Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel', 'doParallel', and 'doRNG' packages.
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.2-3 dated 2025-11-02 and 1.2-4 dated 2025-12-14
ChangeLog | 32 ++++++++ DESCRIPTION | 12 +-- MD5 | 52 ++++++------- NAMESPACE | 5 - R/cpfa.R | 8 ++ R/cpm.R | 3 R/kcv.gbm.R | 21 +++-- R/kcv.nn.R | 4 - R/kcv.rda.R | 6 - R/kcv.rf.R | 4 - R/kcv.svm.R | 4 - R/predict.tunecpfa.R | 2 R/print.tunecpfa.R | 9 +- R/simcpfa.R | 181 +++++++++++++++++++++++++++++------------------- R/tunecpfa.R | 53 ++++++-------- build/vignette.rds |binary inst/doc/cpfa.Rmd | 7 - inst/doc/cpfa.pdf |binary man/cpfa.Rd | 21 ++--- man/cpm.Rd | 13 ++- man/cpm.all.Rd | 18 ++-- man/plotcpfa.Rd | 11 ++ man/predict.tunecpfa.Rd | 29 ++++--- man/print.tunecpfa.Rd | 13 ++- man/simcpfa.Rd | 84 +++++++++++----------- man/tunecpfa.Rd | 15 ++- vignettes/cpfa.Rmd | 7 - 27 files changed, 359 insertions(+), 255 deletions(-)
Title: Time to Event Outcome in Experimental Designs of Pre-Clinical
Studies
Description: Conduct simulation-based customized power calculation
for clustered time to event data in a mixed crossed/nested design,
where a number of cell lines and a number of mice within each cell line are considered to achieve a desired statistical power,
motivated by Eckel-Passow and colleagues (2021) <doi:10.1093/neuonc/noab137> and Li and colleagues (2025) <doi:10.51387/25-NEJSDS76>.
This package provides two commonly used models for powering a design, linear mixed effects and Cox frailty model. Both models account for
within-subject (cell line) correlation while holding different distributional assumptions about the outcome.
Alternatively, the counterparts of fixed effects model are also available, which produces similar estimates of statistical power.
Author: Shanpeng Li [aut, cre],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between PDXpower versions 1.0.4 dated 2025-01-24 and 1.0.5 dated 2025-12-14
PDXpower-1.0.4/PDXpower/man/PowerTable.Rd |only PDXpower-1.0.5/PDXpower/DESCRIPTION | 17 PDXpower-1.0.5/PDXpower/MD5 | 47 - PDXpower-1.0.5/PDXpower/NAMESPACE | 32 PDXpower-1.0.5/PDXpower/R/PDXpower.R |only PDXpower-1.0.5/PDXpower/R/PowANOVA.R | 8 PDXpower-1.0.5/PDXpower/R/PowANOVADat.R | 4 PDXpower-1.0.5/PDXpower/R/PowFrailty.R | 11 PDXpower-1.0.5/PDXpower/R/PowFrailtyDat.R | 14 PDXpower-1.0.5/PDXpower/R/PowerTable.R | 148 ---- PDXpower-1.0.5/PDXpower/R/bootfit.R | 314 ++------- PDXpower-1.0.5/PDXpower/R/globals.R | 2 PDXpower-1.0.5/PDXpower/R/plotpower.R | 321 +++------- PDXpower-1.0.5/PDXpower/R/print.PowerTable.R | 36 - PDXpower-1.0.5/PDXpower/R/simfit.R | 106 +-- PDXpower-1.0.5/PDXpower/README.md | 94 +- PDXpower-1.0.5/PDXpower/inst/WORDLIST | 4 PDXpower-1.0.5/PDXpower/man/PowANOVA.Rd | 3 PDXpower-1.0.5/PDXpower/man/PowANOVADat.Rd | 3 PDXpower-1.0.5/PDXpower/man/PowFrailty.Rd | 9 PDXpower-1.0.5/PDXpower/man/PowFrailtyDat.Rd | 13 PDXpower-1.0.5/PDXpower/man/figures/README-unnamed-chunk-3-1.png |binary PDXpower-1.0.5/PDXpower/man/figures/README-unnamed-chunk-4-1.png |only PDXpower-1.0.5/PDXpower/man/figures/README-unnamed-chunk-5-1.png |only PDXpower-1.0.5/PDXpower/man/figures/README-unnamed-chunk-6-1.png |binary PDXpower-1.0.5/PDXpower/man/figures/README-unnamed-chunk-7-1.png |only PDXpower-1.0.5/PDXpower/man/print.PowerTable.Rd | 3 27 files changed, 386 insertions(+), 803 deletions(-)
Title: Downscaling Species Occupancy
Description: Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) <doi:10.18637/jss.v086.c03>.
Author: Charles Marsh [aut, cre, cph]
Maintainer: Charles Marsh <charlie.marsh@mailbox.org>
Diff between downscale versions 5.1.3 dated 2025-09-18 and 5.1.4 dated 2025-12-14
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/Downscaling.html | 12 ++++++------ inst/doc/Upgraining.html | 4 ++-- man/Downscale-package.Rd | 4 ++-- man/downscale.Rd | 4 ++-- man/ensemble.downscale.Rd | 2 +- man/upgrain.Rd | 6 +++--- man/upgrain.threshold.Rd | 12 ++++++------ 11 files changed, 40 insertions(+), 36 deletions(-)
Title: Characterizing Observed and Expected Representation
Description: A system for analyzing descriptive representation, especially for comparing the composition of a political body to the population it represents. Users can compute the expected degree of representation for a body under a random sampling model, the expected degree of representation variability, as well as representation scores from observed political bodies. The package is based on Gerring, Jerzak, and Oncel (2024) <doi:10.1017/S0003055423000680>.
Author: Connor Jerzak [aut, cre] ,
John Gerring [aut] ,
Erzen Oncel [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Diff between DescriptiveRepresentationCalculator versions 1.1.0 dated 2025-01-14 and 1.1.1 dated 2025-12-14
DESCRIPTION | 17 +++--- MD5 | 35 +++++++----- NAMESPACE | 1 NEWS.md |only R/ExpectedRep.R | 5 + R/HelperFxns.R | 43 +++++++++++++++ R/ObservedRep.R | 26 ++++++++- R/RelativeRep.R |only R/VarRep.R | 5 + build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 +- inst/doc/MainVignette.R | 24 ++++++++ inst/doc/MainVignette.Rmd | 76 ++++++++++++++++++++++++--- inst/doc/MainVignette.html | 108 +++++++++++++++++++++++++++++++++------ man/ObservedRepresentation.Rd | 2 man/RelativeRepresentation.Rd |only man/checkUnmatchedBodyMembers.Rd |only man/validatePopShares.Rd |only tests |only vignettes/MainVignette.Rmd | 76 ++++++++++++++++++++++++--- 21 files changed, 359 insertions(+), 65 deletions(-)
More information about DescriptiveRepresentationCalculator at CRAN
Permanent link
Title: Uncertainty Estimation and Contribution Analysis
Description: Implements the Gaussian method of first and second order, the Kragten numerical method and the Monte Carlo simulation method for uncertainty estimation and analysis.
Author: Hugo Gasca-Aragon [aut, cre]
Maintainer: Hugo Gasca-Aragon <hugo_gasca_aragon@hotmail.com>
Diff between uncertainty versions 0.2.0 dated 2018-05-06 and 0.3.0 dated 2025-12-14
DESCRIPTION | 12 - MD5 | 37 ++-- R/print.uncertainty.R | 23 +- R/print.uncertaintyBudget.R | 4 R/summary.uncertainty.R | 4 R/uncertainty-internal.R | 349 ++++++++++++++++++++++++++++----------- R/uncertainty.default.R | 25 +- R/uncertaintyBudget.default.R | 35 +++ build |only man/plot.summary.uncertainty.Rd | 30 ++- man/plot.uncertainty.Rd | 28 +-- man/print.summary.uncertainty.Rd | 29 ++- man/print.uncertainty.Rd | 31 ++- man/print.uncertaintyBudget.Rd | 18 +- man/summary.uncertainty.Rd | 29 ++- man/uncertainty-package.Rd | 192 ++++++++++----------- man/uncertainty.Rd | 14 - man/uncertainty.default.Rd | 34 ++- man/uncertaintyBudget.Rd | 8 man/uncertaintyBudget.default.Rd | 31 ++- 20 files changed, 591 insertions(+), 342 deletions(-)
Title: Parametric Iterative Conditional Expectation G-Formula
Description: Implements iterative conditional expectation (ICE) estimators of the plug-in g-formula (Wen, Young, Robins, and Hernán (2020) <doi: 10.1111/biom.13321>).
Both singly robust and doubly robust ICE estimators based on parametric models are available.
The package can be used to estimate survival curves under sustained treatment strategies (interventions) using longitudinal data with time-varying treatments, time-varying confounders, censoring, and competing events.
The interventions can be static or dynamic, and deterministic or stochastic (including threshold interventions). Both prespecified and user-defined interventions are available.
Author: Zhaoxi Cheng [aut],
Jing Li [aut, cre],
Sophia Rein [aut],
Ryan O'Dea [aut],
Sean McGrath [aut],
Lan Wen [aut],
Miguel A. Hernan [aut],
2024 The President and Fellows of Harvard College [cph]
Maintainer: Jing Li <jing_li@hsph.harvard.edu>
Diff between gfoRmulaICE versions 0.1.1 dated 2025-11-05 and 1.1.1 dated 2025-12-14
DESCRIPTION | 14 +-- MD5 | 18 +-- NEWS.md | 17 +++ R/ICE.R | 20 ++-- R/ICE_pool.R | 112 ++++++++++++++++++++++-- R/ICE_stratify.R | 207 ++++++++++++++++++++++++++++++++++++++++++--- R/bootstrap_ice.R | 6 + R/helper.R | 61 ++++++++++--- README.md | 4 tests/testthat/test_plot.R | 6 + 10 files changed, 404 insertions(+), 61 deletions(-)
Title: Find and Fix Lints in R Code
Description: Lints are code patterns that are not optimal because they are
inefficient, forget corner cases, or are less readable. 'flir' provides a
small set of functions to detect those lints and automatically fix them.
It builds on 'astgrepr', which itself uses the 'Rust' crate 'ast-grep' to
parse and navigate R code.
