Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.3.2 dated 2025-09-24 and 4.4.0 dated 2025-12-02
OlinkAnalyze-4.3.2/OlinkAnalyze/R/utils.R |only OlinkAnalyze-4.3.2/OlinkAnalyze/man/is_testing.Rd |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_boxplot |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Olink_plate_randomizer |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/Volcano_plot |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/dist_plot |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/linear_mixed_model |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_bridgeability_plot |only OlinkAnalyze-4.3.2/OlinkAnalyze/tests/testthat/_snaps/olink_qc_plot |only OlinkAnalyze-4.4.0/OlinkAnalyze/DESCRIPTION | 8 OlinkAnalyze-4.4.0/OlinkAnalyze/MD5 | 120 +- OlinkAnalyze-4.4.0/OlinkAnalyze/NEWS.md | 11 OlinkAnalyze-4.4.0/OlinkAnalyze/R/Olink_theme.R | 2 OlinkAnalyze-4.4.0/OlinkAnalyze/R/Read_NPX_data.R | 52 + OlinkAnalyze-4.4.0/OlinkAnalyze/R/npxCheck.R | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/R/olink_lod.R | 24 OlinkAnalyze-4.4.0/OlinkAnalyze/R/olink_normalization.R | 14 OlinkAnalyze-4.4.0/OlinkAnalyze/R/olink_normalization_product.R | 66 - OlinkAnalyze-4.4.0/OlinkAnalyze/R/olink_normalization_utils.R | 87 + OlinkAnalyze-4.4.0/OlinkAnalyze/R/sysdata.rda |binary OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/LOD.Rmd | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/LOD.html | 12 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/OutlierExclusion.html | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/Vignett.html | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/bridging_crossproduct.R | 24 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/bridging_crossproduct.Rmd | 135 +- OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/bridging_crossproduct.html | 274 +++-- OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/bridging_introduction.R | 2 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/bridging_introduction.Rmd | 27 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/bridging_introduction.html | 47 - OlinkAnalyze-4.4.0/OlinkAnalyze/inst/doc/plate_randomizer.html | 14 OlinkAnalyze-4.4.0/OlinkAnalyze/inst/extdata/OlinkID_Reveal_HT_mapping.rds |only OlinkAnalyze-4.4.0/OlinkAnalyze/man/check_darid.Rd |only OlinkAnalyze-4.4.0/OlinkAnalyze/man/check_lod_darid.Rd |only OlinkAnalyze-4.4.0/OlinkAnalyze/man/figures/Bridging_schematic.png |binary OlinkAnalyze-4.4.0/OlinkAnalyze/man/mapping_file_id.Rd | 7 OlinkAnalyze-4.4.0/OlinkAnalyze/man/norm_internal_cross_product.Rd | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/man/olink_normalization_product_format.Rd | 27 OlinkAnalyze-4.4.0/OlinkAnalyze/man/olink_normalization_qs.Rd | 7 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md | 24 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/_snaps/npxProcessing.md | 130 +- OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/helper-get_example_olink_data.R | 23 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-Olink_boxplot.R | 24 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-Olink_plate_randomizer.R | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-Read_NPX_data.R | 58 + OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-Volcano_plot.R | 9 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-dist_plot.R | 9 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-linear_mixed_model.R | 9 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_Pathway_Enrichment.R | 8 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_Pathway_Heatmap.R | 10 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_Pathway_Visualization.R | 21 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_bridgeability_plot.R | 40 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_lod.R |only OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_normalization_product.R | 355 +++++++ OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 457 +++++++++- OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-olink_qc_plot.R | 9 OlinkAnalyze-4.4.0/OlinkAnalyze/tests/testthat/test-pca_plot.R | 62 - OlinkAnalyze-4.4.0/OlinkAnalyze/vignettes/LOD.Rmd | 4 OlinkAnalyze-4.4.0/OlinkAnalyze/vignettes/bridging_crossproduct.Rmd | 135 +- OlinkAnalyze-4.4.0/OlinkAnalyze/vignettes/bridging_introduction.Rmd | 27 60 files changed, 1742 insertions(+), 656 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb] ,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-37 dated 2025-03-26 and 1.1-38 dated 2025-12-02
lme4-1.1-37/lme4/inst/tinytest |only lme4-1.1-37/lme4/man/expandDoubleVerts.Rd |only lme4-1.1-37/lme4/man/findbars.Rd |only lme4-1.1-37/lme4/man/isNested.Rd |only lme4-1.1-37/lme4/man/mkReTrms.Rd |only lme4-1.1-37/lme4/man/nobars.Rd |only lme4-1.1-37/lme4/man/subbars.Rd |only lme4-1.1-38/lme4/DESCRIPTION | 46 +- lme4-1.1-38/lme4/MD5 | 203 +++++---- lme4-1.1-38/lme4/NAMESPACE | 25 - lme4-1.1-38/lme4/R/allFit.R | 44 + lme4-1.1-38/lme4/R/checkConv.R | 23 - lme4-1.1-38/lme4/R/lmList.R | 2 lme4-1.1-38/lme4/R/lmer.R | 126 ++++- lme4-1.1-38/lme4/R/lmerControl.R | 15 lme4-1.1-38/lme4/R/methods.R | 2 lme4-1.1-38/lme4/R/modular.R | 52 +- lme4-1.1-38/lme4/R/plot.R | 2 lme4-1.1-38/lme4/R/predict.R | 83 ++- lme4-1.1-38/lme4/R/profile.R | 13 lme4-1.1-38/lme4/R/reformulas_imports.R |only lme4-1.1-38/lme4/R/utilities.R | 243 ++++------- lme4-1.1-38/lme4/R/zzz.R | 72 +-- lme4-1.1-38/lme4/build/partial.rdb |binary lme4-1.1-38/lme4/build/vignette.rds |binary lme4-1.1-38/lme4/data/cbpp2.rda |only lme4-1.1-38/lme4/data/culcitalogreg.rda |only lme4-1.1-38/lme4/data/culcitalvolume.rda |only lme4-1.1-38/lme4/data/gopherdat2.rda |only lme4-1.1-38/lme4/data/salamander.rda |only lme4-1.1-38/lme4/data/schizophrenia.rda |only lme4-1.1-38/lme4/data/toenail.rda |only lme4-1.1-38/lme4/inst/NEWS.Rd | 67 ++- lme4-1.1-38/lme4/inst/REFERENCES.bib |only lme4-1.1-38/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-38/lme4/inst/doc/Theory.pdf |binary lme4-1.1-38/lme4/inst/doc/autoscale.R |only lme4-1.1-38/lme4/inst/doc/autoscale.Rmd |only lme4-1.1-38/lme4/inst/doc/autoscale.html |only lme4-1.1-38/lme4/inst/doc/lmer.R | 162 ------- lme4-1.1-38/lme4/inst/doc/lmer.Rnw | 5 lme4-1.1-38/lme4/inst/doc/lmer.pdf |binary lme4-1.1-38/lme4/inst/doc/lmerperf.html | 4 lme4-1.1-38/lme4/man/Arabidopsis.Rd | 8 lme4-1.1-38/lme4/man/Dyestuff.Rd | 13 lme4-1.1-38/lme4/man/GHrule.Rd | 4 lme4-1.1-38/lme4/man/Pastes.Rd | 6 lme4-1.1-38/lme4/man/Penicillin.Rd | 6 lme4-1.1-38/lme4/man/VarCorr.Rd | 21 lme4-1.1-38/lme4/man/VerbAgg.Rd | 3 lme4-1.1-38/lme4/man/allFit.Rd | 33 - lme4-1.1-38/lme4/man/bootMer.Rd | 12 lme4-1.1-38/lme4/man/cake.Rd | 15 lme4-1.1-38/lme4/man/cbpp.Rd | 16 lme4-1.1-38/lme4/man/cbpp2.Rd |only lme4-1.1-38/lme4/man/checkConv.Rd | 7 lme4-1.1-38/lme4/man/confint.merMod.Rd | 27 - lme4-1.1-38/lme4/man/culcitalogreg.Rd |only lme4-1.1-38/lme4/man/culcitalvolume.Rd |only lme4-1.1-38/lme4/man/fixef.Rd | 7 lme4-1.1-38/lme4/man/gopherdat2.Rd |only lme4-1.1-38/lme4/man/grouseticks.Rd | 5 lme4-1.1-38/lme4/man/influence.merMod.Rd | 3 lme4-1.1-38/lme4/man/isSingular.Rd | 41 - lme4-1.1-38/lme4/man/lmer.Rd | 12 lme4-1.1-38/lme4/man/lmerControl.Rd | 41 + lme4-1.1-38/lme4/man/merMod-class.Rd | 63 -- lme4-1.1-38/lme4/man/mkMerMod.Rd | 2 lme4-1.1-38/lme4/man/mkNewReTrms.Rd |only lme4-1.1-38/lme4/man/mkRespMod.Rd | 6 lme4-1.1-38/lme4/man/modular.Rd | 4 lme4-1.1-38/lme4/man/nlformula.Rd | 6 lme4-1.1-38/lme4/man/plot.merMod.Rd | 23 - lme4-1.1-38/lme4/man/profile-methods.Rd | 22 lme4-1.1-38/lme4/man/rePCA.Rd | 4 lme4-1.1-38/lme4/man/reformulas_imports.Rd |only lme4-1.1-38/lme4/man/salamander.Rd |only lme4-1.1-38/lme4/man/schizophrenia.Rd |only lme4-1.1-38/lme4/man/sigma.Rd | 44 + lme4-1.1-38/lme4/man/simulate.merMod.Rd | 11 lme4-1.1-38/lme4/man/sleepstudy.Rd | 8 lme4-1.1-38/lme4/man/summary.merMod.Rd |only lme4-1.1-38/lme4/man/toenail.Rd |only lme4-1.1-38/lme4/man/vcov.merMod.Rd | 5 lme4-1.1-38/lme4/src/lme4CholmodDecomposition.h | 2 lme4-1.1-38/lme4/tests/testthat/test-NAhandling.R | 2 lme4-1.1-38/lme4/tests/testthat/test-allFit.R | 39 + lme4-1.1-38/lme4/tests/testthat/test-catch.R | 5 lme4-1.1-38/lme4/tests/testthat/test-doubleVertNotation.R | 76 --- lme4-1.1-38/lme4/tests/testthat/test-eval.R | 1 lme4-1.1-38/lme4/tests/testthat/test-factors.R | 4 lme4-1.1-38/lme4/tests/testthat/test-formulaEval.R | 5 lme4-1.1-38/lme4/tests/testthat/test-glmFamily.R | 74 +++ lme4-1.1-38/lme4/tests/testthat/test-glmer.R | 66 ++ lme4-1.1-38/lme4/tests/testthat/test-glmernb.R | 4 lme4-1.1-38/lme4/tests/testthat/test-glmernbref.R | 1 lme4-1.1-38/lme4/tests/testthat/test-glmmFail.R | 4 lme4-1.1-38/lme4/tests/testthat/test-lmList.R | 7 lme4-1.1-38/lme4/tests/testthat/test-lmer.R | 122 +++++ lme4-1.1-38/lme4/tests/testthat/test-lmerResp.R | 6 lme4-1.1-38/lme4/tests/testthat/test-methods.R | 29 - lme4-1.1-38/lme4/tests/testthat/test-nbinom.R | 4 lme4-1.1-38/lme4/tests/testthat/test-nlmer.R | 4 lme4-1.1-38/lme4/tests/testthat/test-oldRZXfailure.R | 2 lme4-1.1-38/lme4/tests/testthat/test-predict.R | 175 +++++++ lme4-1.1-38/lme4/tests/testthat/test-ranef.R | 4 lme4-1.1-38/lme4/tests/testthat/test-rank.R | 5 lme4-1.1-38/lme4/tests/testthat/test-reformulas-import.R |only lme4-1.1-38/lme4/tests/testthat/test-resids.R | 5 lme4-1.1-38/lme4/tests/testthat/test-simulate_formula.R | 3 lme4-1.1-38/lme4/tests/testthat/test-start.R | 11 lme4-1.1-38/lme4/tests/testthat/test-stepHalving.R | 2 lme4-1.1-38/lme4/tests/testthat/test-summary.R | 87 +++ lme4-1.1-38/lme4/tests/testthat/test-summary_testlevel_1.rda |binary lme4-1.1-38/lme4/tests/testthat/test-utils.R | 22 lme4-1.1-38/lme4/vignettes/autoscale.Rmd |only lme4-1.1-38/lme4/vignettes/autoscale_ref.bib |only lme4-1.1-38/lme4/vignettes/downstream_methods.html |only lme4-1.1-38/lme4/vignettes/lmer.Rnw | 5 119 files changed, 1473 insertions(+), 970 deletions(-)
Title: Interval Estimation by Likelihoodist (LI) Compared to
Frequentist (CI)
Description: Parameter estimation via likelihood interval (LI) compared to traditional method (CI). This is the expanded version for 'LBI'- and 'wnl'-package, formulated by Kyun-Seop Bae <k@acr.kr>.
Author: Kim Minkyu [aut, cre]
Maintainer: Kim Minkyu <mkim@acr.kr>
Diff between inteli versions 0.1.0 dated 2025-10-25 and 0.1.1 dated 2025-12-02
inteli-0.1.0/inteli/README.md |only inteli-0.1.0/inteli/build |only inteli-0.1.0/inteli/inst |only inteli-0.1.0/inteli/vignettes |only inteli-0.1.1/inteli/DESCRIPTION | 8 +++----- inteli-0.1.1/inteli/MD5 | 27 +++++++++++---------------- inteli-0.1.1/inteli/NEWS.md | 3 ++- inteli-0.1.1/inteli/R/varE.R | 12 ++++++------ inteli-0.1.1/inteli/R/varEplot.R | 12 ++++++------ inteli-0.1.1/inteli/R/varR.R | 14 +++++++------- inteli-0.1.1/inteli/R/varRplot.R | 12 ++++++------ inteli-0.1.1/inteli/man/inteli-package.Rd |only inteli-0.1.1/inteli/man/varE.Rd | 10 +++++----- inteli-0.1.1/inteli/man/varEplot.Rd | 12 ++++++------ inteli-0.1.1/inteli/man/varR.Rd | 14 +++++++------- inteli-0.1.1/inteli/man/varRplot.Rd | 12 ++++++------ 16 files changed, 65 insertions(+), 71 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: 'HDF5' (Hierarchical Data Format 5) is a high-performance
library and file format for storing and managing large, complex
data. This package provides the static libraries and headers for
the 'HDF5' 'C' library (release 2.0.0). It is intended for R
package developers to use in the 'LinkingTo' field, which
eliminates the need for users to install system-level 'HDF5'
dependencies. This build is compiled with thread-safety enabled
and supports dynamic loading of external compression filters.
'HDF5' is developed by 'The HDF Group' <https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
The HDF Group [cph] ,
Jean-loup Mark [cph] ,
Gailly Adler [cph]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
This is a re-admission after prior archival of version 1.14.6.8 dated 2025-11-19
Diff between hdf5lib versions 1.14.6.8 dated 2025-11-19 and 2.0.0.2 dated 2025-12-02
hdf5lib-1.14.6.8/hdf5lib/src/empty.c |only hdf5lib-1.14.6.8/hdf5lib/src/hdf5.tar.gz |only hdf5lib-1.14.6.8/hdf5lib/src/zlib.tar.gz |only hdf5lib-2.0.0.2/hdf5lib/DESCRIPTION | 15 - hdf5lib-2.0.0.2/hdf5lib/MD5 | 29 +- hdf5lib-2.0.0.2/hdf5lib/NEWS.md | 15 + hdf5lib-2.0.0.2/hdf5lib/R/flags.r | 33 ++ hdf5lib-2.0.0.2/hdf5lib/README.md | 18 - hdf5lib-2.0.0.2/hdf5lib/configure | 235 +++++++++++++-------- hdf5lib-2.0.0.2/hdf5lib/configure.win | 97 -------- hdf5lib-2.0.0.2/hdf5lib/man/c_flags.Rd | 21 + hdf5lib-2.0.0.2/hdf5lib/man/figures/logo.png |binary hdf5lib-2.0.0.2/hdf5lib/man/hdf5lib-package.Rd | 9 hdf5lib-2.0.0.2/hdf5lib/man/ld_flags.Rd | 19 - hdf5lib-2.0.0.2/hdf5lib/src/H5pubconf.h |only hdf5lib-2.0.0.2/hdf5lib/src/find_byte_widths.c |only hdf5lib-2.0.0.2/hdf5lib/src/hdf5-2.0.0.tar.gz |only hdf5lib-2.0.0.2/hdf5lib/src/zlib-1.3.1.tar.gz |only hdf5lib-2.0.0.2/hdf5lib/tests/testthat/test-hdf5.r | 5 19 files changed, 270 insertions(+), 226 deletions(-)
Title: Geospatial Semantic Segmentation with Torch and Terra
Description: Provides tools for semantic segmentation of geospatial data using convolutional neural
network-based deep learning. Utility functions allow for creating masks, image chips, data frames listing image
chips in a directory, and DataSets for use within DataLoaders. Additional functions are provided to serve as checks
during the data preparation and training process. A UNet architecture can be defined with 4 blocks in the encoder, a
bottleneck block, and 4 blocks in the decoder. The UNet can accept a variable number of input channels, and the user
can define the number of feature maps produced in each encoder and decoder block and the bottleneck. Users can also
choose to (1) replace all rectified linear unit (ReLU) activation functions with leaky ReLU or swish, (2) implement attention gates along the
skip connections, (3) implement squeeze and excitation modules within the encoder blocks, (4) add residual connections
within all blocks, (5) replace the bottleneck with a modified atrous spati [...truncated...]
