Title: The 'Seven Bridges Platform' API Client
Description: R client and utilities for 'Seven Bridges Platform' API, from 'Cancer Genomics Cloud'
to other 'Seven Bridges' supported platforms. API documentation is hosted publicly
at <https://docs.sevenbridges.com/docs/the-api>.
Author: Marko Trifunovic [aut, cre],
Marija Gacic [aut],
Vladimir Obucina [aut],
Velsera [cph, fnd]
Maintainer: Marko Trifunovic <marko.trifunovic@velsera.com>
Diff between sevenbridges2 versions 0.2.0 dated 2024-07-02 and 0.3.0 dated 2025-02-24
DESCRIPTION | 6 MD5 | 58 +- NAMESPACE | 1 NEWS.md | 92 +++- R/api-utils.R | 2 R/class-AsyncJob.R |only R/class-app.R | 2 R/class-apps.R | 29 - R/class-files.R | 615 ++++++++++++++++++++++++++++- R/class-project.R | 13 R/class-projects.R | 21 inst/WORDLIST | 34 + inst/doc/Authentication_and_Billing.html | 4 inst/doc/Files_upload_and_Volumes.html | 4 inst/doc/Projects_and_Tasks_execution.R | 76 +++ inst/doc/Projects_and_Tasks_execution.Rmd | 145 ++++++ inst/doc/Projects_and_Tasks_execution.html | 140 ++++++ inst/doc/quickstart.R | 20 inst/doc/quickstart.Rmd | 100 ++-- inst/doc/quickstart.html | 87 ++-- man/App.Rd | 2 man/Apps.Rd | 14 man/AsyncJob.Rd |only man/Files.Rd | 532 ++++++++++++++++++++++++- man/Project.Rd | 13 man/Projects.Rd | 6 tests/testthat/_snaps/class-asyncjob.md |only tests/testthat/setup.R | 17 tests/testthat/test-class-asyncjob.R |only tests/testthat/test-class-files.R | 361 ++++++++++++++++- vignettes/Projects_and_Tasks_execution.Rmd | 145 ++++++ vignettes/quickstart.Rmd | 100 ++-- 32 files changed, 2386 insertions(+), 253 deletions(-)
Title: Tools for Identifying Important Nodes in Networks
Description: Includes assorted tools for network analysis. Bridge centrality; goldbricker; MDS, PCA, & eigenmodel network plotting.
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <paytonjjones@gmail.com>
Diff between networktools versions 1.5.2 dated 2024-02-23 and 1.6.0 dated 2025-02-24
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 4 ++++ R/bridge.R | 2 +- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.utils versions 2.12.3 dated 2023-11-17 and 2.13.0 dated 2025-02-24
DESCRIPTION | 6 +-- MD5 | 53 +++++++++++++++++----------------- NEWS.md | 31 +++++++++++++++++++- R/Sys.readlink.Windows.R |only R/Sys.readlink2.R | 52 ---------------------------------- R/System.R | 2 - R/TimeoutException.R | 4 +- R/downloadFile.R | 18 +++++++++++ R/popBackupFile.R | 2 - R/popTemporaryFile.R | 2 - R/zzz.R | 11 +++++++ man/Arguments.Rd | 30 +++++++++---------- man/Assert.Rd | 10 +++--- man/FileProgressBar.Rd | 4 +- man/GString-class.Rd | 32 ++++++++++----------- man/Java.Rd | 24 +++++++-------- man/MultiVerbose.Rd | 4 +- man/NullVerbose.Rd | 6 +-- man/Options.Rd | 20 ++++++------- man/ProgressBar.Rd | 22 +++++++------- man/Settings.Rd | 12 +++---- man/SmartComments.Rd | 10 +++--- man/System.Rd | 14 ++++----- man/TextStatusBar.Rd | 16 +++++----- man/TimeoutException.Rd | 6 +-- man/VComments.Rd | 6 +-- man/Verbose.Rd | 64 +++++++++++++++++++++--------------------- man/findGhostscript.System.Rd | 2 - 28 files changed, 236 insertions(+), 227 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.1.2 dated 2025-01-27 and 4.2.0 dated 2025-02-24
OlinkAnalyze-4.1.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.R |only OlinkAnalyze-4.1.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.Rmd |only OlinkAnalyze-4.1.2/OlinkAnalyze/inst/doc/bridging_E3072toEHT.html |only OlinkAnalyze-4.1.2/OlinkAnalyze/inst/extdata/OlinkIDMapping.rds |only OlinkAnalyze-4.1.2/OlinkAnalyze/vignettes/bridging_E3072toEHT.Rmd |only OlinkAnalyze-4.2.0/OlinkAnalyze/DESCRIPTION | 13 OlinkAnalyze-4.2.0/OlinkAnalyze/MD5 | 82 OlinkAnalyze-4.2.0/OlinkAnalyze/NEWS.md | 13 OlinkAnalyze-4.2.0/OlinkAnalyze/R/Read_NPX_data.R | 67 OlinkAnalyze-4.2.0/OlinkAnalyze/R/olink_normalization.R | 77 OlinkAnalyze-4.2.0/OlinkAnalyze/R/olink_normalization_product.R | 97 OlinkAnalyze-4.2.0/OlinkAnalyze/R/olink_normalization_utils.R | 314 ++- OlinkAnalyze-4.2.0/OlinkAnalyze/R/sysdata.rda |binary OlinkAnalyze-4.2.0/OlinkAnalyze/build/vignette.rds |binary OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/LOD.html | 2 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/OutlierExclusion.html | 4 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/Vignett.Rmd | 4 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/Vignett.html | 12 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/bridging_crossproduct.R |only OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/bridging_crossproduct.Rmd |only OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/bridging_crossproduct.html |only OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/bridging_introduction.R | 20 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/bridging_introduction.Rmd | 178 + OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/bridging_introduction.html | 16 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/doc/plate_randomizer.html | 4 OlinkAnalyze-4.2.0/OlinkAnalyze/inst/extdata/OlinkID_HT_mapping.rds |only OlinkAnalyze-4.2.0/OlinkAnalyze/inst/extdata/OlinkID_Reveal_mapping.rds |only OlinkAnalyze-4.2.0/OlinkAnalyze/man/figures/Bridging_schematic.png |binary OlinkAnalyze-4.2.0/OlinkAnalyze/man/mapping_file_id.Rd |only OlinkAnalyze-4.2.0/OlinkAnalyze/man/norm_internal_cross_product.Rd | 7 OlinkAnalyze-4.2.0/OlinkAnalyze/man/norm_internal_update_maxlod.Rd |only OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_input_assay_overlap.Rd | 2 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_input_check.Rd | 2 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_input_check_samples.Rd | 2 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_input_clean_assays.Rd | 2 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_input_cross_product.Rd | 26 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_product_id.Rd |only OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_norm_reference_id.Rd |only OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_normalization.Rd | 8 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_normalization_bridgeable.Rd | 7 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_normalization_product_format.Rd | 10 OlinkAnalyze-4.2.0/OlinkAnalyze/man/olink_normalization_qs.Rd | 19 OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/data/example_reveal_data.R |only OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/data/ref_results_norm.R | 86 OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 249 ++ OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/test-olink_normalization_product.R | 300 ++ OlinkAnalyze-4.2.0/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 1029 ++++++++-- OlinkAnalyze-4.2.0/OlinkAnalyze/vignettes/Vignett.Rmd | 4 OlinkAnalyze-4.2.0/OlinkAnalyze/vignettes/bridging_crossproduct.Rmd |only OlinkAnalyze-4.2.0/OlinkAnalyze/vignettes/bridging_introduction.Rmd | 178 + 50 files changed, 2288 insertions(+), 546 deletions(-)
Title: An R Interface for Downloading, Reading, and Handling IPUMS Data
Description: An easy way to work with census, survey, and geographic data
provided by IPUMS in R. Generate and download data through the IPUMS
API and load IPUMS files into R with their associated metadata to
make analysis easier. IPUMS data describing 1.4 billion individuals
drawn from over 750 censuses and surveys is available free of charge
from the IPUMS website <https://www.ipums.org>.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Finn Roberts [aut],
Joe Grover [ctb],
Dan Ehrlich [ctb],
Renae Rodgers [ctb],
Institute for Social Research and Data Innovation [cph]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between ipumsr versions 0.8.1 dated 2024-07-17 and 0.8.2 dated 2025-02-24