Author: Etienne Bacher [aut, cre, cph],
lintr authors [aut],
Trevor L. Davis [ctb]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between flir versions 0.5.0 dated 2025-06-28 and 0.6.0 dated 2025-12-14
DESCRIPTION | 23 LICENSE | 5 MD5 | 165 NAMESPACE | 4 NEWS.md | 30 R/config.R | 36 R/lint.R | 2 R/linters_factory.R | 72 R/list-linters.R | 9 R/utils.R | 28 README.md | 391 - build/vignette.rds |binary inst/WORDLIST | 57 inst/bench/test.R | 6514 ++++++++++++++--------------- inst/config.yml | 4 inst/doc/adding_rules.html | 3 inst/doc/automatic_fixes.html | 2 inst/doc/sharing_rules.html | 3 inst/doc/tips-and-tricks.R |only inst/doc/tips-and-tricks.Rmd |only inst/doc/tips-and-tricks.html |only inst/rules/builtin/expect_s3_class.yml |only inst/rules/builtin/expect_s4_class.yml |only inst/rules/builtin/expect_type.yml | 170 inst/rules/builtin/nzchar.yml |only inst/rules/builtin/vector_logic.yml |only man/expect_s3_class_linter.Rd |only man/expect_s4_class_linter.Rd |only man/flir-package.Rd | 10 man/lint.Rd | 2 man/list_linters.Rd | 4 man/nzchar_linter.Rd |only man/vector_logic_linter.Rd |only tests/testthat/_snaps/expect_s4_class.md |only tests/testthat/_snaps/expect_type.md | 29 tests/testthat/helpers.R | 242 - tests/testthat/test-T_and_F_symbol.R | 46 tests/testthat/test-any_duplicated.R | 244 - tests/testthat/test-any_is_na.R | 76 tests/testthat/test-assignment_linter.R | 360 - tests/testthat/test-class_equals.R | 160 tests/testthat/test-condition_message.R | 377 - tests/testthat/test-config_yml.R | 48 tests/testthat/test-custom_linters.R | 62 tests/testthat/test-duplicate_argument.R | 585 +- tests/testthat/test-empty_assignment.R | 94 tests/testthat/test-equals_na.R | 148 tests/testthat/test-exclude_linters.R | 33 tests/testthat/test-expect_comparison.R | 112 tests/testthat/test-expect_identical.R | 154 tests/testthat/test-expect_length.R | 136 tests/testthat/test-expect_named.R | 160 tests/testthat/test-expect_not.R | 100 tests/testthat/test-expect_null.R | 146 tests/testthat/test-expect_s3_class.R |only tests/testthat/test-expect_s4_class.R |only tests/testthat/test-expect_true_false.R | 130 tests/testthat/test-expect_type.R | 307 - tests/testthat/test-flint_ignore.R | 14 tests/testthat/test-for_loop_index.R | 77 tests/testthat/test-function_return.R | 182 tests/testthat/test-implicit_assignment.R | 1059 ++-- tests/testthat/test-is_numeric.R | 186 tests/testthat/test-length_levels.R | 32 tests/testthat/test-length_test.R | 76 tests/testthat/test-lengths.R | 116 tests/testthat/test-library_call.R | 543 +- tests/testthat/test-list_comparison.R | 78 tests/testthat/test-literal_coercion.R | 321 - tests/testthat/test-matrix_apply.R | 220 tests/testthat/test-missing_argument.R | 232 - tests/testthat/test-nested_ifelse.R | 128 tests/testthat/test-numeric_leading_zero.R | 68 tests/testthat/test-nzchar.R |only tests/testthat/test-outer_negation.R | 102 tests/testthat/test-package_hooks.R | 610 +- tests/testthat/test-paste.R | 586 +- tests/testthat/test-redundant_equals.R | 104 tests/testthat/test-redundant_ifelse.R | 254 - tests/testthat/test-rep_len.R | 12 tests/testthat/test-sample_int.R | 178 tests/testthat/test-seq.R | 32 tests/testthat/test-sort.R | 254 - tests/testthat/test-stopifnot_all.R | 82 tests/testthat/test-todo_comment.R | 58 tests/testthat/test-undesirable_function.R | 50 tests/testthat/test-undesirable_operator.R | 68 tests/testthat/test-unnecessary_nesting.R | 1621 +++---- tests/testthat/test-unreachable_code.R | 34 tests/testthat/test-vector_logic.R |only tests/testthat/test-which_grepl.R | 84 vignettes/tips-and-tricks.Rmd |only 92 files changed, 9464 insertions(+), 9280 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear algebra functions for sta [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between broadcast versions 0.1.6.1 dated 2025-11-09 and 0.1.7 dated 2025-12-14
broadcast-0.1.6.1/broadcast/inst/tinytest/bc_b/test-bc_b.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-binary_attr_broadcaster.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_d_rel0.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-integer_gcd.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-integer_mod.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_rel_attr/test-binary_attr_broadcaster.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_rel_attr/test-main.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_attr_broadcaster.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_zerolen.R |only broadcast-0.1.7/broadcast/DESCRIPTION | 8 broadcast-0.1.7/broadcast/MD5 | 200 +- broadcast-0.1.7/broadcast/NEWS.md | 33 broadcast-0.1.7/broadcast/R/aaa01_broadcast_operators.R | 28 broadcast-0.1.7/broadcast/R/aaa03_broadcast_bind.R | 30 broadcast-0.1.7/broadcast/R/aaa05_broadcast_typecast.R | 4 broadcast-0.1.7/broadcast/R/acast.R | 9 broadcast-0.1.7/broadcast/R/bc_b.R | 41 broadcast-0.1.7/broadcast/R/bc_bit.R | 8 broadcast-0.1.7/broadcast/R/bc_cplx.R | 6 broadcast-0.1.7/broadcast/R/bc_d.R | 24 broadcast-0.1.7/broadcast/R/bc_i.R | 8 broadcast-0.1.7/broadcast/R/bc_ifelse.R | 8 broadcast-0.1.7/broadcast/R/bc_list.R | 2 broadcast-0.1.7/broadcast/R/bc_raw.R | 4 broadcast-0.1.7/broadcast/R/bc_str.R | 10 broadcast-0.1.7/broadcast/R/bc_strrep.R | 2 broadcast-0.1.7/broadcast/R/bcapply.R | 15 broadcast-0.1.7/broadcast/R/cast_dim2flat.R | 8 broadcast-0.1.7/broadcast/R/cast_dim2hier.R | 2 broadcast-0.1.7/broadcast/R/cast_hier2dim.R | 2 broadcast-0.1.7/broadcast/R/cast_shallow2atomic.R | 30 broadcast-0.1.7/broadcast/R/hier2dim.R | 2 broadcast-0.1.7/broadcast/R/internal_acast_names.R | 2 broadcast-0.1.7/broadcast/R/internal_binary.R | 61 broadcast-0.1.7/broadcast/R/internal_binary_names.R | 23 broadcast-0.1.7/broadcast/R/internal_bind.R | 4 broadcast-0.1.7/broadcast/R/internal_functions.R | 1 broadcast-0.1.7/broadcast/R/internal_hiercast.R | 10 broadcast-0.1.7/broadcast/R/meta_functions.R | 248 ++- broadcast-0.1.7/broadcast/R/overload_relops.R | 10 broadcast-0.1.7/broadcast/R/rep_dim.R | 2 broadcast-0.1.7/broadcast/R/typecast.R | 85 - broadcast-0.1.7/broadcast/R/vector2array.R | 14 broadcast-0.1.7/broadcast/R/zzz.R | 7 broadcast-0.1.7/broadcast/inst/examples/acast.R | 30 broadcast-0.1.7/broadcast/inst/examples/bc_cplx.R | 11 broadcast-0.1.7/broadcast/inst/examples/bc_list.R | 3 broadcast-0.1.7/broadcast/inst/examples/bcapply.R | 40 broadcast-0.1.7/broadcast/inst/examples/bind_array.R | 58 broadcast-0.1.7/broadcast/inst/examples/cast_hier2dim.R | 5 broadcast-0.1.7/broadcast/inst/examples/linear_algebra_stats.R | 3 broadcast-0.1.7/broadcast/inst/tinytest/acast/test-acast-crashtest.R | 100 - broadcast-0.1.7/broadcast/inst/tinytest/acast/test-broadcaster.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_b/test-bc_b-coercion.R | 4 broadcast-0.1.7/broadcast/inst/tinytest/bc_b/test-bc_b_andor.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_b/test-bc_b_rel.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_bytes/test-bc_bit_int.R | 771 +-------- broadcast-0.1.7/broadcast/inst/tinytest/bc_bytes/test-bc_bit_raw.R | 808 +--------- broadcast-0.1.7/broadcast/inst/tinytest/bc_bytes/test-bc_raw_byte.R | 226 -- broadcast-0.1.7/broadcast/inst/tinytest/bc_bytes/test-bc_raw_rel.R | 509 ------ broadcast-0.1.7/broadcast/inst/tinytest/bc_cplx/test-bc_cplx_math.R | 33 broadcast-0.1.7/broadcast/inst/tinytest/bc_cplx/test-bc_cplx_rel.R | 196 -- broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bc_ifelse.R | 57 broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bc_ifelse_attr.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bc_strrep.R | 42 broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bcapply-attr.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bcapply_atomic.R | 455 +---- broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bcapply_default.R | 10 broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bcapply_names_1d.R | 4 broadcast-0.1.7/broadcast/inst/tinytest/bc_general/test-bcapply_names_vector.R | 4 broadcast-0.1.7/broadcast/inst/tinytest/bc_list/test-bc_list.R | 107 - broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-bc_d_dist.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-bc_d_math.R | 34 broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-bc_d_rel.R | 438 ----- broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-bc_i_d.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-bc_i_math.R | 70 broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-bc_i_rel.R | 35 broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-integer_noncircular.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_num/test-integer_overflow.R | 23 broadcast-0.1.7/broadcast/inst/tinytest/bc_rel_attr/test-equneq.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_rel_attr/test-greatersmaller.R |only broadcast-0.1.7/broadcast/inst/tinytest/bc_rel_attr/test-rel_names_1d.R | 4 broadcast-0.1.7/broadcast/inst/tinytest/bc_rel_attr/test-rel_names_vector.R | 4 broadcast-0.1.7/broadcast/inst/tinytest/bc_str/test-bc_str_conc.R | 120 - broadcast-0.1.7/broadcast/inst/tinytest/bc_str/test-bc_str_dist.R | 36 broadcast-0.1.7/broadcast/inst/tinytest/bc_str/test-bc_str_rel.R | 199 -- broadcast-0.1.7/broadcast/inst/tinytest/binary_names/test-1d.R | 7 broadcast-0.1.7/broadcast/inst/tinytest/binary_names/test-vector.R | 4 broadcast-0.1.7/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array_internal.R | 38 broadcast-0.1.7/broadcast/inst/tinytest/class/test-mbroadcasters.R | 22 broadcast-0.1.7/broadcast/inst/tinytest/helper/test-ndim.R | 43 broadcast-0.1.7/broadcast/inst/tinytest/helper/test-undim.R | 10 broadcast-0.1.7/broadcast/inst/tinytest/helper/test-vector2array.R | 9 broadcast-0.1.7/broadcast/inst/tinytest/overload/test-precedence.R | 8 broadcast-0.1.7/broadcast/inst/tinytest/shallow2atomic/test-specialcoercion.R |only broadcast-0.1.7/broadcast/inst/tinytest/typecast/test-broadcasterclass.R | 116 + broadcast-0.1.7/broadcast/man/aaa00_broadcast_help.Rd | 2 broadcast-0.1.7/broadcast/man/aaa01_broadcast_operators.Rd | 28 broadcast-0.1.7/broadcast/man/acast.Rd | 30 broadcast-0.1.7/broadcast/man/bc.b.Rd | 5 broadcast-0.1.7/broadcast/man/bc.cplx.Rd | 11 broadcast-0.1.7/broadcast/man/bc.list.Rd | 3 broadcast-0.1.7/broadcast/man/bcapply.Rd | 44 broadcast-0.1.7/broadcast/man/bind_array.Rd | 85 - broadcast-0.1.7/broadcast/man/cast_hier2dim.Rd | 5 broadcast-0.1.7/broadcast/man/cast_shallow2atomic.Rd | 29 broadcast-0.1.7/broadcast/man/hier2dim.Rd | 5 broadcast-0.1.7/broadcast/man/linear_algebra_stats.Rd | 3 broadcast-0.1.7/broadcast/man/typecast.Rd | 4 broadcast-0.1.7/broadcast/src/broadcast.h | 2 broadcast-0.1.7/broadcast/src/rcpp_bcD_int.cpp | 4 111 files changed, 2217 insertions(+), 3690 deletions(-)
Title: Bayesian QTL Mapping Toolkit
Description: QTL mapping toolkit for inbred crosses and recombinant
inbred lines. Includes maximum likelihood and Bayesian tools.
