Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.32 dated 2025-09-24 and 0.4.33 dated 2026-03-13
photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/2013-05-01.hel |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/2014-08-21_cum.hel |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/2014-08-22_cum.hel |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/LI-180-irradiance.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/cr6-day.dat |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/cr6-hour.dat |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/drygrass-spectrum.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-absorbance.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-absorbance.json |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-raman.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-scope.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-scope.json |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-transmission.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/garbage.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/reflectance.PRN |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/reflectance.jaz |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-avaspec.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-comma.JazIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-comma.SSIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-comma.jaz |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-licor-long.PRN |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-psi-spectrapen-SP.csv |only 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photobiologyInOut-0.4.33/photobiologyInOut/NAMESPACE | 1 photobiologyInOut-0.4.33/photobiologyInOut/NEWS.md | 10 photobiologyInOut-0.4.33/photobiologyInOut/R/foreign-conversion.r | 65 photobiologyInOut-0.4.33/photobiologyInOut/R/read-asd-txt.r |only photobiologyInOut-0.4.33/photobiologyInOut/R/read-aster-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-avaspec-csv.r | 12 photobiologyInOut-0.4.33/photobiologyInOut/R/read-fmi-cum.R | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-licor-prn.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-licor-txt.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-macam-dta.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-oojaz-file.r | 4 photobiologyInOut-0.4.33/photobiologyInOut/R/read-ooov-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-oopi-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-ooss-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-psi-spectrapen-csv.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-wasatch-csv.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/README.md | 60 photobiologyInOut-0.4.33/photobiologyInOut/build/partial.rdb |binary photobiologyInOut-0.4.33/photobiologyInOut/build/vignette.rds |binary photobiologyInOut-0.4.33/photobiologyInOut/inst/doc/user-guide.R | 128 - photobiologyInOut-0.4.33/photobiologyInOut/inst/doc/user-guide.Rmd | 381 ++- photobiologyInOut-0.4.33/photobiologyInOut/inst/doc/user-guide.html | 1164 ++++++---- photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-Rfr-panel-50pc.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-Rfr-soil.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-e-irrad-sky.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-e-irrad-sky.csv2 |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-e-irrad-sky.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-raw-gravel.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/aster-Rpc-drygrass.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/avantes-avaspec-e-irrad.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/bad-input-test.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/campbellsci-cr6-day.dat |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/campbellsci-cr6-hour.dat |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/fmi-al-2013-05-01.hel |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/fmi-al-2014-08-21_cum.hel |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/fmi-al-2014-08-22_cum.hel |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li180-irrad.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li1800-Rfr.PRN |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li1800-q-irrad-long.PRN |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li1800-q-irrad.PRN |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/macam-e-irrad.DTA |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-reflectance.jaz |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-comma.SSIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-comma.jaz |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-comma.jazIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-seq-dark.pi |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-seq0.pi |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.OVIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.SSIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.jaz |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.jazIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.pi |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/psi-spectrapen-SP.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/tuv-usrout.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/tuv-usrout2.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-absorbance.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-absorbance.json |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-raman.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-scope.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-scope.json |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-transmission.csv |only photobiologyInOut-0.4.33/photobiologyInOut/man/read_ASTER_txt.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_asd_txt.Rd |only photobiologyInOut-0.4.33/photobiologyInOut/man/read_avaspec_csv.Rd | 10 photobiologyInOut-0.4.33/photobiologyInOut/man/read_fmi_cum.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_li180_txt.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_licor_prn.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_macam_dta.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_jazirrad.Rd | 4 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_ovirrad.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_pidata.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_ssirrad.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_spectrapen_csv.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_wasatch_csv.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/rspec2mspct.Rd | 62 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-asd.R |only photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-aster.R | 5 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-avantes.R | 2 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-fmi.R | 14 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-licor.R | 22 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-macam.R | 2 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-oo.R | 44 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-psi.R | 4 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-tuv.R | 16 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-wasatch.R | 14 photobiologyInOut-0.4.33/photobiologyInOut/vignettes/user-guide.Rmd | 381 ++- 121 files changed, 1750 insertions(+), 885 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] ,
Laura DeCicco [ctb],
Emily Riederer [rev],
Margaret Siple [rev],
Cagri Alican [rev]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.6.3 dated 2025-09-01 and 0.7.0 dated 2026-03-13
DESCRIPTION | 20 MD5 | 88 +- NAMESPACE | 100 +-- NEWS.md | 255 +++----- R/disambi.R | 128 ++-- R/distances.R |only R/fct.R | 86 +- R/fixmob.R | 267 ++++---- R/fixreg.R | 512 ++++++++-------- R/fixregint.R | 498 ++++++++-------- R/helpers.R | 170 ++--- R/map.R | 580 +++++++++--------- R/mapint.R | 1239 +++++++++++++++++++--------------------- R/naijR-package.R | 36 - R/regdata.R | 93 ++- R/regions.R | 1165 ++++++++++++++++++------------------- R/regionsint.R | 302 ++++----- R/sysdata.rda |binary R/zzz.R | 22 README.md | 84 +- build/vignette.rds |binary data/ngdist.rda |only inst/doc/interactive.R | 120 +-- inst/doc/interactive.Rmd | 228 +++---- inst/doc/interactive.html | 1076 +++++++++++++++++----------------- inst/doc/nigeria-maps.R | 156 ++--- inst/doc/nigeria-maps.Rmd | 297 ++++----- inst/doc/nigeria-maps.html | 1078 +++++++++++++++++----------------- man/disambiguate_lga.Rd | 80 +- man/fix_mobile.Rd | 63 +- man/fix_region.Rd | 154 ++-- man/lgas.Rd | 192 +++--- man/lgas_nigeria.Rd | 4 man/naijR-package.Rd | 56 - man/ng_distance.Rd |only man/ngdist.Rd |only man/states_nigeria.Rd | 42 - tests/testthat.R | 24 tests/testthat/data/numbers.rds |only tests/testthat/test-asreg.R | 156 ++--- tests/testthat/test-distances.R |only tests/testthat/test-fixmob.R | 318 +++++----- tests/testthat/test-fixreg.R | 370 +++++------ tests/testthat/test-isreg.R | 314 +++++----- tests/testthat/test-map.R | 904 ++++++++++++++--------------- tests/testthat/test-regions.R | 442 +++++++------- vignettes/interactive.Rmd | 228 +++---- vignettes/nigeria-maps.Rmd | 297 ++++----- 48 files changed, 6132 insertions(+), 6112 deletions(-)
Title: Native R 'torch' Implementation of 'OpenAI' 'Whisper'
Description: Speech-to-text transcription using a native R 'torch' implementation
of 'OpenAI' 'Whisper' model <https://github.com/openai/whisper>. Supports
multiple model sizes from tiny (39M parameters) to large-v3 (1.5B parameters)
with integrated download from 'HuggingFace' <https://huggingface.co/> via the
'hfhub' package. Provides automatic speech recognition with optional language
detection and translation to English. Audio preprocessing, mel spectrogram
computation, and transformer-based encoder-decoder inference are all
implemented in R using the 'torch' package.
Author: Troy Hernandez [aut, cre],
cornball.ai [cph],
OpenAI [cph] )
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between whisper versions 0.1.0 dated 2026-02-06 and 0.3.0 dated 2026-03-13
whisper-0.1.0/whisper/man/load_added_tokens.Rd |only whisper-0.3.0/whisper/DESCRIPTION | 6 whisper-0.3.0/whisper/MD5 | 66 whisper-0.3.0/whisper/NAMESPACE | 5 whisper-0.3.0/whisper/NEWS.md | 16 whisper-0.3.0/whisper/R/alignment.R |only whisper-0.3.0/whisper/R/config.R | 128 - whisper-0.3.0/whisper/R/decoder.R | 30 whisper-0.3.0/whisper/R/encoder.R | 49 whisper-0.3.0/whisper/R/language.R |only whisper-0.3.0/whisper/R/model.R | 14 whisper-0.3.0/whisper/R/tokenizer.R | 59 whisper-0.3.0/whisper/R/transcribe.R | 1311 +++++++++++- whisper-0.3.0/whisper/README.md | 52 whisper-0.3.0/whisper/inst/tinytest/test_alignment.R |only whisper-0.3.0/whisper/inst/tinytest/test_beam_search.R |only whisper-0.3.0/whisper/inst/tinytest/test_language.R |only whisper-0.3.0/whisper/inst/tinytest/test_tokenizer.R | 25 whisper-0.3.0/whisper/inst/tinytest/test_transcribe.R | 76 whisper-0.3.0/whisper/man/apply_timestamp_rules.Rd |only whisper-0.3.0/whisper/man/beam_search_decode.Rd |only whisper-0.3.0/whisper/man/build_byte_decoder.Rd |only whisper-0.3.0/whisper/man/compression_ratio.Rd |only whisper-0.3.0/whisper/man/compute_word_timestamps.Rd |only whisper-0.3.0/whisper/man/create_mel_filterbank_fallback.Rd | 7 whisper-0.3.0/whisper/man/decode_bpe_bytes.Rd | 5 whisper-0.3.0/whisper/man/decode_with_fallback.Rd |only whisper-0.3.0/whisper/man/detect_language.Rd |only whisper-0.3.0/whisper/man/detect_language_from_mel.Rd |only whisper-0.3.0/whisper/man/detect_language_from_pipeline.Rd |only whisper-0.3.0/whisper/man/dtw_align.Rd |only whisper-0.3.0/whisper/man/expand_kv_cache.Rd |only whisper-0.3.0/whisper/man/forced_decode.Rd |only whisper-0.3.0/whisper/man/get_initial_tokens.Rd | 8 whisper-0.3.0/whisper/man/greedy_decode.Rd | 18 whisper-0.3.0/whisper/man/group_into_words.Rd |only whisper-0.3.0/whisper/man/load_whisper_model.Rd | 9 whisper-0.3.0/whisper/man/medfilt1.Rd |only whisper-0.3.0/whisper/man/pipeline_transcribe.Rd |only whisper-0.3.0/whisper/man/rearrange_kv_cache.Rd |only whisper-0.3.0/whisper/man/sample_decode.Rd |only whisper-0.3.0/whisper/man/transcribe.Rd | 58 whisper-0.3.0/whisper/man/transcribe_chunk.Rd | 37 whisper-0.3.0/whisper/man/transcribe_long.Rd | 34 whisper-0.3.0/whisper/man/whisper_lang_from_id.Rd |only whisper-0.3.0/whisper/man/whisper_language_table.Rd |only whisper-0.3.0/whisper/man/whisper_pipeline.Rd |only 47 files changed, 1703 insertions(+), 310 deletions(-)
Title: Treatment Switching
Description: Implements rank preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), marginal structural model (MSM), simple two-stage estimation (TSEsimp), and improved two-stage estimation with g-estimation (TSEgest) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.2.4 dated 2026-02-12 and 0.2.5 dated 2026-03-13
DESCRIPTION | 6 MD5 | 66 NAMESPACE | 6 NEWS.md | 4 R/RcppExports.R | 16 R/ipcw.R | 1 R/msm.R | 2 R/trtswitch-package.R | 7 R/utilities.R | 1 man/ipcw.Rd | 1 man/kmdiff.Rd | 2 man/lrtest.Rd | 8 man/merge_append.Rd | 1 man/msm.Rd | 2 man/rmdiff.Rd | 2 src/RcppExports.cpp | 56 src/dataframe_list.cpp | 428 ++-- src/dataframe_list.h | 329 ++- src/ipcw.cpp | 400 +-- src/ipe.cpp | 191 - src/logistic_regression.cpp | 576 ++--- src/msm.cpp | 351 +-- src/recensor_sim_rpsftm.cpp | 132 - src/rpsftm.cpp | 201 + src/splines.cpp | 304 +-- src/splines.h | 12 src/survival_analysis.cpp | 4426 ++++++++++++++++++++++---------------------- src/survival_analysis.h | 10 src/tsegest.cpp | 347 +-- src/tsegestsim.cpp | 33 src/tsesimp.cpp | 240 +- src/tssim.cpp | 95 src/utilities.cpp | 635 +++--- src/utilities.h | 299 ++ 34 files changed, 4845 insertions(+), 4345 deletions(-)
Title: Response Data for Light Sensors
Description: Spectral response data for broadband ultraviolet and visible
radiation sensors. Angular response data for broadband ultraviolet and visible
radiation sensors and diffusers used as entrance optics. Data obtained from
multiple sources were used: author-supplied data from scientific research
papers, sensor-manufacturer supplied data, and published sensor
specifications. Part of the 'r4photobiology' suite Aphalo P. J. (2015)
<doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologySensors versions 0.5.2 dated 2025-09-24 and 0.5.3 dated 2026-03-13
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More information about photobiologySensors at CRAN
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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 0.2.8 dated 2026-02-18 and 0.2.9 dated 2026-03-13
DESCRIPTION | 6 ++-- MD5 | 21 +++++++------- NAMESPACE | 1 NEWS.md | 5 +++ R/PriceIndices.R | 66 +++++++++++++++++++++++---------------------- R/f_data_processing.R | 52 +++++++++++++++++++++++++++++++++++ README.md | 51 ++++++++++++++++------------------ inst/doc/PriceIndices.Rmd | 2 - inst/doc/PriceIndices.html | 5 ++- man/PriceIndices.Rd | 52 ++++++++++++++++++----------------- man/outlet_check.Rd |only vignettes/PriceIndices.Rmd | 2 - 12 files changed, 163 insertions(+), 100 deletions(-)
Title: Kinase-Substrate Enrichment Analysis
Description: Infers relative kinase activity from phosphoproteomics data
using the method described by Casado et al. (2013) <doi:10.1126/scisignal.2003573>.
Author: Danica Wiredja [aut, cre]
Maintainer: Danica Wiredja <dwiredja@gmail.com>
Diff between KSEAapp versions 0.99.0 dated 2017-05-02 and 2.0 dated 2026-03-13
KSEAapp-0.99.0/KSEAapp/R/KSEA.Complete.R |only KSEAapp-0.99.0/KSEAapp/man/KSEA.Complete.Rd |only KSEAapp-2.0/KSEAapp/DESCRIPTION | 18 KSEAapp-2.0/KSEAapp/LICENSE | 4 KSEAapp-2.0/KSEAapp/MD5 | 50 - KSEAapp-2.0/KSEAapp/NAMESPACE | 33 KSEAapp-2.0/KSEAapp/R/KSEA.Barplot.R | 342 ++++----- KSEAapp-2.0/KSEAapp/R/KSEA.Heatmap.R | 334 ++++----- KSEAapp-2.0/KSEAapp/R/KSEA.KS_table.R | 242 +++--- KSEAapp-2.0/KSEAapp/R/KSEA.Scores.1.R | 51 - KSEAapp-2.0/KSEAapp/R/KSEA.Scores.2.R | 51 - KSEAapp-2.0/KSEAapp/R/KSEA.Scores.3.R | 51 - KSEAapp-2.0/KSEAapp/R/KSEA.Scores.R | 279 +++---- KSEAapp-2.0/KSEAapp/R/PX.R | 54 - KSEAapp-2.0/KSEAapp/build/vignette.rds |binary KSEAapp-2.0/KSEAapp/inst/doc/Overview.Rmd | 361 ++++----- KSEAapp-2.0/KSEAapp/inst/doc/Overview.html | 1018 ++++++++++++++++------------ KSEAapp-2.0/KSEAapp/man/KSData.Rd | 44 - KSEAapp-2.0/KSEAapp/man/KSEA.Barplot.Rd | 101 +- KSEAapp-2.0/KSEAapp/man/KSEA.Heatmap.Rd | 118 +-- KSEAapp-2.0/KSEAapp/man/KSEA.KS_table.Rd | 84 +- KSEAapp-2.0/KSEAapp/man/KSEA.Scores.1.Rd | 55 - KSEAapp-2.0/KSEAapp/man/KSEA.Scores.2.Rd | 55 - KSEAapp-2.0/KSEAapp/man/KSEA.Scores.3.Rd | 55 - KSEAapp-2.0/KSEAapp/man/KSEA.Scores.Rd | 82 +- KSEAapp-2.0/KSEAapp/man/PX.Rd | 60 - KSEAapp-2.0/KSEAapp/vignettes/Overview.Rmd | 361 ++++----- 27 files changed, 2026 insertions(+), 1877 deletions(-)
Title: Visualizing Pedigrees with 'ggplot2' and 'plotly'
Description: Provides plotting functions for visualizing pedigrees and family trees. The package complements a behavior genetics package 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization. Due to the impending deprecation of kinship2, version 1.0 incorporates the layout helper functions from kinship2. The pedigree alignment algorithms are adapted from 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. We gratefully acknowledge the original authors: Jason Sinnwell, Terry Therneau, Daniel Schaid, and Elizabeth Atkinson for their foundational work.