ipumsr-0.8.1/ipumsr/tests/fixtures/nhgis1270_csv.zip |only ipumsr-0.8.1/ipumsr/tests/fixtures/nhgis1270_shape.zip |only ipumsr-0.8.1/ipumsr/tests/fixtures/nhgis1271_shape.zip |only ipumsr-0.8.1/ipumsr/tests/fixtures/recent-nhgis-extracts-tbl-one.yml |only ipumsr-0.8.1/ipumsr/tests/fixtures/recent-nhgis-extracts-tbl-two.yml |only ipumsr-0.8.1/ipumsr/tests/fixtures/recent-nhgis-extracts-tbl.yml |only ipumsr-0.8.1/ipumsr/tests/fixtures/recent-usa-extracts-tbl-two.yml |only ipumsr-0.8.1/ipumsr/tests/fixtures/recent-usa-extracts-tbl.yml |only ipumsr-0.8.1/ipumsr/tests/fixtures/usa_00301.dat.gz |only ipumsr-0.8.1/ipumsr/tests/fixtures/usa_00301.xml |only ipumsr-0.8.2/ipumsr/DESCRIPTION | 6 ipumsr-0.8.2/ipumsr/MD5 | 231 - ipumsr-0.8.2/ipumsr/NAMESPACE | 2 ipumsr-0.8.2/ipumsr/NEWS.md | 19 ipumsr-0.8.2/ipumsr/R/api_define_extract.R | 15 ipumsr-0.8.2/ipumsr/R/api_helpers.R | 140 ipumsr-0.8.2/ipumsr/R/api_metadata.R | 5 ipumsr-0.8.2/ipumsr/R/api_process_extract.R | 72 ipumsr-0.8.2/ipumsr/R/ddi_read.R | 4 ipumsr-0.8.2/ipumsr/R/list_files.R | 93 ipumsr-0.8.2/ipumsr/R/micro_read.R | 2 ipumsr-0.8.2/ipumsr/R/micro_read_chunked.R | 2 ipumsr-0.8.2/ipumsr/R/micro_read_yield.R | 2 ipumsr-0.8.2/ipumsr/R/shape_join.R | 5 ipumsr-0.8.2/ipumsr/R/shape_read.R | 2 ipumsr-0.8.2/ipumsr/README.md | 722 +-- ipumsr-0.8.2/ipumsr/build/vignette.rds |binary ipumsr-0.8.2/ipumsr/inst/doc/ipums-api-micro.R | 428 +- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api-micro.Rmd | 1102 ++--- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api-micro.html | 1758 ++++---- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api-nhgis.R | 406 - ipumsr-0.8.2/ipumsr/inst/doc/ipums-api-nhgis.Rmd | 900 ++-- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api-nhgis.html | 1562 +++---- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api.R | 542 +- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api.Rmd | 1256 ++--- ipumsr-0.8.2/ipumsr/inst/doc/ipums-api.html | 1660 +++---- ipumsr-0.8.2/ipumsr/inst/doc/ipums-bigdata.R | 558 +- ipumsr-0.8.2/ipumsr/inst/doc/ipums-bigdata.Rmd | 1332 +++--- ipumsr-0.8.2/ipumsr/inst/doc/ipums-bigdata.html | 2122 +++++----- ipumsr-0.8.2/ipumsr/inst/doc/ipums-read.R | 250 - ipumsr-0.8.2/ipumsr/inst/doc/ipums-read.Rmd | 764 +-- ipumsr-0.8.2/ipumsr/inst/doc/ipums-read.html | 1844 ++++---- ipumsr-0.8.2/ipumsr/inst/doc/ipums.R | 166 ipumsr-0.8.2/ipumsr/inst/doc/ipums.Rmd | 588 +- ipumsr-0.8.2/ipumsr/inst/doc/ipums.html | 1329 +++--- ipumsr-0.8.2/ipumsr/inst/doc/value-labels.R | 348 - ipumsr-0.8.2/ipumsr/inst/doc/value-labels.Rmd | 4 ipumsr-0.8.2/ipumsr/inst/doc/value-labels.html | 1890 ++++---- ipumsr-0.8.2/ipumsr/man/add_to_extract.nhgis_extract.Rd | 12 ipumsr-0.8.2/ipumsr/man/define_extract_nhgis.Rd | 15 ipumsr-0.8.2/ipumsr/man/download_supplemental_data.Rd |only ipumsr-0.8.2/ipumsr/man/get_metadata_nhgis.Rd | 5 ipumsr-0.8.2/ipumsr/man/ipums_ddi-class.Rd | 2 ipumsr-0.8.2/ipumsr/man/ipums_list_files.Rd | 22 ipumsr-0.8.2/ipumsr/man/read_ipums_ddi.Rd | 2 ipumsr-0.8.2/ipumsr/man/read_ipums_micro.Rd | 2 ipumsr-0.8.2/ipumsr/man/read_ipums_micro_chunked.Rd | 2 ipumsr-0.8.2/ipumsr/man/read_ipums_micro_yield.Rd | 2 ipumsr-0.8.2/ipumsr/man/read_ipums_sf.Rd | 2 ipumsr-0.8.2/ipumsr/tests/fixtures/api-errors-authorization.yml | 10 ipumsr-0.8.2/ipumsr/tests/fixtures/api-errors-invalid-collection.yml | 13 ipumsr-0.8.2/ipumsr/tests/fixtures/api-errors-invalid-extract-number.yml | 38 ipumsr-0.8.2/ipumsr/tests/fixtures/api-errors-invalid-extract.yml | 48 ipumsr-0.8.2/ipumsr/tests/fixtures/api-errors-invalid-metadata.yml | 35 ipumsr-0.8.2/ipumsr/tests/fixtures/api-errors-paged-extract.yml | 15 ipumsr-0.8.2/ipumsr/tests/fixtures/api-warnings-unsupported.yml | 21 ipumsr-0.8.2/ipumsr/tests/fixtures/atus-submission-error.yml | 13 ipumsr-0.8.2/ipumsr/tests/fixtures/download-extract-not-ready.yml | 168 ipumsr-0.8.2/ipumsr/tests/fixtures/download-nhgis-extract-shp.yml | 60 ipumsr-0.8.2/ipumsr/tests/fixtures/download-nhgis-extract.yml | 122 ipumsr-0.8.2/ipumsr/tests/fixtures/download-supplemental-data.yml |only ipumsr-0.8.2/ipumsr/tests/fixtures/download-usa-extract-collection-number.yml | 141 ipumsr-0.8.2/ipumsr/tests/fixtures/download-usa-extract.yml | 122 ipumsr-0.8.2/ipumsr/tests/fixtures/extract-history-all-records.yml | 246 - 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Title: Adversarial Random Forests
Description: Adversarial random forests (ARFs) recursively partition data into
fully factorized leaves, where features are jointly independent. The
procedure is iterative, with alternating rounds of generation and
discrimination. Data becomes increasingly realistic at each round, until
original and synthetic samples can no longer be reliably distinguished.
This is useful for several unsupervised learning tasks, such as density
estimation and data synthesis. Methods for both are implemented in this
package. ARFs naturally handle unstructured data with mixed continuous and
categorical covariates. They inherit many of the benefits of random forests,
including speed, flexibility, and solid performance with default parameters.
For details, see Watson et al. (2023) <https://proceedings.mlr.press/v206/watson23a.html>.
Author: Marvin N. Wright [aut, cre] ,
David S. Watson [aut] ,
Kristin Blesch [aut] ,
Jan Kapar [aut]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between arf versions 0.2.0 dated 2024-01-24 and 0.2.4 dated 2025-02-24
arf-0.2.0/arf/inst/doc/vignette.R |only arf-0.2.0/arf/inst/doc/vignette.Rmd |only arf-0.2.0/arf/inst/doc/vignette.html |only arf-0.2.0/arf/man/leaf_posterior.Rd |only arf-0.2.0/arf/man/prep_evi.Rd |only arf-0.2.0/arf/vignettes/vignette.Rmd |only arf-0.2.4/arf/DESCRIPTION | 18 arf-0.2.4/arf/MD5 | 70 +- arf-0.2.4/arf/NAMESPACE | 9 arf-0.2.4/arf/NEWS.md | 13 arf-0.2.4/arf/R/adversarial_rf.R | 105 ++- arf-0.2.4/arf/R/arf-package.R |only arf-0.2.4/arf/R/expct.R | 250 +++++-- arf-0.2.4/arf/R/forde.R | 209 ++++-- arf-0.2.4/arf/R/forge.R | 342 +++++++--- arf-0.2.4/arf/R/impute.R |only arf-0.2.4/arf/R/lik.R | 34 - arf-0.2.4/arf/R/shortcut_functions.R |only arf-0.2.4/arf/R/utils.R | 724 ++++++++++++++++------- arf-0.2.4/arf/README.md | 3 arf-0.2.4/arf/build/vignette.rds |binary arf-0.2.4/arf/inst/CITATION |only arf-0.2.4/arf/inst/doc/arf.R |only arf-0.2.4/arf/inst/doc/arf.Rmd |only arf-0.2.4/arf/inst/doc/arf.html |only arf-0.2.4/arf/man/adversarial_rf.Rd | 43 + arf-0.2.4/arf/man/arf-package.Rd |only arf-0.2.4/arf/man/cforde.Rd |only arf-0.2.4/arf/man/col_rename.Rd | 7 arf-0.2.4/arf/man/col_rename_all.Rd |only arf-0.2.4/arf/man/darf.Rd |only arf-0.2.4/arf/man/earf.Rd |only arf-0.2.4/arf/man/expct.Rd | 82 ++ arf-0.2.4/arf/man/forde.Rd | 55 + arf-0.2.4/arf/man/forge.Rd | 91 ++ arf-0.2.4/arf/man/impute.Rd |only arf-0.2.4/arf/man/lik.Rd | 21 arf-0.2.4/arf/man/post_x.Rd | 5 arf-0.2.4/arf/man/prep_cond.Rd |only arf-0.2.4/arf/man/prep_x.Rd | 5 arf-0.2.4/arf/man/rarf.Rd |only arf-0.2.4/arf/man/resample.Rd |only arf-0.2.4/arf/man/which.max.random.Rd |only arf-0.2.4/arf/tests/testthat/test-conditions.R |only arf-0.2.4/arf/tests/testthat/test-impute.R |only arf-0.2.4/arf/tests/testthat/test-input_data.R |only arf-0.2.4/arf/tests/testthat/test-return_types.R | 56 + arf-0.2.4/arf/tests/testthat/test_expct.R |only arf-0.2.4/arf/vignettes/arf.Rmd |only arf-0.2.4/arf/vignettes/vignette.R |only arf-0.2.4/arf/vignettes/vignette.html |only 51 files changed, 1533 insertions(+), 609 deletions(-)
Title: Pattern-Oriented Ensemble Modeling System
Description: A framework of interoperable R6 classes (Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, <doi:10.1126/science.1116681>). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, <doi:10.1093/genetics/162.4.2025>), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, [...truncated...]
Author: Sean Haythorne [aut],
Damien Fordham [aut],
Stuart Brown [aut] ,
Jessie Buettel [aut],
Barry Brook [aut],
July Pilowsky [aut, cre]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>
Diff between poems versions 1.3.1 dated 2024-09-19 and 1.3.2 dated 2025-02-24
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 5 README.md | 67 ++-- inst/doc/translocation_example.pdf |binary man/figures/README-example-2.png |binary tests/testthat/test_results_manager.R | 515 +++++++++++++++++++++++++--------- vignettes/simple_example.html | 93 +++--- vignettes/thylacine_example.html | 39 +- 9 files changed, 516 insertions(+), 227 deletions(-)
Title: Estimators for Two-Sample Capture-Recapture Studies
Description: A comprehensive implementation of Petersen-type estimators
and its many variants for two-sample capture-recapture studies.