Author: Charles C. Berry [aut, cre]
Maintainer: Charles C. Berry <cberry@ucsd.edu>
Diff between bqtl versions 1.0-38 dated 2024-09-24 and 1.0-39 dated 2025-12-14
CHANGES | 8 +++++++- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/lapadj.h | 6 +++--- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: Variogram Diagnostics
Description: Interactive variogram diagnostics.
Author: Ernst Glatzer [aut],
Edzer Pebesma [cre]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between vardiag versions 0.2-1 dated 2015-07-08 and 0.2-2 dated 2025-12-14
DESCRIPTION | 21 +++++++++++++++------ MD5 | 2 +- 2 files changed, 16 insertions(+), 7 deletions(-)
Title: Easily Build Command Line Applications
Description: Run simple 'R' scripts as command line applications, with
automatic robust and convenient support for command line arguments.
This package provides 'Rapp', an alternative 'R' front-end similar to
'Rscript', that enables this.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between Rapp versions 0.2.0 dated 2024-07-15 and 0.3.0 dated 2025-12-14
DESCRIPTION | 12 MD5 | 58 ++- NAMESPACE | 2 NEWS.md | 27 + R/app.R | 293 ++++++++++++++---- R/args.R | 299 +++++++++---------- R/help.R |only R/install.R | 517 +++++++++++++++++++++++++++++++++ R/utils.R | 64 +++- R/yaml.R | 32 +- README.md | 452 ++++++++++++++++++++++++---- inst/add-path-entry.ps1 |only inst/examples/flip-coin.R | 28 + inst/examples/install-pkg.R | 12 inst/examples/magic-8-ball.R | 4 inst/examples/todo.R |only inst/examples/unique.R | 14 man/install_pkg_cli_apps.Rd |only man/run.Rd | 8 tests/testthat/_snaps |only tests/testthat/apps |only tests/testthat/helpers.R | 148 +++++++++ tests/testthat/test-basics.R | 42 ++ tests/testthat/test-help-annotations.R |only tests/testthat/test-help-snapshots.R |only tests/testthat/test-install.R |only tests/testthat/test-kitchen-sink.R |only tests/testthat/test-multi-options.R |only tests/testthat/test-regressions.R |only tests/testthat/test-required.R |only tests/testthat/test-run.R |only tests/testthat/test-subcommands.R |only tests/testthat/test-todo.R |only 33 files changed, 1634 insertions(+), 378 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple
rectangular data. The 'rtables' package provides a framework for
declaring complex multi-level tabulations and then applying them to
data. This framework models both tabulation and the resulting tables
as hierarchical, tree-like objects which support sibling sub-tables,
arbitrary splitting or grouping of data in row and column dimensions,
cells containing multiple values, and the concept of contextual
summary computations. A convenient pipe-able interface is provided for
declaring table layouts and the corresponding computations, and then
applying them to data.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables versions 0.6.14 dated 2025-11-18 and 0.6.15 dated 2025-12-14
DESCRIPTION | 17 MD5 | 121 NAMESPACE | 2 NEWS.md | 6 R/00tabletrees.R | 4271 +++++++------- R/argument_conventions.R | 498 - R/as_html.R | 7 R/colby_constructors.R | 4451 +++++++-------- R/format_rcell.R | 10 R/tree_accessors.R | 9327 ++++++++++++++++---------------- R/tt_afun_utils.R | 8 R/tt_as_df.R | 7 R/tt_compatibility.R | 22 R/tt_dotabulation.R | 4378 +++++++-------- R/tt_paginate.R | 6 R/tt_pos_and_access.R | 28 R/tt_toString.R | 27 inst/WORDLIST | 230 inst/doc/advanced_usage.html | 4 inst/doc/ard_how_to.html | 4 inst/doc/baseline.html | 4 inst/doc/clinical_trials.html | 4 inst/doc/col_counts.html | 4 inst/doc/custom_appearance.html | 4 inst/doc/example_analysis_coxreg.html | 4 inst/doc/exploratory_analysis.html | 6 inst/doc/format_precedence.html | 4 inst/doc/introspecting_tables.html | 4 inst/doc/manual_table_construction.html | 4 inst/doc/pathing.html | 4 inst/doc/rtables.html | 4 inst/doc/sorting_pruning.html | 8 inst/doc/split_functions.html | 4 inst/doc/subsetting_tables.html | 4 inst/doc/tabulation_dplyr.html | 4 inst/doc/title_footer.html | 4 man/CellValue.Rd | 6 man/analyze.Rd | 340 - man/as_html.Rd | 6 man/avarspl.Rd | 270 man/basic_table.Rd | 6 man/build_table.Rd | 5 man/data.frame_export.Rd | 4 man/format_rcell.Rd | 7 man/formatters_methods.Rd | 30 man/gen_args.Rd | 4 man/gfc.Rd | 15 man/int_methods.Rd | 2678 ++++----- man/lyt_args.Rd | 422 - man/matrix_form-VTableTree-method.Rd | 7 man/rcell.Rd | 6 man/rowclasses.Rd | 9 man/rrow.Rd | 12 man/rrowl.Rd | 12 man/rtable.Rd | 12 man/tabclasses.Rd | 9 man/tostring.Rd | 8 tests/testthat/setup-fakedata.R | 111 tests/testthat/test-lyt-tabulation.R | 4091 +++++++------- tests/testthat/test-printing.R | 233 tests/testthat/test-round_type.R |only tests/testthat/test-subset-access.R | 194 62 files changed, 16674 insertions(+), 15317 deletions(-)
Title: Download and Process Public Domain Works from Project Gutenberg
Description: Download and process public domain works in the Project
Gutenberg collection <https://www.gutenberg.org/>. Includes metadata
for all Project Gutenberg works, so that they can be searched and
retrieved.
Author: Jon Harmon [aut, cre] ,
Myfanwy Johnston [aut],
Jordan Bradford [aut] ,
David Robinson [aut, cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between gutenbergr versions 0.3.0 dated 2025-05-29 and 0.3.1 dated 2025-12-14
DESCRIPTION | 8 - MD5 | 57 +++++----- NAMESPACE | 2 NEWS.md | 152 +++++++++++++------------- R/data.R | 2 R/gutenberg_download.R | 12 +- R/gutenberg_mirrors.R | 36 +++--- R/gutenberg_strip.R | 3 R/gutenberg_works.R | 41 +++---- R/gutenbergr-package.R | 2 R/utils.R | 15 +- README.md | 5 build/vignette.rds |binary data/gutenberg_authors.rda |binary data/gutenberg_languages.rda |binary data/gutenberg_metadata.rda |binary data/gutenberg_subjects.rda |binary data/sample_books.rda |binary inst/WORDLIST |only inst/doc/gutenbergr.html | 126 +++++++++++----------- man/gutenberg_download.Rd | 126 +++++++++++----------- man/gutenberg_get_all_mirrors.Rd | 74 ++++++------- man/gutenberg_get_mirror.Rd | 50 ++++---- man/gutenberg_metadata.Rd | 4 man/gutenberg_strip.Rd | 70 ++++++------ man/gutenberg_subjects.Rd | 138 ++++++++++++------------ man/gutenberg_works.Rd | 182 ++++++++++++++++---------------- tests/testthat/test-data.R | 53 +++++++++ tests/testthat/test-gutenberg_mirrors.R | 26 ++-- tests/testthat/test-gutenberg_works.R | 5 30 files changed, 635 insertions(+), 554 deletions(-)
Title: Ecological Niche Modeling using Presence-Absence Data
Description: A set of tools to perform Ecological Niche Modeling with
presence-absence data. It includes algorithms for data partitioning,
model fitting, calibration, evaluation, selection, and prediction.
Other functions help to explore signals of ecological niche using univariate
and multivariate analyses, and model features such as variable response
curves and variable importance. Unique characteristics of this package are
the ability to exclude models with concave quadratic responses, and the
option to clamp model predictions to specific variables. These tools are
implemented following principles proposed in
Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>,
Cobos et al., (2019) <doi:10.7717/peerj.6281>,
and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.
Author: Luis F. Arias-Giraldo [aut, cre] ,
Marlon E. Cobos [aut] ,
A. Townsend Peterson [ctb]
Maintainer: Luis F. Arias-Giraldo <lfarias.giraldo@gmail.com>
Diff between enmpa versions 0.2.1 dated 2025-06-12 and 0.2.2 dated 2025-12-14
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NEWS.md | 6 ++ R/response_curve.R | 33 ++++++++------ R/short_helpers.R | 116 +++++++++++++++++++++++++++----------------------- man/response_curve.Rd | 14 +++--- 6 files changed, 108 insertions(+), 81 deletions(-)
More information about CrownScorchTLS at CRAN
Permanent link
Title: Trajectory Miner: a Sequence Analysis Toolkit
Description: Set of sequence analysis tools for manipulating, describing and rendering categorical sequences, and more generally mining sequence data in the field of social sciences. Although this sequence analysis package is primarily intended for state or event sequences that describe time use or life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent event subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] ,
Nicolas Mueller [aut],
Reto Buergin [aut] ,
Pierre-Alexandre Fonta [ctb],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.2-12 dated 2025-06-29 and 2.2-13 dated 2025-12-14
DESCRIPTION | 8 MD5 | 58 ++--- NEWS | 28 ++ R/dissrf.R | 368 ++++++++++++++++++---------------- R/plot.stslist.R | 61 ++++- R/stslist-methods.R | 7 build/partial.rdb |binary build/vignette.rds |binary data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/NEWS.Rd | 42 +++ inst/doc/TraMineR-state-sequence.Rnw | 30 +- inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 man/actcal.Rd | 12 + man/actcal.tse.Rd | 1 man/bfspell.Rd | 1 man/biofam.Rd | 17 + man/disscenter.Rd | 4 man/disstree-assign.Rd | 2 man/disstree-get-rules.Rd | 2 man/disstreeleaf.Rd | 2 man/ex1.Rd | 3 man/ex2.Rd | 1 man/famform.Rd | 10 man/mvad.Rd | 18 + man/plot.stslist.Rd | 33 ++- man/seqmeant.Rd | 4 vignettes/TraMineR-state-sequence.Rnw | 30 +- 30 files changed, 480 insertions(+), 264 deletions(-)
Title: Handle Ambiguity of Protein Identifications from Shotgun
Proteomics
Description: In shotgun proteomics, shared peptides (i.e., peptides that might
originate from different proteins sharing homology, from different
proteoforms due to alternative mRNA splicing, post-translational
modifications, proteolytic cleavages, and/or allelic variants) represent a
major source of ambiguity in protein identifications. The 'net4pg' package
allows to assess and handle ambiguity of protein identifications. It
implements methods for two main applications. First, it allows to represent
and quantify ambiguity of protein identifications by means of graph
connected components (CCs). In graph theory, CCs are defined as the largest
subgraphs in which any two vertices are connected to each other by a path
and not connected to any other of the vertices in the supergraph. Here,
proteins sharing one or more peptides are thus gathered in the same CC
(multi-protein CC), while unambiguous protein identifications constitute CCs
with a single protein vertex (single-protein CCs). Therefore, the pro [...truncated...]