Author: Aaron Maxwell [aut, cre, cph],
Sarah Farhadpour [aut],
Srinjoy Das [aut],
Yalin Yang [aut]
Maintainer: Aaron Maxwell <Aaron.Maxwell@mail.wvu.edu>
Diff between geodl versions 0.3.0 dated 2025-11-12 and 0.3.1 dated 2025-12-02
DESCRIPTION | 8 +++--- MD5 | 14 ++++++------ R/segModels.R | 56 ------------------------------------------------ R/utilities.R | 21 ------------------ man/countParams.Rd | 22 ------------------ man/defineMobileUNet.Rd | 17 -------------- man/defineUNet.Rd | 23 ------------------- man/defineUNet3p.Rd | 17 -------------- 8 files changed, 11 insertions(+), 167 deletions(-)
More information about StealLikeBayes at CRAN
Permanent link
Title: Error Detection in Science
Description: Test published summary statistics for consistency
(Brown and Heathers, 2017, <doi:10.1177/1948550616673876>;
Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>;
Heathers and Brown, 2019, <https://osf.io/5vb3u/>).
The package also provides infrastructure for implementing new
error detection techniques.
Author: Lukas Jung [aut, cre],
Aurelien Allard [ctb],
Nicolas Roman Posner [ctb]
Maintainer: Lukas Jung <jung-lukas@gmx.net>
Diff between scrutiny versions 0.6.0 dated 2025-08-22 and 0.6.1 dated 2025-12-02
DESCRIPTION | 8 MD5 | 56 NEWS.md | 14 R/function-map-total-n.R | 8 R/grimmer-map-seq.R | 7 R/grimmer.R | 73 README.md | 9 build/partial.rdb |binary build/vignette.rds |binary inst/doc/consistency-tests-in-depth.Rmd | 2 inst/doc/consistency-tests-in-depth.html | 147 inst/doc/consistency-tests-simple.html | 5 inst/doc/debit.html | 29 inst/doc/devtools.html | 5 inst/doc/duplicates.html | 5 inst/doc/grim.html | 15 inst/doc/grimmer.html | 5184 ++++++++++++++++++++++++++++++- inst/doc/related.Rmd | 32 inst/doc/related.html | 55 inst/doc/rounding-in-depth.Rmd | 4 inst/doc/rounding-in-depth.html | 39 inst/doc/wrangling.html | 5 man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/grimmer_map_seq.Rd | 5 tests/testthat/helper-expectations.R | 2 vignettes/consistency-tests-in-depth.Rmd | 2 vignettes/related.Rmd | 32 vignettes/rounding-in-depth.Rmd | 4 29 files changed, 5455 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-25 1.5.6
2024-07-26 1.5.3
2024-05-02 1.5.2
2024-02-05 1.5.1
2023-09-19 1.5.0
2023-03-10 1.4.5
2022-12-14 1.4.4
2022-08-10 1.4.3
2022-06-14 1.4.2
2022-05-02 1.4.1
2022-01-05 1.4.0
2021-10-27 1.3.4
2021-10-08 1.3.3
2021-09-16 1.3.2
2021-09-13 1.3.1
2021-08-22 1.3.0
2021-08-09 1.2.0
2021-08-03 1.1.0
2021-07-12 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-21 0.3.1
2025-11-07 0.3
2025-09-21 0.2
2025-07-13 0.1.5
2025-05-16 0.1.4
2024-11-15 0.1.3
2024-11-01 0.1.1
2024-09-19 0.1.0
Title: Transmutation of Languages
Description: Tools for transforming 'R' expressions. Provides functions for
finding, extracting, and replacing patterns in 'R' language objects, similarly
to how regular expressions can be used to find, extract, and replace patterns
in text. Also provides functions for generating code using specially-formatted
template files and for translating 'R' expressions into similar expressions in
other programming languages. The package may be helpful for advanced uses of
'R' expressions, such as developing domain-specific languages.
Author: Nicholas Davies [cre, aut, cph]
Maintainer: Nicholas Davies <nicholas.davies@lshtm.ac.uk>
Diff between elixir versions 0.1.0 dated 2025-09-24 and 0.1.1 dated 2025-12-02
DESCRIPTION | 8 ++--- MD5 | 60 +++++++++++++++++++------------------- NAMESPACE | 11 ------ NEWS.md | 5 +++ R/apply.R | 13 ++++---- R/basic.R | 39 +++++++++++++++++------- R/convenience.R | 6 +-- R/elixir-package.R | 11 ------ R/helper.R |only R/match.R | 16 +++++----- R/meld.R | 2 - R/reindent.R | 6 +-- R/replace.R | 9 +++-- R/translate.R | 7 +--- inst/doc/elixir.Rmd | 8 ++--- inst/doc/elixir.html | 2 - man/elixir-expression.Rd | 4 +- man/expr_apply.Rd | 9 +++-- man/expr_list.Rd | 4 +- man/expr_match.Rd | 6 ++- man/expr_replace.Rd | 3 + man/expr_sub.Rd | 2 - man/meld.Rd | 2 - man/translate.Rd | 1 tests/testthat/test-apply.R | 15 ++++++++- tests/testthat/test-basic.R | 4 ++ tests/testthat/test-convenience.R | 9 +++++ tests/testthat/test-helper.R |only tests/testthat/test-match.R | 32 +++++++++++++------- tests/testthat/test-reindent.R | 6 +++ tests/testthat/test-replace.R | 9 +++++ vignettes/elixir.Rmd | 8 ++--- 32 files changed, 188 insertions(+), 129 deletions(-)
Title: Assurance Methods for Clinical Trials with a Delayed Treatment
Effect
Description: Provides functions for planning clinical trials subject to a delayed
treatment effect using assurance-based methods. Includes two 'shiny'
applications for interactive exploration, simulation, and visualisation of
trial designs and outcomes. The methodology is described in:
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Assurance methods for designing a clinical trial with a delayed treatment
effect" <doi:10.1002/sim.10136>,
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Adaptive clinical trial design with delayed treatment effects using
elicited prior distributions" <doi:10.48550/arXiv.2509.07602>.
Author: James Salsbury [aut, cre]
Maintainer: James Salsbury <jsalsbury1@sheffield.ac.uk>
Diff between DTEAssurance versions 1.0.1 dated 2025-10-24 and 1.1.0 dated 2025-12-02
DTEAssurance-1.0.1/DTEAssurance/inst/shiny/AdaptiveApp |only DTEAssurance-1.0.1/DTEAssurance/inst/shiny/AssuranceApp |only DTEAssurance-1.0.1/DTEAssurance/man/assurance_GSD_shiny_app.Rd |only DTEAssurance-1.0.1/DTEAssurance/man/calc_dte_assurance_interim.Rd |only DTEAssurance-1.0.1/DTEAssurance/tests/testthat/test-assurance_GSD_shiny_app.R |only DTEAssurance-1.0.1/DTEAssurance/tests/testthat/test-calc_dte_assurance_interim.R |only DTEAssurance-1.1.0/DTEAssurance/DESCRIPTION | 10 DTEAssurance-1.1.0/DTEAssurance/MD5 | 61 DTEAssurance-1.1.0/DTEAssurance/NAMESPACE | 8 DTEAssurance-1.1.0/DTEAssurance/NEWS.md | 26 DTEAssurance-1.1.0/DTEAssurance/R/main.R | 1145 +++++++++- DTEAssurance-1.1.0/DTEAssurance/R/shiny_apps.R | 24 DTEAssurance-1.1.0/DTEAssurance/R/utils.R | 619 ++--- DTEAssurance-1.1.0/DTEAssurance/inst/shiny/adaptive_app |only DTEAssurance-1.1.0/DTEAssurance/inst/shiny/assurance_app |only DTEAssurance-1.1.0/DTEAssurance/man/BPP_func.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/add_recruitment_time.Rd | 4 DTEAssurance-1.1.0/DTEAssurance/man/assurance_adaptive_shiny_app.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/assurance_shiny_app.Rd | 9 DTEAssurance-1.1.0/DTEAssurance/man/calc_dte_assurance.Rd | 2 DTEAssurance-1.1.0/DTEAssurance/man/calc_dte_assurance_adaptive.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/calibrate_BPP_threshold.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/calibrate_BPP_timing.Rd |only DTEAssurance-1.1.0/DTEAssurance/man/cens_data.Rd | 2 DTEAssurance-1.1.0/DTEAssurance/man/update_priors.Rd |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat.R | 8 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-BPP_func.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-apply_GSD_to_trial.R | 84 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-assurance_adaptive_shiny_app.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-assurance_shiny_app.R | 26 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calc_dte_assurance.R | 136 - DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calc_dte_assurance_adaptive.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calibrate_BPP_threshold.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-calibrate_BPP_timing.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-cens_data.R | 90 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-make_prior_name_jags.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-make_rpact_design_from_GSD_model.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-sim_dte.R | 31 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-simulate_trial_with_recruitment.R | 103 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-single_calibration_rep.R |only DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-survival_test.R | 54 DTEAssurance-1.1.0/DTEAssurance/tests/testthat/test-update_priors.R |only 42 files changed, 1921 insertions(+), 521 deletions(-)
Title: Handling Hierarchically Structured Risk Factors using Random
Effects Models
Description: Using this package, you can fit a random effects model using either the hierarchical credibility model, a combination of the hierarchical credibility model with a generalized linear model or a Tweedie generalized linear mixed model. See Campo, B.D.C. and Antonio, K. (2023) <doi:10.1080/03461238.2022.2161413>.
