rd | 2 man/summary.dma.Rd | 5 + man/summary.grid.dma.Rd | 5 + man/summary.grid.roll.reg.Rd | 5 + man/summary.grid.tvp.Rd | 5 + man/summary.reg.Rd | 5 + man/summary.tvp.Rd | 5 + man/trends.Rd | 21 ++++--- man/tvp.Rd | 5 + src/RcppExports.cpp | 5 + 62 files changed, 330 insertions(+), 166 deletions(-)
Title: Estimation of Dynamic Finite Mixtures
Description: Allows to perform the dynamic mixture estimation with state-space components and normal regression components, and clustering with normal mixture. Quasi-Bayesian estimation, as well as, that based on the Kerridge inaccuracy approximation are implemented. Main references: Nagy and Suzdaleva (2013) <doi:10.1016/j.apm.2013.05.038>; Nagy et al. (2011) <doi:10.1002/acs.1239>.
Author: Krzysztof Drachal [aut, cre]
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between dynmix versions 2.0 dated 2023-06-13 and 2.1 dated 2025-01-24
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 8 ++++++++ data/oil.RData |binary man/cauimp.Rd | 4 ++-- man/convts.Rd | 4 ++-- man/oil.Rd | 30 +++++++++++++++++++++--------- src/RcppExports.cpp | 5 +++++ 8 files changed, 49 insertions(+), 24 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-14 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-21 0.3.0
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb],
Roger Bivand [ctb] ,
Andrew Brown [ctb],
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-10 dated 2025-01-13 and 1.8-15 dated 2025-01-24
DESCRIPTION | 14 MD5 | 60 +-- NEWS.md | 23 + R/Zdeprecated.R | 3 R/distance.R | 67 ++-- R/divide.R | 20 - R/k_means.R | 19 + R/messages.R | 19 - R/plot.R | 737 +++++++++++++++++++++++----------------------- R/relate.R | 2 R/time.R | 7 R/wrap.R | 45 ++ R/write.R | 2 inst/tinytest/test_rds.R |only inst/tinytest/test_time.R |only man/adjacent.Rd | 124 +++---- man/bestMatch.Rd | 21 - man/cellSize.Rd | 6 man/combineGeoms.Rd | 160 ++++----- man/ext.Rd | 158 ++++----- man/mem.Rd | 3 man/plot.Rd | 2 man/union.Rd | 164 +++++----- man/vect.Rd | 294 +++++++++--------- src/gdalio.cpp | 1 src/geos_methods.cpp | 3 src/ram.cpp | 36 ++ src/raster_methods.cpp | 37 +- src/read_gdal.cpp | 8 src/read_ogr.cpp | 33 ++ src/write_gdal.cpp | 11 src/write_ogr.cpp | 15 32 files changed, 1152 insertions(+), 942 deletions(-)
Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020)
<doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>
Diff between PriceIndices versions 0.2.2 dated 2024-10-09 and 0.2.3 dated 2025-01-24
PriceIndices-0.2.2/PriceIndices/man/figures/README-unnamed-chunk-62-1.png |only PriceIndices-0.2.2/PriceIndices/man/figures/README-unnamed-chunk-64-1.png |only PriceIndices-0.2.2/PriceIndices/man/figures/README-unnamed-chunk-69-1.png |only PriceIndices-0.2.3/PriceIndices/DESCRIPTION | 6 PriceIndices-0.2.3/PriceIndices/MD5 | 43 PriceIndices-0.2.3/PriceIndices/NAMESPACE | 1 PriceIndices-0.2.3/PriceIndices/NEWS.md | 9 PriceIndices-0.2.3/PriceIndices/R/PriceIndices.R | 80 + PriceIndices-0.2.3/PriceIndices/R/f_data_processing.R | 105 - PriceIndices-0.2.3/PriceIndices/R/f_full_multilateral_indices.R | 543 +++++++++- PriceIndices-0.2.3/PriceIndices/README.md | 98 + PriceIndices-0.2.3/PriceIndices/inst/doc/PriceIndices.R | 6 PriceIndices-0.2.3/PriceIndices/inst/doc/PriceIndices.Rmd | 9 PriceIndices-0.2.3/PriceIndices/inst/doc/PriceIndices.html | 5 PriceIndices-0.2.3/PriceIndices/man/PriceIndices.Rd | 84 + PriceIndices-0.2.3/PriceIndices/man/data_norm.Rd | 4 PriceIndices-0.2.3/PriceIndices/man/data_selecting.Rd | 2 PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-19-1.png |binary PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-20-1.png |binary PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-63-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-65-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-70-1.png |binary PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-71-1.png |only PriceIndices-0.2.3/PriceIndices/man/m_decomposition.Rd |only PriceIndices-0.2.3/PriceIndices/man/shrinkflation.Rd | 26 PriceIndices-0.2.3/PriceIndices/vignettes/PriceIndices.Rmd | 9 26 files changed, 838 insertions(+), 192 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.6.1 dated 2024-11-18 and 0.7.0 dated 2025-01-24
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tinytable-0.7.0/tinytable/R/package.R | 2 tinytable-0.7.0/tinytable/R/plot_tt.R | 16 tinytable-0.7.0/tinytable/R/print.R | 3 tinytable-0.7.0/tinytable/R/rbind2.R | 81 - tinytable-0.7.0/tinytable/R/sanity.R | 626 ++++---- tinytable-0.7.0/tinytable/R/save_tt.R | 13 tinytable-0.7.0/tinytable/R/style_bootstrap.R | 212 +- tinytable-0.7.0/tinytable/R/style_grid.R | 38 tinytable-0.7.0/tinytable/R/style_grid_dataframe.R | 27 tinytable-0.7.0/tinytable/R/style_notes.R |only tinytable-0.7.0/tinytable/R/style_string.R |only tinytable-0.7.0/tinytable/R/style_tabularray.R | 45 tinytable-0.7.0/tinytable/R/style_tt.R | 539 +++---- tinytable-0.7.0/tinytable/R/style_typst.R | 224 +-- tinytable-0.7.0/tinytable/R/theme_bootstrap.R | 45 tinytable-0.7.0/tinytable/R/theme_default.R | 39 tinytable-0.7.0/tinytable/R/theme_grid.R | 39 tinytable-0.7.0/tinytable/R/theme_multipage.R | 72 tinytable-0.7.0/tinytable/R/theme_placement.R | 48 tinytable-0.7.0/tinytable/R/theme_resize.R | 74 - 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Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.2.0 dated 2025-01-13 and 5.2.1 dated 2025-01-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ build/Seurat.pdf |binary build/stage23.rdb |binary tests/testthat/test_find_clusters.R | 16 ++++++++++------ 6 files changed, 24 insertions(+), 14 deletions(-)
Title: Classes and Helper Functions for Working with Epidemiological
Parameters
Description: Classes and helper functions for loading, extracting, converting,
manipulating, plotting and aggregating epidemiological parameters for infectious diseases.
Epidemiological parameters extracted from the literature are loaded from the 'epiparameterDB'
R package.
Author: Joshua W. Lambert [aut, cre, cph]
,
Adam Kucharski [aut, cph] ,
Carmen Tamayo [aut] ,
Hugo Gruson [ctb, rev] ,
Sebastian Funk [ctb] ,
Pratik Gupte [rev] ,
James M. Azam [rev] ,
Chris Hartgerink [rev] ,
Tim Taylor [rev]
Maintainer: Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Diff between epiparameter versions 0.4.0 dated 2025-01-08 and 0.4.1 dated 2025-01-24
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