Author: Laura Fancello [aut, cre] ,
Thomas Burger [aut, ctb]
Maintainer: Laura Fancello <laura.fancello@gmail.com>
Diff between net4pg versions 0.1.1 dated 2022-09-07 and 0.1.2 dated 2025-12-14
DESCRIPTION | 14 MD5 | 19 R/net4pg-package.R |only R/plot_cc.R | 377 ++--- build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 5 inst/doc/Intro_To_net4pg.R | 664 ++++----- inst/doc/Intro_To_net4pg.html | 2948 ++++++++++++++++++++---------------------- man/net4pg-package.Rd |only man/plot_cc.Rd | 54 man/transcriptome_filter.Rd | 2 12 files changed, 2040 insertions(+), 2043 deletions(-)
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] ,
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut] ,
Mattan S. Ben-Shachar [aut],
Soeren Hoejsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathon Love [ctb],
Russell Lenth [ctb],
Rune [...truncated...]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between afex versions 1.5-0 dated 2025-08-24 and 1.5-1 dated 2025-12-14
DESCRIPTION | 10 MD5 | 38 +- NEWS | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/afex_analysing_accuracy_data.html | 11 inst/doc/afex_anova_example.html | 117 ++++---- inst/doc/afex_mixed_example.Rmd | 2 inst/doc/afex_mixed_example.html | 39 +- inst/doc/afex_plot_introduction.R | 103 ++++--- inst/doc/afex_plot_introduction.Rmd | 96 ++++-- inst/doc/afex_plot_introduction.html | 173 +++++++----- inst/doc/afex_plot_supported_models.R | 2 inst/doc/afex_plot_supported_models.Rmd | 2 inst/doc/afex_plot_supported_models.html | 399 ++++++++++++++--------------- inst/doc/assumptions_of_ANOVAs.html | 9 inst/doc/introduction-mixed-models.pdf |binary vignettes/afex_mixed_example.Rmd | 2 vignettes/afex_plot_introduction.Rmd | 96 ++++-- vignettes/afex_plot_supported_models.Rmd | 2 20 files changed, 602 insertions(+), 501 deletions(-)
Title: Marker Gene Detection via Penalized Principal Component Analysis
Description: Implementation of the 'MarkerPen' algorithm, short for marker gene detection
via penalized principal component analysis, described in the paper by Qiu, Wang, Lei,
and Roeder (2021, <doi:10.1093/bioinformatics/btab257>). 'MarkerPen' is a semi-supervised
algorithm for detecting marker genes by combining prior marker information with bulk
transcriptome data.
Author: Yixuan Qiu [aut, cre],
Jiebiao Wang [aut],
Jing Lei [aut],
Kathryn Roeder [aut]
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between markerpen versions 0.1.1 dated 2021-03-16 and 0.1.2 dated 2025-12-14
DESCRIPTION | 29 ++- MD5 | 26 +-- README.md | 23 +-- build/vignette.rds |binary inst/NEWS.Rd | 14 + inst/doc/introduction.R | 62 ++++---- inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 329 +++++++++++++++++++++---------------------- src/Makevars | 2 src/RcppExports.cpp | 5 src/inceig_tridiag_spectra.h | 26 ++- src/pca_pen.cpp | 21 ++ src/tridiag.h | 3 vignettes/introduction.Rmd | 2 14 files changed, 306 insertions(+), 238 deletions(-)
Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins [aut, cre] ,
Bob Rudis [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.5.6 dated 2023-09-30 and 2.6.0 dated 2025-12-14
DESCRIPTION | 20 MD5 | 67 +- NAMESPACE | 3 NEWS.md | 14 R/a-rect.R | 2 R/geom_treemap.R | 24 - R/geom_treemap_text.R | 6 R/treemap_fixed.R | 11 R/treemap_squarified.R | 8 R/treemapify-package.R |only R/treemapify.R | 34 - R/utils.R | 7 README.md | 6 build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/introduction-to-treemapify.html | 15 man/figures/README-complex_treemap-1.png |binary man/figures/animated_treemap.gif |binary man/geom_treemap.Rd | 2 man/treemapify-ggproto.Rd |only man/treemapify-package.Rd |only man/treemapify.Rd | 2 tests/testthat/_snaps/plots/basic-treemap.svg | 18 tests/testthat/_snaps/plots/chequer-pattern-fill.svg |only tests/testthat/_snaps/plots/colour-is-drawn-correctly-in-legend.svg | 60 +- tests/testthat/_snaps/plots/correct-colours-for-subgroup-text-differently.svg | 18 tests/testthat/_snaps/plots/correct-colours-for-subgroup-text.svg | 18 tests/testthat/_snaps/plots/fixed-layout.svg | 18 tests/testthat/_snaps/plots/lineargradient-fills.svg |only tests/testthat/_snaps/plots/scol-layout.svg | 18 tests/testthat/_snaps/plots/squarified-layout-starting-from-top-right.svg | 18 tests/testthat/_snaps/plots/srow-layout-starting-from-bottom-right-with-subgroups.svg | 18 tests/testthat/_snaps/plots/srow-layout.svg | 18 tests/testthat/_snaps/plots/understands-variants-of-centre.svg | 18 tests/testthat/test_layout_functions.R | 7 tests/testthat/test_plots.R | 226 ++++++++-- tests/testthat/test_treemapify.R | 5 37 files changed, 453 insertions(+), 234 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut] ,
Rong Wei Sun [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.3.1 dated 2025-08-22 and 0.3.2 dated 2025-12-14
DESCRIPTION | 8 +- MD5 | 42 +++++++------ NEWS.md | 31 +++++++++ R/cond_indirect.R | 54 +++++++++++++--- R/cond_indirect_diff.R | 67 ++++++++++++++++----- R/cond_indirect_effects_math.R | 35 +++++++++- R/delta_med.R | 24 +++++-- R/find_product.R | 4 - R/index_mome.R | 49 ++++++++++++--- R/print_indirect_list.R | 6 + README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mod_levels.html | 6 - inst/extdata/mi_test_data.RData |binary man/cond_indirect.Rd | 10 ++- tests/testthat/test_est2p_mc_1.R |only tests/testthat/test_est2p_mc_2.R |only tests/testthat/test_est2p_min_size_1.R |only tests/testthat/test_est2p_min_size_2.R |only tests/testthat/test_fit2boot_out_do_boot_missing.R | 2 tests/testthat/test_q_fct_mediation_plot_sem.R | 2 tests/testthat/test_skip_ci_mc_1.R |only tests/testthat/test_skip_ci_mc_2.R |only tests/testthat/test_skip_ci_min_size_1.R |only tests/testthat/test_skip_ci_min_size_2.R |only 26 files changed, 263 insertions(+), 79 deletions(-)
Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for
Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between DR.SC versions 3.6 dated 2025-10-03 and 3.7 dated 2025-12-14
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/main.R | 6 +++--- README.md | 2 ++ inst/doc/DR.SC.DLPFC.html | 4 ++-- inst/doc/DR.SC.Simu.html | 4 ++-- man/DR.SC.fit.Rd | 4 ++-- man/selectModel.Rd | 2 +- 8 files changed, 24 insertions(+), 22 deletions(-)
Title: Drag-and-Drop in 'shiny' Apps with 'SortableJS'
Description: Enables drag-and-drop behaviour in Shiny apps, by exposing
the functionality of the 'SortableJS'
<https://sortablejs.github.io/Sortable/> JavaScript library as an
'htmlwidget'. You can use this in Shiny apps and widgets, 'learnr'
tutorials as well as R Markdown. In addition, provides a custom
'learnr' question type - 'question_rank()' - that allows ranking
questions with drag-and-drop.
Author: Andrie de Vries [cre, aut],
Barret Schloerke [aut],
Kenton Russell [aut, ccp] ,
Posit [cph, fnd],
Lebedev Konstantin [cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between sortable versions 0.5.0 dated 2023-03-26 and 0.6.0 dated 2025-12-14
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Title: Probabilistic Factor Analysis for Spatially-Aware Dimension
Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations.
More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre],
Xiao Zhang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between ProFAST versions 1.6 dated 2025-03-27 and 1.7 dated 2025-12-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/CoFAST.R | 16 ++++++++-------- R/main.R | 16 ++++++++-------- README.md | 2 ++ inst/doc/CosMx.html | 4 ++-- inst/doc/FASTdlpfc.html | 4 ++-- inst/doc/FASTdlpfc2.html | 4 ++-- inst/doc/FASTsimu.html | 4 ++-- inst/doc/pbmc3k.html | 4 ++-- 10 files changed, 41 insertions(+), 39 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.5.0 dated 2025-11-07 and 1.5.1 dated 2025-12-14
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 14 +++++++++----- R/TunerBatchCmaes.R | 3 +++ R/TunerBatchGenSA.R | 32 +++++++++++++++++++++++++++++++- R/TunerBatchInternal.R | 5 ++++- R/TunerBatchIrace.R | 4 +++- R/TunerBatchNLoptr.R | 4 +++- R/mlr_callbacks.R | 5 +++-- build/partial.rdb |binary build/vignette.rds |binary man/mlr3tuning.asnyc_mlflow.Rd | 6 +++--- man/mlr_tuners_cmaes.Rd | 3 +++ man/mlr_tuners_gensa.Rd | 10 +++++++--- man/mlr_tuners_internal.Rd | 5 +++-- man/mlr_tuners_irace.Rd | 4 +++- man/mlr_tuners_nloptr.Rd | 4 +++- 17 files changed, 99 insertions(+), 42 deletions(-)
Title: Seasonal Adjustment of Weekly Data
Description: Perform seasonal adjustment and forecasting of weekly data.
The package provides a user-friendly interface for computing seasonally
adjusted estimates and forecasts of weekly time series and includes
functions for the construction of country-specific prior adjustment
variables, as well as diagnostic tools to assess the quality of the
adjustments. The methodology is described in more detail in
Ginker (2024) <doi:10.13140/RG.2.2.12221.44000>.