A conditional likelihood approach is used that allows
for tag loss; non reporting of tags; reward tags; categorical, geographical and temporal stratification;
partial stratification; reverse capture-recapture;
and continuous variables in modeling the probability of capture.
Many examples from fisheries management are presented.
Author: Carl Schwarz [aut, cre]
Maintainer: Carl Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between Petersen versions 2024.6.1 dated 2024-05-31 and 2025.3.1 dated 2025-02-24
DESCRIPTION | 16 ++++++++-------- MD5 | 28 +++++++++++++++------------- NAMESPACE | 3 +++ NEWS.md | 7 +++++++ R/LP_fit.R | 2 +- R/n1_n2_m2_to_cap_hist.R |only README.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/PackageDocumentation.html | 4 ++-- man/LP_BTSPAS_fit_Diag.Rd | 5 ++++- man/LP_BTSPAS_fit_NonDiag.Rd | 5 ++++- man/LP_IS_fit.Rd | 5 ++++- man/LP_TL_fit.Rd | 5 ++++- man/LP_fit.Rd | 7 +++++-- man/n1_n2_m2_to_cap_hist.Rd |only 16 files changed, 61 insertions(+), 30 deletions(-)
Title: Estimate and Simulate from Location Dependent Marked Point
Processes
Description: A suite of tools for estimating, assessing model fit, simulating from, and visualizing location dependent marked point processes characterized by regularity in the pattern.
You provide a reference marked point process, a set of raster images containing location specific covariates, and select the estimation algorithm and type of mark model.
'ldmppr' estimates the process and mark models and allows you to check the appropriateness of the model using a variety of diagnostic tools.
Once a satisfactory model fit is obtained, you can simulate from the model and visualize the results.
Documentation for the package 'ldmppr' is available in the form of a vignette.
Author: Lane Drew [aut, cre, cph] ,
Andee Kaplan [aut]
Maintainer: Lane Drew <lanetdrew@gmail.com>
Diff between ldmppr versions 1.0.3 dated 2024-12-02 and 1.0.4 dated 2025-02-24
DESCRIPTION | 6 MD5 | 42 +++--- NEWS.md | 10 + R/check_model_fit.R | 20 ++ R/data.R | 24 +++ R/plot_mpp.R | 2 R/predict_marks.R | 15 +- R/simulate_mpp.R | 7 + R/train_mark_model.R | 17 +- R/zzz.R | 4 README.md | 2 data/medium_example_data.rda |only inst/doc/ldmppr_howto.R | 4 inst/doc/ldmppr_howto.Rmd | 8 - inst/doc/ldmppr_howto.html | 143 ++++++++++----------- inst/extdata/Snodgrass_DEM_1m_med.tif |only inst/extdata/Snodgrass_aspect_southness_1m_med.tif |only inst/extdata/Snodgrass_slope_1m_med.tif |only inst/extdata/Snodgrass_wetness_index_1m_med.tif |only man/check_model_fit.Rd | 5 man/medium_example_data.Rd |only man/predict_marks.Rd | 4 man/simulate_mpp.Rd | 5 man/train_mark_model.Rd | 5 vignettes/ldmppr_howto.Rmd | 8 - 25 files changed, 225 insertions(+), 106 deletions(-)
Title: Difference-in-Differences with Unpoolable Data
Description: A framework for estimating difference-in-differences with
unpoolable data, based on Karim, Webb, Austin, and Strumpf (2024)
<doi:10.48550/arXiv.2403.15910>. Supports common or staggered adoption, multiple
groups, and the inclusion of covariates. Also computes p-values for the
aggregate average treatment effect on the treated via the
randomization inference procedure described in MacKinnon and Webb (2020)
<doi:10.1016/j.jeconom.2020.04.024>.
Author: Eric Jamieson [aut, cre, cph]
Maintainer: Eric Jamieson <ericbrucejamieson@gmail.com>
Diff between undidR versions 1.0.0 dated 2025-01-23 and 1.0.1 dated 2025-02-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/undid_stage_two.r | 6 +++--- README.md | 10 +++++----- inst/doc/undidR.html | 20 ++++++++++---------- 6 files changed, 30 insertions(+), 26 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Groq','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://groq.com>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.3.0 dated 2024-12-08 and 0.3.1 dated 2025-02-24
DESCRIPTION | 8 LICENSE | 2 MD5 | 81 +++-- NAMESPACE | 16 + NEWS.md | 69 ++++ R/APIProvider.R | 2 R/LLMMessage.R | 14 R/api_azure_openai.R | 554 ++++++++++++++++++++++++++++++++++++++- R/api_claude.R | 68 ++++ R/api_gemini.R | 16 - R/api_groq.R | 75 +++++ R/api_mistral.R | 75 +++++ R/api_ollama.R | 217 ++++++++++++++- R/api_openai.R | 203 ++++++++++++-- R/api_perplexity.R | 4 R/llm_verbs.R | 39 ++ R/message_retrieval.R | 71 ++++ R/perform_api_requests.R | 2 R/tidyllm_schema.R | 297 +++++++++++++------- R/utilites.R | 22 + README.md | 8 build/vignette.rds |binary inst/doc/tidyllm.R | 4 inst/doc/tidyllm.Rmd | 21 + inst/doc/tidyllm.html | 210 ++++++++++---- man/azure_openai.Rd | 5 man/azure_openai_chat.Rd | 2 man/check_azure_openai_batch.Rd |only man/claude_list_models.Rd |only man/fetch_azure_openai_batch.Rd |only man/field_chr.Rd |only man/gemini_chat.Rd | 4 man/get_logprobs.Rd |only man/groq_list_models.Rd |only man/list_azure_openai_batches.Rd |only man/list_models.Rd |only man/mistral_list_models.Rd |only man/ollama.Rd | 1 man/ollama_delete_model.Rd |only man/openai_chat.Rd | 13 man/openai_list_models.Rd |only man/perplexity_chat.Rd | 4 man/send_azure_openai_batch.Rd |only man/send_ollama_batch.Rd |only man/send_openai_batch.Rd | 11 man/tidyllm_schema.Rd | 60 +--- tests/testthat/test_api_gemini.R | 4 vignettes/tidyllm.Rmd | 21 + 48 files changed, 1886 insertions(+), 317 deletions(-)
Title: Swash-Backwash Model for the Single Epidemic Wave
Description: The Swash-Backwash Model for the Single Epidemic Wave was developed by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> to model the velocity of spread of infectious diseases across space. This package enables the calculation of the Swash-Backwash Model for user-supplied panel data on regional infections. The package also provides additional functions for bootstrap confidence intervals, country comparison, visualization of results, and data management.
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Diff between swash versions 1.0.0 dated 2025-02-13 and 1.1.0 dated 2025-02-24
DESCRIPTION | 10 MD5 | 40 +- NAMESPACE | 12 R/swash.R | 632 ++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary data/COVID19Cases_geoRegion.rda |binary data/Oesterreich_Faelle.rda |only data/datalist | 1 man/COVID19Cases_geoRegion.Rd | 9 man/Oesterreich_Faelle.Rd |only man/as_balanced.Rd |only man/compare_countries.Rd |only man/confint-methods.Rd | 28 + man/countries-class.Rd |only man/hist_ci.Rd | 23 - man/is_balanced.Rd | 46 ++ man/plot-methods.Rd | 3 man/plot_regions-methods.Rd |only man/plot_regions.Rd |only man/quantile_ci.Rd |only man/sbm-class.Rd | 12 man/sbm_ci-class.Rd | 18 + man/summary-methods.Rd | 4 man/swash-package.Rd | 13 man/swash.Rd | 8 25 files changed, 723 insertions(+), 136 deletions(-)
Title: Miscellaneous Functions for Passive Acoustic Analysis
Description: A collection of miscellaneous functions for passive acoustics.
Much of the content here is adapted to R from code written by other people.
If you have any ideas of functions to add, please contact Taiki Sakai.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Julie Oswald [ctb],
Val Schmidt [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMmisc versions 1.12.3 dated 2024-12-11 and 1.12.4 dated 2025-02-24
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 12 +++ R/edinfoToURL.R | 11 ++ R/erddapToEdinfo.R | 31 ++++++++ R/formatURL.R | 45 +++++++++++- R/ncToData.R | 195 +++++++++++++++++++++++++++++++++++++++++++++++------ R/ncUtils.R | 70 +++++++++++-------- R/pwelch.R | 9 +- R/soundtrapQAQC.R | 2 man/pwelch.Rd | 5 + src/file.c | 1 12 files changed, 343 insertions(+), 66 deletions(-)
Title: Automate the Creation of Generalized Additive Models (GAMs)
Description: This wrapper package for 'mgcv' makes it easier to create high-performing Generalized Additive Models (GAMs). With its central function autogam(), by entering just a dataset and the name of the outcome column as inputs, 'AutoGAM' tries to automate the procedure of configuring a highly accurate GAM which performs at reasonably high speed, even for large datasets.
Author: Chitu Okoli [aut, cre]
Maintainer: Chitu Okoli <Chitu.Okoli@skema.edu>
Diff between autogam versions 0.0.1 dated 2024-10-02 and 0.1.0 dated 2025-02-24
DESCRIPTION | 12 MD5 | 29 +- NAMESPACE | 34 ++ NEWS.md | 6 R/autogam-package.R |only R/autogam.R | 373 +++++++++++++++++++++++++++- R/smooth_formula_string.R | 198 +++++++------- R/unpackaged_utils.R |only README.md | 43 +-- inst/WORDLIST | 7 man/autogam-package.Rd |only man/autogam.Rd | 52 ++- man/generic-method.Rd |only man/plot.autogam.Rd |only man/print.autogam.Rd |only man/smooth_formula_string.Rd | 80 +++--- man/summary.autogam.Rd |only tests/testthat/test-autogam.R | 41 ++- tests/testthat/test-smooth_formula_string.R | 13 19 files changed, 658 insertions(+), 230 deletions(-)
Title: Get Data Frame Representations of 'Elasticsearch' Results
Description: 'Elasticsearch' is an open-source, distributed, document-based datastore
(<https://www.elastic.co/products/elasticsearch>).