Author: Campo Bavo D.C. [aut, cre]
Maintainer: Campo Bavo D.C. <bavo.decock@kuleuven.be>
Diff between actuaRE versions 0.1.6 dated 2025-07-31 and 0.1.7 dated 2025-12-02
DESCRIPTION | 12 - MD5 | 23 +- NAMESPACE | 3 R/hierCredGLM.R | 4 R/plotRE.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/tweedietestdata.rda |only data/tweedietraindata.rda |only inst/doc/actuaRE.R | 16 - inst/doc/actuaRE.Rmd | 12 - inst/doc/actuaRE.html | 378 +++++++++++++++++++++++----------------------- man/tweedietraindata.Rd |only vignettes/actuaRE.Rmd | 12 - 14 files changed, 243 insertions(+), 219 deletions(-)
Title: 'shiny' Widgets for 'teal' Applications
Description: Collection of 'shiny' widgets to support 'teal' applications.
Enables the manipulation of application layout and plot or table
settings.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.widgets versions 0.5.0 dated 2025-08-19 and 0.5.1 dated 2025-12-02
DESCRIPTION | 11 - MD5 | 43 ++-- NEWS.md | 5 R/get_dt_rows.R | 2 R/plot_with_settings.R | 2 build/vignette.rds |binary man/get_dt_rows.Rd | 2 man/plot_with_settings.Rd | 3 tests/testthat.R | 7 tests/testthat/Rplots.pdf |only tests/testthat/_snaps |only tests/testthat/test-draggable_buckets.R | 35 +++ tests/testthat/test-get_dt_rows_ui.R | 4 tests/testthat/test-optionalInput.R | 115 ++++++++++++ tests/testthat/test-optionalSelectInput_ui.R | 108 ++++++++++++ tests/testthat/test-optionalSliderInputValMinMax_ui.R | 14 + tests/testthat/test-plot_with_settings.R | 6 tests/testthat/test-plot_with_settings_ui.R | 98 ++++++----- tests/testthat/test-standard_layout.R | 23 ++ tests/testthat/test-table_with_settings_ui.R | 33 ++- tests/testthat/test-verbatim_popup.R | 160 ++++++++++++++++++ tests/testthat/test-verbatim_popup_ui.R | 70 +++++++ tests/testthat/test-white_small_well.R |only 23 files changed, 665 insertions(+), 76 deletions(-)
Title: A Sky Illuminance Location Tracker
Description: Calculate geolocations by light using template matching.
The routine uses a calibration free optimization of a sky illuminance model to
determine locations robustly using a template matching approach,
as described by Ekstrom (2004) <https://nipr.repo.nii.ac.jp/records/2496>,
and behaviourly informed constraints (step-selection).
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between skytrackr versions 1.0 dated 2025-10-08 and 2.0 dated 2025-12-02
skytrackr-1.0/skytrackr/R/log_lux.R |only skytrackr-1.0/skytrackr/man/log_lux.Rd |only skytrackr-2.0/skytrackr/DESCRIPTION | 12 skytrackr-2.0/skytrackr/MD5 | 88 +- skytrackr-2.0/skytrackr/NAMESPACE | 8 skytrackr-2.0/skytrackr/R/data.R | 20 skytrackr-2.0/skytrackr/R/illuminance_models.R |only skytrackr-2.0/skytrackr/R/likelihood.R | 10 skytrackr-2.0/skytrackr/R/skytrackr.R | 336 ++++++++-- skytrackr-2.0/skytrackr/R/stk_calibrate.R |only skytrackr-2.0/skytrackr/R/stk_center.R |only skytrackr-2.0/skytrackr/R/stk_filter.R |only skytrackr-2.0/skytrackr/R/stk_fit.R | 67 + skytrackr-2.0/skytrackr/R/stk_map.R | 286 +++++++- skytrackr-2.0/skytrackr/R/stk_mask.R | 7 skytrackr-2.0/skytrackr/R/stk_profile.R | 21 skytrackr-2.0/skytrackr/R/stk_read.R | 3 skytrackr-2.0/skytrackr/R/stk_screen_twl.R | 34 - skytrackr-2.0/skytrackr/build/vignette.rds |binary skytrackr-2.0/skytrackr/data/lakes.rda |only skytrackr-2.0/skytrackr/data/rivers.rda |only skytrackr-2.0/skytrackr/inst/doc/skytrackr_benchmark.R |only skytrackr-2.0/skytrackr/inst/doc/skytrackr_benchmark.Rmd |only skytrackr-2.0/skytrackr/inst/doc/skytrackr_benchmark.html |only skytrackr-2.0/skytrackr/inst/doc/skytrackr_optimization.R | 59 + skytrackr-2.0/skytrackr/inst/doc/skytrackr_optimization.Rmd | 113 +++ skytrackr-2.0/skytrackr/inst/doc/skytrackr_optimization.html | 231 ++++++ skytrackr-2.0/skytrackr/inst/doc/skytrackr_parallel_processing.R | 58 - skytrackr-2.0/skytrackr/inst/doc/skytrackr_parallel_processing.Rmd | 16 skytrackr-2.0/skytrackr/inst/doc/skytrackr_parallel_processing.html | 37 - skytrackr-2.0/skytrackr/inst/doc/skytrackr_vignette.R | 21 skytrackr-2.0/skytrackr/inst/doc/skytrackr_vignette.Rmd | 26 skytrackr-2.0/skytrackr/inst/doc/skytrackr_vignette.html | 101 +-- skytrackr-2.0/skytrackr/inst/extdata/shadedrelief.tif |only skytrackr-2.0/skytrackr/man/diurnal.Rd |only skytrackr-2.0/skytrackr/man/individual.Rd |only skytrackr-2.0/skytrackr/man/lakes.Rd |only skytrackr-2.0/skytrackr/man/likelihood.Rd | 4 skytrackr-2.0/skytrackr/man/rivers.Rd |only skytrackr-2.0/skytrackr/man/skytrackr.Rd | 57 + skytrackr-2.0/skytrackr/man/stk_calibrate.Rd |only skytrackr-2.0/skytrackr/man/stk_center.Rd |only skytrackr-2.0/skytrackr/man/stk_filter.Rd |only skytrackr-2.0/skytrackr/man/stk_fit.Rd | 15 skytrackr-2.0/skytrackr/man/stk_map.Rd | 24 skytrackr-2.0/skytrackr/man/stk_profile.Rd | 9 skytrackr-2.0/skytrackr/tests/testthat/Rplots.pdf |only skytrackr-2.0/skytrackr/tests/testthat/test_skytrackr.R | 63 + skytrackr-2.0/skytrackr/vignettes/mask.png |only skytrackr-2.0/skytrackr/vignettes/poor_fit.png |only skytrackr-2.0/skytrackr/vignettes/sgat_locations.rds |only skytrackr-2.0/skytrackr/vignettes/skytrackr_benchmark.Rmd |only skytrackr-2.0/skytrackr/vignettes/skytrackr_final_plot.png |binary skytrackr-2.0/skytrackr/vignettes/skytrackr_optimization.Rmd | 113 +++ skytrackr-2.0/skytrackr/vignettes/skytrackr_parallel_processing.Rmd | 16 skytrackr-2.0/skytrackr/vignettes/skytrackr_preview.png |binary skytrackr-2.0/skytrackr/vignettes/skytrackr_vignette.Rmd | 26 57 files changed, 1484 insertions(+), 397 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-9 dated 2025-11-18 and 0.3-10 dated 2025-12-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 7 +++++++ inst/doc/tbm_supplement.Rnw | 2 +- inst/doc/tbm_supplement.pdf |binary vignettes/tbm_supplement.Rnw | 2 +- 6 files changed, 18 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-05 1.9.1
2020-07-03 1.9.0
2020-04-03 1.7.1
2020-01-31 1.7.0
Title: Parameterized Unit Testing
Description: This is an extension of the 'testthat' package that
lets you add parameters to your unit tests. Parameterized unit tests
are often easier to read and more reliable, since they follow the DNRY
(do not repeat yourself) rule.