Author: Tim Ginker [aut, cre, cph] ,
Jon Lachman [ctb]
Maintainer: Tim Ginker <tim.ginker@gmail.com>
Diff between boiwsa versions 1.1.3 dated 2025-02-05 and 1.1.4 dated 2025-12-14
DESCRIPTION | 19 +++-- MD5 | 37 +++++---- NEWS.md | 4 + R/boiwsa.R | 58 ++++++++++----- R/find_opt.R | 32 +++++--- R/find_outliers.R | 49 +++++++++---- R/fourier_vars.R | 192 ++++++++++++++++++++++++++------------------------- R/genhol.R | 164 ++++++++++++++++++++++++------------------- R/my_ao.R | 103 ++++++++++++++------------- R/plot_spec.R | 93 +++++++++++++----------- R/simple_td.R | 150 +++++++++++++++++++++------------------ inst |only man/boiwsa.Rd | 60 +++++++++------ man/find_opt.Rd | 32 +++++--- man/find_outliers.Rd | 45 ++++++++--- man/fourier_vars.Rd | 21 +++-- man/genhol.Rd | 37 +++++++-- man/my_ao.Rd | 18 +++- man/plot_spec.Rd | 15 ++- man/simple_td.Rd | 21 ++++- 20 files changed, 679 insertions(+), 471 deletions(-)
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided. As of release 1.84.0-0, the following Boost libraries are
included: 'accumulators' 'algorithm' 'align' 'any' 'atomic' 'beast'
'bimap' 'bind' 'circular_buffer' 'compute' 'concept' 'config'
'container' 'date_time' 'detail' 'dynamic_bitset' 'exception'
'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap'
'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams'
'iterator' 'lambda2' 'math' 'move' 'mp11' 'mpl' 'multiprecision'
'numeric' 'pending' 'phoenix' 'polygon' 'preprocessor' 'process'
'propery_tree' 'qvm' 'rando [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
John W. Emerson [aut],
Michael J. Kane [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.87.0-1 dated 2024-12-17 and 1.90.0-1 dated 2025-12-14
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BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/select_rings.hpp | 16 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/self_turn_points.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/stream_info.hpp | 1 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/traversal_info.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/traverse.hpp | 55 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/turn_info.hpp | 28 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/overlay/turn_operation_id.hpp |only BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/partition.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/point_is_spike_or_equal.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/point_on_border.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/position_code.hpp |only BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/areal_areal.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/boundary_checker.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/follow_helpers.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/implementation_gc.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/interface.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/linear_areal.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/multi_point_geometry.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/point_point.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/relate_impl.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/topology_check.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relate/turns.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/relation/interface.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/sections/range_by_section.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/sections/section_functions.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/sections/sectionalize.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/select_geometry_type.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/sub_range.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/touches/implementation.hpp | 24 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/touches/interface.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/tupled_output.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/visit.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/within/interface.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/detail/within/point_in_geometry.hpp | 9 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/difference.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/discrete_frechet_distance.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/discrete_hausdorff_distance.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/envelope.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/expand.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/is_simple.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/dispatch/is_valid.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/for_each.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/is_convex.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/is_empty.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/length.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/line_interpolate.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/make.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/merge_elements.hpp | 16 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/num_interior_rings.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/num_points.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/num_segments.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/perimeter.hpp | 12 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/point_on_surface.hpp | 14 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/remove_spikes.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/reverse.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/simplify.hpp | 24 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/sym_difference.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/transform.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/union.hpp | 14 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/unique.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/algorithms/validity_failure_type.hpp | 24 BH-1.90.0-1/BH/inst/include/boost/geometry/arithmetic/arithmetic.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/arithmetic/determinant.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/arithmetic/infinite_line_functions.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/arithmetic/normalize.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/geometry/core/access.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/core/closure.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/core/config.hpp | 14 BH-1.90.0-1/BH/inst/include/boost/geometry/core/coordinate_promotion.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/core/coordinate_system.hpp | 27 BH-1.90.0-1/BH/inst/include/boost/geometry/core/cs.hpp | 30 BH-1.90.0-1/BH/inst/include/boost/geometry/core/exception.hpp | 25 BH-1.90.0-1/BH/inst/include/boost/geometry/core/exterior_ring.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/core/geometry_id.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/core/geometry_types.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/core/interior_rings.hpp | 13 BH-1.90.0-1/BH/inst/include/boost/geometry/core/interior_type.hpp | 32 BH-1.90.0-1/BH/inst/include/boost/geometry/core/point_type.hpp | 49 BH-1.90.0-1/BH/inst/include/boost/geometry/core/radian_access.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/core/ring_type.hpp | 48 BH-1.90.0-1/BH/inst/include/boost/geometry/core/tag.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/core/tags.hpp | 9 BH-1.90.0-1/BH/inst/include/boost/geometry/core/topological_dimension.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/authalic_radius_sqr.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/eccentricity_sqr.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/flattening.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/geographic.hpp | 26 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/mean_radius.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/meridian_inverse.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/quarter_meridian.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/sjoberg_intersection.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/spherical.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/formulas/vincenty_inverse.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_array.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_fusion.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_polygon/box.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_polygon/point.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_polygon/polygon.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_polygon/ring.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_polygon/ring_proxy.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_range/adjacent_filtered.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_range/filtered.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_range/reversed.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_range/sliced.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_range/strided.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_range/uniqued.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/boost_tuple.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/c_array.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/std_array.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/adapted/std_pair_as_segment.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/box.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/concepts/check.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/concepts/concept_type.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/concepts/geometry_collection_concept.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/concepts/point_concept.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/concepts/polyhedral_surface_concept.hpp |only BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/geometries.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/helper_geometry.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/linestring.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/multi_linestring.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/multi_point.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/multi_polygon.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/point.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/point_xy.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/point_xyz.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/pointing_segment.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/polygon.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/polyhedral_surface.hpp |only BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/box.hpp | 22 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/linestring.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/multi_linestring.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/multi_point.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/multi_polygon.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/point.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/ring.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/register/segment.hpp | 20 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/ring.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/geometries/segment.hpp | 12 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/bounds.hpp | 33 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/comparable_distance_centroid.hpp | 19 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/comparable_distance_far.hpp | 19 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/comparable_distance_near.hpp | 21 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/content.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/is_valid.hpp | 3 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/margin.hpp | 11 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/minmaxdist.hpp | 17 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/path_intersection.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/algorithms/segment_intersection.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/bounded_view.hpp | 24 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/is_bounding_geometry.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/is_indexable.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/predicates.hpp | 60 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/iterators.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/linear/redistribute_elements.hpp | 46 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/pack_create.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/quadratic/redistribute_elements.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/query_iterators.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/rstar/choose_next_node.hpp | 22 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/rstar/redistribute_elements.hpp | 88 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/utilities/gl_draw.hpp | 29 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/utilities/print.hpp | 9 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/visitors/insert.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/visitors/iterator.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/visitors/remove.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/rtree/visitors/spatial_query.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/serialization.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/index/detail/utilities.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/index/equal_to.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/index/indexable.hpp | 12 BH-1.90.0-1/BH/inst/include/boost/geometry/index/rtree.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/io/dsv/write.hpp | 46 BH-1.90.0-1/BH/inst/include/boost/geometry/io/io.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/io/svg/svg_mapper.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/io/svg/write.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/io/wkt/detail/prefix.hpp | 5 BH-1.90.0-1/BH/inst/include/boost/geometry/io/wkt/read.hpp | 62 BH-1.90.0-1/BH/inst/include/boost/geometry/io/wkt/write.hpp | 41 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/detail/point_iterator/inner_range_type.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/detail/point_iterator/iterator_type.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/detail/point_iterator/value_type.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/detail/segment_iterator/iterator_type.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/detail/segment_iterator/value_type.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/dispatch/point_iterator.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/iterators/dispatch/segment_iterator.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/policies/robustness/segment_ratio.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projection.hpp | 15 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/code.hpp | 91 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/dpar.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/epsg.hpp | 8744 +++++----- BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/esri.hpp | 909 - BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/iau2000.hpp | 4774 ++--- BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/impl/pj_ell_set.hpp | 8 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/impl/pj_transform.hpp | 60 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/projections/proj/imw_p.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/srs/transformation.hpp | 26 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/agnostic/point_in_poly_winding.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/area/services.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/azimuth/services.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/buffer/services.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/buffer_end_round.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/buffer_join_miter.hpp | 7 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/buffer_join_round.hpp | 14 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BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/distance_segment_box.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/intersection.hpp | 24 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/line_interpolate.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/point_in_point.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/point_in_poly_crossings_multiply.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/point_in_poly_winding.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/side_3d_rounded_input.hpp |only BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/cartesian/side_rounded_input.hpp | 45 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/centroid/cartesian.hpp | 18 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/centroid/geographic.hpp | 41 BH-1.90.0-1/BH/inst/include/boost/geometry/strategies/centroid/services.hpp | 2 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BH-1.90.0-1/BH/inst/include/boost/url/rfc/absolute_uri_rule.hpp | 38 BH-1.90.0-1/BH/inst/include/boost/url/rfc/authority_rule.hpp | 33 BH-1.90.0-1/BH/inst/include/boost/url/rfc/ipv4_address_rule.hpp | 40 BH-1.90.0-1/BH/inst/include/boost/url/rfc/ipv6_address_rule.hpp | 48 BH-1.90.0-1/BH/inst/include/boost/url/rfc/origin_form_rule.hpp | 39 BH-1.90.0-1/BH/inst/include/boost/url/rfc/pct_encoded_rule.hpp | 63 BH-1.90.0-1/BH/inst/include/boost/url/rfc/query_rule.hpp | 43 BH-1.90.0-1/BH/inst/include/boost/url/rfc/relative_ref_rule.hpp | 32 BH-1.90.0-1/BH/inst/include/boost/url/rfc/uri_reference_rule.hpp | 35 BH-1.90.0-1/BH/inst/include/boost/url/rfc/uri_rule.hpp | 32 BH-1.90.0-1/BH/inst/include/boost/url/segments_base.hpp | 46 BH-1.90.0-1/BH/inst/include/boost/url/segments_encoded_base.hpp | 49 BH-1.90.0-1/BH/inst/include/boost/url/segments_encoded_ref.hpp | 40 BH-1.90.0-1/BH/inst/include/boost/url/segments_encoded_view.hpp | 104 BH-1.90.0-1/BH/inst/include/boost/url/segments_ref.hpp | 34 BH-1.90.0-1/BH/inst/include/boost/url/segments_view.hpp | 72 BH-1.90.0-1/BH/inst/include/boost/url/static_url.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/url/url.hpp | 10 BH-1.90.0-1/BH/inst/include/boost/url/url_base.hpp | 329 BH-1.90.0-1/BH/inst/include/boost/url/url_view.hpp | 16 BH-1.90.0-1/BH/inst/include/boost/url/url_view_base.hpp | 358 BH-1.90.0-1/BH/inst/include/boost/uuid.hpp | 3 BH-1.90.0-1/BH/inst/include/boost/uuid/basic_random_generator.hpp | 39 BH-1.90.0-1/BH/inst/include/boost/uuid/constants.hpp |only BH-1.90.0-1/BH/inst/include/boost/uuid/detail/nil_uuid.hpp |only BH-1.90.0-1/BH/inst/include/boost/uuid/detail/uuid_x86.ipp | 2 BH-1.90.0-1/BH/inst/include/boost/uuid/entropy_error.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/uuid/generators.hpp |only BH-1.90.0-1/BH/inst/include/boost/uuid/namespaces.hpp | 21 BH-1.90.0-1/BH/inst/include/boost/uuid/nil_generator.hpp | 6 BH-1.90.0-1/BH/inst/include/boost/uuid/string_generator.hpp | 161 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BH-1.90.0-1/BH/inst/include/boost/variant/recursive_wrapper_fwd.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/variant/variant.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/variant/variant_fwd.hpp | 2 BH-1.90.0-1/BH/inst/include/boost/variant2/variant.hpp | 206 BH-1.90.0-1/BH/inst/include/boost/version.hpp | 4 BH-1.90.0-1/BH/inst/include/boost/winapi/condition_variable.hpp | 67 BH-1.90.0-1/BH/inst/include/boost/winapi/critical_section.hpp | 47 BH-1.90.0-1/BH/inst/include/boost/winapi/handles.hpp | 16 BH-1.90.0-1/BH/inst/include/boost/winapi/srw_lock.hpp | 58 2025 files changed, 44932 insertions(+), 43872 deletions(-)
Title: Spectrally Deconfounded Models
Description: Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.1080/10618600.2025.2569602>).