It provides an 'HTTP' 'API' for querying the database and extracting datasets, but that
'API' was not designed for common data science workflows like pulling large batches of
records and normalizing those documents into a data frame that can be used as a training
dataset for statistical models. 'uptasticsearch' provides an interface for 'Elasticsearch'
that is explicitly designed to make these data science workflows easy and fun.
Author: James Lamb [aut, cre],
Nick Paras [aut],
Austin Dickey [aut],
Michael Frasco [ctb],
Weiwen Gu [ctb],
Will Dearden [ctb],
Uptake Technologies Inc. [cph]
Maintainer: James Lamb <jaylamb20@gmail.com>
Diff between uptasticsearch versions 0.4.0 dated 2019-09-11 and 1.0.0 dated 2025-02-24
uptasticsearch-0.4.0/uptasticsearch/NEWS.md |only uptasticsearch-0.4.0/uptasticsearch/README.md |only uptasticsearch-0.4.0/uptasticsearch/tests/testthat/test-repo_characteristics.R |only uptasticsearch-1.0.0/uptasticsearch/DESCRIPTION | 23 uptasticsearch-1.0.0/uptasticsearch/LICENSE | 2 uptasticsearch-1.0.0/uptasticsearch/MD5 | 63 - uptasticsearch-1.0.0/uptasticsearch/NAMESPACE | 21 uptasticsearch-1.0.0/uptasticsearch/R/assertions.R | 77 + uptasticsearch-1.0.0/uptasticsearch/R/chomp_aggs.R | 72 - uptasticsearch-1.0.0/uptasticsearch/R/chomp_hits.R | 28 uptasticsearch-1.0.0/uptasticsearch/R/es_search.R | 354 +++--- uptasticsearch-1.0.0/uptasticsearch/R/get_fields.R | 193 +-- uptasticsearch-1.0.0/uptasticsearch/R/helperfuns.R |only uptasticsearch-1.0.0/uptasticsearch/R/logging.R | 20 uptasticsearch-1.0.0/uptasticsearch/R/parse_date_time.R | 43 uptasticsearch-1.0.0/uptasticsearch/R/unpack_nested_data.R | 38 uptasticsearch-1.0.0/uptasticsearch/R/uptasticsearch.R | 25 uptasticsearch-1.0.0/uptasticsearch/build/vignette.rds |binary uptasticsearch-1.0.0/uptasticsearch/inst/doc/FAQ.Rmd | 22 uptasticsearch-1.0.0/uptasticsearch/inst/doc/FAQ.html | 355 +----- uptasticsearch-1.0.0/uptasticsearch/man/chomp_aggs.Rd | 4 uptasticsearch-1.0.0/uptasticsearch/man/doc_shared.Rd | 5 uptasticsearch-1.0.0/uptasticsearch/man/es_search.Rd | 35 uptasticsearch-1.0.0/uptasticsearch/man/get_fields.Rd | 2 uptasticsearch-1.0.0/uptasticsearch/man/unpack_nested_data.Rd | 15 uptasticsearch-1.0.0/uptasticsearch/tests/testthat.R | 19 uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-assertions.R |only uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-chomp_aggs.R | 509 ++++------ uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-chomp_hits.R | 84 - uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-es_search.R | 32 uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-get_fields.R | 142 +- uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-integration.R | 186 ++- uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-parse_date_time.R | 66 - uptasticsearch-1.0.0/uptasticsearch/tests/testthat/test-unpack_nested_data.R | 101 + uptasticsearch-1.0.0/uptasticsearch/vignettes/FAQ.Rmd | 22 35 files changed, 1237 insertions(+), 1321 deletions(-)
More information about uptasticsearch at CRAN
Permanent link
Title: Database Interface and MariaDB Driver
Description: Implements a DBI-compliant interface to MariaDB
(<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>)
databases.
Author: Kirill Mueller [aut, cre] ,
Jeroen Ooms [aut] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RMariaDB versions 1.3.3 dated 2024-11-18 and 1.3.4 dated 2025-02-24
DESCRIPTION | 9 +++++---- MD5 | 9 ++++++--- NEWS.md | 11 +++++++++++ R/dbQuoteLiteral_MySQLConnection.R |only R/quote-mysql.R |only man/mysql-quoting.Rd |only src/Makevars.win | 37 +++++++++++++++++++++---------------- 7 files changed, 43 insertions(+), 23 deletions(-)
Title: Hypothesis Testing for Markov Switching Models
Description: Implementation of hypothesis testing procedures described in Hansen (1992) <doi:10.1002/jae.3950070506>, Carrasco, Hu, & Ploberger (2014) <doi:10.3982/ECTA8609>, Dufour & Luger (2017) <doi:10.1080/07474938.2017.1307548>, and Rodriguez Rondon & Dufour (2024) <https://grodriguezrondon.com/files/RodriguezRondon_Dufour_2024_MonteCarlo_LikelihoodRatioTest_MarkovSwitchingModels_20241015.pdf> that can be used to identify the number of regimes in Markov switching models.
Author: Gabriel Rodriguez Rondon [cre, aut],
Jean-Marie Dufour [aut]
Maintainer: Gabriel Rodriguez Rondon <gabriel.rodriguezrondon@mail.mcgill.ca>
Diff between MSTest versions 0.1.3 dated 2024-10-30 and 0.1.5 dated 2025-02-24
DESCRIPTION | 10 +++--- MD5 | 9 +++-- NEWS.md | 6 +++ inst/examples/article.R |only src/htest_MomentTests.cpp | 4 +- src/methods.cpp | 70 +++++++++++++++++++++++----------------------- 6 files changed, 52 insertions(+), 47 deletions(-)
Title: Process Data from Wearable Light Loggers and Optical Radiation
Dosimeters
Description: Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
Author: Johannes Zauner [aut, cre] ,
Manuel Spitschan [aut] ,
Steffen Hartmeyer [aut] ,
MeLiDos [fnd],
EURAMET [fnd] has received funding from
the European Partnership on Metrology, co-financed from the
European Union’s Horizon Europe Research and Innovatio [...truncated...]
Maintainer: Johannes Zauner <johannes.zauner@tum.de>
Diff between LightLogR versions 0.3.8 dated 2024-07-04 and 0.5.3 dated 2025-02-24
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Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 1.1.0 dated 2024-10-14 and 1.2.0 dated 2025-02-24
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Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parametric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.3.2 dated 2024-11-05 and 1.4.0 dated 2025-02-24
DESCRIPTION | 18 MD5 | 175 +++--- NAMESPACE | 11 NEWS.md | 38 + R/ESS.R | 21 R/anova.glm_weightit.R | 220 +++---- R/as.weightit.R | 69 +- R/calibrate.R | 77 +- R/chk-utilities.R | 43 - R/dist_functions.R | 107 +-- R/functions_for_processing.R | 929 ++++++++++++++++++++++---------- R/get_w_from_ps.R | 202 +++--- R/glm_weightit-methods.R | 547 +++++++++++++++--- R/glm_weightit.R | 369 ++++++++---- R/glm_weightit_helpers.R | 474 ++++++++-------- R/make_full_rank.R | 64 +- R/msmdata.R | 18 R/multinom_weightit.R | 187 ++---- R/ordinal_weightit.R | 93 +-- R/plot.weightit.R | 45 + R/predict.glm_weightit.R | 113 ++- R/sbps.R | 244 ++++---- R/summary.weightit.R | 159 +++-- R/trim.R | 142 ++-- R/utils.R | 516 +++++++++++------ R/weightit.R | 302 ++++++---- R/weightit.fit.R | 254 ++++---- R/weightit2bart.R | 184 ++++-- R/weightit2cbps.R | 747 +++++++++++++++++++------ R/weightit2ebal.R | 427 ++++++++++---- R/weightit2energy.R | 300 ++++++---- R/weightit2gbm.R | 467 +++++++++------- R/weightit2glm.R | 792 +++++++++++++++------------ R/weightit2ipt.R | 378 ++++++++++--- R/weightit2npcbps.R | 86 +- R/weightit2null.R | 4 R/weightit2optweight.R | 286 +++++---- R/weightit2ps.R | 44 - R/weightit2super.R | 393 ++++++++----- R/weightit2user.R | 42 - R/weightitMSM.R | 279 +++++---- R/weightit_methods.R | 49 - README.md | 19 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/WeightIt.Rmd | 16 inst/doc/WeightIt.html | 64 -- inst/doc/estimating-effects.Rmd | 40 - inst/doc/estimating-effects.html | 365 +++++------- inst/doc/installing-packages.html | 4 man/ESS.Rd | 10 man/anova.glm_weightit.Rd | 54 + man/as.weightit.Rd | 41 - man/calibrate.Rd | 35 - man/dot-weightit_methods.Rd | 16 man/get_w_from_ps.Rd | 153 ++--- man/glm_weightit-methods.Rd | 107 +++ man/glm_weightit.Rd | 235 +++++--- man/make_full_rank.Rd | 25 man/method_bart.Rd | 108 ++- man/method_cbps.Rd | 146 +++-- man/method_ebal.Rd | 98 ++- man/method_energy.Rd | 139 +++- man/method_gbm.Rd | 125 +++- man/method_glm.Rd | 161 ++++- man/method_ipt.Rd | 73 +- man/method_npcbps.Rd | 51 + man/method_optweight.Rd | 95 ++- man/method_super.Rd | 125 +++- man/method_user.Rd | 2 man/msmdata.Rd | 17 man/plot.weightit.Rd | 30 - man/predict.glm_weightit.Rd | 69 +- man/sbps.Rd | 110 +-- man/summary.weightit.Rd | 52 + man/trim.Rd | 84 +- man/weightit.Rd | 229 ++++--- man/weightit.fit.Rd | 171 ++--- man/weightitMSM.Rd | 191 +++--- tests/testthat/helper-M_est.R | 77 ++ tests/testthat/helpers.R |only tests/testthat/test-glm_weightit.R | 80 ++ tests/testthat/test-method_cbps.R |only tests/testthat/test-method_ebal.R |only tests/testthat/test-method_glm.R | 149 ++++- tests/testthat/test-method_ipt.R |only tests/testthat/test-multinom_weightit.R | 25 tests/testthat/test-ordinal_weightit.R | 26 tests/testthat/test-update.R |only vignettes/WeightIt.Rmd | 16 vignettes/estimating-effects.Rmd | 40 - 91 files changed, 8752 insertions(+), 4836 deletions(-)
Title: Machine Learning for Merging Satellite and Ground Precipitation
Data
Description: A machine learning algorithm that merges satellite and ground precipitation data using Random Forest for spatial prediction, residual modeling for bias correction, and quantile mapping for adjustment, ensuring accurate estimates across temporal scales and regions.