Author: S. Mason Garrison [aut, cre, cph]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between ggpedigree versions 1.1.0.3 dated 2026-01-11 and 1.1.1.0.0 dated 2026-03-13
ggpedigree-1.1.0.3/ggpedigree/inst/doc/v10_configuration.R |only ggpedigree-1.1.0.3/ggpedigree/inst/doc/v10_configuration.Rmd |only ggpedigree-1.1.0.3/ggpedigree/inst/doc/v10_configuration.html |only ggpedigree-1.1.0.3/ggpedigree/vignettes/v10_configuration.Rmd |only ggpedigree-1.1.1.0.0/ggpedigree/DESCRIPTION | 6 ggpedigree-1.1.1.0.0/ggpedigree/MD5 | 103 +++++----- ggpedigree-1.1.1.0.0/ggpedigree/NEWS.md | 8 ggpedigree-1.1.1.0.0/ggpedigree/R/buildPlotConfig.R | 27 ++ ggpedigree-1.1.1.0.0/ggpedigree/R/calcCoordinates.R | 9 ggpedigree-1.1.1.0.0/ggpedigree/R/defaultPlotConfig.R | 26 +- ggpedigree-1.1.1.0.0/ggpedigree/R/ggPedigreeInteractive.R | 37 +-- ggpedigree-1.1.1.0.0/ggpedigree/R/ggPhenotypeByDegree.R | 20 + ggpedigree-1.1.1.0.0/ggpedigree/R/ggRelatednessMatrix.R | 3 ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigree.R | 16 - ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigreeCore.R | 38 ++- ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigreeCoreHelpers.R | 38 ++- ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigreeHelpers.R | 11 - ggpedigree-1.1.1.0.0/ggpedigree/R/kinship2_alignped3.R | 4 ggpedigree-1.1.1.0.0/ggpedigree/R/kinship2_pedigree.R | 35 ++- ggpedigree-1.1.1.0.0/ggpedigree/R/processExtras.R | 14 - ggpedigree-1.1.1.0.0/ggpedigree/README.md | 23 +- ggpedigree-1.1.1.0.0/ggpedigree/build/partial.rdb |binary ggpedigree-1.1.1.0.0/ggpedigree/build/vignette.rds |binary ggpedigree-1.1.1.0.0/ggpedigree/inst/CITATION |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v00_plots.R | 6 ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v00_plots.Rmd | 6 ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v00_plots.html | 2 ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v02_configuration.R |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v02_configuration.Rmd |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v02_configuration.html |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v20_interactiveplots.html | 28 -- ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v30_matrix.html | 41 --- ggpedigree-1.1.1.0.0/ggpedigree/man/addFocalFillColumn.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addLabels.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addNodes.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addOverlay.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addScales.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addSelfSegment.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addTwins.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-adjustSpacing.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-preparePhenotypeByDegreeData.Rd | 6 ggpedigree-1.1.1.0.0/ggpedigree/man/dot-restoreNames.Rd | 10 ggpedigree-1.1.1.0.0/ggpedigree/man/figures/README-basic-usage-1.png |binary ggpedigree-1.1.1.0.0/ggpedigree/man/figures/README-slightly-usage-1.png |binary ggpedigree-1.1.1.0.0/ggpedigree/man/getDefaultPlotConfig.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/ggPedigree.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/ggPedigree.core.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/ggPedigreeInteractive.Rd | 15 - ggpedigree-1.1.1.0.0/ggpedigree/man/preparePedigreeData.Rd | 17 + ggpedigree-1.1.1.0.0/ggpedigree/man/recodeMissingIDs.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/transformPed.Rd | 15 - ggpedigree-1.1.1.0.0/ggpedigree/tests/testthat/Rplots.pdf |binary ggpedigree-1.1.1.0.0/ggpedigree/tests/testthat/test-defaultPlotConfig.R | 10 ggpedigree-1.1.1.0.0/ggpedigree/tests/testthat/test-ggpedigree_datainputs.R | 95 +++++---- ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v00_plots.Rmd | 6 ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v02_configuration.Rmd |only ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v10_configuration.R |only ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v10_configuration.html |only 58 files changed, 480 insertions(+), 339 deletions(-)
Title: Scalable Causal Discovery and Model Selection on Mixed Datasets
with 'rCausalMGM'
Description: Scalable methods for learning causal graphical models from mixed data, including continuous, discrete, and censored variables. The package implements CausalMGM, which combines a convex, score-based approach for learning an initial moralized graph with a producer-consumer scheme that enables efficient parallel conditional independence testing in constraint-based causal discovery algorithms. The implementation supports high-dimensional datasets and provides individual access to core components of the workflow, including MGM and the PC-Stable and FCI-Stable causal discovery algorithms. To support practical applications, the package includes multiple model selection strategies, including information criteria based on likelihood and model complexity, cross-validation for out-of-sample likelihood estimation, and stability-based approaches that assess graph robustness across subsamples.
Author: Tyler C Lovelace [aut],
Max Dudek [aut],
Jack Fiore [aut],
Panayiotis V Benos [aut, cre]
Maintainer: Panayiotis V Benos <pbenos@ufl.edu>
Diff between rCausalMGM versions 1.0 dated 2026-03-03 and 1.0.1 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS |only src/CensoredVariable.cpp | 12 ++++++------ src/ContinuousVariable.cpp | 2 +- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple
GUI controls for R functions. These are built on the 'tcltk' package.
Uses could include changing a parameter on a graph by animating it
with a slider or a "doublebutton", up to more sophisticated control
panels.
Some functions for specific graphical tasks, referred to as 'cartoons',
are provided.
Author: Adrian Bowman [aut, cre, cph],
Ewan Crawford [aut],
Gavin Alexander [aut],
Richard Bowman [aut]
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between rpanel versions 1.1-6 dated 2026-03-12 and 1.1-6.1 dated 2026-03-13
ChangeLog | 2 ++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/rp-plot4d.r | 2 +- R/rp_drop1.R | 2 +- R/rp_sample.r | 5 +++-- R/rpanel.r | 2 +- tests/testthat/test-rp.sample.r | 15 ++++++++++++--- 8 files changed, 30 insertions(+), 18 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951, Stuiver & Suess 1966, Pearson & Stuiver 1986) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre] ,
Christopher Bronk Ramsey [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.3.1 dated 2025-12-07 and 1.4.0 dated 2026-03-13
DESCRIPTION | 6 - MD5 | 26 +++--- NEWS.md | 7 + R/data.R | 187 ++++++++++++++++++++++------------------------ R/intcal_json.R | 73 ++++++++++------- R/rintcal.R | 53 +++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/rintcal.html | 23 ++--- man/ccurve.Rd | 33 +++----- man/intcal.data.Rd | 160 +++++++++++++++++++-------------------- man/intcal.plot.record.Rd | 10 +- man/intcal.write.data.Rd | 2 man/rintcal-package.Rd | 2 14 files changed, 307 insertions(+), 275 deletions(-)
Title: Empirical Bayes Methods for Pharmacovigilance
Description: A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.48550/arXiv.2502.09816>, <doi:10.48550/arXiv.2512.01057>; Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224>; Efron (2016) <doi:10.1093/biomet/asv068>.
Author: Yihao Tan [aut, cre] ,
Marianthi Markatou [aut] ,
Saptarshi Chakraborty [aut] ,
Raktim Mukhopadhyay [aut]
Maintainer: Yihao Tan <yihaotan@buffalo.edu>
Diff between pvEBayes versions 0.2.1 dated 2026-01-11 and 0.2.2 dated 2026-03-13
DESCRIPTION | 6 MD5 | 20 - R/pvEBayes-package.R | 3 R/pvEBayes_main_function.R | 78 ++++- README.md | 127 +++++---- inst/doc/pvEBayes-introduction.Rmd | 368 +++++++++++++++------------ inst/doc/pvEBayes-introduction.html | 80 ++++- man/dot-KM_fit.Rd | 2 man/pvEBayes-package.Rd | 3 tests/testthat/test-pvEBayes_main_function.R | 17 - vignettes/pvEBayes-introduction.Rmd | 368 +++++++++++++++------------ 11 files changed, 631 insertions(+), 441 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-26 dated 2026-03-06 and 1.2-27 dated 2026-03-13
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++---------- build/partial.rdb |binary inst/NEWS.Rd | 10 +++++ inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary tests/Rplots.pdf |only tests/bugfixes.R | 2 - tests/bugfixes.Rout.save | 16 ++++---- tests/constparty.Rout.save | 6 +-- tests/regtest-MIA.Rout.save | 6 +-- tests/regtest-cforest.Rout.save | 6 +-- tests/regtest-ctree.Rout.save | 6 +-- tests/regtest-glmtree.Rout.save | 6 +-- tests/regtest-nmax.Rout.save | 6 +-- tests/regtest-node.Rout.save | 6 +-- tests/regtest-party.Rout.save | 78 ++++++++++++++++++++-------------------- tests/regtest-split.Rout.save | 6 +-- tests/regtest-weights.Rout.save | 6 +-- 21 files changed, 109 insertions(+), 98 deletions(-)
Title: Explainable Ensemble Trees
Description: The Explainable Ensemble Trees 'e2tree' approach has been proposed by Aria et al. (2024) <doi:10.1007/s00180-022-01312-6>. It aims to explain and interpret decision tree ensemble models using a single tree-like structure. 'e2tree' is a new way of explaining an ensemble tree trained through 'randomForest' or 'xgboost' packages.
Author: Massimo Aria [aut, cre, cph] ,
Agostino Gnasso [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between e2tree versions 0.2.0 dated 2025-07-16 and 1.0.0 dated 2026-03-13
e2tree-0.2.0/e2tree/R/eComparison.R |only e2tree-0.2.0/e2tree/man/eComparison.Rd |only e2tree-0.2.0/e2tree/tests/testthat.R |only e2tree-0.2.0/e2tree/tests/testthat/Rplots.pdf |only e2tree-0.2.0/e2tree/tests/testthat/test-eComparison.R |only e2tree-1.0.0/e2tree/DESCRIPTION | 20 e2tree-1.0.0/e2tree/MD5 | 92 + e2tree-1.0.0/e2tree/NAMESPACE | 37 e2tree-1.0.0/e2tree/NEWS.md | 34 e2tree-1.0.0/e2tree/R/RcppExports.R | 16 e2tree-1.0.0/e2tree/R/aaa_utils.R |only e2tree-1.0.0/e2tree/R/createDisMatrix.R | 477 ++++++---- e2tree-1.0.0/e2tree/R/credit.R |only e2tree-1.0.0/e2tree/R/e2tree.R | 282 +++-- e2tree-1.0.0/e2tree/R/eImpurity.R | 65 - e2tree-1.0.0/e2tree/R/ePredTree.R | 160 ++- e2tree-1.0.0/e2tree/R/eStoppingRules.R | 30 e2tree-1.0.0/e2tree/R/eValidation.R |only e2tree-1.0.0/e2tree/R/goi.R |only e2tree-1.0.0/e2tree/R/plot_e2tree_click.R |only e2tree-1.0.0/e2tree/R/plot_e2tree_vis.R |only e2tree-1.0.0/e2tree/R/proximity_longer.R | 2 e2tree-1.0.0/e2tree/R/roc.R | 10 e2tree-1.0.0/e2tree/R/rpart2Tree.R | 22 e2tree-1.0.0/e2tree/R/split.R | 118 +- e2tree-1.0.0/e2tree/R/vimp.R | 78 + e2tree-1.0.0/e2tree/R/zzz.R | 22 e2tree-1.0.0/e2tree/README.md | 43 e2tree-1.0.0/e2tree/data |only e2tree-1.0.0/e2tree/inst/CITATION | 12 e2tree-1.0.0/e2tree/man/check_package.Rd |only e2tree-1.0.0/e2tree/man/createDisMatrix.Rd | 93 + e2tree-1.0.0/e2tree/man/credit.Rd |only e2tree-1.0.0/e2tree/man/e2_variance.Rd |only e2tree-1.0.0/e2tree/man/e2tree.Rd | 22 e2tree-1.0.0/e2tree/man/ePredTree.Rd | 10 e2tree-1.0.0/e2tree/man/eValidation.Rd |only e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-10-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-15-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-15-2.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-18-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-19-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-19-2.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-19-3.png |binary e2tree-1.0.0/e2tree/man/get_ensemble_type.Rd |only e2tree-1.0.0/e2tree/man/goi.Rd |only e2tree-1.0.0/e2tree/man/goi_analysis.Rd |only e2tree-1.0.0/e2tree/man/goi_perm.Rd |only e2tree-1.0.0/e2tree/man/plot.goi_perm.Rd |only e2tree-1.0.0/e2tree/man/plot_e2tree.Rd |only e2tree-1.0.0/e2tree/man/plot_e2tree_click.Rd |only e2tree-1.0.0/e2tree/man/plot_e2tree_vis.Rd |only e2tree-1.0.0/e2tree/man/print_e2tree_summary.Rd |only e2tree-1.0.0/e2tree/man/rpart2Tree.Rd | 18 e2tree-1.0.0/e2tree/man/save_e2tree_html.Rd |only e2tree-1.0.0/e2tree/src/CoOccurrences.cpp | 365 +++++++ e2tree-1.0.0/e2tree/src/Makevars |only e2tree-1.0.0/e2tree/src/Makevars.win |only e2tree-1.0.0/e2tree/src/RcppExports.cpp | 57 + e2tree-1.0.0/e2tree/tests/testthat.zip |only e2tree-1.0.0/e2tree/tests/testthat/test-createDisMatrix.R | 4 e2tree-1.0.0/e2tree/tests/testthat/test-eValidation.R |only 62 files changed, 1437 insertions(+), 652 deletions(-)
Title: Descriptive, Reliability, and Inferential Tables for
Psychometric Scales and Demographic Data
Description: Provides functions to format and summarise already computed outputs from commonly used statistical and psychometric functions into compact, single-row tables and simple graphs, with utilities to export results to CSV, Word, and Excel formats. The package does not implement new statistical methods or estimation procedures; instead, it organises and presents results obtained from existing functions such as psych::describe(), psych::alpha(), stats::t.test(), and gtsummary::tbl_summary() to streamline reporting workflows in clinical and psychological research.
Author: Darshankumar Dharaiya [aut, cre]
Maintainer: Darshankumar Dharaiya <dharaiya.darshan@gmail.com>
Diff between scaledescr versions 0.2.1 dated 2026-03-06 and 0.2.2 dated 2026-03-13
DESCRIPTION | 8 ++--- MD5 | 14 +++++---- NAMESPACE | 3 ++ NEWS.md | 9 ++++-- R/make_demographic_table.R | 46 +++++++++++++++++++++++--------- R/make_demographic_table_to_output.R |only inst/CITATION | 2 - man/make_demographic_table.Rd | 7 ++-- man/make_demographic_table_to_output.Rd |only 9 files changed, 59 insertions(+), 30 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [c [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-37 dated 2026-02-28 and 5.2.1-41 dated 2026-03-13
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS | 29 ++++++++++++++++---- R/zzz.R | 2 - man/RMUMPS_PERM.Rd | 8 +++-- src/lib/MUMPS_5.2.1/include/mumps_c_types.h | 2 - src/lib/MUMPS_5.2.1/src/dmumps_ooc.F | 20 ++++++------- src/lib/MUMPS_5.2.1/src/dmumps_save_restore_files.F | 4 +- src/lib/MUMPS_5.2.1/src/dsol_bwd_aux.F | 2 - tests/testthat/test_rmumps.R | 4 +- 10 files changed, 58 insertions(+), 37 deletions(-)
Title: Simplifies Plotting Data Inside Databases
Description: Leverages 'dplyr' to process the calculations of a plot inside a database.