Author: Markus Ulmer [aut, cre, cph] ,
Cyrill Scheidegger [aut]
Maintainer: Markus Ulmer <markus.ulmer@stat.math.ethz.ch>
Diff between SDModels versions 2.0.0 dated 2025-12-04 and 2.0.2 dated 2025-12-14
DESCRIPTION | 15 -- MD5 | 56 +++---- NEWS.md | 10 + R/SDAM.R | 85 ++++++++--- R/SDForest.R | 57 +++---- R/SDTree.R | 249 ---------------------------------- R/partDependence.R | 41 +++-- R/paths.R | 48 +++++- R/plot.R | 42 +++-- R/predict.R | 32 +--- R/utility.R | 266 ++++++++++++++++++++++++++++++++++++- README.md | 12 - build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 12 + inst/doc/Runtime.R | 17 ++ inst/doc/Runtime.Rmd | 27 ++- inst/doc/Runtime.html | 56 ++++--- man/SDAM.Rd | 11 - man/SDForest.Rd | 11 + man/partDependence.Rd | 17 +- man/plot.SDForest.Rd | 5 man/predict.SDForest.Rd | 10 - man/regPath.SDForest.Rd | 18 ++ man/stabilitySelection.SDForest.Rd | 5 tests/testthat/test-parallel.R | 2 tests/testthat/test-tree.R | 10 + tests/testthat/test_OneForest.R | 10 + vignettes/Runtime.Rmd | 27 ++- 29 files changed, 686 insertions(+), 465 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre] ,
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
Rishi Kumar Tyagi [aut],
ICAR-NBGPR [cph] ,
Maurice Aubrey [ctb] ,
Kevin Atkinson [ctb] ,
Lawrence Philips [ctb]
Maintainer: J. Aravind <j.aravind@icar.org.in>
Diff between PGRdup versions 0.2.3.9 dated 2023-08-31 and 0.2.4.0 dated 2025-12-14
DESCRIPTION | 20 ++-- MD5 | 75 +++++++-------- R/AddProbDup.R | 2 R/DataClean.R | 2 R/DisProbDup.R | 2 R/DoubleMetaphone.R | 2 R/GN1000.R | 29 ++--- R/KWCounts.R | 2 R/KWIC.R | 2 R/MergeKW.R | 2 R/MergeProbDup.R | 2 R/PGRdup-package.R | 14 +- R/ParseProbDup.R | 2 R/ProbDup.R | 4 R/ReconstructProbDup.R | 2 R/ReviewProbDup.R | 4 R/SplitProbDup.R | 2 R/ValidatePrimKey.R | 4 R/ViewProbDup.R | 4 R/globals.R | 2 R/print.KWIC.R | 2 R/print.ProbDup.R | 2 R/read.genesys.R | 2 R/xtra.R | 2 README.md | 43 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/Introduction.Rmd | 16 ++- inst/doc/Introduction.pdf |binary inst/extdata/PGRdup_v1.svg |only inst/extdata/PGRdup_v2.svg |only inst/pkgdown.yml |only man/GN1000.Rd | 53 +++++----- man/KWIC.Rd | 210 +++++++++++++++++++++--------------------- man/PGRdup-package.Rd | 21 +++- man/ProbDup.Rd | 2 man/ReviewProbDup.Rd | 2 vignettes/Introduction.Rmd | 16 ++- vignettes/bibliography.bibtex | 16 +-- 40 files changed, 297 insertions(+), 270 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>
Diff between hdf5lib versions 2.0.0.2 dated 2025-12-02 and 2.0.0.3 dated 2025-12-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ R/flags.r | 30 ++++++++++++++++++------------ README.md | 2 ++ configure | 33 ++++++++++++++++++++++++--------- man/c_flags.Rd | 13 +++++++------ man/ld_flags.Rd | 8 +++----- src/hdf5-2.0.0.tar.gz |binary 9 files changed, 73 insertions(+), 43 deletions(-)
Title: Seed Germination Indices and Curve Fitting
Description: Provides functions to compute various germination indices
such as germinability, median germination time, mean germination time,
mean germination rate, speed of germination, Timson's index,
germination value, coefficient of uniformity of germination,
uncertainty of germination process, synchrony of germination etc. from
germination count data. Includes functions for fitting cumulative seed
germination curves using four-parameter hill function and computation
of associated parameters. See the vignette for more, including full
list of citations for the methods implemented.
Author: J. Aravind [aut, cre] ,
S. Vimala Devi [aut],
J. Radhamani [aut],
Sherry Rachel Jacob [aut],
Kalyani Srinivasan [aut],
ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.org.in>
Diff between germinationmetrics versions 0.1.8 dated 2023-08-18 and 0.1.9 dated 2025-12-14
germinationmetrics-0.1.8/germinationmetrics/build/germinationmetrics.pdf |only germinationmetrics-0.1.9/germinationmetrics/DESCRIPTION | 27 germinationmetrics-0.1.9/germinationmetrics/MD5 | 88 +- germinationmetrics-0.1.9/germinationmetrics/NAMESPACE | 22 germinationmetrics-0.1.9/germinationmetrics/NEWS.md | 16 germinationmetrics-0.1.9/germinationmetrics/R/CUGerm.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/EmergenceRateIndex.R | 86 +- germinationmetrics-0.1.9/germinationmetrics/R/FirstGermTime.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/FourPHFfit.R | 368 ++++++---- germinationmetrics-0.1.9/germinationmetrics/R/FourPHFfit.bulk.R | 49 - germinationmetrics-0.1.9/germinationmetrics/R/GermIndex.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/GermPercent.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/GermSpeed.R | 22 germinationmetrics-0.1.9/germinationmetrics/R/GermSynchrony.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/GermValue.R | 99 +- germinationmetrics-0.1.9/germinationmetrics/R/MeanGermPercent.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/MeanGermRate.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/MeanGermTime.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/TimsonsIndex.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/WeightGermPercent.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/gcdata.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/geom_line2.R |only germinationmetrics-0.1.9/germinationmetrics/R/germination.indices.R | 2 germinationmetrics-0.1.9/germinationmetrics/R/globals.R | 4 germinationmetrics-0.1.9/germinationmetrics/R/plot.FourPHFfit.R | 4 germinationmetrics-0.1.9/germinationmetrics/R/plot.FourPHFfit.bulk.R | 72 + germinationmetrics-0.1.9/germinationmetrics/R/t50.R | 26 germinationmetrics-0.1.9/germinationmetrics/R/xtra.R | 2 germinationmetrics-0.1.9/germinationmetrics/README.md | 47 - germinationmetrics-0.1.9/germinationmetrics/build/partial.rdb |binary germinationmetrics-0.1.9/germinationmetrics/build/stage23.rdb |binary germinationmetrics-0.1.9/germinationmetrics/build/vignette.rds |binary germinationmetrics-0.1.9/germinationmetrics/inst/CITATION | 6 germinationmetrics-0.1.9/germinationmetrics/inst/REFERENCES.bib | 109 ++ germinationmetrics-0.1.9/germinationmetrics/inst/doc/Introduction.Rmd | 6 germinationmetrics-0.1.9/germinationmetrics/inst/doc/Introduction.pdf |binary germinationmetrics-0.1.9/germinationmetrics/inst/pkgdown.yml |only germinationmetrics-0.1.9/germinationmetrics/man/EmergenceRateIndex.Rd | 29 germinationmetrics-0.1.9/germinationmetrics/man/FourPHF.Rd | 2 germinationmetrics-0.1.9/germinationmetrics/man/GermSpeed.Rd | 16 germinationmetrics-0.1.9/germinationmetrics/man/draw_key_path2.Rd |only germinationmetrics-0.1.9/germinationmetrics/tests/testthat/test-EmergenceRateIndex.R | 40 + germinationmetrics-0.1.9/germinationmetrics/tests/testthat/test-FourPHFfit.R | 35 germinationmetrics-0.1.9/germinationmetrics/tests/testthat/test-t50.R | 17 germinationmetrics-0.1.9/germinationmetrics/vignettes/Indices.rda |binary germinationmetrics-0.1.9/germinationmetrics/vignettes/Introduction.Rmd | 6 germinationmetrics-0.1.9/germinationmetrics/vignettes/REFERENCES.bib | 153 +++- 47 files changed, 939 insertions(+), 436 deletions(-)
More information about germinationmetrics at CRAN
Permanent link
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] ,
Michael Sumner [ctb] ,
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb],
Krzysztof Dyba [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.6-8 dated 2025-02-01 and 0.7-0 dated 2025-12-14
stars-0.6-8/stars/man/st_sfc2xy.Rd |only stars-0.7-0/stars/DESCRIPTION | 35 +- stars-0.7-0/stars/MD5 | 166 ++++++------- stars-0.7-0/stars/NAMESPACE | 3 stars-0.7-0/stars/NEWS.md | 36 ++ stars-0.7-0/stars/R/aggregate.R | 38 ++- stars-0.7-0/stars/R/cf.R |only stars-0.7-0/stars/R/dimensions.R | 199 +++++++++------ stars-0.7-0/stars/R/extract.R | 144 +++++++++-- stars-0.7-0/stars/R/intervals.R | 7 stars-0.7-0/stars/R/mdim.R | 81 +++--- stars-0.7-0/stars/R/ncdf.R | 225 +++--------------- stars-0.7-0/stars/R/ncproxy.R | 32 +- stars-0.7-0/stars/R/plot.R | 3 stars-0.7-0/stars/R/prcomp.R | 4 stars-0.7-0/stars/R/proxy.R | 5 stars-0.7-0/stars/R/rasterize.R | 66 +---- stars-0.7-0/stars/R/read.R | 27 +- stars-0.7-0/stars/R/sample.R | 36 +- stars-0.7-0/stars/R/sf.R | 43 +++ stars-0.7-0/stars/R/stars.R | 23 + stars-0.7-0/stars/R/subset.R | 39 ++- stars-0.7-0/stars/R/tidyverse.R | 3 stars-0.7-0/stars/R/values.R | 5 stars-0.7-0/stars/build/vignette.rds |binary stars-0.7-0/stars/inst/doc/stars1.R | 2 stars-0.7-0/stars/inst/doc/stars1.Rmd | 2 stars-0.7-0/stars/inst/doc/stars1.html | 88 +++---- stars-0.7-0/stars/inst/doc/stars2.R | 2 stars-0.7-0/stars/inst/doc/stars2.Rmd | 2 stars-0.7-0/stars/inst/doc/stars2.html | 58 ++-- stars-0.7-0/stars/inst/doc/stars3.html | 34 +- stars-0.7-0/stars/inst/doc/stars4.R | 2 stars-0.7-0/stars/inst/doc/stars4.Rmd | 2 stars-0.7-0/stars/inst/doc/stars4.html | 34 +- stars-0.7-0/stars/inst/doc/stars6.R | 2 stars-0.7-0/stars/inst/doc/stars6.Rmd | 2 stars-0.7-0/stars/inst/doc/stars6.html | 10 stars-0.7-0/stars/inst/doc/stars8.html | 30 +- stars-0.7-0/stars/man/aggregate.stars.Rd | 2 stars-0.7-0/stars/man/mdim.Rd | 8 stars-0.7-0/stars/man/prcomp.Rd | 4 stars-0.7-0/stars/man/print_stars.Rd | 2 stars-0.7-0/stars/man/read_ncdf.Rd | 7 stars-0.7-0/stars/man/st_as_stars.Rd | 34 ++ stars-0.7-0/stars/man/st_extract.Rd | 41 +++ stars-0.7-0/stars/man/st_xy2sfc.Rd | 26 +- stars-0.7-0/stars/man/stars_subset.Rd | 2 stars-0.7-0/stars/tests/aggregate.Rout.save | 6 stars-0.7-0/stars/tests/align.Rout.save | 4 stars-0.7-0/stars/tests/area.Rout.save | 4 stars-0.7-0/stars/tests/crop.Rout.save | 4 