Author: Michael Quinn [aut],
Michael Chirico [aut, cre]
Maintainer: Michael Chirico <chiricom@google.com>
Diff between patrick versions 0.3.0 dated 2025-01-27 and 0.3.1 dated 2025-12-02
DESCRIPTION | 22 ++-- MD5 | 12 +- NAMESPACE | 13 ++ NEWS.md | 7 + R/patrick-package.R | 4 R/with_parameters.R | 47 ++++---- tests/testthat/test-with_parameters.R | 182 ++++++++++++++++------------------ 7 files changed, 155 insertions(+), 132 deletions(-)
Title: Interactive Volcano Plot
Description: Generate interactive volcano plots for exploring gene expression data. Built with 'ggplot2', the plots are rendered interactive using 'ggiraph', enabling users to hover over points to display detailed information or click to trigger custom actions.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ivolcano versions 0.0.2 dated 2025-11-17 and 0.0.4 dated 2025-12-02
DESCRIPTION | 10 - MD5 | 35 ++- NAMESPACE | 59 ++++-- NEWS.md |only R/geom-ivolcano-gene.R |only R/geom-ivolcano-line.R |only R/ivolcano.R | 320 ++++++++++++++++++++++------------- R/onclick.R | 81 ++++++++ R/print.R |only R/scales.R |only README.md | 19 +- inst/doc/ivolcano.R | 157 ++++++++++++++++- inst/doc/ivolcano.html | 210 +++++++++++++++++++++- inst/doc/ivolcano.qmd | 212 ++++++++++++++++++++++- inst/extdata/easy_input_limma.rds |only inst/extdata/easy_input_selected.rds |only man/geom_ivolcano_line.Rd |only man/ivolcano.Rd | 182 +++++++++++-------- man/ivolcano_point.Rd |only man/onclick_ensembl.Rd |only man/onclick_hgnc.Rd |only man/onclick_ncbi.Rd |only man/onclick_pubmed.Rd |only man/onclick_uniprot.Rd |only man/scale_color_figureya.Rd |only vignettes/ivolcano.qmd | 212 ++++++++++++++++++++++- 26 files changed, 1227 insertions(+), 270 deletions(-)
Title: Modified Generalized Estimating Equations for Binary Outcome
Description: Analyze small-sample clustered or longitudinal data with binary
outcome using modified generalized estimating equations (GEE) with
bias-adjusted covariance estimator. The package provides any combination of
three GEE methods and 12 covariance estimators.
Author: Ryota Ishii [aut, cre],
Tomohiro Ohigashi [ctb],
Kazushi Maruo [ctb],
Masahiko Gosho [ctb]
Maintainer: Ryota Ishii <r.ishii0808@gmail.com>
Diff between geessbin versions 1.0.0 dated 2024-09-08 and 1.0.1 dated 2025-12-02
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NAMESPACE | 6 +++++ NEWS.md | 5 ++++ R/geessbin.R | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++---- README.md | 5 ++-- build/partial.rdb |binary 7 files changed, 78 insertions(+), 15 deletions(-)
Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for
interactive filtering of data stored in 'data.frame' and
'MultiAssayExperiment' objects. Also displays filtered and unfiltered
observation counts.
Author: Dawid Kaledkowski [aut, cre] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Marcin Kosinski [aut],
Chendi Liao [rev],
Dony Unardi [rev],
Andrew Bates [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.slice versions 0.7.0 dated 2025-08-20 and 0.7.1 dated 2025-12-02
DESCRIPTION | 12 MD5 | 28 NEWS.md | 6 R/FilterStateChoices.R | 31 R/FilteredData.R | 2 R/choices_labeled.R | 49 - build/vignette.rds |binary man/FilteredData.Rd | 2 man/MAEFilteredDataset.Rd | 2 man/choices_labeled.Rd | 6 tests/testthat/helpers-testing-depth.R | 2 tests/testthat/test-FilteredData.R | 589 ++++++++++++++ tests/testthat/test-shinytest2_DataframeFilteredDataset.R | 2 tests/testthat/test-shinytest2_MAEFilteredDataset.R | 1 tests/testthat/test-teal_slice.R | 5 15 files changed, 641 insertions(+), 96 deletions(-)
Title: Propensity Score Predictive Inference for Generalizability
Description: Provides a suite of Propensity Score Predictive Inference (PSPI) methods to generalize treatment effects in trials to target populations. The package includes an existing model Bayesian Causal Forest (BCF) and four PSPI models (BCF-PS, FullBART, SplineBART, DSplineBART). These methods leverage Bayesian Additive Regression Trees (BART) to adjust for high-dimensional covariates and nonlinear associations, while SplineBART and DSplineBART further use propensity score based splines to address covariate shift between trial data and target population.
Author: Jungang Zou [aut, cre],
Qixuan Chen [aut],
Joseph Schwartz [aut],
Nathalie Moise [aut],
Roderick Little [aut],
Robert McCulloch [ctb],
Rodney Sparapani [ctb],
Charles Spanbauer [ctb],
Robert Gramacy [ctb],
Jean-Sebastien Roy [ctb]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between PSPI versions 1.1 dated 2025-12-01 and 1.2 dated 2025-12-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ R/MCMC_PSPI_R.R | 2 +- README.md | 4 ++-- src/BART/bart.h | 7 ++++--- 6 files changed, 18 insertions(+), 14 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut] ,
Malan Bosman [aut] ,
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.7.0 dated 2025-08-27 and 0.7.1 dated 2025-12-02
cards-0.7.0/cards/man/shuffle_ard.Rd |only cards-0.7.1/cards/DESCRIPTION | 16 cards-0.7.1/cards/MD5 | 66 +- cards-0.7.1/cards/NEWS.md | 8 cards-0.7.1/cards/R/ard_attributes.R | 1 cards-0.7.1/cards/R/ard_stack.R | 13 cards-0.7.1/cards/R/ard_stack_hierarchical.R | 105 +-- cards-0.7.1/cards/R/ard_summary.R | 2 cards-0.7.1/cards/R/ard_tabulate.R | 2 cards-0.7.1/cards/R/deprecated.R | 3 cards-0.7.1/cards/R/import-standalone-check_pkg_installed.R | 95 +-- cards-0.7.1/cards/R/import-standalone-cli_call_env.R | 4 cards-0.7.1/cards/R/mock.R | 11 cards-0.7.1/cards/R/shuffle_ard.R | 10 cards-0.7.1/cards/R/sort_ard_hierarchical.R | 6 cards-0.7.1/cards/README.md | 2 cards-0.7.1/cards/inst/WORDLIST | 1 cards-0.7.1/cards/man/ard_stack.Rd | 6 cards-0.7.1/cards/man/ard_stack_hierarchical.Rd | 4 cards-0.7.1/cards/man/cards-package.Rd | 2 cards-0.7.1/cards/man/deprecated.Rd | 34 + cards-0.7.1/cards/man/figures/logo.png |only cards-0.7.1/cards/man/filter_ard_hierarchical.Rd | 2 cards-0.7.1/cards/man/sort_ard_hierarchical.Rd | 2 cards-0.7.1/cards/tests/testthat/_snaps/shuffle_ard.md | 32 + cards-0.7.1/cards/tests/testthat/test-ard_attributes.R | 2 cards-0.7.1/cards/tests/testthat/test-ard_hierarchical.R | 2 cards-0.7.1/cards/tests/testthat/test-ard_stack.R | 67 -- cards-0.7.1/cards/tests/testthat/test-ard_stack_hierarchical.R | 60 + cards-0.7.1/cards/tests/testthat/test-ard_tabulate.R | 2 cards-0.7.1/cards/tests/testthat/test-filter_ard_hierarchical.R | 8 cards-0.7.1/cards/tests/testthat/test-options.R | 2 cards-0.7.1/cards/tests/testthat/test-shuffle_ard.R | 304 +++++++--- cards-0.7.1/cards/tests/testthat/test-tidy_ard_column_order.R | 2 cards-0.7.1/cards/tests/testthat/test-tidy_ard_row_order.R | 2 35 files changed, 526 insertions(+), 352 deletions(-)
Title: Bayesian Gaussian Graphical Models
Description: Fit Bayesian Gaussian graphical models. The methods are separated into
two Bayesian approaches for inference: hypothesis testing and estimation. There are
extensions for confirmatory hypothesis testing, comparing Gaussian graphical models,
and node wise predictability. These methods were recently introduced in the Gaussian
graphical model literature, including
Williams (2019) <doi:10.31234/osf.io/x8dpr>,
Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>,
Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.