Author: Jonnathan Augusto Landi Bermeo [aut, cre, cph]
,
Alex Aviles [aut] ,
Dario Zhina [aut] ,
Marco Mogro [aut]
Maintainer: Jonnathan Augusto Landi Bermeo <jonnathan.landi@outlook.com>
Diff between RFplus versions 1.2-2 dated 2025-02-04 and 1.3-0 dated 2025-02-24
DESCRIPTION | 27 ++- MD5 | 20 +- NAMESPACE | 6 NEWS.md | 21 ++ R/RFplus.R | 384 +++++++++++++++++++++++++++++-------------- R/RFplusNews.R |only R/zzz.R |only README.md | 85 +++++---- inst/NEWS |only inst/doc/RFplus.html | 88 +++++---- man/RFplus.Rd | 44 +++- man/figures |only tests/testthat/test-RFplus.R | 9 - 13 files changed, 443 insertions(+), 241 deletions(-)
Title: Cluster Analysis with Missing Values by Multiple Imputation
Description: Allows clustering of incomplete observations by addressing missing values using multiple imputation. For achieving this goal, the methodology consists in three steps, following Audigier and Niang 2022 <doi:10.1007/s11634-022-00519-1>. I) Missing data imputation using dedicated models. Four multiple imputation methods are proposed, two are based on joint modelling and two are fully sequential methods, as discussed in Audigier et al. (2021) <doi:10.48550/arXiv.2106.04424>. II) cluster analysis of imputed data sets. Six clustering methods are available (distances-based or model-based), but custom methods can also be easily used. III) Partition pooling. The set of partitions is aggregated using Non-negative Matrix Factorization based method. An associated instability measure is computed by bootstrap (see Fang, Y. and Wang, J., 2012 <doi:10.1016/j.csda.2011.09.003>). Among applications, this instability measure can be used to choose a number of clusters with missing value [...truncated...]
Author: Vincent Audigier [aut, cre] ,
Hang Joon Kim [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between clusterMI versions 1.4.0 dated 2025-02-12 and 1.5 dated 2025-02-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/cluster.intern.R | 2 +- R/imputedata.R | 6 ++---- build/vignette.rds |binary inst/doc/clusterMI.pdf |binary man/cluster.intern.Rd | 2 +- 7 files changed, 14 insertions(+), 16 deletions(-)
Title: Flexible and Robust Agreement and Reliability Analyses
Description: Reliability and agreement analyses often have limited software support. Therefore, this package was created to make agreement and reliability analyses easier for the average researcher. The functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability. In addition, this package contains a set of functions to help when planning studies looking to assess measurement agreement.
Author: Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between SimplyAgree versions 0.2.0 dated 2024-03-21 and 0.2.1 dated 2025-02-24
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SimplyAgree-0.2.1/SimplyAgree/man/simple_agree-methods.Rd | 114 SimplyAgree-0.2.1/SimplyAgree/man/simple_eiv-methods.Rd | 72 SimplyAgree-0.2.1/SimplyAgree/man/simple_reli-methods.Rd | 62 SimplyAgree-0.2.1/SimplyAgree/man/temps.Rd | 74 SimplyAgree-0.2.1/SimplyAgree/man/tolerance_delta-methods.Rd | 88 SimplyAgree-0.2.1/SimplyAgree/man/tolerance_limit.Rd | 195 SimplyAgree-0.2.1/SimplyAgree/tests/testthat.R | 8 SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-agree_nest.R | 636 +- SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-agree_np.R | 256 - SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-agree_reps.R | 368 - SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-blandPowerCurve.R | 228 SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-dem_reg.R | 162 SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-loa_lme.R | 270 - SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-loa_mixed.R | 172 SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-reli_stats.R | 786 +-- SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test-tolerance_limit.R | 598 +- SimplyAgree-0.2.1/SimplyAgree/tests/testthat/test_agree_test.R | 416 - SimplyAgree-0.2.1/SimplyAgree/vignettes/Deming.Rmd | 418 - SimplyAgree-0.2.1/SimplyAgree/vignettes/agree_tests.Rmd | 1078 ++-- SimplyAgree-0.2.1/SimplyAgree/vignettes/agreement_analysis.Rmd | 1133 ++-- SimplyAgree-0.2.1/SimplyAgree/vignettes/reanalysis.Rmd | 550 +- SimplyAgree-0.2.1/SimplyAgree/vignettes/ref.bib | 174 SimplyAgree-0.2.1/SimplyAgree/vignettes/refs.bib | 692 +- SimplyAgree-0.2.1/SimplyAgree/vignettes/reliability_analysis.Rmd | 1000 ++-- 117 files changed, 24337 insertions(+), 24078 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.40.0 dated 2024-11-14 and 1.41.0 dated 2025-02-24
DESCRIPTION | 6 MD5 | 82 +++-- NAMESPACE | 3 NEWS.md | 26 + R/config.R | 115 +++++--- R/install.R | 19 + R/package.R | 9 R/pip.R | 10 R/py_require.R |only R/repl.R | 7 R/use_python.R | 10 R/utils.R | 80 +++++ R/virtualenv.R | 21 + inst/config/config.py | 2 inst/doc/arrays.html | 5 inst/doc/calling_python.html | 5 inst/doc/package.Rmd | 358 ++++++++++++++++++++------ inst/doc/package.html | 452 ++++++++++++++++++++------------- inst/doc/python_dependencies.Rmd | 8 inst/doc/python_dependencies.html | 16 + inst/doc/python_packages.Rmd | 299 +++++++++++++++++++-- inst/doc/python_packages.html | 225 +++++++++++++--- inst/doc/python_primer.html | 5 inst/doc/versions.Rmd | 192 ++++++++++---- inst/doc/versions.html | 81 +++-- man/py_require.Rd |only man/py_version.Rd | 5 man/use_python.Rd | 7 man/uv_run_tool.Rd |only src/libpython.cpp | 6 src/libpython.h | 53 +++ src/pending_py_calls_notifier.cpp | 2 src/python.cpp | 56 +++- tests/testthat/_snaps/py_require.md |only tests/testthat/helper-py-require.R |only tests/testthat/resources/import-test.R | 1 tests/testthat/test-finalize.R | 4 tests/testthat/test-interrupts.R | 12 tests/testthat/test-py_require.R |only tests/testthat/test-python-arrays.R | 2 tests/testthat/test-python-numpy.R | 65 ++++ vignettes/package.Rmd | 358 ++++++++++++++++++++------ vignettes/python_dependencies.Rmd | 8 vignettes/python_packages.Rmd | 299 +++++++++++++++++++-- vignettes/versions.Rmd | 192 ++++++++++---- 45 files changed, 2387 insertions(+), 719 deletions(-)
Title: Get Basic Information from Chinese ID Number
Description: The Chinese ID number contains a lot of information,
this package helps you get the date of birth, age, age based
on year, gender, region, zodiac, constellation information from
the Chinese ID number.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between CNID versions 1.3.1 dated 2023-10-24 and 2.0.1 dated 2025-02-24
CNID-1.3.1/CNID/R/birth_day.R |only CNID-1.3.1/CNID/R/birth_month.R |only CNID-1.3.1/CNID/R/birth_year.R |only CNID-1.3.1/CNID/man/birth_day.Rd |only CNID-1.3.1/CNID/man/birth_month.Rd |only CNID-1.3.1/CNID/man/birth_year.Rd |only CNID-2.0.1/CNID/DESCRIPTION | 10 CNID-2.0.1/CNID/LICENSE | 2 CNID-2.0.1/CNID/MD5 | 30 +- CNID-2.0.1/CNID/NAMESPACE | 4 CNID-2.0.1/CNID/R/check_id.R | 6 CNID-2.0.1/CNID/R/cnid_info.R | 400 +++++++++++++------------------------ CNID-2.0.1/CNID/R/leap_year.R |only CNID-2.0.1/CNID/R/mdays.R | 45 ---- CNID-2.0.1/CNID/R/ydays.R | 28 -- CNID-2.0.1/CNID/README.md | 20 + CNID-2.0.1/CNID/man/check_id.Rd | 4 CNID-2.0.1/CNID/man/leap_year.Rd |only CNID-2.0.1/CNID/man/mdays.Rd | 14 - CNID-2.0.1/CNID/man/ydays.Rd | 12 - 20 files changed, 212 insertions(+), 363 deletions(-)
Title: Bayesian Evaluation, Analysis, and Simulation Software Tools for
Trials
Description: Bayesian dynamic borrowing with covariate adjustment via inverse probability
weighting for simulations and data analyses in clinical trials. This makes it easy to use
propensity score methods to balance covariate distributions between external and internal
data.