This package provides helper functions that abstract the work at three levels:
outputs a 'ggplot', outputs the calculations, outputs the formula
needed to calculate bins.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between dbplot versions 0.3.3 dated 2020-02-06 and 0.4.0 dated 2026-03-13
dbplot-0.3.3/dbplot/R/utils-pipe.R |only dbplot-0.3.3/dbplot/man/pipe.Rd |only dbplot-0.4.0/dbplot/DESCRIPTION | 18 dbplot-0.4.0/dbplot/LICENSE |only dbplot-0.4.0/dbplot/MD5 | 101 +- dbplot-0.4.0/dbplot/NAMESPACE | 6 dbplot-0.4.0/dbplot/NEWS.md | 42 + dbplot-0.4.0/dbplot/R/boxplot.R | 80 +- dbplot-0.4.0/dbplot/R/dbbin.R | 46 - dbplot-0.4.0/dbplot/R/dbplot-package.R |only dbplot-0.4.0/dbplot/R/dbplot.R | 23 dbplot-0.4.0/dbplot/R/discrete.R | 72 + dbplot-0.4.0/dbplot/R/histogram.R | 61 + dbplot-0.4.0/dbplot/R/raster.R | 95 +- dbplot-0.4.0/dbplot/README.md | 379 ++++++---- dbplot-0.4.0/dbplot/inst |only dbplot-0.4.0/dbplot/man/db_bin.Rd | 29 dbplot-0.4.0/dbplot/man/db_compute_bins.Rd | 22 dbplot-0.4.0/dbplot/man/db_compute_boxplot.Rd | 30 dbplot-0.4.0/dbplot/man/db_compute_count.Rd | 25 dbplot-0.4.0/dbplot/man/db_compute_raster.Rd | 29 dbplot-0.4.0/dbplot/man/dbplot-package.Rd |only dbplot-0.4.0/dbplot/man/dbplot_bar.Rd | 24 dbplot-0.4.0/dbplot/man/dbplot_boxplot.Rd | 25 dbplot-0.4.0/dbplot/man/dbplot_histogram.Rd | 23 dbplot-0.4.0/dbplot/man/dbplot_line.Rd | 26 dbplot-0.4.0/dbplot/man/dbplot_raster.Rd | 26 dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-10-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-11-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-12-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-13-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-14-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-15-1.png |only dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-16-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-17-1.png |only dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-19-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-20-1.png |only dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-4-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-5-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-6-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-7-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-8-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-9-1.png |binary dbplot-0.4.0/dbplot/man/figures/logo.png |binary dbplot-0.4.0/dbplot/man/figures/logo.svg |only dbplot-0.4.0/dbplot/tests/testthat.R | 3 dbplot-0.4.0/dbplot/tests/testthat/_snaps |only dbplot-0.4.0/dbplot/tests/testthat/helper-snapshots.R |only dbplot-0.4.0/dbplot/tests/testthat/test-boxplots.R | 23 dbplot-0.4.0/dbplot/tests/testthat/test-dbbin.R | 2 dbplot-0.4.0/dbplot/tests/testthat/test-dbplots.R | 53 + dbplot-0.4.0/dbplot/tests/testthat/test-discrete.R | 66 + dbplot-0.4.0/dbplot/tests/testthat/test-duckdb-computations.R |only dbplot-0.4.0/dbplot/tests/testthat/test-edge-cases.R |only dbplot-0.4.0/dbplot/tests/testthat/test-input-validation.R |only dbplot-0.4.0/dbplot/tests/testthat/test-raster.R | 27 56 files changed, 996 insertions(+), 360 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2025) <doi:10.1007/s10519-025-10225-1>]. For a full overview,
see [Garrison et al. (2024) <doi:10.21105/joss.06203>]. For a big data application see [Burt et al. (2025) <doi: 10.1016/j.ebiom.2025.105911>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.5.2 dated 2026-01-11 and 1.6.0.1 dated 2026-03-13
BGmisc-1.5.2/BGmisc/R/cleanPedigree.R |only BGmisc-1.5.2/BGmisc/R/helpPedigree.R |only BGmisc-1.5.2/BGmisc/R/insertEven.R |only BGmisc-1.5.2/BGmisc/man/buildBetweenGenerations.Rd |only BGmisc-1.6.0.1/BGmisc/DESCRIPTION | 12 BGmisc-1.6.0.1/BGmisc/MD5 | 146 - BGmisc-1.6.0.1/BGmisc/NAMESPACE | 7 BGmisc-1.6.0.1/BGmisc/NEWS.md | 16 BGmisc-1.6.0.1/BGmisc/R/buildComponent.R | 187 + BGmisc-1.6.0.1/BGmisc/R/buildmxPedigrees.R |only BGmisc-1.6.0.1/BGmisc/R/checkIDs.R | 23 BGmisc-1.6.0.1/BGmisc/R/checkParents.R | 22 BGmisc-1.6.0.1/BGmisc/R/constructAdjacency.R | 5 BGmisc-1.6.0.1/BGmisc/R/helpChecks.R |only BGmisc-1.6.0.1/BGmisc/R/helpInsertEven.R |only BGmisc-1.6.0.1/BGmisc/R/helpNames.R |only BGmisc-1.6.0.1/BGmisc/R/helpSimulatePedigree.R |only BGmisc-1.6.0.1/BGmisc/R/helpSimulatePedigree_beta.R |only BGmisc-1.6.0.1/BGmisc/R/helpTwins.R |only BGmisc-1.6.0.1/BGmisc/R/readGedcom.R | 42 BGmisc-1.6.0.1/BGmisc/R/segmentPedigree.R | 48 BGmisc-1.6.0.1/BGmisc/R/simulatePedigree.R | 984 +++++++--- BGmisc-1.6.0.1/BGmisc/R/simulatePedigree_within.R |only BGmisc-1.6.0.1/BGmisc/R/summarizePedigree.R | 18 BGmisc-1.6.0.1/BGmisc/R/tweakPedigree.R | 295 ++ BGmisc-1.6.0.1/BGmisc/README.md | 1 BGmisc-1.6.0.1/BGmisc/build/partial.rdb |binary BGmisc-1.6.0.1/BGmisc/build/vignette.rds |binary BGmisc-1.6.0.1/BGmisc/inst/doc/v0_network.Rmd | 2 BGmisc-1.6.0.1/BGmisc/inst/doc/v0_network.html | 6 BGmisc-1.6.0.1/BGmisc/inst/doc/v1_modelingvariancecomponents.R | 27 BGmisc-1.6.0.1/BGmisc/inst/doc/v1_modelingvariancecomponents.Rmd | 47 BGmisc-1.6.0.1/BGmisc/inst/doc/v1_modelingvariancecomponents.html | 210 +- BGmisc-1.6.0.1/BGmisc/inst/doc/v2_pedigree.Rmd | 3 BGmisc-1.6.0.1/BGmisc/inst/doc/v2_pedigree.html | 4 BGmisc-1.6.0.1/BGmisc/inst/doc/v3_analyticrelatedness.html | 4 BGmisc-1.6.0.1/BGmisc/inst/doc/v5_ASOIAF.R | 41 BGmisc-1.6.0.1/BGmisc/inst/doc/v5_ASOIAF.Rmd | 49 BGmisc-1.6.0.1/BGmisc/inst/doc/v5_ASOIAF.html | 273 +- BGmisc-1.6.0.1/BGmisc/inst/doc/v6_pedigree_model_fitting.R |only BGmisc-1.6.0.1/BGmisc/inst/doc/v6_pedigree_model_fitting.Rmd |only BGmisc-1.6.0.1/BGmisc/inst/doc/v6_pedigree_model_fitting.html |only BGmisc-1.6.0.1/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.6.0.1/BGmisc/man/addIfAny.Rd |only BGmisc-1.6.0.1/BGmisc/man/adjustKidsPerCouple.Rd | 21 BGmisc-1.6.0.1/BGmisc/man/assignCoupleIDs.Rd | 12 BGmisc-1.6.0.1/BGmisc/man/buildBtwnGenerations.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildFamilyGroups.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildOneFamilyGroup.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildPedigreeModelCovariance.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildPedigreeMx.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildWithinGenerations.Rd | 19 BGmisc-1.6.0.1/BGmisc/man/createGenDataFrame.Rd | 18 BGmisc-1.6.0.1/BGmisc/man/determineSex.Rd | 10 BGmisc-1.6.0.1/BGmisc/man/dot-adjBeta.Rd | 4 BGmisc-1.6.0.1/BGmisc/man/dropIdenticalDuplicateIDs.Rd |only BGmisc-1.6.0.1/BGmisc/man/dropLink.Rd | 5 BGmisc-1.6.0.1/BGmisc/man/findMZtwins.Rd |only BGmisc-1.6.0.1/BGmisc/man/fitPedigreeModel.Rd |only BGmisc-1.6.0.1/BGmisc/man/fuseTwins.Rd |only BGmisc-1.6.0.1/BGmisc/man/insertEven.Rd | 2 BGmisc-1.6.0.1/BGmisc/man/isTwin.Rd |only BGmisc-1.6.0.1/BGmisc/man/makeInbreeding.Rd | 5 BGmisc-1.6.0.1/BGmisc/man/makeTwins.Rd | 5 BGmisc-1.6.0.1/BGmisc/man/markPotentialChildren.Rd | 22 BGmisc-1.6.0.1/BGmisc/man/ped2add.Rd | 10 BGmisc-1.6.0.1/BGmisc/man/ped2cn.Rd | 4 BGmisc-1.6.0.1/BGmisc/man/ped2com.Rd | 15 BGmisc-1.6.0.1/BGmisc/man/ped2fam.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/ped2gen.Rd | 136 - BGmisc-1.6.0.1/BGmisc/man/ped2graph.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/ped2maternal.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/ped2mit.Rd | 4 BGmisc-1.6.0.1/BGmisc/man/ped2paternal.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/restorePedColnames.Rd |only BGmisc-1.6.0.1/BGmisc/man/simulatePedigree.Rd | 19 BGmisc-1.6.0.1/BGmisc/man/standardizeColnames.Rd | 2 BGmisc-1.6.0.1/BGmisc/tests/testthat/test-buildComponent.R | 246 ++ BGmisc-1.6.0.1/BGmisc/tests/testthat/test-buildmxPedigrees.R |only BGmisc-1.6.0.1/BGmisc/tests/testthat/test-checkSex.R | 2 BGmisc-1.6.0.1/BGmisc/tests/testthat/test-helpTwins.R |only BGmisc-1.6.0.1/BGmisc/tests/testthat/test-segmentPedigree.R | 25 BGmisc-1.6.0.1/BGmisc/tests/testthat/test-simulatePedigree.R | 294 ++ BGmisc-1.6.0.1/BGmisc/tests/testthat/test-tweakPedigree.R | 358 +++ BGmisc-1.6.0.1/BGmisc/vignettes/v0_network.Rmd | 2 BGmisc-1.6.0.1/BGmisc/vignettes/v1_modelingvariancecomponents.Rmd | 47 BGmisc-1.6.0.1/BGmisc/vignettes/v2_pedigree.Rmd | 3 BGmisc-1.6.0.1/BGmisc/vignettes/v5_ASOIAF.Rmd | 49 BGmisc-1.6.0.1/BGmisc/vignettes/v6_pedigree_model_fitting.Rmd |only 89 files changed, 2961 insertions(+), 864 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.2.2 dated 2026-01-12 and 1.3.0 dated 2026-03-13
DESCRIPTION | 10 +-- MD5 | 56 +++++++++++---------- NAMESPACE | 1 R/BasicQuerySet.R |only R/checks.R | 44 ++++++++++++----- R/file_loaders.R | 2 R/import.R | 13 ++--- R/install.R | 2 R/lamindb.R | 61 +---------------------- R/require.R | 18 ++++--- R/status.R | 25 ++++++--- R/temporary-instance.R | 75 +++++++++++------------------ R/utils.R | 92 ++++++++++++++++++------------------ R/zzz.R | 2 build/vignette.rds |binary man/get_current_lamin_instance.Rd | 12 ++-- man/get_current_lamin_settings.Rd | 8 +-- man/get_current_lamin_user.Rd | 9 +-- man/import_module.Rd | 4 - man/install_lamindb.Rd | 2 man/require_module.Rd | 2 tests/testthat/setup.R | 8 +-- tests/testthat/test-BasicQuerySet.R |only tests/testthat/test-Registry.R | 2 tests/testthat/test-checks.R | 9 +++ tests/testthat/test-import.R | 8 +-- tests/testthat/test-install.R | 11 +++- tests/testthat/test-unwrap-python.R | 6 +- tests/testthat/test-utils.R | 8 +-- tests/testthat/test-wrap-python.R | 3 - 30 files changed, 239 insertions(+), 254 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery [aut],
Jennifer Hoeting [aut],
Chris Volinsky [aut],
Ian Painter [aut],
Ka Yee Yeung [aut],
Hana Sevcikova [cre]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.20 dated 2025-01-11 and 3.18.21 dated 2026-03-13
ChangeLog | 5 DESCRIPTION | 8 MD5 | 16 - R/bicreg.R | 2 R/iBMA.bicreg.R | 488 ++++++++++++++++++++++++++-------------------------- R/iBMA.glm.R | 63 ------ R/iBMA.surv.R | 58 ------ R/predict.bic.glm.R | 2 man/iBMA.Rd | 2 9 files changed, 282 insertions(+), 362 deletions(-)
Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write
facilities for files created with (or for) the 'NumPy' extension for 'Python'.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with as C++11 which should be the default on
all platforms since the release of R 3.3.0.
Author: Dirk Eddelbuettel [aut, cre] ,
Wush Wu [aut] ,
Carl Rogers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCNPy versions 0.2.14 dated 2025-11-03 and 0.2.15 dated 2026-03-13
ChangeLog | 17 +++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++- inst/doc/RcppCNPy-intro.pdf |binary inst/doc/UsingReticulate.pdf |binary src/cnpy.cpp | 47 +++++++++++++++++++++---------------------- src/cnpy.h | 16 ++++++-------- src/cnpyMod.cpp | 19 ++++++++--------- 10 files changed, 77 insertions(+), 57 deletions(-)
Title: Analysis of Designed High-Dimensional Data using the
Comprehensive MultANOVA Framework
Description: A comprehensive and computationally fast framework to analyze high dimensional data associated with an experimental design based on Multiple ANOVAs (MultANOVA). It includes testing the overall significance of terms in the model, post-hoc analyses of significant terms and variable selection. Details may be found in Mahieu, B., & Cariou, V. (2025). MultANOVA Followed by Post Hoc Analyses for Designed High‐Dimensional Data: A Comprehensive Framework That Outperforms ASCA, rMANOVA, and VASCA. Journal of Chemometrics, 39(7). <doi:10.1002/cem.70039>.
Author: Benjamin Mahieu [aut, cre],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MultANOVA versions 1.0.1 dated 2025-09-01 and 1.1.0 dated 2026-03-13
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/plot.DCDA.R | 2 +- build/partial.rdb |binary 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Animated Glass-Style Tabs and Multi-Select Filter for 'Shiny'
Description: Tools for creating animated glassmorphism-style tab
navigation and multi-select dropdown filters in 'shiny' applications.