Author: Donald Williams [aut],
Joris Mulder [aut],
Philippe Rast [aut, cre]
Maintainer: Philippe Rast <rast.ph@gmail.com>
Diff between BGGM versions 2.1.5 dated 2024-12-22 and 2.1.6 dated 2025-12-02
DESCRIPTION | 12 - MD5 | 48 +++--- NEWS.md | 21 ++ R/bggm_missing.R | 4 R/confirm.R | 18 +- R/estimate.R | 16 +- R/explore.default.R | 17 +- R/ggm_compare_confirm.R | 17 +- R/ggm_compare_estimate.default.R | 14 + build/partial.rdb |binary build/vignette.rds |binary configure.ac | 1 inst/doc/hyp_3_ways.R | 16 +- inst/doc/hyp_3_ways.html | 5 inst/doc/mcmc_diagnostics.R | 116 +++++++------- inst/doc/netplot.R | 72 ++++----- inst/doc/netplot.html | 24 +-- inst/doc/netstat_custom.R | 258 ++++++++++++++++----------------- inst/doc/netstat_custom.html | 11 - inst/doc/ppc_custom.R | 18 +- inst/doc/ppc_custom.html | 57 +++---- inst/doc/predictability.R | 190 ++++++++++++------------ inst/doc/predictability.html | 7 inst/doc/test_sum.R | 16 +- src/bggm_fast.cpp | 302 +++++++++++++++++++++++++++++---------- 25 files changed, 719 insertions(+), 541 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-12 0.1.1
2025-08-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-17 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-20 1.0.1
2025-02-06 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-08 1.0.4
Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types of machine learning models in R. Aside from some standard model-
specific variable importance measures, this package also provides model-
agnostic approaches that can be applied to any supervised learning algorithm.
These include 1) an efficient permutation-based variable importance measure,
2) variable importance based on Shapley values (Strumbelj and Kononenko,
2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based
approach described in Greenwell et al. (2018) <doi:10.48550/arXiv.1805.04755>. A
variance-based method for quantifying the relative strength of interaction
effects is also included (see the previous reference for details).
Author: Brandon M. Greenwell [aut, cre] ,
Brad Boehmke [aut]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between vip versions 0.4.1 dated 2023-08-21 and 0.4.2 dated 2025-12-02
DESCRIPTION | 17 - MD5 | 36 +- NEWS.md | 40 ++ R/data.R | 18 - R/vi_permute.R | 4 README.md | 293 ++++++++++++----- build/vignette.rds |binary inst/doc/vip.Rmd | 2 inst/doc/vip.html | 633 +++++++++++++++++++------------------- inst/references.bib | 4 inst/tinytest/test_pkg_lightgbm.R | 7 inst/tinytest/test_pkg_nnet.R | 7 inst/tinytest/test_pkg_xgboost.R | 7 inst/tinytest/test_vi_permute.R | 66 +++ man/titanic.Rd | 5 man/titanic_mice.Rd | 10 man/vi_permute.Rd | 2 vignettes/vip.Rmd | 2 vignettes/vip.Rmd.orig | 2 19 files changed, 690 insertions(+), 465 deletions(-)
Title: Logging Setup for the 'teal' Family of Packages
Description: Utilizing the 'logger' framework to record events within a
package, specific to 'teal' family of packages. Supports logging
namespaces, hierarchical logging, various log destinations,
vectorization, and more.
Author: Dawid Kaledkowski [aut, cre],
Konrad Pagacz [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.logger versions 0.4.0 dated 2025-07-08 and 0.4.1 dated 2025-12-02
DESCRIPTION | 21 ++--- MD5 | 24 +++--- NAMESPACE | 1 NEWS.md | 5 + R/log_shiny_input_changes.R | 13 +-- R/register_logger.R | 2 R/supress_logs.R | 11 ++- R/teal.logger-package.R | 4 - build/vignette.rds |binary man/register_logger.Rd | 2 man/suppress_logs.Rd | 2 tests/testthat/test-log_formatter.R | 94 +++++++++++++------------- tests/testthat/test-log_shiny_input_changes.R |only tests/testthat/test-supress_logs.R |only 14 files changed, 96 insertions(+), 83 deletions(-)
Title: Spatial Resampling Infrastructure
Description: Functions and classes for spatial resampling to use with the
'rsample' package, such as spatial cross-validation (Brenning, 2012)
<doi:10.1109/IGARSS.2012.6352393>. The scope of 'rsample' and
'spatialsample' is to provide the basic building blocks for creating
and analyzing resamples of a spatial data set, but neither package
includes functions for modeling or computing statistics. The resampled
spatial data sets created by 'spatialsample' do not contain much
overhead in memory.
Author: Michael Mahoney [aut, cre] ,
Julia Silge [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between spatialsample versions 0.6.0 dated 2024-10-02 and 0.6.1 dated 2025-12-02
DESCRIPTION | 13 +-- MD5 | 42 +++++----- NEWS.md | 4 R/spatial_vfold_cv.R | 40 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/spatialsample.R | 2 inst/doc/spatialsample.html | 2 man/spatial_clustering_cv.Rd | 2 man/spatial_nndm_cv.Rd | 2 man/spatial_vfold.Rd | 2 tests/testthat/_snaps/autoplot/block-plots-with-grid.svg | 20 ++-- tests/testthat/_snaps/autoplot/buffered-rsample-plot.svg | 6 - tests/testthat/_snaps/autoplot/buffered-rset-plot.svg | 40 ++++----- tests/testthat/_snaps/autoplot/buffered-vfold-plot.svg | 20 ++-- tests/testthat/_snaps/autoplot/buffered-vfold-split.svg | 6 - tests/testthat/_snaps/autoplot/expand-bbox.svg | 16 +-- tests/testthat/_snaps/autoplot/repeated-block-cv.svg | 40 ++++----- tests/testthat/_snaps/autoplot/repeated-vfold.svg | 20 ++-- tests/testthat/_snaps/autoplot/snake-flips-rows-the-right-way.svg | 40 ++++----- tests/testthat/_snaps/spatial_vfold_cv.md | 6 - tests/testthat/test-autoplot.R | 3 22 files changed, 171 insertions(+), 155 deletions(-)
Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is
an open source distributed SQL query engine for running interactive
analytic queries against data sources of all sizes ranging from
gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut],
Sergey Goder [aut],
Jarod G.R. Meng [aut, cre],
Thomas J. Leeper [ctb],
John Myles White [ctb]
Maintainer: Jarod G.R. Meng <jarodm@fb.com>
Diff between RPresto versions 1.4.7 dated 2025-01-08 and 1.4.8 dated 2025-12-02
DESCRIPTION | 17 + MD5 | 114 ++++++++----- NAMESPACE | 38 ++++ NEWS.md | 27 +++ R/PrestoQuery.R | 19 +- R/PrestoSession.R | 17 + R/cte.R | 6 R/dbAppendTableAs.R |only R/dbClearResult.R | 6 R/dbColumnInfo.R |only R/dbColumnType.R |only R/dbConnect.R | 3 R/dbGetQuery.R | 4 R/dbListFields.R | 5 R/dbplyr-db.R | 83 +++++++++ R/dbplyr-src.R | 3 R/presto.field.R | 57 +++++- R/presto.field_utilities.R | 91 ++++++++++ R/presto_type.R |only R/presto_unnest.R |only R/sqlAppendTableAs.R |only README.md | 31 +-- inst/doc/common-table-expressions.html | 11 - inst/doc/complex-types.html | 45 ++--- inst/doc/primitive-types.html | 39 ++-- man/Presto.Rd | 3 man/PrestoConnection-class.Rd | 59 ++++-- man/PrestoResult-class.Rd | 24 ++ man/dbAppendTableAs.Rd |only man/dbplyr-db.Rd | 33 +++ man/dplyr_function_implementations.Rd | 3 man/get_query_columns.Rd |only man/get_table_columns.Rd |only man/op_frame.lazy_unnest_query.Rd |only man/op_grps.lazy_unnest_query.Rd |only man/op_sort.lazy_unnest_query.Rd |only man/op_vars.lazy_unnest_query.Rd |only man/presto_type.Rd |only man/presto_unnest.Rd |only man/reorder_select_columns.Rd |only man/sqlAppendTableAs.Rd |only man/sql_build.lazy_unnest_query.Rd |only man/sql_render.unnest_query.Rd |only man/validate_column_match.Rd |only tests/testthat/helper-mock_connection.R | 44 ++--- tests/testthat/test-PrestoQuery.R | 24 +- tests/testthat/test-bigint_handling.R | 6 tests/testthat/test-bigint_overflow_warning.R |only tests/testthat/test-dbAppendTableAs.R |only tests/testthat/test-dbClearResult.R | 30 +-- tests/testthat/test-dbColumnInfo.R |only tests/testthat/test-dbColumnType.R |only tests/testthat/test-dbConnect.R | 22 +- tests/testthat/test-dbFetch.R | 222 +++++++++++++------------- tests/testthat/test-dbGetInfo.R | 54 +++--- tests/testthat/test-dbGetQuery.R | 80 ++++----- tests/testthat/test-dbGetRowCount.R | 28 +-- tests/testthat/test-dbGetStatement.R | 24 +- tests/testthat/test-dbHasCompleted.R | 6 tests/testthat/test-dbIsValid.R | 146 ++++++++--------- tests/testthat/test-dbListFields.R | 156 +++++++++--------- tests/testthat/test-dbListTables.R | 16 - tests/testthat/test-dbSendQuery.R | 144 ++++++++-------- tests/testthat/test-db_explain.R | 16 - tests/testthat/test-db_query_fields.R | 74 ++++---- tests/testthat/test-dbplyr-db.R |only tests/testthat/test-dplyr.integration.R | 3 tests/testthat/test-fetch.R | 34 +-- tests/testthat/test-presto_field.R | 3 tests/testthat/test-presto_type.R |only tests/testthat/test-presto_unnest.R |only tests/testthat/test-sqlAppendTableAs.R |only 72 files changed, 1133 insertions(+), 737 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features.