Author: Christina Fillmore [aut, cre] ,
Ben Arancibia [aut],
Nate Bean [aut] ,
Abi Terry [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd],
Trustees of Columbia University [cph]
Maintainer: Christina Fillmore <christina.e.fillmore@gsk.com>
Diff between beastt versions 0.0.1 dated 2024-06-20 and 0.0.2 dated 2025-02-24
DESCRIPTION | 46 +- MD5 | 103 ++++-- NAMESPACE | 28 + NEWS.md | 6 R/beastt-package.R |only R/data.R | 44 ++ R/import-standalone-check_pkg_installed.R |only R/import-standalone-cli_call_env.R |only R/post.R | 320 ++++++++++++++++--- R/ps.R | 39 +- R/pwr_prior.R | 280 ++++++++++++++-- R/stanmodels.R |only R/utils.R | 158 ++++++++- R/zzz.R | 3 README.md | 10 build/vignette.rds |binary configure |only configure.win |only data/ex_binary_df.rda |binary data/ex_norm_df.rda |binary data/ex_tte_df.rda |only data/int_binary_df.rda |binary data/int_norm_df.rda |binary data/int_tte_df.rda |only inst/WORDLIST | 17 + inst/doc/binary.R | 100 +++++ inst/doc/binary.Rmd | 183 +++++++++- inst/doc/binary.html | 431 +++++++++++++++++-------- inst/doc/continuous.R | 112 +++++- inst/doc/continuous.Rmd | 201 +++++++++--- inst/doc/continuous.html | 469 ++++++++++++++++++++-------- inst/doc/tte.R |only inst/doc/tte.Rmd |only inst/doc/tte.html |only inst/include |only inst/stan |only man/beastt-package.Rd |only man/calc_post_beta.Rd | 9 man/calc_post_norm.Rd | 5 man/calc_post_weibull.Rd |only man/calc_power_prior_beta.Rd | 33 + man/calc_power_prior_norm.Rd | 23 - man/calc_power_prior_weibull.Rd |only man/ex_tte_df.Rd |only man/int_tte_df.Rd |only man/mix_means.Rd |only man/mix_sigmas.Rd |only man/robustify_mvnorm.Rd |only man/robustify_norm.Rd | 4 man/tidy.prop_scr.Rd |only src |only tests/testthat/_snaps |only tests/testthat/code_for_normal_tests_Stan.R |only tests/testthat/code_for_tte_tests_Stan.R |only tests/testthat/test-binary.R |only tests/testthat/test-normal.R |only tests/testthat/test-plot_dist.R |only tests/testthat/test-prop_scr_dens.R |only tests/testthat/test-prop_scr_hist.R |only tests/testthat/test-prop_scr_love.R |only tests/testthat/test-tte.R |only vignettes/binary.Rmd | 183 +++++++++- vignettes/continuous.Rmd | 201 +++++++++--- vignettes/tte.Rmd |only 64 files changed, 2368 insertions(+), 640 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner [aut, cre] ,
Andreas Mayr [aut],
Nora Fenske [aut],
Janek Thomas [aut],
Matthias Schmid [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between gamboostLSS versions 2.0-7 dated 2023-03-09 and 2.1-0 dated 2025-02-24
ChangeLog | 73 +++++++++++++++++++++++++++ DESCRIPTION | 13 ++-- MD5 | 42 +++++++-------- NAMESPACE | 2 R/as.families.R | 18 ++++++ R/families.R | 100 ++++++++++++++++++++++++++++++++++++++ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/india.RData |binary data/india.bnd.RData |binary inst/NEWS.Rd | 19 ++++++- inst/doc/gamboostLSS_Tutorial.pdf |binary man/as.families.Rd | 6 +- man/cvrisk.Rd | 6 +- man/families.Rd | 31 +++++++++-- man/gamboostLSS-package.Rd | 6 +- man/india.Rd | 2 man/mboostLSS.Rd | 30 +++++------ man/methods.Rd | 2 man/stabsel.mboostLSS.Rd | 2 tests/regtest-families.R | 79 ++++++++++++++++++++++++++++++ 22 files changed, 366 insertions(+), 67 deletions(-)
Title: Brazilian Population Estimatives
Description: Functions to handle and aggregate population estimates for Brazilian municipalities by sex and age groups.
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.saldanha@fiocruz.br>
Diff between brpop versions 0.5.0 dated 2024-10-17 and 0.6.0 dated 2025-02-24
DESCRIPTION | 10 +-- MD5 | 84 +++++++++++++++--------------- NEWS.md | 5 + R/datasus2024_mun_female_pop.R |only R/datasus2024_mun_male_pop.R |only R/mun_female_pop_totals.R | 6 +- R/mun_male_pop_totals.R | 6 +- R/mun_pop_age.R | 7 +- R/mun_pop_totals.R | 9 ++- R/mun_sex_pop.R | 7 +- R/regsaude_female_pop.R | 6 +- R/regsaude_female_pop_totals.R | 4 - R/regsaude_male_pop.R | 6 +- R/regsaude_male_pop_totals.R | 4 - R/regsaude_pop_age.R | 4 - R/regsaude_pop_totals.R | 6 +- R/regsaude_sex_pop.R | 4 - R/uf_female_pop_totals.R | 6 +- R/uf_male_pop_totals.R | 6 +- R/uf_pop_age.R | 7 +- R/uf_pop_totals.R | 9 ++- R/uf_sex_pop.R | 7 +- R/zenodo_deposit.R | 2 man/brpop-package.Rd | 2 man/datasus2024_mun_female_pop.Rd |only man/datasus2024_mun_male_pop.Rd |only man/mun_female_pop_totals.Rd | 2 man/mun_male_pop_totals.Rd | 2 man/mun_pop_age.Rd | 2 man/mun_pop_totals.Rd | 2 man/mun_sex_pop.Rd | 2 man/regsaude_female_pop.Rd | 2 man/regsaude_female_pop_totals.Rd | 2 man/regsaude_male_pop.Rd | 2 man/regsaude_male_pop_totals.Rd | 2 man/regsaude_pop_age.Rd | 2 man/regsaude_pop_totals.Rd | 2 man/regsaude_sex_pop.Rd | 2 man/uf_female_pop_totals.Rd | 2 man/uf_male_pop_totals.Rd | 2 man/uf_pop_age.Rd | 2 man/uf_pop_totals.Rd | 2 man/uf_sex_pop.Rd | 2 tests/testthat/test-pop_mun_consistency.R | 36 ++++++++++++ tests/testthat/test-pop_uf_consistency.R | 10 +++ 45 files changed, 186 insertions(+), 101 deletions(-)
Title: ISO11784 PIT Tag ID Format Converters
Description: Some tools to assist with converting International Organization for Standardization (ISO) standard 11784 (ISO11784) animal ID codes between 4 recognised formats commonly displayed on Passive Integrated Transponder (PIT) tag readers.
The most common formats are 15 digit decimal, e.g., 999123456789012, and 13 character hexadecimal 'dot' format, e.g., 3E7.1CBE991A14. These are referred
to in this package as isodecimal and isodothex. The other two formats are the raw hexadecimal representation of the ISO11784 binary
structure (see <https://en.wikipedia.org/wiki/ISO_11784_and_ISO_11785>). There are two 'flavours' of this format, a left and a right variation. Which flavour
a reader happens to output depends on if the developers decided to reverse the binary number or not before converting to hexadecimal, a decision based on
the fact that the PIT tags will transmit their binary code Least Significant Bit (LSB) first, or backwards basically.
Author: Graeme Diack [aut, cre]
Maintainer: Graeme Diack <graemediack@hotmail.com>
Diff between ISO11784Tools versions 1.1.4 dated 2023-03-01 and 1.2.0 dated 2025-02-24
DESCRIPTION | 6 +- MD5 | 24 +++++------ R/from_isodecimal_tform.R | 12 +++++ R/utilities.R | 8 ++- README.md | 9 +++- build/vignette.rds |binary inst/doc/ISO11784Tools.R | 8 +-- inst/doc/ISO11784Tools.Rmd | 6 -- inst/doc/ISO11784Tools.html | 58 ++++++++++++---------------- tests/testthat/test-from_isodecimal_tform.R | 27 +++++++++++-- tests/testthat/test-to_isodecimal_tform.R | 9 ++-- tests/testthat/test-utilities.R | 17 +++++--- vignettes/ISO11784Tools.Rmd | 6 -- 13 files changed, 109 insertions(+), 81 deletions(-)
Title: Estimating Aboveground Biomass and Its Uncertainty in Tropical
Forests
Description: Contains functions to estimate aboveground biomass/carbon and its uncertainty in tropical forests.
These functions allow to (1) retrieve and to correct taxonomy, (2) estimate wood density and its uncertainty,
(3) construct height-diameter models, (4) manage tree and plot coordinates,
(5) estimate the aboveground biomass/carbon at the stand level with associated uncertainty.
To cite 'BIOMASS', please use citation("BIOMASS").
See more in the article of Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.
Author: Maxime Rejou-Mechain [aut, dtc],
Guillaume Cornu [aut] ,
Dominique Lamonica [aut, cre],
Arthur Bailly [aut],
Arthur Pere [aut],
Ariane Tanguy [aut],
Jerome Chave [dtc],
Ted Feldpausch [dtc],
Philippe Verley [ctb],
Camille Piponiot [aut],
Bruno Heraul [...truncated...]