stars-0.7-0/stars/tests/curvilinear.Rout.save | 4 stars-0.7-0/stars/tests/datasets.Rout.save | 4 stars-0.7-0/stars/tests/dimensions.Rout.save | 20 - stars-0.7-0/stars/tests/downsample.Rout.save | 4 stars-0.7-0/stars/tests/ee.Rout.save | 4 stars-0.7-0/stars/tests/extract.Rout.save | 4 stars-0.7-0/stars/tests/gridtypes.Rout.save | 4 stars-0.7-0/stars/tests/mdim.Rout.save | 4 stars-0.7-0/stars/tests/nc.Rout.save | 4 stars-0.7-0/stars/tests/plot.Rout.save | 4 stars-0.7-0/stars/tests/predict.Rout.save | 8 stars-0.7-0/stars/tests/proxy.Rout.save | 20 - stars-0.7-0/stars/tests/raster.Rout.save | 4 stars-0.7-0/stars/tests/rasterize.Rout.save | 4 stars-0.7-0/stars/tests/rectilinear.Rout.save | 4 stars-0.7-0/stars/tests/redimension.Rout.save | 4 stars-0.7-0/stars/tests/sf.Rout.save | 4 stars-0.7-0/stars/tests/sp.Rout.save | 4 stars-0.7-0/stars/tests/spacetime.Rout.save | 4 stars-0.7-0/stars/tests/spatstat.Rout.save | 4 stars-0.7-0/stars/tests/stars.R | 4 stars-0.7-0/stars/tests/stars.Rout.save | 18 - stars-0.7-0/stars/tests/subset.Rout.save | 4 stars-0.7-0/stars/tests/testthat/test-OpenStreetMap.R | 6 stars-0.7-0/stars/tests/testthat/test-ncdf.R | 18 - stars-0.7-0/stars/tests/tidy.Rout.save | 4 stars-0.7-0/stars/tests/transform.Rout.save | 10 stars-0.7-0/stars/tests/warp.Rout.save | 4 stars-0.7-0/stars/tests/write.Rout.save | 4 stars-0.7-0/stars/vignettes/stars1.Rmd | 2 stars-0.7-0/stars/vignettes/stars2.Rmd | 2 stars-0.7-0/stars/vignettes/stars4.Rmd | 2 stars-0.7-0/stars/vignettes/stars6.Rmd | 2 85 files changed, 1008 insertions(+), 822 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.3.1 dated 2025-10-29 and 5.4.0 dated 2025-12-14
Seurat-5.3.1/Seurat/tests/testthat/test_dimplot.R |only Seurat-5.4.0/Seurat/DESCRIPTION | 35 Seurat-5.4.0/Seurat/MD5 | 57 Seurat-5.4.0/Seurat/NAMESPACE | 8 Seurat-5.4.0/Seurat/NEWS.md | 19 Seurat-5.4.0/Seurat/R/clustering.R | 6 Seurat-5.4.0/Seurat/R/convenience.R | 12 Seurat-5.4.0/Seurat/R/data.R | 4 Seurat-5.4.0/Seurat/R/objects.R | 13 Seurat-5.4.0/Seurat/R/preprocessing.R | 423 +++++- Seurat-5.4.0/Seurat/R/utilities.R | 2 Seurat-5.4.0/Seurat/R/visualization.R | 621 ++++++++-- Seurat-5.4.0/Seurat/build/Seurat.pdf |binary Seurat-5.4.0/Seurat/build/stage23.rdb |binary Seurat-5.4.0/Seurat/man/CustomDistance.Rd | 2 Seurat-5.4.0/Seurat/man/Format10X_GeoJson_CellID.Rd |only Seurat-5.4.0/Seurat/man/InteractiveSpatialPlot.Rd |only Seurat-5.4.0/Seurat/man/Load10X_Spatial.Rd | 14 Seurat-5.4.0/Seurat/man/Read10X_HD_GeoJson.Rd |only Seurat-5.4.0/Seurat/man/Read10X_Segmentations.Rd |only Seurat-5.4.0/Seurat/man/SCTransform.Rd | 4 Seurat-5.4.0/Seurat/man/SampleUMI.Rd | 2 Seurat-5.4.0/Seurat/man/Seurat-package.Rd | 1 Seurat-5.4.0/Seurat/man/SingleSpatialPlot.Rd | 7 Seurat-5.4.0/Seurat/man/SpatialPlot.Rd | 11 Seurat-5.4.0/Seurat/man/cc.genes.Rd | 2 Seurat-5.4.0/Seurat/man/cc.genes.updated.2019.Rd | 2 Seurat-5.4.0/Seurat/tests/testthat/test_differential_expression.R | 10 Seurat-5.4.0/Seurat/tests/testthat/test_find_clusters.R | 8 Seurat-5.4.0/Seurat/tests/testthat/test_integration.R | 2 Seurat-5.4.0/Seurat/tests/testthat/test_load_10X.R | 6 Seurat-5.4.0/Seurat/tests/testthat/test_preprocessing.R | 5 32 files changed, 1033 insertions(+), 243 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-28 1.2.0
2024-05-08 1.0.7
2023-06-14 1.0.6
2016-09-16 1.0.5
2016-06-14 1.0.4
2016-06-13 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-12 1.5.7
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:
2019-11-22 0.1.4
2019-03-13 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-19 0.3.2
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team [aut],
Yuta Koike [cre]
Maintainer: Yuta Koike <kyuta@ms.u-tokyo.ac.jp>
Diff between yuima versions 1.15.30 dated 2025-04-16 and 1.15.34 dated 2025-12-14
DESCRIPTION | 20 ++--- MD5 | 44 ++++++----- NAMESPACE | 9 +- NEWS | 18 ++++ R/AllClasses.R | 98 +++++++++++++++++++++----- R/kalmanBucyFilter.R | 23 ++++-- R/lm.jumptest.R | 2 R/params_in_expr.R | 18 ++-- R/poest.R |only R/qmle.degenerate.R |only R/qmle_linear_state_space_model.R | 18 +++- R/yuima.data.R | 66 +++++++++++++++-- R/yuima.model.R | 26 +++++- R/yuima.state_space_model.R | 4 - build/partial.rdb |binary man/kalmanBucyFilter.Rd | 2 man/llag.test.Rd | 4 - man/plot-yuima.kalmanBucyFilter-ANY-method.Rd | 18 ++++ man/poest.Rd |only man/qmle.degenerate.Rd |only man/qmle_linear_state_space_model.Rd | 2 man/setModel.Rd | 5 - man/simBmllag.Rd | 2 man/yuima-class.Rd | 6 + man/yuima.data-class.Rd | 7 + 25 files changed, 296 insertions(+), 96 deletions(-)
Title: Model-Independent Variable Selection via the Rule-Based Variable
Priority
Description: A new framework of variable selection, which instead of generating artificial covariates such as permutation importance and knockoffs, creates release rules to examine the affect on the response for each covariate where the conditional distribution of the response variable can be arbitrary and unknown.
Author: Min Lu [aut],
Aster K. Shear [aut],
Udaya B. Kogalur [aut, cre],
Hemant Ishwaran [aut]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between varPro versions 1.0.0 dated 2025-12-11 and 1.0.1 dated 2025-12-14
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/varpro.strength.R | 2 +- inst/NEWS | 4 ++-- src/entryGeneric.c | 2 +- src/entryGeneric.h | 2 +- src/shared/preprocessForestRecord.c | 2 +- src/shared/preprocessForestRecord.h | 2 +- src/stackOutput.c | 4 ++-- src/stackOutput.h | 2 ++ src/termOps.c | 2 +- src/termOps.h | 2 +- src/varProMain.c | 2 +- src/varProMain.h | 2 +- 14 files changed, 32 insertions(+), 30 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise
components such as animal vocalizations or human voice. Also offers tools
for audio manipulation and acoustic analysis, including pitch tracking,
spectral analysis, audio segmentation, pitch and formant shifting, etc.
Includes four interactive web apps for synthesizing and annotating audio,
manually correcting pitch contours, and measuring formant frequencies.
Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <andrey.anikin@cogsci.se>
Diff between soundgen versions 2.7.4 dated 2025-09-29 and 2.8.0 dated 2025-12-14
soundgen-2.7.4/soundgen/inst/shiny/annotation_app/www/nrm66nuk.wav |only soundgen-2.8.0/soundgen/DESCRIPTION | 13 soundgen-2.8.0/soundgen/MD5 | 121 soundgen-2.8.0/soundgen/NAMESPACE | 4 soundgen-2.8.0/soundgen/NEWS | 19 soundgen-2.8.0/soundgen/R/analyze.R | 13 soundgen-2.8.0/soundgen/R/analyze_utilities.R | 8 soundgen-2.8.0/soundgen/R/apps.R | 142 - soundgen-2.8.0/soundgen/R/detectNLP.R | 12 soundgen-2.8.0/soundgen/R/filters.R | 4 soundgen-2.8.0/soundgen/R/formants.R | 1 soundgen-2.8.0/soundgen/R/frequency_scales.R | 10 soundgen-2.8.0/soundgen/R/loudness.R | 141 - soundgen-2.8.0/soundgen/R/loudness_utilities.R | 64 soundgen-2.8.0/soundgen/R/modulationSpectrum.R | 54 soundgen-2.8.0/soundgen/R/phasegram.R | 13 soundgen-2.8.0/soundgen/R/pitchTrackers.R | 11 soundgen-2.8.0/soundgen/R/pitch_postprocessing.R | 2 soundgen-2.8.0/soundgen/R/postprocessing.R | 4 soundgen-2.8.0/soundgen/R/prosody.R | 2 soundgen-2.8.0/soundgen/R/rolloff.R | 4 soundgen-2.8.0/soundgen/R/segment.R | 161 + soundgen-2.8.0/soundgen/R/soundgen.R | 114 soundgen-2.8.0/soundgen/R/source.R | 2 soundgen-2.8.0/soundgen/R/spectrogram.R | 88 soundgen-2.8.0/soundgen/R/surprisal.R | 17 soundgen-2.8.0/soundgen/README.md | 120 soundgen-2.8.0/soundgen/inst/shiny/annotation_app/server.R | 99 soundgen-2.8.0/soundgen/inst/shiny/annotation_app/ui.R | 424 +-- soundgen-2.8.0/soundgen/inst/shiny/formant_app/server.R | 185 - soundgen-2.8.0/soundgen/inst/shiny/formant_app/ui.R | 799 +++--- soundgen-2.8.0/soundgen/inst/shiny/pitch_app/server.R | 156 - soundgen-2.8.0/soundgen/inst/shiny/pitch_app/ui.R | 1287 +++++----- soundgen-2.8.0/soundgen/inst/shiny/pitch_app/www/temp.wav |binary soundgen-2.8.0/soundgen/inst/shiny/soundgen_main/server.R | 96 soundgen-2.8.0/soundgen/inst/shiny/soundgen_main/ui.R | 763 +++-- soundgen-2.8.0/soundgen/man/analyze.Rd | 4 soundgen-2.8.0/soundgen/man/annotation_app.Rd | 24 soundgen-2.8.0/soundgen/man/detectNLP.Rd | 4 soundgen-2.8.0/soundgen/man/dot-analyze.Rd | 4 soundgen-2.8.0/soundgen/man/dot-detectNLP.Rd | 2 soundgen-2.8.0/soundgen/man/dot-segment.Rd | 12 soundgen-2.8.0/soundgen/man/figures/README-analysis-1.png |binary soundgen-2.8.0/soundgen/man/figures/README-synthsesis-1.png |binary soundgen-2.8.0/soundgen/man/figures/s.mp3 |binary soundgen-2.8.0/soundgen/man/filled.contour.mod.Rd | 3 soundgen-2.8.0/soundgen/man/findVoicedSegments.Rd | 4 soundgen-2.8.0/soundgen/man/formant_app.Rd | 31 soundgen-2.8.0/soundgen/man/generateNoise.Rd | 10 soundgen-2.8.0/soundgen/man/getLoudness.Rd | 2 soundgen-2.8.0/soundgen/man/getPitchZc.Rd | 9 soundgen-2.8.0/soundgen/man/getSurprisal.Rd | 3 soundgen-2.8.0/soundgen/man/modulationSpectrum.Rd | 19 soundgen-2.8.0/soundgen/man/phasegram.Rd | 12 soundgen-2.8.0/soundgen/man/phon2sone.Rd | 19 soundgen-2.8.0/soundgen/man/pitchSmoothPraat.Rd | 4 soundgen-2.8.0/soundgen/man/pitch_app.Rd | 42 soundgen-2.8.0/soundgen/man/plotUnrasterized.Rd | 3 soundgen-2.8.0/soundgen/man/segment.Rd | 62 soundgen-2.8.0/soundgen/man/soundgen.Rd | 36 soundgen-2.8.0/soundgen/man/spectrogram.Rd | 6 soundgen-2.8.0/soundgen/man/updateAnalyze.Rd | 2 62 files changed, 2921 insertions(+), 2349 deletions(-)
Title: Polychoric and Polyserial Correlations
Description: Computes polychoric and polyserial correlations by quick "two-step" methods or ML,
optionally with standard errors; tetrachoric and biserial correlations are special cases.