All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] ,
Edzer Pebesma [ctb] ,
Roger Bivand [ctb],
Jeroen Ooms [ctb] ,
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kaminski [cph] [...truncated...]
Maintainer: Marius Appel <marius.appel@hs-bochum.de>
Diff between gdalcubes versions 0.7.1 dated 2025-03-19 and 0.7.2 dated 2025-12-02
DESCRIPTION | 17 +++++++++-------- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/image_collection.R | 14 +++++++++----- R/stac.R | 7 +++++-- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- inst/doc/gc01_MODIS.html | 6 +++--- src/gdalcubes/src/build_info.h | 12 ++++++------ src/gdalcubes/src/coord_types.h | 2 +- src/gdalcubes/src/image_collection.h | 2 +- src/gdalcubes/src/view.h | 8 +++++++- 13 files changed, 70 insertions(+), 49 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 3.2.1 dated 2025-09-22 and 3.3.0 dated 2025-12-02
DESCRIPTION | 13 MD5 | 202 - NAMESPACE | 15 NEWS.md | 14 R/EMC2-package.R | 2 R/MRI.R | 7 R/RcppExports.R | 16 R/SBC.R | 266 + R/design.R | 11 R/factor_analysis.R | 253 + R/fitting.R | 54 R/get_type_objects.R | 97 R/group_design.R | 8 R/make_data.R | 138 - R/map.R | 239 + R/model_DDM.R | 59 R/model_SS.R | 57 R/new_map.R | 455 ++- R/objects.R | 34 R/plot_data.R | 672 ++++ R/plotting.R | 153 + R/plotting_ss.R |only R/priors.R | 31 R/s3_funcs.R | 59 R/sampling.R | 90 R/statistics.R | 62 R/trend.R | 960 +++++-- R/utils.R | 39 R/variant_SEM.R | 1108 +++++--- R/variant_diag_gamma.R | 2 R/variant_factor.R | 7 R/variant_infnt_factor.R | 2 R/variant_standard.R | 54 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Simulation-based-Calibration.R | 4 inst/doc/Simulation-based-Calibration.Rmd | 4 inst/doc/Simulation-based-Calibration.html | 10 inst/doc/trends.R |only inst/doc/trends.Rmd |only inst/doc/trends.html |only inst/include |only man/compare_subject.Rd | 13 man/fit.Rd | 8 man/get_group_design.Rd |only man/init_chains.Rd | 9 man/make_SEM_diagram.Rd |only man/make_emc.Rd | 5 man/make_sem_structure.Rd |only man/make_trend.Rd | 19 man/plot.emc.prior.Rd | 8 man/plot_caf.Rd |only man/plot_cdf.Rd | 5 man/plot_delta.Rd |only man/plot_sbc_ecdf.Rd | 6 man/plot_sbc_hist.Rd | 4 man/plot_ss_if.Rd |only man/plot_ss_srrt.Rd |only man/plot_trend.Rd |only man/predict.emc.Rd | 2 man/profile_plot.Rd | 6 man/register_trend.Rd |only man/rotate_loadings.Rd |only man/run_emc.Rd | 9 man/run_hyper.Rd |only man/summary.emc.group_design.Rd |only src/Makevars | 2 src/Makevars.ucrt | 2 src/Makevars.win | 2 src/RcppExports.cpp | 51 src/group_designs.cpp | 196 + src/particle_ll.cpp | 288 -- src/trend.h | 568 +++- src/utility_functions.h | 137 - tests/testthat/_snaps/Darwin/fMRI.md | 56 tests/testthat/_snaps/Darwin/fit.md | 60 tests/testthat/_snaps/Darwin/variant_funs.md | 215 - tests/testthat/_snaps/Linux |only tests/testthat/_snaps/S3/prior-plot.svg | 663 ++-- tests/testthat/_snaps/Windows |only tests/testthat/_snaps/compare.md | 2 tests/testthat/_snaps/fMRI/prior-fmri.svg | 942 +++--- tests/testthat/_snaps/group.md | 224 - tests/testthat/_snaps/joint.md | 6 tests/testthat/_snaps/make_emc.md | 114 tests/testthat/_snaps/map.md | 60 tests/testthat/_snaps/model_functions.md | 258 - tests/testthat/_snaps/new_models.md | 50 tests/testthat/_snaps/pairs_posterior/pairs-plot.svg | 1502 +++++------ tests/testthat/_snaps/plot_chains/chain-plots.svg | 454 +-- tests/testthat/_snaps/plot_fit/cdf-plot-fit.svg | 842 +++--- tests/testthat/_snaps/plot_fit/dens-plot-fit.svg | 148 - tests/testthat/_snaps/plot_fit/stat-plot-fit.svg | 124 tests/testthat/_snaps/plot_pars/density-alpha.svg | 478 +-- tests/testthat/_snaps/plot_pars/density-plots.svg | 470 +-- tests/testthat/_snaps/plot_relations/plot-relations-cred.svg | 660 ++-- tests/testthat/_snaps/plot_relations/plot-relations-mean.svg | 660 ++-- tests/testthat/_snaps/profile/profile-plot.svg | 426 +-- tests/testthat/_snaps/stopS.md | 2 tests/testthat/_snaps/trend.md | 370 +- tests/testthat/test-S3.R | 2 tests/testthat/test-fMRI.R | 2 tests/testthat/test-fit.R | 22 tests/testthat/test-group.R | 11 tests/testthat/test-map.R | 7 tests/testthat/test-plot_fit.R | 1 tests/testthat/test-trend.R | 158 + tests/testthat/test-variant_funs.R | 74 vignettes/Simulation-based-Calibration.Rmd | 4 vignettes/trends.Rmd |only 110 files changed, 9780 insertions(+), 5824 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry [aut, cre],
Amy Gill [aut]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between dslabs versions 0.9.0 dated 2025-09-17 and 0.9.1 dated 2025-12-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/mnist_127.R | 4 +--- R/mnist_27.R | 2 +- man/mnist_127.Rd | 4 +--- man/mnist_27.Rd | 2 +- 6 files changed, 12 insertions(+), 16 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Description: Utility package containing: Main categories: Working with grouped data: 'do' something to data when stratified 'by' some variables. General linear estimates. Data handling utilities. Functional programming, in particular restrict functions to a smaller domain. Miscellaneous functions for data handling. Model stability in connection with model selection. Miscellaneous other tools.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.7.0 dated 2025-06-29 and 4.7.1 dated 2025-12-02