Maintainer: Dominique Lamonica <dominique.lamonica@ird.fr>
Diff between BIOMASS versions 2.1.12 dated 2025-02-12 and 2.2.3 dated 2025-02-24
BIOMASS-2.1.12/BIOMASS/R/pkgname.R |only BIOMASS-2.1.12/BIOMASS/data/APG.rda |only BIOMASS-2.1.12/BIOMASS/data/KarnatakaForest.rda |only BIOMASS-2.1.12/BIOMASS/data/Taxo.rda |only BIOMASS-2.1.12/BIOMASS/inst/doc/BIOMASS.R |only BIOMASS-2.1.12/BIOMASS/inst/doc/BIOMASS.Rmd |only BIOMASS-2.1.12/BIOMASS/inst/doc/BIOMASS.html |only BIOMASS-2.1.12/BIOMASS/inst/doc/plot.R |only BIOMASS-2.1.12/BIOMASS/inst/doc/plot.Rmd |only BIOMASS-2.1.12/BIOMASS/inst/doc/plot.html |only BIOMASS-2.1.12/BIOMASS/inst/external |only BIOMASS-2.1.12/BIOMASS/man/APG.Rd |only BIOMASS-2.1.12/BIOMASS/man/KarnatakaForest.Rd |only BIOMASS-2.1.12/BIOMASS/man/Taxo.Rd |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_00_correctTaxo.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_00_cutplot.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_00_modelHD.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_01_correctCoordGPS.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_01_numberCorner.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_01_small_function.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_02_attributeTree.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_02_getWoodDensity.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_02_retrieveH.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_03_AGBmonteCarlo.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_03_attributeTreeCoord.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_03_computeAGB.R |only BIOMASS-2.1.12/BIOMASS/tests/testthat/test_04_summaryByPlot.R |only BIOMASS-2.1.12/BIOMASS/vignettes/BIOMASS.Rmd |only BIOMASS-2.1.12/BIOMASS/vignettes/plot.Rmd |only BIOMASS-2.2.3/BIOMASS/DESCRIPTION | 32 - 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Title: R Analyzer for Large-Scale Assessments
Description: Download, prepare and analyze data from large-scale assessments and
surveys with complex sampling and assessment design (see 'Rutkowski',
2010 <doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of
the package, see 'Mirazchiyski', 2021b (< [...truncated...]
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.5.0 dated 2024-09-23 and 1.5.5 dated 2025-02-24
DESCRIPTION | 26 MD5 | 24 NAMESPACE | 7 NEWS.md | 44 + R/RALSA.r | 10 R/common.r | 1503 ++++++++++++++++++++++++++++++++++++++++++----- R/lsa.convert.data.r | 13 R/lsa.download.data.r |only R/lsa.merge.data.r | 13 R/lsa.pcts.means.r | 2 inst/shiny/GUI/server.r | 1044 ++++++++++++++++++++++++++++---- inst/shiny/GUI/ui.r | 113 +++ man/RALSA.Rd | 1 man/lsa.download.data.Rd |only 14 files changed, 2478 insertions(+), 322 deletions(-)
Title: High-Performance Geocoding using 'photon'
Description: Features unstructured, structured and reverse geocoding using the
'photon' geocoding API <https://photon.komoot.io/>.
Facilitates the setup of local 'photon' instances to enable offline
geocoding.
Author: Jonas Lieth [aut, cre, cph]
Maintainer: Jonas Lieth <jonas.lieth@gesis.org>
Diff between photon versions 0.3.1 dated 2024-11-11 and 0.3.5 dated 2025-02-24
DESCRIPTION | 8 - MD5 | 81 +++++++------- NAMESPACE | 1 NEWS.md | 18 +++ R/assert.R | 84 +++++++++----- R/download-db.R | 11 - R/download-photon.R | 10 + R/geocode.R | 81 +++++++++++--- R/java.R | 3 R/new_photon.R | 6 - R/photon-package.R | 2 R/photon_local.R | 40 ++++--- R/purge.R | 21 +-- R/query_photon.R | 13 +- R/reverse.R | 29 ++--- R/run_photon.R | 52 ++++++--- R/structured.R | 30 ++--- R/utils.R | 57 ++++++++++ README.md | 4 inst/doc/nominatim-import.R | 230 ++++++++++++++++++++--------------------- inst/doc/nominatim-import.Rmd | 8 - inst/doc/nominatim-import.html | 10 - inst/doc/photon.R | 120 ++++++++++----------- inst/doc/photon.Rmd | 8 - inst/doc/photon.html | 10 - man/cmd_options.Rd | 10 - man/download_photon.Rd | 5 man/download_searchindex.Rd | 4 man/geocode.Rd | 74 ++++++++----- man/get_instance.Rd | 4 man/latinize.Rd |only man/new_photon.Rd | 6 - man/photon-package.Rd | 34 +++--- man/photon_local.Rd | 8 - man/purge_java.Rd | 6 - man/reverse.Rd | 60 +++++----- man/structured.Rd | 60 +++++----- tests/testthat/test-geocode.R | 39 ++++-- tests/testthat/test-setup.R | 5 tests/testthat/test-utils.R | 13 +- vignettes/nominatim-import.Rmd | 8 - vignettes/photon.Rmd | 8 - 42 files changed, 751 insertions(+), 530 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and
predictions of any machine learning model. Implemented methods are:
Feature importance described by Fisher et al. (2018)
<doi:10.48550/arxiv.1801.01489>, accumulated local effects plots described by Apley
(2018) <doi:10.48550/arxiv.1612.08468>, partial dependence plots described by
Friedman (2001) <www.jstor.org/stable/2699986>, individual conditional
expectation ('ice') plots described by Goldstein et al. (2013)
<doi:10.1080/10618600.2014.907095>, local models (variant of 'lime')
described by Ribeiro et. al (2016) <doi:10.48550/arXiv.1602.04938>, the Shapley
Value described by Strumbelj et. al (2014)
<doi:10.1007/s10115-013-0679-x>, feature interactions described by
Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Giuseppe Casalicchio [aut, cre],
Christoph Molnar [aut],
Patrick Schratz [aut]
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@lmu.de>
Diff between iml versions 0.11.3 dated 2024-04-27 and 0.11.4 dated 2025-02-24
DESCRIPTION | 8 MD5 | 24 NEWS.md | 296 ++++---- R/FeatureEffect.R | 1536 +++++++++++++++++++++---------------------- R/Shapley.R | 489 ++++++------- R/utils.R | 661 +++++++++--------- build/vignette.rds |binary inst/doc/intro.html | 109 +-- inst/doc/parallel.html | 51 - man/calculate.ale.cat.Rd | 2 man/calculate.ale.num.Rd | 2 man/calculate.ale.num.cat.Rd | 2 man/calculate.ale.num.num.Rd | 2 13 files changed, 1575 insertions(+), 1607 deletions(-)
Title: Fit, Simulate, and Diagnose Hierarchical Exponential-Family
Models for Big Networks
Description: A toolbox for analyzing and simulating large networks based on hierarchical exponential-family random graph models (HERGMs).'bigergm' implements the estimation for large networks efficiently building on the 'lighthergm' and 'hergm' packages. Moreover, the package contains tools for simulating networks with local dependence to assess the goodness-of-fit.
Author: Cornelius Fritz [aut, cre],
Michael Schweinberger [aut],
Shota Komatsu [aut],
Juan Nelson Martinez Dahbura [aut],
Takanori Nishida [aut],
Angelo Mele [aut]
Maintainer: Cornelius Fritz <corneliusfritz2010@gmail.com>
Diff between bigergm versions 1.2.3 dated 2024-10-23 and 1.2.4 dated 2025-02-24
DESCRIPTION | 6 +-- MD5 | 14 +++---- R/bigergm.R | 2 - R/est_within.R | 2 - R/preprocess.R | 6 +-- inst/doc/bigergm.R | 2 - tests/testthat/test-start-from-given-cluster.R | 4 +- vignettes/bigergm.html | 44 +++++++++++++------------ 8 files changed, 41 insertions(+), 39 deletions(-)
Title: Package for Sequence Analysis by Local Score
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://pmc.ncbi.nlm.nih.gov/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Author: Sebastian Simon [aut],
Chris Verschelden [aut],
Charly Marty [aut],
David Robelin [aut, cre],
Sabine Mercier [aut],
Sebastien Dejean [aut],
The authors of Eigen the library for the included version of Eigen
[cph]
Maintainer: David Robelin <david.robelin@inrae.fr>
Diff between localScore versions 1.0.10 dated 2023-11-02 and 2.0.1 dated 2025-02-24