The package provides a tab navigation component and a searchable
multi-select widget with multiple checkbox indicator styles,
select-all controls, and customizable colour themes. The widgets are
compatible with standard 'shiny' layouts and 'bs4Dash' dashboards.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between glasstabs versions 0.1.0 dated 2026-03-11 and 0.1.1 dated 2026-03-13
glasstabs-0.1.0/glasstabs/man/glassMultiSelectServer.Rd |only glasstabs-0.1.1/glasstabs/DESCRIPTION | 9 glasstabs-0.1.1/glasstabs/LICENSE | 4 glasstabs-0.1.1/glasstabs/MD5 | 78 glasstabs-0.1.1/glasstabs/NAMESPACE | 26 glasstabs-0.1.1/glasstabs/NEWS.md | 41 glasstabs-0.1.1/glasstabs/R/dependencies.R | 66 glasstabs-0.1.1/glasstabs/R/glassSelect.R |only glasstabs-0.1.1/glasstabs/R/glass_multiselect.R | 610 ++++- glasstabs-0.1.1/glasstabs/R/glass_select_theme.R | 37 glasstabs-0.1.1/glasstabs/R/zzz.R | 50 glasstabs-0.1.1/glasstabs/README.md | 263 ++ glasstabs-0.1.1/glasstabs/build/vignette.rds |binary glasstabs-0.1.1/glasstabs/inst/WORDLIST | 7 glasstabs-0.1.1/glasstabs/inst/doc/getting-started.R | 70 glasstabs-0.1.1/glasstabs/inst/doc/getting-started.Rmd | 133 + glasstabs-0.1.1/glasstabs/inst/doc/getting-started.html | 273 +- glasstabs-0.1.1/glasstabs/inst/doc/glassSelect.R |only glasstabs-0.1.1/glasstabs/inst/doc/glassSelect.Rmd |only glasstabs-0.1.1/glasstabs/inst/doc/glassSelect.html |only glasstabs-0.1.1/glasstabs/inst/doc/multiselect.R | 65 glasstabs-0.1.1/glasstabs/inst/doc/multiselect.Rmd | 105 glasstabs-0.1.1/glasstabs/inst/doc/multiselect.html | 260 +- glasstabs-0.1.1/glasstabs/inst/doc/tabs.Rmd | 392 +-- glasstabs-0.1.1/glasstabs/inst/doc/tabs.html | 5 glasstabs-0.1.1/glasstabs/inst/www/glass.css | 891 +++++--- glasstabs-0.1.1/glasstabs/inst/www/glass.js | 1273 ++++++++---- glasstabs-0.1.1/glasstabs/man/glassFilterTags.Rd | 42 glasstabs-0.1.1/glasstabs/man/glassMultiSelect.Rd | 182 - glasstabs-0.1.1/glasstabs/man/glassMultiSelectValue.Rd |only glasstabs-0.1.1/glasstabs/man/glassSelect.Rd |only glasstabs-0.1.1/glasstabs/man/glassSelectValue.Rd |only glasstabs-0.1.1/glasstabs/man/glassTabPanel.Rd | 64 glasstabs-0.1.1/glasstabs/man/glassTabsServer.Rd | 70 glasstabs-0.1.1/glasstabs/man/glassTabsUI.Rd | 68 glasstabs-0.1.1/glasstabs/man/glass_select_theme.Rd | 66 glasstabs-0.1.1/glasstabs/man/updateGlassMultiSelect.Rd |only glasstabs-0.1.1/glasstabs/man/updateGlassSelect.Rd |only glasstabs-0.1.1/glasstabs/man/useGlassTabs.Rd | 64 glasstabs-0.1.1/glasstabs/tests/testthat.R | 24 glasstabs-0.1.1/glasstabs/tests/testthat/test-glassselect.R |only glasstabs-0.1.1/glasstabs/tests/testthat/test-multiselect.R | 260 ++ glasstabs-0.1.1/glasstabs/vignettes/getting-started.Rmd | 133 + glasstabs-0.1.1/glasstabs/vignettes/glassSelect.Rmd |only glasstabs-0.1.1/glasstabs/vignettes/multiselect.Rmd | 105 glasstabs-0.1.1/glasstabs/vignettes/tabs.Rmd | 392 +-- 46 files changed, 4172 insertions(+), 1956 deletions(-)
More information about freebsdcontribs at CRAN
Permanent link
Title: Coherent Forecast Combination for Linearly Constrained Multiple
Time Series
Description: Methods and tools designed to improve the forecast accuracy for a linearly
constrained multiple time series, while fulfilling the linear/aggregation relationships
linking the components (Girolimetto and Di Fonzo, 2024 <doi:10.48550/arXiv.2412.03429>).
'FoCo2' offers multi-task forecast combination and reconciliation
approaches leveraging input from multiple forecasting models or experts and ensuring
that the resulting forecasts satisfy specified linear constraints. In addition, linear
inequality constraints (e.g., non-negativity of the forecasts) can be imposed, if needed.
Author: Daniele Girolimetto [aut, cre] ,
Tommaso Di Fonzo [aut]
Maintainer: Daniele Girolimetto <daniele.girolimetto@unipd.it>
Diff between FoCo2 versions 0.1.2 dated 2025-06-14 and 0.1.3 dated 2026-03-13
DESCRIPTION | 23 - MD5 | 26 +- NEWS.md | 6 R/mtfc_fun.R | 296 +++++++++++++++--------- R/optimal.R | 207 ++++++++++------- R/resemble.R | 567 ++++++++++++++++++++++++++++++----------------- README.md | 10 build/partial.rdb |binary man/FoCo2-package.Rd | 10 man/csscr.Rd | 2 man/cssrc.Rd | 2 man/figures/foreco.svg | 455 ++++++++----------------------------- man/figures/logo.svg | 198 ++++++---------- tests/testthat/test-cs.R | 278 +++++++++++++++++------ 14 files changed, 1125 insertions(+), 955 deletions(-)
Title: Broken Stick Model for Irregular Longitudinal Data
Description: Data on multiple individuals through time are often sampled at
times that differ between persons. Irregular observation times can severely
complicate the statistical analysis of the data. The broken stick model
approximates each subject’s trajectory by one or more connected line segments.
The times at which segments connect (breakpoints) are identical for all
subjects and under control of the user. A well-fitting broken stick model
effectively transforms individual measurements made at irregular times into
regular trajectories with common observation times. Specification of the
model requires three variables: time, measurement and subject. The
model is a special case of the linear mixed model, with time as a linear
B-spline and subject as the grouping factor. The main assumptions are:
subjects are exchangeable, trajectories between consecutive breakpoints are
straight, random effects follow a multivariate normal distribution, and
unobserved data are missing at random. The package conta [...truncated...]
Author: Stef van Buuren [aut, cre]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
This is a re-admission after prior archival of version 2.6.0 dated 2025-03-31
Diff between brokenstick versions 2.6.0 dated 2025-03-31 and 2.7.0 dated 2026-03-13
DESCRIPTION | 8 - MD5 | 54 +++---- NAMESPACE | 1 NEWS.md | 9 + R/EB.R | 4 R/brokenstick-class.R | 44 +++-- R/brokenstick.R | 71 ++++++--- R/coef.R | 23 +-- R/get.R | 110 ++++++++------ R/import.R | 2 R/internals.R | 79 +++++++--- R/kr.R | 62 +++++--- R/model.frame.R | 4 R/plot.R | 229 ++++++++++++++++++------------ R/predict.R | 132 +++++++++++------ R/print.R | 99 ++++++++++-- R/set_control.R | 34 ++-- R/summary.R | 16 +- README.md | 7 build/vignette.rds |binary inst/doc/mainfunctions.Rmd | 2 inst/doc/mainfunctions.html | 7 inst/doc/oldfriends.html | 5 inst/doc/perfectmodel.html | 57 +++---- tests/testthat/test-brokenstick_edge.R | 110 +++++++++----- tests/testthat/test-predict.brokenstick.R | 41 ++++- tests/testthat/test-smooth_covariance.R | 39 +++-- vignettes/mainfunctions.Rmd | 2 28 files changed, 811 insertions(+), 440 deletions(-)
Title: Companion to Portfolio Construction and Risk Analysis
Description: A collection of functions and data sets that support teaching a quantitative finance MS level course on Portfolio Construction and Risk Analysis, and the writing of a textbook for such a course. The package provides several real-world data sets for problem assignments and student projects, including cross-sections of stock data from the Center for Research on Security Prices, LLC (CRSP), corresponding factor exposures from S&P Global, and several S&P 500 data sets.
Author: Doug Martin [cre, aut],
Alexios Galanos [ctb],
Kirk Li [aut, ctb],
Jon Spinney [ctb],
Thomas Philips [ctb]
Maintainer: Doug Martin <martinrd3d@gmail.com>
Diff between PCRA versions 1.2 dated 2023-08-30 and 1.2.1 dated 2026-03-13
DESCRIPTION | 43 +++++++++++++++---------------------------- MD5 | 16 ++++++++-------- R/PCRAData.R | 2 +- R/factorsSPGMI.R | 2 +- build/vignette.rds |binary inst/doc/PCRAVignette.pdf |binary man/PCRA-package.Rd | 2 +- man/factorsSPGMI.Rd | 2 +- man/getPCRAData.Rd | 2 +- 9 files changed, 28 insertions(+), 41 deletions(-)
Title: Multiblock Exploratory and Predictive Data Analysis
Description: Exploratory and predictive methods for the analysis of several blocks of variables measured on the same individuals.
Author: Benjamin Mahieu [aut, cre],
Essomanda Tchandao Mangamana [aut],
Evelyne Vigneau [aut],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MBAnalysis versions 2.1.1 dated 2025-10-08 and 2.2.0 dated 2026-03-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/MBplotBlocks.R | 10 +++++----- R/MBplotScores.R | 2 +- R/MBplotVars.R | 4 ++-- build/partial.rdb |binary 6 files changed, 18 insertions(+), 18 deletions(-)
Title: A Driver Discovery Tool for Cancer Whole Genomes
Description: A method for finding enrichments of somatic single nucleotide variants (SNVs) and small insertions-deletions (Indels) in functional elements in the human genome. 'ActiveDriverWGS' detects coding and noncoding cancer driver elements using whole genome sequencing data. The method is part of the publication H. Zhu et al. (2020) <doi:10.1016/j.molcel.2019.12.027> "Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks" in Molecular Cell.
Author: Juri Reimand [aut, cre],
Helen Zhu [ctb],
Kevin Cheng [ctb]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
This is a re-admission after prior archival of version 1.2.0 dated 2022-09-03
Diff between ActiveDriverWGS versions 1.2.0 dated 2022-09-03 and 1.2.1 dated 2026-03-13
DESCRIPTION | 24 - MD5 | 32 - NEWS.md | 5 R/ADWGS_test.R | 29 - R/ActiveDriverWGS.R | 44 ++ R/format_muts.R | 13 R/prepare_elements.R | 18 - README.md | 4 build/vignette.rds |binary inst/doc/ActiveDriverWGSR.R | 13 inst/doc/ActiveDriverWGSR.Rmd | 13 inst/doc/ActiveDriverWGSR.html | 598 ++++++++++++++++++++++------------ tests/testthat/test_ADWGS_test.R | 1 tests/testthat/test_ActiveDriverWGS.R | 1 tests/testthat/test_format_muts.R | 11 tests/testthat/test_input_format.R | 33 + vignettes/ActiveDriverWGSR.Rmd | 13 17 files changed, 553 insertions(+), 299 deletions(-)
More information about ActiveDriverWGS at CRAN
Permanent link
Title: A Unified Tidy Interface to R's Machine Learning Ecosystem
Description: Provides a unified tidyverse-compatible interface to R's machine
learning packages. Wraps established implementations from 'glmnet',
'randomForest', 'xgboost', 'e1071', 'rpart', 'gbm', 'nnet', 'cluster',
'dbscan', and others - providing consistent function signatures, tidy tibble
output, and unified 'ggplot2'-based visualization. The underlying algorithms
are unchanged; 'tidylearn' simply makes them easier to use together. Access
raw model objects via the $fit slot for package-specific functionality.
Methods include random forests Breiman (2001) <doi:10.1023/A:1010933404324>,
LASSO regression Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>,
elastic net Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>,
support vector machines Cortes and Vapnik (1995) <doi:10.1007/BF00994018>,
and gradient boosting Friedman (2001) <doi:10.1214/aos/1013203451>.
Author: Cesaire Tobias [aut, cre]
Maintainer: Cesaire Tobias <cesaire@sheetsolved.com>
Diff between tidylearn versions 0.1.0 dated 2026-02-06 and 0.1.1 dated 2026-03-13
DESCRIPTION | 8 MD5 | 26 NEWS.md | 122 +- R/core.R | 867 ++++++++------- R/supervised-classification.R | 694 ++++++------ R/supervised-regression.R | 758 ++++++------- R/unsupervised-market-basket.R | 2 R/visualization.R | 2366 ++++++++++++++++++++--------------------- README.md | 2 build/vignette.rds |binary inst/doc/automl.html | 3 inst/doc/getting-started.html | 4 man/tidy_apriori.Rd | 104 - man/tl_plot_model.Rd |only man/tl_plot_unsupervised.Rd |only 15 files changed, 2527 insertions(+), 2429 deletions(-)
Title: Simulation of Bird Flight Range
Description: Functions for range estimation in birds based on Pennycuick (2008)
and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008)
requires manual entry of birds which can be tedious when there are hundreds
of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975)
and time-marching computation methods as in Pennycuick (1998) and Pennycuick (2008).
See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>,
and Pennycuick (2008, ISBN:9780080557816).
Author: Brian Masinde [aut, cre],
Krzysztof Bartoszek [ctb, ths]
Maintainer: Brian Masinde <masindeb@live.com>
Diff between FlyingR versions 0.2.2 dated 2022-06-27 and 0.2.3 dated 2026-03-13
DESCRIPTION | 19 - MD5 | 35 ++- NEWS.md | 13 - R/curlew_sandpiper.R |only R/garden_wablers.R |only R/input_match.R | 10 R/lesser_whitethroats.R |only R/migrate.R | 106 +++++++-- README.md | 467 +++++++++++++++++++++++++++++++++++------- build/vignette.rds |binary data/curlew_sandpiper.rda |only data/garden_wablers.rda |only data/lesser_whitethroats.rda |only inst/doc/documentation.R | 170 +++++++++++++++ inst/doc/documentation.Rmd | 243 +++++++++++++++++++++ inst/doc/documentation.html | 362 +++++++++++++++++++++++++------- man/curlew_sandpiper.Rd |only man/figures |only man/garden_wablers.Rd |only man/lesser_whitethroats.Rd |only tests/testthat/test_migrate.R | 64 ++++- vignettes/documentation.Rmd | 243 +++++++++++++++++++++ vignettes/references.bib | 74 ++++++ 23 files changed, 1586 insertions(+), 220 deletions(-)
Title: Multiple Imputation with Denoising Autoencoders
Description: A tool for multiply imputing missing data using 'MIDAS', a deep learning method based on denoising autoencoder neural networks (see Lall and Robinson, 2022; <doi:10.1017/pan.2020.49>). This algorithm offers significant accuracy and efficiency advantages over other multiple imputation strategies, particularly when applied to large datasets with complex features. Alongside interfacing with 'Python' to run the core algorithm, this package contains functions for processing data before and after model training, running imputation model diagnostics, generating multiple completed datasets, and estimating regression models on these datasets. For more information see Lall and Robinson (2023) <doi:10.18637/jss.v107.i09>. This package is deprecated in favor of 'rMIDAS2'; it remains available for existing workflows but will receive only compatibility and documentation updates.