doBy-4.7.0/doBy/R/linear_modelling.R |only doBy-4.7.0/doBy/inst/doc/linest_lsmeans.R |only doBy-4.7.0/doBy/inst/doc/linest_lsmeans.Rnw |only doBy-4.7.0/doBy/inst/doc/linest_lsmeans.pdf |only doBy-4.7.0/doBy/inst/doc/section_fun.R |only doBy-4.7.0/doBy/inst/doc/section_fun.Rmd |only doBy-4.7.0/doBy/inst/doc/section_fun.html |only doBy-4.7.0/doBy/man/NIRmilk.Rd |only doBy-4.7.0/doBy/man/pow.Rd |only doBy-4.7.0/doBy/man/reciprocal.Rd |only doBy-4.7.0/doBy/vignettes/linest_lsmeans.Rnw |only doBy-4.7.0/doBy/vignettes/section_fun.Rmd |only doBy-4.7.1/doBy/DESCRIPTION | 16 - doBy-4.7.1/doBy/MD5 | 171 ++++++++--------- doBy-4.7.1/doBy/NAMESPACE | 12 + doBy-4.7.1/doBy/NEWS.md | 7 doBy-4.7.1/doBy/R/DATA_doby.R | 169 ++++++++-------- doBy-4.7.1/doBy/R/NAMESPACE_doby.R | 3 doBy-4.7.1/doBy/R/by_lapplyBy.R | 2 doBy-4.7.1/doBy/R/by_lmBy.R | 2 doBy-4.7.1/doBy/R/by_orderBy.R | 1 doBy-4.7.1/doBy/R/by_sampleBy.R | 1 doBy-4.7.1/doBy/R/by_scaleBy.R | 2 doBy-4.7.1/doBy/R/by_splitBy.R | 1 doBy-4.7.1/doBy/R/by_subsetBy.R | 2 doBy-4.7.1/doBy/R/by_summaryBy.R | 1 doBy-4.7.1/doBy/R/by_transformBy.R | 2 doBy-4.7.1/doBy/R/compute_on_forecast.R |only doBy-4.7.1/doBy/R/data_firstobs_lastobs.R | 4 doBy-4.7.1/doBy/R/data_rbind_list.R | 2 doBy-4.7.1/doBy/R/data_scale_df.R | 2 doBy-4.7.1/doBy/R/functional_bquote_list.R | 6 doBy-4.7.1/doBy/R/functional_coerce_expr_to_function.R | 4 doBy-4.7.1/doBy/R/functional_section_fun.R | 113 +++++++++-- doBy-4.7.1/doBy/R/modelling.R |only doBy-4.7.1/doBy/R/pipe_friendly.R |only doBy-4.7.1/doBy/R/plot_functions.r | 4 doBy-4.7.1/doBy/README.md | 13 - doBy-4.7.1/doBy/build/vignette.rds |binary doBy-4.7.1/doBy/data/shoes_long.RData |only doBy-4.7.1/doBy/inst/doc/doby.Rmd | 3 doBy-4.7.1/doBy/inst/doc/doby.html | 64 +----- doBy-4.7.1/doBy/inst/doc/pipe_arithmetic.Rmd |only doBy-4.7.1/doBy/inst/doc/pipe_arithmetic.html |only doBy-4.7.1/doBy/inst/doc/sectioning_fun.R |only doBy-4.7.1/doBy/inst/doc/sectioning_fun.Rmd |only doBy-4.7.1/doBy/inst/doc/sectioning_fun.html |only doBy-4.7.1/doBy/inst/doc/vtools.Rmd | 7 doBy-4.7.1/doBy/inst/doc/vtools.html | 8 doBy-4.7.1/doBy/man/add_int.Rd | 2 doBy-4.7.1/doBy/man/add_pred.Rd | 2 doBy-4.7.1/doBy/man/add_resid.Rd | 2 doBy-4.7.1/doBy/man/align_coefs.Rd |only doBy-4.7.1/doBy/man/beets.Rd | 1 doBy-4.7.1/doBy/man/bquote_fun_list.Rd | 1 doBy-4.7.1/doBy/man/by-lapply.Rd | 1 doBy-4.7.1/doBy/man/by-lmby.Rd | 1 doBy-4.7.1/doBy/man/by-order.Rd | 1 doBy-4.7.1/doBy/man/by-sample.Rd | 1 doBy-4.7.1/doBy/man/by-split.Rd | 1 doBy-4.7.1/doBy/man/by-subset.Rd | 1 doBy-4.7.1/doBy/man/by-summary.Rd | 1 doBy-4.7.1/doBy/man/by-transform.Rd | 1 doBy-4.7.1/doBy/man/by_scale.Rd | 1 doBy-4.7.1/doBy/man/carcass.Rd | 1 doBy-4.7.1/doBy/man/child_growth.Rd | 15 - doBy-4.7.1/doBy/man/codstom.Rd | 1 doBy-4.7.1/doBy/man/crickets.Rd | 1 doBy-4.7.1/doBy/man/crimeRate.Rd | 1 doBy-4.7.1/doBy/man/crime_rate.Rd | 1 doBy-4.7.1/doBy/man/data_breastcancer.Rd | 1 doBy-4.7.1/doBy/man/data_budworm.Rd | 1 doBy-4.7.1/doBy/man/data_cad.Rd | 2 doBy-4.7.1/doBy/man/data_mathmark.Rd | 1 doBy-4.7.1/doBy/man/data_personality.Rd | 1 doBy-4.7.1/doBy/man/dietox.Rd | 1 doBy-4.7.1/doBy/man/expr_to_fun.Rd | 1 doBy-4.7.1/doBy/man/fatacid.Rd | 1 doBy-4.7.1/doBy/man/firstlastobs.Rd | 1 doBy-4.7.1/doBy/man/haldCement.Rd | 1 doBy-4.7.1/doBy/man/income.Rd | 3 doBy-4.7.1/doBy/man/interaction-plot.Rd | 1 doBy-4.7.1/doBy/man/math_teachers.Rd | 11 - doBy-4.7.1/doBy/man/milkman.Rd | 1 doBy-4.7.1/doBy/man/nir_milk.Rd | 36 ++- doBy-4.7.1/doBy/man/pipe_arithmetic.Rd |only doBy-4.7.1/doBy/man/plot_lm.Rd | 1 doBy-4.7.1/doBy/man/potatoes.Rd | 1 doBy-4.7.1/doBy/man/rbind_list.Rd | 1 doBy-4.7.1/doBy/man/response.Rd | 2 doBy-4.7.1/doBy/man/response_plot.Rd | 1 doBy-4.7.1/doBy/man/scale_df.Rd | 1 doBy-4.7.1/doBy/man/section_fun.Rd | 4 doBy-4.7.1/doBy/man/set_default.Rd |only doBy-4.7.1/doBy/man/shoes.Rd | 10 doBy-4.7.1/doBy/man/transform_forecast.Rd |only doBy-4.7.1/doBy/vignettes/doby.Rmd | 3 doBy-4.7.1/doBy/vignettes/pipe_arithmetic.Rmd |only doBy-4.7.1/doBy/vignettes/sectioning_fun.Rmd |only doBy-4.7.1/doBy/vignettes/vtools.Rmd | 7 100 files changed, 452 insertions(+), 301 deletions(-)
Title: Model Wrappers for Discriminant Analysis
Description: Bindings for additional classification models for use with
the 'parsnip' package. Models include flavors of discriminant
analysis, such as linear (Fisher (1936)
<doi:10.1111/j.1469-1809.1936.tb02137.x>), regularized (Friedman
(1989) <doi:10.1080/01621459.1989.10478752>), and flexible (Hastie,
Tibshirani, and Buja (1994) <doi:10.1080/01621459.1994.10476866>), as
well as naive Bayes classifiers (Hand and Yu (2007)
<doi:10.1111/j.1751-5823.2001.tb00465.x>).
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between discrim versions 1.0.2 dated 2025-08-22 and 1.1.0 dated 2025-12-02
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 4 ++ R/discrim_flexible_data.R | 29 +++++++++++++--- R/discrim_linear_data.R | 74 ++++++++++++++++++++++++++++++++++++------- R/discrim_quad_data.R | 34 ++++++++++++++++--- R/discrim_regularized_data.R | 20 +++++++++-- R/naive_Bayes_data.R | 34 ++++++++++++++++--- inst/WORDLIST | 1 man/discrim-package.Rd | 9 ++++- 10 files changed, 187 insertions(+), 44 deletions(-)