localScore-1.0.10/localScore/data/dico.rda |only localScore-1.0.10/localScore/inst/doc/localScorePackageDocumentation.html |only localScore-1.0.10/localScore/man/LongSeq.Rd |only localScore-1.0.10/localScore/man/MidSeq.Rd |only localScore-1.0.10/localScore/man/MySeqList.Rd |only localScore-1.0.10/localScore/man/SJSyndrome.data.Rd |only localScore-1.0.10/localScore/man/ShortSeq.Rd |only localScore-1.0.10/localScore/man/dico.Rd |only localScore-1.0.10/localScore/man/karlinMonteCarlo_double.Rd |only localScore-1.0.10/localScore/man/localScoreC_double.Rd |only localScore-1.0.10/localScore/man/monteCarlo_double.Rd |only localScore-1.0.10/localScore/man/scoreDictionnary2probabilityVector.Rd |only localScore-1.0.10/localScore/tests/testthat/test-markov_generic.R |only localScore-2.0.1/localScore/DESCRIPTION | 16 localScore-2.0.1/localScore/MD5 | 145 - localScore-2.0.1/localScore/NAMESPACE | 8 localScore-2.0.1/localScore/R/RcppExports.R | 152 - localScore-2.0.1/localScore/R/data.R | 126 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localScore-2.0.1/localScore/inst/doc/localScorePackageDocumentation.R | 454 ++- localScore-2.0.1/localScore/inst/doc/localScorePackageDocumentation.Rmd | 616 +++- localScore-2.0.1/localScore/inst/doc/localScorePackageDocumentation.pdf |only localScore-2.0.1/localScore/man/Aeso.Rd | 2 localScore-2.0.1/localScore/man/CharSequence2ScoreSequence.Rd | 19 localScore-2.0.1/localScore/man/CharSequences2ScoreSequences.Rd | 21 localScore-2.0.1/localScore/man/HydroScore.Rd | 6 localScore-2.0.1/localScore/man/MarkovParameters.Rd |only localScore-2.0.1/localScore/man/SJSyndrome.Rd |only localScore-2.0.1/localScore/man/Seq1093.Rd | 24 localScore-2.0.1/localScore/man/Seq219.Rd | 12 localScore-2.0.1/localScore/man/Seq31.Rd | 22 localScore-2.0.1/localScore/man/SeqListSCOPe.Rd | 8 localScore-2.0.1/localScore/man/aeso.data.Rd | 32 localScore-2.0.1/localScore/man/automatic_analysis.Rd | 6 localScore-2.0.1/localScore/man/daudin.Rd | 13 localScore-2.0.1/localScore/man/exact_mc.Rd | 29 localScore-2.0.1/localScore/man/karlin.Rd | 19 localScore-2.0.1/localScore/man/karlinMonteCarlo.Rd | 115 localScore-2.0.1/localScore/man/lindley.Rd | 6 localScore-2.0.1/localScore/man/loadScoreFromFile.Rd | 13 localScore-2.0.1/localScore/man/localScore-package.Rd | 73 localScore-2.0.1/localScore/man/localScoreC.Rd | 55 localScore-2.0.1/localScore/man/maxPartialSumd.Rd | 2 localScore-2.0.1/localScore/man/mcc.Rd | 9 localScore-2.0.1/localScore/man/monteCarlo.Rd | 67 localScore-2.0.1/localScore/man/proba_theoretical_first_excursion_iid.Rd |only localScore-2.0.1/localScore/man/proba_theoretical_ith_excursion_iid.Rd |only localScore-2.0.1/localScore/man/proba_theoretical_ith_excursion_markov.Rd |only localScore-2.0.1/localScore/man/recordTimes.Rd |only localScore-2.0.1/localScore/man/sequences2transmatrix.Rd | 19 localScore-2.0.1/localScore/man/transmatrix2sequence.Rd | 17 localScore-2.0.1/localScore/src/Eigen/CMakeLists.txt |only localScore-2.0.1/localScore/src/Eigen/COPYRIGHTS |only localScore-2.0.1/localScore/src/Eigen/src/Core/arch/CUDA/Half.h |only localScore-2.0.1/localScore/src/Eigen/src/Core/arch/CUDA/MathFunctions.h |only localScore-2.0.1/localScore/src/Eigen/src/Core/arch/CUDA/PacketMath.h |only localScore-2.0.1/localScore/src/Eigen/src/Core/arch/CUDA/PacketMathHalf.h |only localScore-2.0.1/localScore/src/Eigen/src/Core/arch/CUDA/TypeCasting.h |only localScore-2.0.1/localScore/src/Eigen/src/Geometry/arch/Geometry_SSE.h |only localScore-2.0.1/localScore/src/Eigen/src/LU/arch/Inverse_SSE.h |only localScore-2.0.1/localScore/src/RcppExports.cpp | 69 localScore-2.0.1/localScore/src/function_wrapper.cpp | 214 + localScore-2.0.1/localScore/src/localScoreC.cpp | 321 +- localScore-2.0.1/localScore/src/pValueMethods.cpp | 204 + localScore-2.0.1/localScore/src/pValueMethods.h | 9 localScore-2.0.1/localScore/src/testsCpp |only localScore-2.0.1/localScore/tests/testthat.R | 2 localScore-2.0.1/localScore/tests/testthat/test-daudin.R | 70 localScore-2.0.1/localScore/tests/testthat/test-exact_mc.R | 23 localScore-2.0.1/localScore/tests/testthat/test-excursions.R |only localScore-2.0.1/localScore/tests/testthat/test-karlin.R | 131 - localScore-2.0.1/localScore/tests/testthat/test-localScoreC.R | 191 + localScore-2.0.1/localScore/tests/testthat/test-mcc.R | 77 localScore-2.0.1/localScore/tests/testthat/test-monteCarlo.R |only localScore-2.0.1/localScore/tests/testthat/test-stationary_distribution.R |only localScore-2.0.1/localScore/tests/testthat/test-tools.R |only localScore-2.0.1/localScore/vignettes/ExcursionsheightDocumentation.Rmd |only localScore-2.0.1/localScore/vignettes/localScorePackageDocumentation.Rmd | 616 +++- 94 files changed, 3550 insertions(+), 1770 deletions(-)
Title: 'Schwab API' Interface
Description: Use R to interface with the 'Charles Schwab Trade API' <https://developer.schwab.com/>.
Functions include authentication, trading, price requests, account information, and option
chains. A user will need a Schwab brokerage account and Schwab Individual Developer app. See README
for authentication process and examples.
Author: Anthony Trevisan [aut, cre]
Maintainer: Anthony Trevisan <anthonytrevisan@gmail.com>
Diff between schwabr versions 0.1.2 dated 2025-02-11 and 0.1.3 dated 2025-02-24
DESCRIPTION | 8 +++---- MD5 | 17 ++++++++------- NAMESPACE | 1 NEWS.md | 8 +++++-- R/other.R | 42 ++++++++++++++++++++++++++++++++++++-- README.md | 12 ++++++---- man/schwab_marketHours.Rd | 2 - man/schwab_transactSearch.Rd | 2 - man/schwab_userPreferences.Rd |only tests/testthat/test-testOutputs.R | 6 +++-- 10 files changed, 73 insertions(+), 25 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.17.0 dated 2025-01-13 and 0.18.0 dated 2025-02-24
DESCRIPTION | 8 +- MD5 | 44 +++++++------- NEWS.md | 6 + R/ReadNetCDF.R | 80 +++++++++++++++++++------ R/WriteNetCDF.R | 2 R/geom_contour_tanaka.R | 3 R/geom_streamline.R | 6 - R/label-scales.R | 6 - R/stat_contour2.r | 2 R/zzz.R | 21 ++++++ README.md | 2 inst/doc/Visualization-tools.R | 2 inst/doc/Visualization-tools.Rmd | 18 ++--- inst/doc/Visualization-tools.html | 90 +++++++++++++---------------- inst/doc/Working-with-data.html | 18 ++--- man/ReadNetCDF.Rd | 17 +++++ man/figures/field-1.png |binary man/figures/timeseries-1.png |binary man/label_scales.Rd | 6 - tests/testthat/Rplots.pdf |binary tests/testthat/test-vis-contour2.R | 4 - tests/testthat/test-vis-guide_colorstrip.R | 13 ++-- vignettes/Visualization-tools.Rmd | 18 ++--- 23 files changed, 210 insertions(+), 156 deletions(-)
Title: Multiple Fill and Colour Scales in 'ggplot2'
Description: Use multiple fill and colour scales in 'ggplot2'.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between ggnewscale versions 0.5.0 dated 2024-07-19 and 0.5.1 dated 2025-02-24
DESCRIPTION | 6 MD5 | 9 NEWS.md | 4 R/zzz.R |only README.md | 412 ++++++++++++++++++++----------- man/figures/README-unnamed-chunk-3-1.png |binary 6 files changed, 287 insertions(+), 144 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb],
Wouter van der Bijl [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.2 dated 2024-04-21 and 0.2.3 dated 2025-02-24
DESCRIPTION | 14 ++- MD5 | 74 +++++++++---------- NEWS.md | 37 +++++++++ R/RcppExports.R | 4 - R/init.R | 136 +++++++++++++++++++++++++++--------- R/rspectra_init.R | 37 +++++++-- R/transform.R | 35 +++++++-- R/umap2.R | 33 ++++++-- R/uwot.R | 113 +++++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/uwot.Rmd | 2 inst/doc/uwot.html | 26 +++--- inst/include/uwot/gradient.h | 14 ++- inst/include/uwot/perplexity.h | 4 - inst/include/uwot/smooth_knn.h | 8 +- inst/include/uwot/supervised.h | 4 - inst/include/uwot/tauprng.h | 15 +++ inst/include/uwot/update.h | 3 man/lvish.Rd | 20 ++++- man/optimize_graph_layout.Rd | 20 ++++- man/tumap.Rd | 20 ++++- man/umap.Rd | 20 ++++- man/umap2.Rd | 20 ++++- man/umap_transform.Rd | 9 ++ src/RcppExports.cpp | 8 +- src/nn_parallel.cpp | 4 - src/nn_parallel.h | 12 +-- src/r_uwot.cpp | 55 +++++++++----- src/rng.h | 12 ++- src/smooth_knn.cpp | 17 ++-- src/supervised.cpp | 21 ++--- tests/testthat/test_errors.R | 1 tests/testthat/test_normlaplacian.R | 52 ++++++------- tests/testthat/test_output.R | 52 +++++++++++-- tests/testthat/test_saveload.R | 39 ++++++++++ tests/testthat/test_transform.R | 30 +++++++ vignettes/uwot.Rmd | 2 38 files changed, 718 insertions(+), 255 deletions(-)
Title: Compare Microbial Networks of 'trans_network' Class of
'microeco' Package
Description: Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>.
This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.
Author: Chi Liu [aut, cre],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between meconetcomp versions 0.6.0 dated 2025-01-07 and 0.6.1 dated 2025-02-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/edge_tax_comp.R | 4 ++++ R/robustness.R | 19 +++++++++++-------- man/robustness.Rd | 5 ++++- 5 files changed, 26 insertions(+), 16 deletions(-)
Title: Plots 'D&D'-Style Alignment Charts
Description: 'D&D' alignment charts show 9 boxes with values for good
through evil and values for chaotic through lawful. This package
easily creates these alignment charts from user-provided image paths
and alignment values.
Author: Afton Coombs [aut, cre, cph],
Tan Ho [ctb]
Maintainer: Afton Coombs <aftoncoombs@gmail.com>
Diff between ggalignment versions 1.0.1 dated 2022-11-04 and 1.0.2 dated 2025-02-24
DESCRIPTION | 10 MD5 | 12 README.md | 8 build/vignette.rds |binary inst/doc/ggalignment.html | 162 +++++----- man/figures/README-example-chart-1.png |binary tests/testthat/_snaps/ggalignment/basic-alignment-chart-with-cats.svg | 8 7 files changed, 104 insertions(+), 96 deletions(-)