Author: Thomas Robinson [aut, cre, cph] ,
Ranjit Lall [aut, cph] ,
Alex Stenlake [ctb, cph],
Elviss Dvinskis [ctb]
Maintainer: Thomas Robinson <ts.robinson1994@gmail.com>
Diff between rMIDAS versions 1.0.0 dated 2023-10-11 and 1.0.1 dated 2026-03-13
rMIDAS-1.0.0/rMIDAS/inst/python/__pycache__ |only rMIDAS-1.0.1/rMIDAS/DESCRIPTION | 20 +- rMIDAS-1.0.1/rMIDAS/MD5 | 48 +++--- rMIDAS-1.0.1/rMIDAS/NEWS.md | 6 rMIDAS-1.0.1/rMIDAS/R/rMIDAS-package.R |only rMIDAS-1.0.1/rMIDAS/R/zzz.R | 33 ++++ rMIDAS-1.0.1/rMIDAS/README.md | 64 +++++--- rMIDAS-1.0.1/rMIDAS/build/partial.rdb |binary rMIDAS-1.0.1/rMIDAS/build/vignette.rds |binary rMIDAS-1.0.1/rMIDAS/inst/doc/custom_python_versions.R | 108 +++++++-------- rMIDAS-1.0.1/rMIDAS/inst/doc/custom_python_versions.Rmd | 10 + rMIDAS-1.0.1/rMIDAS/inst/doc/custom_python_versions.html | 14 + rMIDAS-1.0.1/rMIDAS/inst/doc/imputation_demo.R | 92 ++++++------ rMIDAS-1.0.1/rMIDAS/inst/doc/imputation_demo.Rmd | 8 + rMIDAS-1.0.1/rMIDAS/inst/doc/imputation_demo.html | 8 + rMIDAS-1.0.1/rMIDAS/inst/doc/migrating-to-rMIDAS2.R |only rMIDAS-1.0.1/rMIDAS/inst/doc/migrating-to-rMIDAS2.Rmd |only rMIDAS-1.0.1/rMIDAS/inst/doc/migrating-to-rMIDAS2.html |only rMIDAS-1.0.1/rMIDAS/inst/doc/use-server.R | 4 rMIDAS-1.0.1/rMIDAS/inst/doc/use-server.Rmd | 12 + rMIDAS-1.0.1/rMIDAS/inst/doc/use-server.html | 10 + rMIDAS-1.0.1/rMIDAS/man/rMIDAS-package.Rd |only rMIDAS-1.0.1/rMIDAS/tests/testthat.R | 16 ++ rMIDAS-1.0.1/rMIDAS/vignettes/custom_python_versions.Rmd | 10 + rMIDAS-1.0.1/rMIDAS/vignettes/imputation_demo.Rmd | 8 + rMIDAS-1.0.1/rMIDAS/vignettes/migrating-to-rMIDAS2.Rmd |only rMIDAS-1.0.1/rMIDAS/vignettes/use-server.Rmd | 12 + 27 files changed, 309 insertions(+), 174 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.8-2 dated 2025-04-25 and 1.9-0 dated 2026-03-13
RBesT-1.8-2/RBesT/R/deprecation_message.R |only RBesT-1.9-0/RBesT/DESCRIPTION | 21 RBesT-1.9-0/RBesT/MD5 | 179 +- RBesT-1.9-0/RBesT/NAMESPACE | 31 RBesT-1.9-0/RBesT/NEWS.md | 27 RBesT-1.9-0/RBesT/R/BinaryExactCI.R | 4 RBesT-1.9-0/RBesT/R/EM_bmm_ab.R | 12 RBesT-1.9-0/RBesT/R/EM_bmm_mun.R | 12 RBesT-1.9-0/RBesT/R/EM_gmm.R | 12 RBesT-1.9-0/RBesT/R/EM_mnmm.R | 27 RBesT-1.9-0/RBesT/R/EM_msmm.R | 4 RBesT-1.9-0/RBesT/R/EM_plot.R | 38 RBesT-1.9-0/RBesT/R/RBesT-package.R | 3 RBesT-1.9-0/RBesT/R/decision1S.R | 189 ++ RBesT-1.9-0/RBesT/R/decision1S_boundary.R | 197 ++ RBesT-1.9-0/RBesT/R/decision2S.R | 190 ++ RBesT-1.9-0/RBesT/R/decision2S_boundary.R | 327 ++++ RBesT-1.9-0/RBesT/R/forest_plot.R | 31 RBesT-1.9-0/RBesT/R/gMAP.R | 6 RBesT-1.9-0/RBesT/R/mix.R | 121 + RBesT-1.9-0/RBesT/R/mixbeta.R | 8 RBesT-1.9-0/RBesT/R/mixcombine.R | 8 RBesT-1.9-0/RBesT/R/mixess.R | 6 RBesT-1.9-0/RBesT/R/mixfit.R | 4 RBesT-1.9-0/RBesT/R/mixgamma.R | 8 RBesT-1.9-0/RBesT/R/mixmvnorm.R | 3 RBesT-1.9-0/RBesT/R/mixnorm.R | 4 RBesT-1.9-0/RBesT/R/mixplot.R | 28 RBesT-1.9-0/RBesT/R/mixstanvar.R | 3 RBesT-1.9-0/RBesT/R/nsamples.R |only RBesT-1.9-0/RBesT/R/oc1S.R | 130 + RBesT-1.9-0/RBesT/R/oc2S.R | 358 ++++- RBesT-1.9-0/RBesT/R/plot_gMAP.R | 15 RBesT-1.9-0/RBesT/R/pos1S.R | 112 + RBesT-1.9-0/RBesT/R/pos2S.R | 373 ++++- RBesT-1.9-0/RBesT/R/posterior.R |only RBesT-1.9-0/RBesT/R/preddist.R | 3 RBesT-1.9-0/RBesT/R/robustify.R | 3 RBesT-1.9-0/RBesT/R/support.R | 3 RBesT-1.9-0/RBesT/R/sysdata.rda |binary RBesT-1.9-0/RBesT/R/zzz.R | 8 RBesT-1.9-0/RBesT/build/vignette.rds |binary RBesT-1.9-0/RBesT/data/AS.rda |binary RBesT-1.9-0/RBesT/data/colitis.rda |binary RBesT-1.9-0/RBesT/data/crohn.rda |binary RBesT-1.9-0/RBesT/data/transplant.rda |binary RBesT-1.9-0/RBesT/demo/oc2S-tte.R | 71 - RBesT-1.9-0/RBesT/demo/robustMAP.R | 252 ++- RBesT-1.9-0/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.9-0/RBesT/inst/doc/introduction.html | 129 - RBesT-1.9-0/RBesT/inst/examples/ess.R | 9 RBesT-1.9-0/RBesT/inst/examples/predict_gMAP.R | 11 RBesT-1.9-0/RBesT/inst/extra/run-oq.R | 14 RBesT-1.9-0/RBesT/inst/sbc/calibration.md5 | 6 RBesT-1.9-0/RBesT/inst/sbc/make_reference_rankhist.R | 76 - RBesT-1.9-0/RBesT/inst/sbc/sbc_report.R | 18 RBesT-1.9-0/RBesT/inst/sbc/sbc_report.html | 810 ++++++------ RBesT-1.9-0/RBesT/inst/sbc/sbc_tools.R | 96 + RBesT-1.9-0/RBesT/man/RBesT-package.Rd | 2 RBesT-1.9-0/RBesT/man/create_decision1S_1sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision1S_2sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision1S_atomic.Rd |only RBesT-1.9-0/RBesT/man/create_decision2S_1sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision2S_2sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision2S_atomic.Rd |only RBesT-1.9-0/RBesT/man/decision1S.Rd | 59 RBesT-1.9-0/RBesT/man/decision1S_boundary.Rd | 5 RBesT-1.9-0/RBesT/man/decision2S.Rd | 62 RBesT-1.9-0/RBesT/man/decision2S_boundary.Rd | 17 RBesT-1.9-0/RBesT/man/draws-RBesT.Rd |only RBesT-1.9-0/RBesT/man/ess.Rd | 9 RBesT-1.9-0/RBesT/man/forest_plot.Rd | 5 RBesT-1.9-0/RBesT/man/mixplot.Rd | 23 RBesT-1.9-0/RBesT/man/nsamples.gMAP.Rd |only RBesT-1.9-0/RBesT/man/oc1S.Rd | 20 RBesT-1.9-0/RBesT/man/oc2S.Rd | 3 RBesT-1.9-0/RBesT/man/plot.EM.Rd | 14 RBesT-1.9-0/RBesT/man/plot.gMAP.Rd | 6 RBesT-1.9-0/RBesT/man/pos1S.Rd | 2 RBesT-1.9-0/RBesT/man/pos2S.Rd | 3 RBesT-1.9-0/RBesT/man/predict.gMAP.Rd | 11 RBesT-1.9-0/RBesT/tests/testthat.R | 8 RBesT-1.9-0/RBesT/tests/testthat/_snaps |only RBesT-1.9-0/RBesT/tests/testthat/test-EM.R | 15 RBesT-1.9-0/RBesT/tests/testthat/test-decision1S.R |only RBesT-1.9-0/RBesT/tests/testthat/test-decision1S_boundary.R |only RBesT-1.9-0/RBesT/tests/testthat/test-decision2S.R |only RBesT-1.9-0/RBesT/tests/testthat/test-decision2S_boundary.R |only RBesT-1.9-0/RBesT/tests/testthat/test-gMAP.R | 28 RBesT-1.9-0/RBesT/tests/testthat/test-mixdist.R | 8 RBesT-1.9-0/RBesT/tests/testthat/test-mixjson.R | 4 RBesT-1.9-0/RBesT/tests/testthat/test-mixstanvar.R | 218 +-- RBesT-1.9-0/RBesT/tests/testthat/test-oc1S.R | 99 + RBesT-1.9-0/RBesT/tests/testthat/test-oc2S.R | 369 +++++ RBesT-1.9-0/RBesT/tests/testthat/test-pos1S.R | 100 + RBesT-1.9-0/RBesT/tests/testthat/test-pos2S.R | 114 + RBesT-1.9-0/RBesT/tests/testthat/test-posterior.R |only RBesT-1.9-0/RBesT/tests/testthat/test-preddist.R | 16 98 files changed, 3947 insertions(+), 1273 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are implemented.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>), substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>), and features
for the generation of synthetic datasets
(Reiter, 2005, <doi:10. [...truncated...]
Author: Alexander Robitzsch [aut, cre] ,
Simon Grund [aut] ,
Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.18-36 dated 2025-09-12 and 3.19-16 dated 2026-03-13
DESCRIPTION | 8 +-- MD5 | 52 +++++++++++------------ R/RcppExports.R | 2 R/mice.impute.pls.R | 5 -- R/mice.impute.rlm.R | 4 - R/mice.nmi.R | 4 - R/mice_imputation_prepare_2l_functions.R | 25 ++++++----- R/ml_mcmc_fit.R | 4 - R/syn.constant.R | 6 +- R/syn.formula.R | 10 ++-- R/syn.mice.R | 8 +-- R/syn_da.R | 8 +-- R/syn_da_compute_pls_factors.R | 8 +-- R/syn_da_create_formula.R | 6 +- R/syn_da_extend_list.R | 4 - R/syn_da_synthesize_lm.R | 12 ++--- R/syn_mice.R | 8 +-- R/syn_mice_catch_arguments.R | 4 - R/syn_mice_completed_datasets.R | 4 - R/syn_mice_create_design_matrix.R | 8 +-- R/systime.R | 16 +++---- build/partial.rdb |binary inst/NEWS | 11 ++++ man/write.pspp.Rd | 5 -- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 70 +++++++++++++++---------------- 27 files changed, 154 insertions(+), 142 deletions(-)
Title: Data Sets and Code for "Meta-Analysis with R"
Description: Data sets and code supporting the second edition of "Meta-Analysis with R"; first edition: Schwarzer, Carpenter, and Rücker (2015) <DOI:10.1007/978-3-319-21416-0>.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between metabook versions 0.1-0 dated 2026-03-04 and 0.2-0 dated 2026-03-13
metabook-0.1-0/metabook/data/Law1994.rda |only metabook-0.1-0/metabook/man/Law1994.Rd |only metabook-0.2-0/metabook/DESCRIPTION | 14 ++-- metabook-0.2-0/metabook/MD5 | 73 ++++++++++++++---------- metabook-0.2-0/metabook/NAMESPACE | 3 metabook-0.2-0/metabook/NEWS.md | 21 ++++++ metabook-0.2-0/metabook/R/metabook-package.R | 8 -- metabook-0.2-0/metabook/build |only metabook-0.2-0/metabook/data/Hamza2021.rda |only metabook-0.2-0/metabook/data/Hong2015.rda |only metabook-0.2-0/metabook/data/Jalota2011.rda |only metabook-0.2-0/metabook/data/Linde2015.rda |binary metabook-0.2-0/metabook/data/Senn2013.rda |only metabook-0.2-0/metabook/data/Senn2024.rda |only metabook-0.2-0/metabook/data/Su2018.rda |only metabook-0.2-0/metabook/data/Thompson1999.rda |only metabook-0.2-0/metabook/man/Baker2009.Rd | 49 +++++++++++----- metabook-0.2-0/metabook/man/Bassler2004.Rd | 46 ++++++++++----- metabook-0.2-0/metabook/man/Curtin2002.Rd | 47 ++++++++++----- metabook-0.2-0/metabook/man/Dogliotti2014.Rd | 42 +++++++++---- metabook-0.2-0/metabook/man/Dong2013.Rd | 15 ++-- metabook-0.2-0/metabook/man/Feng2019.Rd | 36 ++++++++--- metabook-0.2-0/metabook/man/Franchini2012.Rd | 59 +++++++++++++------ metabook-0.2-0/metabook/man/Furukawa2003.Rd | 49 +++++++++++----- metabook-0.2-0/metabook/man/Greb2008.Rd | 46 ++++++++++----- metabook-0.2-0/metabook/man/Greenland1992.Rd | 44 +++++++++----- metabook-0.2-0/metabook/man/Gurusamy2011.Rd | 66 +++++++++++++++------ metabook-0.2-0/metabook/man/Hamza2021.Rd |only metabook-0.2-0/metabook/man/Higgins2008.Rd | 56 +++++++++++------- metabook-0.2-0/metabook/man/Hong2015.Rd |only metabook-0.2-0/metabook/man/Jalota2011.Rd |only metabook-0.2-0/metabook/man/Linde2015.Rd | 17 ++--- metabook-0.2-0/metabook/man/Linde2016.Rd | 17 ++--- metabook-0.2-0/metabook/man/Lloyd2010.Rd | 13 ++-- metabook-0.2-0/metabook/man/Moore1998.Rd | 9 +- metabook-0.2-0/metabook/man/Poole2003.Rd | 13 ++-- metabook-0.2-0/metabook/man/Quan2000.Rd | 13 ++-- metabook-0.2-0/metabook/man/Senn2013.Rd |only metabook-0.2-0/metabook/man/Senn2024.Rd |only metabook-0.2-0/metabook/man/Spooner2002.Rd | 13 ++-- metabook-0.2-0/metabook/man/Steurer2006.Rd | 13 ++-- metabook-0.2-0/metabook/man/Stowe2010.Rd | 15 ++-- metabook-0.2-0/metabook/man/Su2018.Rd |only metabook-0.2-0/metabook/man/Thompson1999.Rd |only metabook-0.2-0/metabook/man/Woods2010.Rd | 38 ++++++++---- metabook-0.2-0/metabook/man/metabook-package.Rd | 2 46 files changed, 547 insertions(+), 290 deletions(-)
Title: Statistics for International Large-Scale Assessments (ILSA)
Description: Calculates point estimates and standard errors using replicate weights and plausible values for International Large-Scale Assessments (ILSA), including: means, proportions, quantiles, correlations, singlelevel regressions, and multilevel regressions.
Author: Andres Christiansen [aut, cre] ,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAstats versions 0.4.0 dated 2025-07-15 and 0.4.4 dated 2026-03-13
ILSAstats-0.4.0/ILSAstats/R/myfunc.R |only ILSAstats-0.4.0/ILSAstats/man/myfunc.Rd |only ILSAstats-0.4.4/ILSAstats/DESCRIPTION | 9 ILSAstats-0.4.4/ILSAstats/MD5 | 67 +- ILSAstats-0.4.4/ILSAstats/NAMESPACE | 9 ILSAstats-0.4.4/ILSAstats/NEWS.md | 19 ILSAstats-0.4.4/ILSAstats/R/argchecks.R | 103 +++ ILSAstats-0.4.4/ILSAstats/R/internal.R | 41 - ILSAstats-0.4.4/ILSAstats/R/leaguetable.R |only ILSAstats-0.4.4/ILSAstats/R/prepILSA.R |only ILSAstats-0.4.4/ILSAstats/R/proflevels.R |only ILSAstats-0.4.4/ILSAstats/R/proflevels.get.R |only ILSAstats-0.4.4/ILSAstats/R/repcreate.R | 231 ++++++-- ILSAstats-0.4.4/ILSAstats/R/replm.R | 123 +++- ILSAstats-0.4.4/ILSAstats/R/repmean.R | 161 ++++- ILSAstats-0.4.4/ILSAstats/R/repmeanCI.R |only ILSAstats-0.4.4/ILSAstats/R/repprop.R | 274 +++++++++- ILSAstats-0.4.4/ILSAstats/R/repprop.table.R |only ILSAstats-0.4.4/ILSAstats/R/repquant.R | 2 ILSAstats-0.4.4/ILSAstats/R/reprho.R | 58 +- ILSAstats-0.4.4/ILSAstats/R/repse.R | 16 ILSAstats-0.4.4/ILSAstats/R/repsetup.R | 5 ILSAstats-0.4.4/ILSAstats/R/timss99.R |only ILSAstats-0.4.4/ILSAstats/data/ILSAinfo.RData |binary ILSAstats-0.4.4/ILSAstats/data/repdata.RData |binary ILSAstats-0.4.4/ILSAstats/data/timss99.RData |only ILSAstats-0.4.4/ILSAstats/inst/examples/repmeanCI_example.R |only ILSAstats-0.4.4/ILSAstats/inst/examples/repprop.table_example.R |only ILSAstats-0.4.4/ILSAstats/man/leaguetable.Rd |only ILSAstats-0.4.4/ILSAstats/man/prepILSA.Rd |only ILSAstats-0.4.4/ILSAstats/man/proflevels.Rd |only ILSAstats-0.4.4/ILSAstats/man/proflevels.get.Rd |only ILSAstats-0.4.4/ILSAstats/man/repcreate.Rd | 6 ILSAstats-0.4.4/ILSAstats/man/repglm.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/replm.Rd | 11 ILSAstats-0.4.4/ILSAstats/man/repmean.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/repmeanCI.Rd |only ILSAstats-0.4.4/ILSAstats/man/repprop.Rd | 11 ILSAstats-0.4.4/ILSAstats/man/repprop.table.Rd |only ILSAstats-0.4.4/ILSAstats/man/repquant.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/reprho.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/repse.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/repsetup.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/timss99.Rd |only 44 files changed, 927 insertions(+), 243 deletions(-)
Title: Estimation of Spatial Weight Matrices
Description: Bayesian estimation of spatial weight matrices in spatial
econometric panel models. Allows for estimation of spatial
autoregressive (SAR), spatial error (SEM), spatial Durbin (SDM),
spatial error Durbin (SDEM) and spatially lagged explanatory variable
(SLX) type specifications featuring an unknown spatial weight matrix.