Author: John Fox [aut],
Adrian Dusa [ctb],
Duncan Murdoch [cre]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between polycor versions 0.8-1 dated 2022-01-11 and 0.8-2 dated 2025-12-14
DESCRIPTION | 22 ++++++++++++---------- MD5 | 5 +++-- NEWS | 8 ++++++++ README.md |only 4 files changed, 23 insertions(+), 12 deletions(-)
Title: Working with the Neotoma Paleoecology Database
Description: Access and manipulation of data using the Neotoma Paleoecology Database.
<https://api.neotomadb.org/api-docs/>.
Examples in functions that require API access are not executed during CRAN checks.
Vignettes do not execute as to avoid API calls during CRAN checks.
Author: Dominguez Vidana Socorro [aut, cre] ,
Simon Goring [aut]
Maintainer: Dominguez Vidana Socorro <dominguezvid@wisc.edu>
Diff between neotoma2 versions 1.0.10 dated 2025-12-06 and 1.0.11 dated 2025-12-14
DESCRIPTION | 10 MD5 | 112 NEWS.md | 6 R/01_classDefinitions.R | 3 R/clean.R | 2 R/filter.R | 2 R/get_datasets.R | 2 R/get_documentation.R | 2 R/get_downloads.R | 2 R/get_manual.R | 2 R/get_publications.R | 2 R/get_sites.R | 31 R/get_speleothems.R | 8 R/get_stats.R | 2 R/get_table.R | 6 R/getids.r | 6 R/pingNeotoma.r | 2 R/plotLeaflet.R | 2 R/samples.R | 7 R/set_server.R | 2 R/site-methods.R | 25 R/speleothemdetails.R | 6 R/speleothems.R | 6 R/taxa.R | 8 R/toWide.R | 9 inst/doc/neotoma2-package.R | 227 - inst/doc/neotoma2-package.Rmd | 35 inst/doc/neotoma2-package.html | 4280 ---------------------------------- man/cite_data-sites-method.Rd | 8 man/clean.Rd | 2 man/contacts_classes.Rd | 2 man/doi-sites-method.Rd | 7 man/filter.Rd | 2 man/get_datasets.Rd | 2 man/get_documentation.Rd | 2 man/get_downloads.Rd | 2 man/get_manual.Rd | 2 man/get_publications.Rd | 2 man/get_sites.Rd | 30 man/get_speleothems.Rd | 8 man/get_stats.Rd | 2 man/get_table.Rd | 6 man/getids.Rd | 6 man/pingNeotoma.Rd | 2 man/plotLeaflet-sites-method.Rd | 2 man/samples-sites-method.Rd | 7 man/set_server.Rd | 2 man/speleothemdetails-sites-method.Rd | 6 man/speleothems-sites-method.Rd | 6 man/sub-sub.Rd | 10 man/taxa-sites-method.Rd | 8 man/toWide.Rd | 6 tests/testthat/test_get_downloads.R | 1 tests/testthat/test_get_table.R | 1 tests/testthat/test_pingNeotoma.R | 1 tests/testthat/test_set_server.R | 2 vignettes/neotoma2-package.Rmd | 35 57 files changed, 325 insertions(+), 4654 deletions(-)
Title: Toolkit for Analysis of Genomic Data
Description: A toolkit for analysis of genomic data. The 'misha' package
implements an efficient data structure for storing genomic data, and
provides a set of functions for data extraction, manipulation and
analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay
(2011) <doi:10.1038/ng.947>.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Eitan Yaffe [aut],
Amos Tanay [aut],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between misha versions 5.3.1 dated 2025-12-10 and 5.3.2 dated 2025-12-14
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ src/Chain2Interval.cpp | 6 +++--- src/ConfigurationManager.h | 2 +- src/GenomeIntervalUtils.cpp | 14 ++++++++++---- src/GseqString.cpp | 20 ++++++++++---------- src/IntervVarProcessor.h | 2 +- src/ValueVarProcessor.h | 2 +- src/misha-init.cpp | 12 ++++++------ src/rdbutils.cpp | 9 ++++----- src/rdbutils.h | 3 ++- 12 files changed, 60 insertions(+), 46 deletions(-)
Title: Draw Gene Arrow Maps in 'ggplot2'
Description: A 'ggplot2' extension for drawing gene arrow maps.
Author: David Wilkins [aut, cre],
Zachary Kurtz [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between gggenes versions 0.5.1 dated 2023-09-05 and 0.6.0 dated 2025-12-14
gggenes-0.5.1/gggenes/tests/testthat/_snaps/geom_subgene_arrow |only gggenes-0.5.1/gggenes/tests/testthat/_snaps/plots |only gggenes-0.5.1/gggenes/tests/testthat/test-geom_feature.R |only gggenes-0.5.1/gggenes/tests/testthat/test-geom_feature_label.R |only gggenes-0.5.1/gggenes/tests/testthat/test-geom_gene_arrow.R |only gggenes-0.5.1/gggenes/tests/testthat/test-geom_gene_label.R |only gggenes-0.5.1/gggenes/tests/testthat/test-geom_subgene_arrow.R |only gggenes-0.5.1/gggenes/tests/testthat/test-geom_subgene_label.R |only gggenes-0.5.1/gggenes/tests/testthat/test-plots.R |only gggenes-0.5.1/gggenes/tests/testthat/test-theme_genes.R |only gggenes-0.6.0/gggenes/DESCRIPTION | 13 gggenes-0.6.0/gggenes/MD5 | 122 +++--- gggenes-0.6.0/gggenes/NAMESPACE | 11 gggenes-0.6.0/gggenes/NEWS.md | 15 gggenes-0.6.0/gggenes/R/data.R | 24 + gggenes-0.6.0/gggenes/R/geom_feature.R | 120 +----- gggenes-0.6.0/gggenes/R/geom_feature_label.R | 185 ++++----- gggenes-0.6.0/gggenes/R/geom_gene_arrow.R | 199 ++++------ gggenes-0.6.0/gggenes/R/geom_gene_label.R | 65 ++- gggenes-0.6.0/gggenes/R/geom_subgene_arrow.R | 65 +-- gggenes-0.6.0/gggenes/R/geom_subgene_label.R | 14 gggenes-0.6.0/gggenes/R/geom_terminator.R |only gggenes-0.6.0/gggenes/R/geom_terminator_label.R |only gggenes-0.6.0/gggenes/R/gggenes-package.R | 1 gggenes-0.6.0/gggenes/R/make_alignment_dummies.R | 2 gggenes-0.6.0/gggenes/R/utilities.R |only gggenes-0.6.0/gggenes/README.md | 54 ++ gggenes-0.6.0/gggenes/build/vignette.rds |binary gggenes-0.6.0/gggenes/data/example_dummies.rda |binary gggenes-0.6.0/gggenes/data/example_features.rda |binary gggenes-0.6.0/gggenes/data/example_features_polar.rda |only gggenes-0.6.0/gggenes/data/example_genes.rda |binary gggenes-0.6.0/gggenes/data/example_genes_polar.rda |only gggenes-0.6.0/gggenes/data/example_subgenes.rda |binary gggenes-0.6.0/gggenes/data/example_subgenes_polar.rda |only gggenes-0.6.0/gggenes/data/example_terminators.rda |only gggenes-0.6.0/gggenes/data/example_terminators_polar.rda |only gggenes-0.6.0/gggenes/inst/WORDLIST | 3 gggenes-0.6.0/gggenes/inst/doc/introduction-to-gggenes.R | 2 gggenes-0.6.0/gggenes/inst/doc/introduction-to-gggenes.html | 23 - gggenes-0.6.0/gggenes/man/example_features.Rd | 5 gggenes-0.6.0/gggenes/man/example_genes.Rd | 10 gggenes-0.6.0/gggenes/man/example_terminators.Rd |only gggenes-0.6.0/gggenes/man/figures/README-geom_gene_arrow-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-labelled_genes-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-make_alignment_dummies-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-reversing_direction-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-subgenes-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-theme_genes-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-unnamed-chunk-2-1.png |binary gggenes-0.6.0/gggenes/man/figures/README-unnamed-chunk-3-1.png |only gggenes-0.6.0/gggenes/man/figures/README-unnamed-chunk-4-1.png |only gggenes-0.6.0/gggenes/man/geom_feature.Rd | 5 gggenes-0.6.0/gggenes/man/geom_gene_arrow.Rd | 3 gggenes-0.6.0/gggenes/man/geom_subgene_arrow.Rd | 3 gggenes-0.6.0/gggenes/man/geom_terminator.Rd |only gggenes-0.6.0/gggenes/man/geom_terminator_label.Rd |only gggenes-0.6.0/gggenes/tests/testthat.R | 8 gggenes-0.6.0/gggenes/tests/testthat/_snaps/feature |only gggenes-0.6.0/gggenes/tests/testthat/_snaps/gene_arrow |only gggenes-0.6.0/gggenes/tests/testthat/_snaps/make_alignment_dummies |only gggenes-0.6.0/gggenes/tests/testthat/_snaps/subgene_arrow |only gggenes-0.6.0/gggenes/tests/testthat/_snaps/terminator |only gggenes-0.6.0/gggenes/tests/testthat/helpers.R |only gggenes-0.6.0/gggenes/tests/testthat/test-feature.R |only gggenes-0.6.0/gggenes/tests/testthat/test-gene_arrow.R |only gggenes-0.6.0/gggenes/tests/testthat/test-make_alignment_dummies.R | 42 -- gggenes-0.6.0/gggenes/tests/testthat/test-subgene_arrow.R |only gggenes-0.6.0/gggenes/tests/testthat/test-terminator.R |only 69 files changed, 540 insertions(+), 454 deletions(-)
Title: Algorithmic Fairness Metrics
Description: Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/328756 [...truncated...]
Author: Nikita Kozodoi [aut, cre],
Tibor V. Varga [aut]
Maintainer: Nikita Kozodoi <n.kozodoi@icloud.com>
This is a re-admission after prior archival of version 1.2.2 dated 2021-04-14
Diff between fairness versions 1.2.2 dated 2021-04-14 and 1.2.3 dated 2025-12-14
DESCRIPTION | 17 - LICENSE | 4 MD5 | 26 +- NAMESPACE | 18 + NEWS.md | 5 R/fairness-package.R | 2 R/import_packages.R | 6 build/vignette.rds |binary data/germancredit.RData |binary inst/doc/fairness.R | 134 +++++++------- inst/doc/fairness.Rmd | 6 inst/doc/fairness.html | 438 ++++++++++++++++++++++++++++++++++++++++++------ man/fairness.Rd | 2 vignettes/fairness.Rmd | 6 14 files changed, 506 insertions(+), 158 deletions(-)