Methodological details are given in Krisztin and Piribauer (2022)
<doi:10.1080/17421772.2022.2095426>.
Author: Tamas Krisztin [aut, cre] ,
Philipp Piribauer [aut]
Maintainer: Tamas Krisztin <krisztin@iiasa.ac.at>
Diff between estimateW versions 0.1.0 dated 2025-05-13 and 0.2.0 dated 2026-03-13
DESCRIPTION | 7 MD5 | 42 - NAMESPACE | 2 NEWS.md | 9 R/R6_samplers.R | 12 R/data.R | 150 +++--- R/logdetPaceBarry.R | 46 ++ R/ngamma.R | 1158 ++++++++++++++++++++++++++++----------------------- R/output.R | 6 R/plotting.R | 6 R/priors.R | 5 R/sdmw.R | 4 R/semw.R | 486 ++++++++++----------- R/slxw.R | 3 data/nuts1growth.rda |binary man/logdetSpline.Rd |only man/nuts1growth.Rd | 21 man/rho_priors.Rd | 5 man/sdem.Rd | 9 man/sdemw.Rd | 9 man/sem.Rd | 11 man/semw.Rd | 9 man/slx.Rd |only 23 files changed, 1125 insertions(+), 875 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.11 dated 2025-12-11 and 0.1.12 dated 2026-03-13
DESCRIPTION | 12 MD5 | 28 NAMESPACE | 116 +-- R/dataset.R | 198 ++--- R/helper.R | 888 +++++++++++------------ R/xtdml_data.R | 1438 +++++++++++++++++++------------------- R/xtdml_main.R | 212 +++++ R/xtdml_plr.R | 1166 +++++++++++++++--------------- R/zzz.R | 40 - README.md | 138 +++ man/make_plpr_data.Rd | 122 +-- man/xtdml.Rd | 997 +++++++++++++------------- man/xtdml_data.Rd | 414 +++++----- man/xtdml_data_from_data_frame.Rd | 152 ++-- man/xtdml_plr.Rd | 655 ++++++++--------- 15 files changed, 3491 insertions(+), 3085 deletions(-)
Title: Adaptive Machine Learning-Powered, Context-Matching Tool for
Single-Cell and Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using context-matching marker datasets. It creates a unified marker list (`Markers_list`) from multiple sources: built-in curated databases ('Cellmarker2', 'PanglaoDB', 'ScType', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects with cell labels, or user-provided Excel tables. SlimR first uses adaptive machine learning for parameter optimization, and then offers two automated annotation approaches: 'cluster-based' and 'per-cell'. Cluster-based annotation assigns one label per cluster, expression-based probability calculation, and AUC validation. Per-cell annotation assigns labels to individual cells using three scoring methods with adaptive thresholds and ratio-based confidence filtering, plus optional UMAP spatial smoothing, making it ideal for heterogeneous clusters and rare cell types. The package also supports semi-automated workflows with heatmaps, feature plots, and combined visualizations for manual annotation. For m [...truncated...]
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.1.1 dated 2026-02-05 and 1.1.2 dated 2026-03-13
DESCRIPTION | 10 MD5 | 53 +- NAMESPACE | 1 NEWS.md | 7 R/Celltype_Annotation_PerCell.R | 35 + R/Database_ScType.R |only R/Markers_filter_ScType.R |only R/onattach.R | 19 - README.md | 609 +++++++++------------------------ data/ScType.rda |only data/ScType_raw.rda |only data/ScType_table.rda |only man/Cellmarker2.Rd | 5 man/Cellmarker2_raw.Rd | 5 man/Cellmarker2_table.Rd | 5 man/Markers_filter_Cellmarker2.Rd | 1 man/Markers_filter_PanglaoDB.Rd | 1 man/Markers_filter_ScType.Rd |only man/Markers_list_PCTAM.Rd | 5 man/Markers_list_PCTIT.Rd | 5 man/Markers_list_TCellSI.Rd | 5 man/Markers_list_scIBD.Rd | 5 man/PanglaoDB.Rd | 5 man/PanglaoDB_raw.Rd | 5 man/PanglaoDB_table.Rd | 5 man/Read_excel_markers.Rd | 1 man/Read_seurat_markers.Rd | 1 man/ScType.Rd |only man/ScType_raw.Rd |only man/ScType_table.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-marker-functions.R | 47 ++ 32 files changed, 339 insertions(+), 496 deletions(-)
Title: Conduct Response Item Network (ResIN) Analysis with Social
Response Data
Description: Contains various tools to estimate, analyze, and visualize Response Item Networks. 'ResIN' dummy-codes ordered and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.
Author: Philip Warncke [cre, aut],
Dino Carpentras [aut],
Adrian Lueders [aut]
Maintainer: Philip Warncke <philip.warncke@ul.ie>
Diff between ResIN versions 2.3.0 dated 2026-03-02 and 2.3.1 dated 2026-03-13
DESCRIPTION | 10 MD5 | 38 - NAMESPACE | 11 NEWS.md | 26 + R/BrJSocPsychol_2024.R | 1 R/ResIN.R | 866 ++++++++++++++++++++++++++++++++---------- R/ResIN_boots_execute.R | 246 ++++++++--- R/ResIN_boots_extract.R | 5 R/ResIN_boots_prepare.R | 7 R/methods-ResIN.R | 16 data/BrJSocPsychol_2024.RData |binary inst/doc/ResIN-VIGNETTE.R | 38 - inst/doc/ResIN-VIGNETTE.Rmd | 77 +-- inst/doc/ResIN-VIGNETTE.html | 132 ++---- man/ResIN.Rd | 254 ++++++------ man/ResIN_boots_execute.Rd | 20 man/ResIN_boots_extract.Rd | 5 man/ResIN_boots_prepare.Rd | 7 man/plot.ResIN.Rd | 4 vignettes/ResIN-VIGNETTE.Rmd | 77 +-- 20 files changed, 1175 insertions(+), 665 deletions(-)
Title: Sparse Additive Modelling
Description: Computationally efficient tools for high dimensional predictive
modeling (regression and classification). SAM is short for sparse
additive modeling, and adopts the computationally efficient basis
spline technique. We solve the optimization problems by various
computational algorithms including the block coordinate descent
algorithm, fast iterative soft-thresholding algorithm, and newton method.
The computation is further accelerated by warm-start and active-set tricks.
Author: Haoming Jiang [aut],
Yukun Ma [aut],
Han Liu [aut],
Kathryn Roeder [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between SAM versions 1.2 dated 2026-02-19 and 1.3 dated 2026-03-13
DESCRIPTION | 6 +- MD5 | 62 ++++++++++++--------- NAMESPACE | 5 + NEWS.md |only R/aaa_sam_utils.R | 51 +++++++++++++++++ R/sam.R |only R/samEL.R | 33 ++++++++--- R/samHL.R | 21 ++++--- R/samLL.R | 32 ++++++++--- R/samQL.R | 50 ++++++++++++++--- README.md |only man/sam.Rd |only man/samEL.Rd | 22 +++++++ man/samHL.Rd | 10 +++ man/samLL.Rd | 22 +++++++ man/samQL.Rd | 37 ++++++++++++ src/amalgamation.cpp | 2 src/c_api.cpp | 16 ++--- src/c_api/c_api_utils.h |only src/c_api/grpLR.cpp | 41 +++++--------- src/c_api/grpPR.cpp | 40 +++++--------- src/c_api/grpSVM.cpp | 76 ++++++++++++++++++-------- src/c_api/grplasso.cpp | 100 ++++++++++++++++++++--------------- src/objective/GLMObjective.cpp | 64 ++++++++++++++-------- src/objective/GLMObjective.h | 7 ++ src/objective/LinearCovObjective.cpp |only src/objective/LinearCovObjective.h |only src/objective/LinearObjective.cpp | 9 +-- src/objective/objective.h | 10 +++ src/solver/actgd.cpp |only src/solver/actgd.h | 20 ++----- src/solver/actnewton.cpp | 66 ++++++++++++++++++++++- src/solver/solver_params.cpp | 5 + src/solver/solver_params.h | 19 +++++- src/utils.h | 10 +++ tests/test_poisson.R |only tests/test_svm.R |only 37 files changed, 604 insertions(+), 232 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph] ,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.2.1 dated 2026-01-12 and 1.3.0 dated 2026-03-13
cffr-1.2.1/cffr/inst/doc/bibtex-cff.Rmd |only cffr-1.2.1/cffr/inst/doc/cffr.Rmd |only cffr-1.2.1/cffr/inst/doc/joss-paper.Rmd |only cffr-1.2.1/cffr/inst/doc/r-cff.Rmd |only cffr-1.2.1/cffr/vignettes/bibtex-cff.Rmd |only cffr-1.2.1/cffr/vignettes/cffr.Rmd |only cffr-1.2.1/cffr/vignettes/joss-paper.Rmd |only cffr-1.2.1/cffr/vignettes/r-cff.Rmd |only cffr-1.3.0/cffr/DESCRIPTION | 16 cffr-1.3.0/cffr/MD5 | 196 cffr-1.3.0/cffr/NEWS.md | 31 cffr-1.3.0/cffr/R/as_bibentry.R | 851 +- cffr-1.3.0/cffr/R/as_cff.R | 15 cffr-1.3.0/cffr/R/as_cff_person.R | 37 cffr-1.3.0/cffr/R/as_cff_reference.R | 2 cffr-1.3.0/cffr/R/assertions.R | 28 cffr-1.3.0/cffr/R/cff.R | 11 cffr-1.3.0/cffr/R/cff_create.R | 31 cffr-1.3.0/cffr/R/cff_gha_update.R | 154 cffr-1.3.0/cffr/R/cff_git_hook.R | 40 cffr-1.3.0/cffr/R/cff_modify.R | 16 cffr-1.3.0/cffr/R/cff_read.R | 584 - cffr-1.3.0/cffr/R/cff_read_bib_text.R | 19 cffr-1.3.0/cffr/R/cff_validate.R | 265 cffr-1.3.0/cffr/R/cff_write.R | 371 cffr-1.3.0/cffr/R/cff_write_misc.R | 290 cffr-1.3.0/cffr/R/deprecated.R | 16 cffr-1.3.0/cffr/R/encoded_utf_to_latex.R | 6 cffr-1.3.0/cffr/R/methods.R | 7 cffr-1.3.0/cffr/R/utils-alerts.R | 178 cffr-1.3.0/cffr/R/utils-bib.R | 1 cffr-1.3.0/cffr/R/utils-cff_read.R | 10 cffr-1.3.0/cffr/R/utils-cff_ref.R | 1 cffr-1.3.0/cffr/R/utils-create.R | 451 - cffr-1.3.0/cffr/R/utils-persons.R | 29 cffr-1.3.0/cffr/R/utils-schema.R | 4 cffr-1.3.0/cffr/R/utils.R | 27 cffr-1.3.0/cffr/README.md | 800 +- cffr-1.3.0/cffr/build/partial.rdb |binary cffr-1.3.0/cffr/build/vignette.rds |binary cffr-1.3.0/cffr/data/cran_to_spdx.rda |binary cffr-1.3.0/cffr/inst/REFERENCES.bib | 95 cffr-1.3.0/cffr/inst/WORDLIST | 1 cffr-1.3.0/cffr/inst/doc/bibtex-cff.R | 371 cffr-1.3.0/cffr/inst/doc/bibtex-cff.html | 4178 +++++------ cffr-1.3.0/cffr/inst/doc/bibtex-cff.qmd |only cffr-1.3.0/cffr/inst/doc/cffr.R | 63 cffr-1.3.0/cffr/inst/doc/cffr.html | 1119 +- cffr-1.3.0/cffr/inst/doc/cffr.qmd |only cffr-1.3.0/cffr/inst/doc/joss-paper.html | 377 cffr-1.3.0/cffr/inst/doc/joss-paper.qmd |only cffr-1.3.0/cffr/inst/doc/r-cff.R | 172 cffr-1.3.0/cffr/inst/doc/r-cff.html | 2964 +++---- cffr-1.3.0/cffr/inst/doc/r-cff.qmd |only cffr-1.3.0/cffr/inst/examples/CITATION_basic.cff | 2 cffr-1.3.0/cffr/inst/examples/CITATION_rmarkdown | 4 cffr-1.3.0/cffr/inst/schemaorg.json | 4 cffr-1.3.0/cffr/inst/yaml/update-citation-cff.yaml | 76 cffr-1.3.0/cffr/man/as_bibentry.Rd | 21 cffr-1.3.0/cffr/man/as_cff.Rd | 14 cffr-1.3.0/cffr/man/as_cff_person.Rd | 27 cffr-1.3.0/cffr/man/cff.Rd | 8 cffr-1.3.0/cffr/man/cff_class.Rd | 36 cffr-1.3.0/cffr/man/cff_create.Rd | 23 cffr-1.3.0/cffr/man/cff_gha_update.Rd | 12 cffr-1.3.0/cffr/man/cff_git_hook.Rd | 38 cffr-1.3.0/cffr/man/cff_modify.Rd | 13 cffr-1.3.0/cffr/man/cff_read.Rd | 18 cffr-1.3.0/cffr/man/cff_read_bib_text.Rd | 15 cffr-1.3.0/cffr/man/cff_schema.Rd | 2 cffr-1.3.0/cffr/man/cff_validate.Rd | 6 cffr-1.3.0/cffr/man/cff_write.Rd | 22 cffr-1.3.0/cffr/man/cff_write_misc.Rd | 24 cffr-1.3.0/cffr/man/chunks/cffclass.Rmd | 31 cffr-1.3.0/cffr/man/chunks/person.Rmd | 6 cffr-1.3.0/cffr/man/deprecated_cff_bibentry.Rd | 3 cffr-1.3.0/cffr/man/deprecated_cff_from_bib.Rd | 8 cffr-1.3.0/cffr/man/deprecated_cff_to_bib.Rd | 14 cffr-1.3.0/cffr/man/deprecated_write.Rd | 10 cffr-1.3.0/cffr/man/encoded_utf_to_latex.Rd | 6 cffr-1.3.0/cffr/tests/testthat/_snaps/as_cff_reference.md | 2 cffr-1.3.0/cffr/tests/testthat/_snaps/cff_gha_update.md | 46 cffr-1.3.0/cffr/tests/testthat/_snaps/utils-create.md | 2387 +++--- cffr-1.3.0/cffr/tests/testthat/test-as_bibentry.R | 1 cffr-1.3.0/cffr/tests/testthat/test-as_cff.R | 1 cffr-1.3.0/cffr/tests/testthat/test-as_cff_person.R | 1 cffr-1.3.0/cffr/tests/testthat/test-as_cff_reference.R | 1521 +--- cffr-1.3.0/cffr/tests/testthat/test-assertions.R | 1 cffr-1.3.0/cffr/tests/testthat/test-cff.R | 1 cffr-1.3.0/cffr/tests/testthat/test-cff_create.R | 1131 +- cffr-1.3.0/cffr/tests/testthat/test-cff_read.R | 505 - cffr-1.3.0/cffr/tests/testthat/test-cff_validate.R | 1 cffr-1.3.0/cffr/tests/testthat/test-cff_write.R | 401 - cffr-1.3.0/cffr/tests/testthat/test-cff_write_misc.R | 273 cffr-1.3.0/cffr/tests/testthat/test-deprecated.R | 1 cffr-1.3.0/cffr/tests/testthat/test-methods.R | 1 cffr-1.3.0/cffr/tests/testthat/test-mock-package.R | 266 cffr-1.3.0/cffr/tests/testthat/test-utils-cff_create.R | 44 cffr-1.3.0/cffr/tests/testthat/test-utils-create.R | 74 cffr-1.3.0/cffr/tests/testthat/test-utils-persons.R | 3 cffr-1.3.0/cffr/tests/testthat/test-utils.R | 84 cffr-1.3.0/cffr/tests/testthat/test-xtra-check-bibtex-ruby.R | 1 cffr-1.3.0/cffr/vignettes/REFERENCES.bib | 104 cffr-1.3.0/cffr/vignettes/bibtex-cff.qmd |only cffr-1.3.0/cffr/vignettes/cffr.qmd |only cffr-1.3.0/cffr/vignettes/joss-paper.qmd |only cffr-1.3.0/cffr/vignettes/r-cff.qmd |only 107 files changed, 10214 insertions(+), 10906 deletions(-)
Title: Calculate High Resolution Water Balance of Starch Potatoes
Description: Calculates the water balance of starch potatoes from Normalized Distance Vegetation Index (NDVI) images, German Weather Service (DWD) reference evapotranspiration, German Weather Service RADOLAN precipitation data and irrigation information. For more details see Piernicke et al. (2025) <doi:10.3390/rs17183227>.
Author: Thomas Piernicke [aut, cre]
Maintainer: Thomas Piernicke <thomasp@gfz.de>
Diff between WaterBalanceR versions 0.1.20 dated 2026-03-11 and 0.1.21 dated 2026-03-13
DESCRIPTION | 6 MD5 | 12 NEWS.md | 424 ++++++++++++++++---------------- R/DownloadSentinel2.R | 2 inst/doc/WaterBalanceR_DataSources.html | 4 inst/doc/WaterBalanceR_Workflow.html | 6 man/DownloadSentinel2.Rd | 2 7 files changed, 232 insertions(+), 224 deletions(-)
Title: Spatial Absorbing Markov Chains
Description: Implements functions for working with absorbing Markov chains. The
implementation is based on the framework described in "Toward a unified
framework for connectivity that disentangles movement and mortality in space
and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies
them to spatial ecology. This framework incorporates both resistance and
absorption with spatial absorbing Markov chains (SAMC) to provide several
short-term and long-term predictions for metrics related to connectivity in
landscapes. Despite the ecological context of the framework, this package
can be used in any application of absorbing Markov chains.
Author: Andrew Marx [aut, cre, cph] ,
Robert Fletcher [ctb] ,
Miguel Acevedo [ctb] ,
Jorge Sefair [ctb] ,
Chao Wang [ctb] ,
Hughes Josie [ctb] ,
Barrett Griffin [ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>
Diff between samc versions 4.1.0 dated 2026-02-05 and 4.2.1 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/internal-functions.R | 40 +++++++++++++++++++++++++++++++--------- R/internal-validation.R | 31 +++++++++++++++++++++++-------- R/pairwise.R | 36 ++++++++++++++++++++++++++---------- R/samc.R | 11 +++++++---- inst/CITATION | 2 +- inst/doc/overview.html | 4 ++-- 9 files changed, 109 insertions(+), 46 deletions(-)
Title: Import Various Northern and Southern Hemisphere Climate Indices
Description: Downloads Southern Oscillation Index, Oceanic Nino
Index, North Pacific Gyre Oscillation data, North Atlantic Oscillation
and Arctic Oscillation. Data sources are described in the help files for each function.
Author: Sam Albers [aut, cre],
Elio Campitelli [ctb]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between rsoi versions 0.5.7 dated 2026-03-06 and 0.5.8 dated 2026-03-13
DESCRIPTION | 6 +- MD5 | 7 +-- NEWS.md | 3 + R/download-roni.R | 75 ++++++++++-------------------------- tests/testthat/test-download-roni.R |only 5 files changed, 32 insertions(+), 59 deletions(-)
Title: Polytomous Variable Latent Class Analysis Parallel
Description: A 'C++' reimplementation of 'poLCA' - latent class analysis and
latent class regression models for polytomous outcome variables, also known
as latent structure analysis. It attempts to reproduce results and be as
similar as possible to the original code, while running faster, especially
with multiple repetitions, by utilising multiple threads. Further reading is
available on the Queen Mary, University of London, IT Services Research blog
<https://blog.hpc.qmul.ac.uk/speeding_up_r_packages/>.
Author: Sherman Lo [aut, cre],
Drew Linzer [aut],
Jeffrey Lewis. [aut]
Maintainer: Sherman Lo <s.lo@qmul.ac.uk>
This is a re-admission after prior archival of version 1.2.6 dated 2026-02-19
Diff between poLCAParallel versions 1.2.6 dated 2026-02-19 and 1.2.7 dated 2026-03-13
DESCRIPTION | 9 +++--- MD5 | 28 ++++++++++---------- src/blrt.cc | 10 +++++-- src/blrt_rcpp.cc | 9 +++++- src/em_algorithm_array.cc | 10 +++++-- src/em_algorithm_rcpp.cc | 16 +++++++---- src/em_algorithm_regress.cc | 61 ++++++++++++++++++-------------------------- src/em_algorithm_regress.h | 40 +++++++++++++++++++++++----- src/goodness_fit_rcpp.cc | 7 +++-- src/polca_rcpp.cc | 14 +++++----- src/regularised_error.cc | 6 ++-- src/standard_error_rcpp.cc | 14 ++++++---- src/util.cc | 7 +++++ src/util.h | 5 +++ src/util_rcpp.cc |only src/util_rcpp.h |only 16 files changed, 146 insertions(+), 90 deletions(-)
Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre],
Marcell T. Kurbucz [aut],
Attila I. Katona [aut],
Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between nda versions 0.2.4 dated 2025-02-16 and 0.2.5 dated 2026-03-13
DESCRIPTION | 6 MD5 | 8 R/ndrlm.R | 1224 +++++++++++++++++++++++++++++------------------------------ inst/NEWS | 222 +++++----- man/ndrlm.Rd | 354 ++++++++--------- 5 files changed, 911 insertions(+), 903 deletions(-)
Title: Missing Morphometric Data Simulation and Estimation
Description: Functions for simulating missing morphometric
data randomly, with taxonomic bias and with anatomical bias. LOST also
includes functions for estimating linear and geometric morphometric data.
Author: J. Arbour [aut, cre],
C. Brown [aut]
Maintainer: J. Arbour <jessica.arbour@mtsu.edu>
Diff between LOST versions 2.1.2 dated 2025-01-27 and 2.1.3 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/align.missing.R | 6 +++++- 3 files changed, 11 insertions(+), 7 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 0.9.0 dated 2025-06-04 and 0.10.0 dated 2026-03-13
DESCRIPTION | 10 MD5 | 100 NEWS.md | 22 R/api_define_extract.R | 6993 +++++++++++++++----------------- R/api_helpers.R | 15 R/api_metadata.R | 4 R/ddi_read.R | 2363 +++++----- R/micro_read.R | 738 +-- R/micro_read_chunked.R | 734 +-- R/micro_read_yield.R | 668 +-- R/proj_config.R | 1 README.md | 896 ++-- build/vignette.rds |binary inst/doc/ipums-api-agg.R | 438 +- inst/doc/ipums-api-agg.html | 1639 +++---- inst/doc/ipums-api-micro.R | 440 +- inst/doc/ipums-api-micro.Rmd | 2 inst/doc/ipums-api-micro.html | 1807 ++++---- inst/doc/ipums-api.R | 548 +- inst/doc/ipums-api.Rmd | 1 inst/doc/ipums-api.html | 1686 +++---- inst/doc/ipums-bigdata.R | 558 +- inst/doc/ipums-bigdata.Rmd | 1331 +++--- inst/doc/ipums-bigdata.html | 2123 ++++----- inst/doc/ipums-read.R | 274 - inst/doc/ipums-read.html | 1823 ++++---- inst/doc/ipums.R | 172 inst/doc/ipums.Rmd | 1 inst/doc/ipums.html | 1350 +++--- inst/doc/value-labels.R | 348 - inst/doc/value-labels.html | 1891 ++++---- man/define_extract_micro.Rd | 1 man/get_sample_info.Rd | 1 man/ipums_data_collections.Rd | 1 man/ipums_ddi-class.Rd | 2 man/ipums_shape_join.Rd | 2 man/read_ipums_ddi.Rd | 3 man/read_ipums_micro.Rd | 2 man/read_ipums_micro_chunked.Rd | 2 man/read_ipums_micro_yield.Rd | 2 man/read_ipums_sf.Rd | 2 man/set_ipums_api_key.Rd | 15 tests/fixtures/cps_00111.xml |only tests/fixtures/ipumsi_00987.xml |only tests/testthat/helper_api.R | 13 tests/testthat/test_api_helpers.R | 2 tests/testthat/test_read_ddi.R | 25 vignettes/fixtures/wait-for-extract.yml | 166 vignettes/ipums-api-micro.Rmd | 2 vignettes/ipums-api.Rmd | 1 vignettes/ipums-bigdata.Rmd | 1331 +++--- vignettes/ipums.Rmd | 1 52 files changed, 15398 insertions(+), 15152 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.9.8.2 dated 2026-02-13 and 1.9.8.3 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/haplostats.R | 4 ++++ inst/doc/haplostats.Rmd | 4 ++++ vignettes/haplostats.Rmd | 4 ++++ 5 files changed, 20 insertions(+), 8 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal,
conservative, or deep-first search). The objective of this package is to
make it as simple as possible to identify global objects for the purpose
of exporting them in parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph],
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.19.0 dated 2026-02-02 and 0.19.1 dated 2026-03-13
DESCRIPTION | 6 MD5 | 34 ++-- NEWS.md | 11 + R/Globals-class.R | 9 + R/call_find_globals_with_dotdotdot.R | 2 R/findGlobalsDFS.R | 3 R/find_globals_ordered.R | 59 ------- R/globalsByName.R | 2 R/utils-debug.R | 2 R/where.R | 2 inst/testme/test-Globals.R | 73 ++++++++- inst/testme/test-cleanup.R | 63 +++++++ inst/testme/test-dotdotdot.R | 18 ++ inst/testme/test-findGlobals,dfs.R | 52 ++++++ inst/testme/test-findGlobals.R | 126 +++++++++++++++ inst/testme/test-globalsByName.R | 19 ++ inst/testme/test-globalsOf.R | 102 ++++++++++++ inst/testme/test-utils.R | 281 +++++++++++++++++++++++++++++++++++ 18 files changed, 776 insertions(+), 88 deletions(-)
Title: Faster Generation of Quantile Quantile Plots with Large Samples
Description: New and faster implementations for quantile quantile plots.
The package also includes a function to prune data for quantile quantile
plots. This can drastically reduce the running time for large samples,
for 100 million samples, you can expect a factor 80X speedup.
Author: Gudmundur Einarsson [aut, cre],
Hafsteinn Einarsson [aut]
Maintainer: Gudmundur Einarsson <gudmundur.einarsson.phd@gmail.com>
Diff between fastqq versions 0.1.3 dated 2022-10-25 and 0.1.4 dated 2026-03-13
DESCRIPTION | 10 +- MD5 | 37 +++++--- NAMESPACE | 2 NEWS.md | 12 ++ R/RcppExports.R | 10 ++ R/qq.R | 129 ++++++++++++++++++++++++++++- README.md | 132 +++++++++++++++++++++++------- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-ggplot-1.png |binary man/figures/README-qqchisq1_ex-1.png |only man/figures/README-qqchisq1_extreme-1.png |only man/figures/README-qqlog_ex-1.png |only man/figures/README-qqnorm_ex-1.png |binary man/figures/README-qqplot_ex-1.png |binary man/figures/README-zero_action_ex-1.png |only man/qq.Rd | 12 ++ man/qqchisq1.Rd |only man/qqlog.Rd |only src/RcppExports.cpp | 26 +++++ src/code.cpp | 115 ++++++++++++++++++++++++++ tests |only 22 files changed, 434 insertions(+), 51 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<https://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.6 dated 2025-09-19 and 0.3.7 dated 2026-03-13
DESCRIPTION | 8 MD5 | 72 ++-- NAMESPACE | 3 R/apollo_classAlloc.R | 3 R/apollo_cnl.R | 3 R/apollo_cnl2.R | 3 R/apollo_deltaMethod.R | 4 R/apollo_el.R | 3 R/apollo_estimate.R | 31 +- R/apollo_estimateHB.R | 62 ++-- R/apollo_firstRow.R | 10 R/apollo_fmnl.R | 3 R/apollo_fnl.R | 3 R/apollo_initialise.R | 2 R/apollo_lcEM.R | 1 R/apollo_lcEM_new.R | 21 - R/apollo_makeCluster.R | 2 R/apollo_mnl.R | 8 R/apollo_modelOutput.R | 31 +- R/apollo_modifyUserDefFunc.R | 19 + R/apollo_nl.R | 3 R/apollo_prediction.R | 4 R/apollo_rrm.R | 1 R/apollo_saveOutput.R | 16 - R/apollo_searchStart.R | 6 R/apollo_speedTest.R | 15 - R/apollo_validateControl.R | 11 R/apollo_validateInputs.R | 4 R/onAttach.R | 5 inst/doc/apollofirstexample.html | 565 +++++++++++++++++++-------------------- man/apollo_estimate.Rd | 2 man/apollo_modelOutput.Rd | 1 man/apollo_prediction.Rd | 1 man/apollo_rrm.Rd | 1 man/apollo_saveOutput.Rd | 2 man/apollo_speedTest.Rd | 2 man/apollo_validateInputs.Rd | 4 37 files changed, 523 insertions(+), 412 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-08 1.0.14
2025-08-18 1.0.13
2024-02-26 1.0.12
2023-08-08 1.0.11
2022-04-19 1.0.10
2022-03-02 1.0.9
2021-12-12 1.0.8
2021-11-15 1.0.7
2021-10-06 1.0.6
2021-08-11 1.0.5
2021-06-29 1.0.4
2021-05-03 1.0.3
2021-03-04 1.0.2
2021-02-23 1.0.1
2021-01-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 1.5.2
2024-01-23 1.5.1
2022-10-17 1.5.0
2022-09-30 1.4.9
2022-09-26 1.4.8
2022-09-04 1.4.7
2022-04-11 1.4.6
2022-01-21 1.4.5
2021-11-08 1.4.4
2021-08-07 1.4.3
2021-06-29 1.4.2
2021-05-15 1.4.1
2021-02-23 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-06 1.0.4
2024-02-26 1.0.2
2024-02-26 1.0.3
2022-01-18 1.0.1
2021-11-19 1.0.0
2020-12-14 0.1.1
2020-09-29 0.1.0
Title: Predict with 'tidymodels' Workflows in Databases
Description: Turn 'tidymodels' workflows into objects containing the
sufficient sequential equations to perform predictions. These smaller
objects allow for low dependency prediction locally or directly in
databases.
Author: Emil Hvitfeldt [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between orbital versions 0.5.0 dated 2026-02-27 and 0.5.1 dated 2026-03-13
DESCRIPTION | 17 +- MD5 | 152 ++++++++++----------- NAMESPACE | 50 ++++++ NEWS.md | 10 + R/adjust_equivocal_zone.R | 8 - R/adjust_numeric_range.R | 23 +++ R/adjust_predictions_custom.R | 10 + R/adjust_probability_threshold.R | 8 - R/estimate-size.R |only R/model-xgboost.R | 17 ++ R/parsnip.R | 34 +++- R/step_adasyn.R | 5 R/step_bsmote.R | 5 R/step_center.R | 10 + R/step_corr.R | 5 R/step_downsample.R | 5 R/step_dummy.R | 14 + R/step_filter_missing.R | 5 R/step_impute_mean.R | 10 + R/step_impute_median.R | 10 + R/step_indicate_na.R | 12 + R/step_lincomb.R | 5 R/step_log.R | 11 + R/step_mutate.R | 6 R/step_nearmiss.R | 5 R/step_normalize.R | 10 + R/step_nzv.R | 5 R/step_pca.R | 10 + R/step_range.R | 10 + R/step_rm.R | 5 R/step_rose.R | 5 R/step_scale.R | 10 + R/step_select.R | 5 R/step_smote.R | 5 R/step_smotenc.R | 5 R/step_sqrt.R | 10 + R/step_tomek.R | 5 R/step_upsample.R | 5 R/step_zv.R | 5 inst/doc/supported-models.html | 110 +++++++-------- man/estimate_orbital_size.Rd |only tests/testthat/_snaps/estimate-size.md |only tests/testthat/_snaps/sql.md | 29 ---- tests/testthat/derby.log | 6 tests/testthat/test-adjust_equivocal_zone.R | 30 ++++ tests/testthat/test-adjust_numeric_range.R | 53 +++++++ tests/testthat/test-adjust_predictions_custom.R | 38 +++++ tests/testthat/test-adjust_probability_threshold.R | 26 +++ tests/testthat/test-estimate-size.R |only tests/testthat/test-model-xgboost.R | 22 +++ tests/testthat/test-sql.R | 12 - tests/testthat/test-step_adasyn.R | 15 ++ tests/testthat/test-step_bsmote.R | 15 ++ tests/testthat/test-step_center.R | 23 +++ tests/testthat/test-step_corr.R | 11 + tests/testthat/test-step_downsample.R | 15 ++ tests/testthat/test-step_dummy.R | 27 +++ tests/testthat/test-step_filter_missing.R | 11 + tests/testthat/test-step_impute_mean.R | 23 +++ tests/testthat/test-step_impute_median.R | 23 +++ tests/testthat/test-step_indicate_na.R | 23 +++ tests/testthat/test-step_lincomb.R | 11 + tests/testthat/test-step_log.R | 23 +++ tests/testthat/test-step_mutate.R | 23 +++ tests/testthat/test-step_nearmiss.R | 15 ++ tests/testthat/test-step_normalize.R | 23 +++ tests/testthat/test-step_nzv.R | 11 + tests/testthat/test-step_pca.R | 15 ++ tests/testthat/test-step_range.R | 23 +++ tests/testthat/test-step_rm.R | 11 + tests/testthat/test-step_rose.R | 15 ++ tests/testthat/test-step_scale.R | 23 +++ tests/testthat/test-step_select.R | 11 + tests/testthat/test-step_smote.R | 15 ++ tests/testthat/test-step_smotenc.R | 15 ++ tests/testthat/test-step_sqrt.R | 23 +++ tests/testthat/test-step_tomek.R | 15 ++ tests/testthat/test-step_upsample.R | 15 ++ tests/testthat/test-step_zv.R | 11 + 79 files changed, 1152 insertions(+), 190 deletions(-)
Title: Multilevel Functions
Description: Tools used by organizational researchers for the analysis of multilevel data. Includes four broad sets of tools. First, functions for estimating within-group agreement and reliability indices. Second, functions for manipulating multilevel and longitudinal (panel) data. Third, simulations for estimating power and generating multilevel data. Fourth, miscellaneous functions for estimating reliability and performing simple calculations and data transformations.
Author: Paul Bliese [aut, cre],
Gilad Chen [ctb],
Patrick Downes [ctb],
Patrick Flynn [ctb],
Jonas Lang [ctb],
Donald Schepker [ctb]
Maintainer: Paul Bliese <pdbliese@gmail.com>
Diff between multilevel versions 2.7.1 dated 2025-09-08 and 2.8 dated 2026-03-13
DESCRIPTION | 18 ++++++++++-------- MD5 | 13 ++++++++----- R/multilevel.R | 32 +++++++++++++++++++++++++------- data/banddat.rda |only man/banddat.Rd |only man/correct.gcor.Rd |only man/paneldat.Rd | 27 ++++++++++++++++----------- man/rwg.j.Rd | 12 ++++++++---- man/rwg.j.lindell.Rd | 22 +++++++++++++--------- 9 files changed, 80 insertions(+), 44 deletions(-)
Title: Intergovernmental Organizations Database
Description: Tools to extract information from the Intergovernmental
Organizations ('IGO') Database (v3), provided by the Correlates of War
Project <https://correlatesofwar.org/>. See also Pevehouse, J. C. et
al. (2020) <doi:10.1177/0022343319881175>.
Author: Diego Hernangomez [aut, cre, cph] ,
The Correlates of War Project [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between igoR versions 1.0.0 dated 2026-01-17 and 1.0.1 dated 2026-03-13
igoR-1.0.0/igoR/inst/doc/igoR.Rmd |only igoR-1.0.0/igoR/inst/doc/mapping.Rmd |only igoR-1.0.0/igoR/vignettes/AustShared-1.png |only igoR-1.0.0/igoR/vignettes/NAShared-1.png |only igoR-1.0.0/igoR/vignettes/UNMaps-1.png |only igoR-1.0.0/igoR/vignettes/igoR.Rmd |only igoR-1.0.0/igoR/vignettes/mapping.Rmd |only igoR-1.0.1/igoR/DESCRIPTION | 14 igoR-1.0.1/igoR/MD5 | 50 - igoR-1.0.1/igoR/NEWS.md | 5 igoR-1.0.1/igoR/R/sysdata.rda |binary igoR-1.0.1/igoR/README.md | 53 - igoR-1.0.1/igoR/build/partial.rdb |binary igoR-1.0.1/igoR/build/vignette.rds |binary igoR-1.0.1/igoR/data/igo_year_format3.rda |binary igoR-1.0.1/igoR/data/state_year_format3.rda |binary igoR-1.0.1/igoR/data/states2016.rda |binary igoR-1.0.1/igoR/inst/CITATION | 73 - igoR-1.0.1/igoR/inst/COPYRIGHTS | 22 igoR-1.0.1/igoR/inst/REFERENCES.bib | 86 - igoR-1.0.1/igoR/inst/WORDLIST | 1 igoR-1.0.1/igoR/inst/doc/igoR.R | 494 ++++++++-- igoR-1.0.1/igoR/inst/doc/igoR.html | 1235 ++++++++++++++----------- igoR-1.0.1/igoR/inst/doc/igoR.qmd |only igoR-1.0.1/igoR/inst/doc/mapping.html | 553 +++-------- igoR-1.0.1/igoR/inst/doc/mapping.qmd |only igoR-1.0.1/igoR/inst/schemaorg.json | 4 igoR-1.0.1/igoR/vignettes/REFERENCES.bib | 86 - igoR-1.0.1/igoR/vignettes/fig-AustShared-1.png |only igoR-1.0.1/igoR/vignettes/fig-NAShared-1.png |only igoR-1.0.1/igoR/vignettes/fig-UNMaps-1.png |only igoR-1.0.1/igoR/vignettes/igoR.qmd |only igoR-1.0.1/igoR/vignettes/mapping.qmd |only 33 files changed, 1524 insertions(+), 1152 deletions(-)
Title: Gaussian and Student-t Copula Models for Count Time Series
Description: Provides likelihood-based inference for Gaussian and Student-t
copula models for univariate count time series. Supports Poisson,
negative binomial, binomial, beta-binomial, and zero-inflated
marginals with ARMA dependence structures. Includes simulation,
maximum-likelihood estimation, residual diagnostics, and predictive
inference. Implements Time Series Minimax Exponential Tilting (TMET)
<doi:10.1016/j.csda.2026.108344>, an adaptation of minimax exponential
tilting of Botev (2017) <doi:10.1111/rssb.12162>. Also provides a
linear-cost implementation of the Geweke–Hajivassiliou–Keane (GHK)
simulator following Masarotto and Varin (2012) <doi:10.1214/12-EJS721>,
and the Continuous Extension (CE) approximation of Nguyen and
De Oliveira (2025) <doi:10.1080/02664763.2025.2498502>. The package
follows the S3 design philosophy of 'gcmr' but is developed independently.
Author: Quynh Nguyen [aut, cre],
Victor De Oliveira [aut]
Maintainer: Quynh Nguyen <nqnhu2209@gmail.com>
Diff between gctsc versions 0.1.3 dated 2025-12-17 and 0.2.0 dated 2026-03-13
gctsc-0.1.3/gctsc/R/copula-utils.R |only gctsc-0.1.3/gctsc/R/core_utils.R |only gctsc-0.1.3/gctsc/R/loglik_vmet.R |only gctsc-0.1.3/gctsc/data/campyl.csv |only gctsc-0.1.3/gctsc/inst/CITATION |only gctsc-0.1.3/gctsc/inst/examples |only gctsc-0.1.3/gctsc/man/pmvn_ce.Rd |only gctsc-0.1.3/gctsc/man/pmvn_ghk.Rd |only gctsc-0.1.3/gctsc/man/pmvn_tmet.Rd |only gctsc-0.1.3/gctsc/src/gctsc_dummy.cpp |only gctsc-0.1.3/gctsc/src/lnNpr.cpp |only gctsc-0.1.3/gctsc/src/mvnkernel.cpp |only gctsc-0.1.3/gctsc/src/predmvn.cpp |only gctsc-0.2.0/gctsc/DESCRIPTION | 34 - gctsc-0.2.0/gctsc/LICENSE | 2 gctsc-0.2.0/gctsc/MD5 | 154 ++-- gctsc-0.2.0/gctsc/NAMESPACE | 11 gctsc-0.2.0/gctsc/R/RcppExports.R | 46 + gctsc-0.2.0/gctsc/R/arma-helpers.R | 187 +++-- gctsc-0.2.0/gctsc/R/cond_mv.R |only gctsc-0.2.0/gctsc/R/cormat.R | 46 + gctsc-0.2.0/gctsc/R/data.R | 9 gctsc-0.2.0/gctsc/R/grad_jac_prod.R |only gctsc-0.2.0/gctsc/R/import.R | 7 gctsc-0.2.0/gctsc/R/loglik_ce.R | 273 +++++--- gctsc-0.2.0/gctsc/R/loglik_factory.R | 70 +- gctsc-0.2.0/gctsc/R/loglik_ghk.R | 315 ++++++---- gctsc-0.2.0/gctsc/R/loglik_tmet.R | 500 ++++++++------- gctsc-0.2.0/gctsc/R/main.R | 330 ++++++---- gctsc-0.2.0/gctsc/R/marg_utils.R | 17 gctsc-0.2.0/gctsc/R/marginals.R | 32 - gctsc-0.2.0/gctsc/R/methods-print.R | 36 - gctsc-0.2.0/gctsc/R/prediction.R | 317 ++++++---- gctsc-0.2.0/gctsc/R/residuals.R | 308 ++++++--- gctsc-0.2.0/gctsc/R/sample_utils.R |only gctsc-0.2.0/gctsc/R/sim-utils.R | 142 +++- gctsc-0.2.0/gctsc/R/simulate-gctsc.R | 272 ++++---- gctsc-0.2.0/gctsc/R/tmet_t_solver.R |only gctsc-0.2.0/gctsc/R/validate-utils.R | 75 +- gctsc-0.2.0/gctsc/README.md | 117 +++ gctsc-0.2.0/gctsc/build/vignette.rds |binary gctsc-0.2.0/gctsc/data/KCWC.rda |binary gctsc-0.2.0/gctsc/data/campyl.rda |binary gctsc-0.2.0/gctsc/data/datalist | 1 gctsc-0.2.0/gctsc/data/rota.csv |only gctsc-0.2.0/gctsc/data/rota.rda |only gctsc-0.2.0/gctsc/inst/Gaussian_copula_examples |only gctsc-0.2.0/gctsc/inst/doc/gctsc_vignette.R | 104 ++- gctsc-0.2.0/gctsc/inst/doc/gctsc_vignette.Rmd | 201 ++++-- gctsc-0.2.0/gctsc/inst/doc/gctsc_vignette.html | 755 +++++++++++++----------- gctsc-0.2.0/gctsc/inst/t_copula_examples |only gctsc-0.2.0/gctsc/man/KCWC.Rd | 32 - gctsc-0.2.0/gctsc/man/arma.cormat.Rd | 41 - gctsc-0.2.0/gctsc/man/coef.gctsc.Rd | 39 - gctsc-0.2.0/gctsc/man/gctsc.Rd | 309 +++++---- gctsc-0.2.0/gctsc/man/gctsc.opts.Rd | 54 - gctsc-0.2.0/gctsc/man/marginal.gctsc.Rd | 156 ++-- gctsc-0.2.0/gctsc/man/plot.gctsc.Rd | 156 ++-- gctsc-0.2.0/gctsc/man/pmv_ce.Rd |only gctsc-0.2.0/gctsc/man/pmv_ghk.Rd |only gctsc-0.2.0/gctsc/man/pmv_tmet.Rd |only gctsc-0.2.0/gctsc/man/predict.gctsc.Rd | 137 +++- gctsc-0.2.0/gctsc/man/print.gctsc.Rd | 40 - gctsc-0.2.0/gctsc/man/print.summary.gctsc.Rd | 40 - gctsc-0.2.0/gctsc/man/residuals.gctsc.Rd | 122 ++- gctsc-0.2.0/gctsc/man/rota.Rd |only gctsc-0.2.0/gctsc/man/sim_gctsc.Rd | 314 ++++++--- gctsc-0.2.0/gctsc/man/summary.gctsc.Rd | 46 - gctsc-0.2.0/gctsc/src/RcppExports.cpp | 120 +++ gctsc-0.2.0/gctsc/src/cond_var.cpp | 5 gctsc-0.2.0/gctsc/src/gauss_utils.cpp | 12 gctsc-0.2.0/gctsc/src/gauss_utils.h | 13 gctsc-0.2.0/gctsc/src/kernel_mvn.cpp |only gctsc-0.2.0/gctsc/src/kernel_mvt.cpp |only gctsc-0.2.0/gctsc/src/lnNpr.h | 9 gctsc-0.2.0/gctsc/src/lnTpr.h |only gctsc-0.2.0/gctsc/src/loglik_ce.cpp | 147 ++++ gctsc-0.2.0/gctsc/src/pred_mvn.cpp |only gctsc-0.2.0/gctsc/src/pred_mvt.cpp |only gctsc-0.2.0/gctsc/src/res_mvn.cpp |only gctsc-0.2.0/gctsc/src/res_mvt.cpp |only gctsc-0.2.0/gctsc/src/sampling_utils.h | 2 gctsc-0.2.0/gctsc/src/t_utils.cpp |only gctsc-0.2.0/gctsc/src/t_utils.h |only gctsc-0.2.0/gctsc/vignettes/gctsc_vignette.Rmd | 201 ++++-- 85 files changed, 4033 insertions(+), 2323 deletions(-)
Title: Efficient Inference on High-Dimensional Linear Model with
Missing Outcomes
Description: A statistically and computationally efficient debiasing method for conducting valid inference on the high-dimensional linear regression function with missing outcomes.
The reference paper is Zhang, Giessing, and Chen (2023) <doi:10.48550/arXiv.2309.06429>.
Author: Yikun Zhang [aut, cre] ,
Alexander Giessing [aut] ,
Yen-Chi Chen [aut]
Maintainer: Yikun Zhang <yikunzhang@foxmail.com>
Diff between DebiasInfer versions 0.2 dated 2023-10-09 and 0.2.1 dated 2026-03-13
DESCRIPTION | 17 +++++++------- MD5 | 12 +++++----- R/DebiasProg.R | 61 ++++++++++++++++++++++++++++++++-------------------- R/DebiasProgCV.R | 22 +++++++++++++++--- build/partial.rdb |binary man/DebiasProg.Rd | 5 ++-- man/DebiasProgCV.Rd | 5 ++-- 7 files changed, 77 insertions(+), 45 deletions(-)