Title: Ecological Inference Applying Entropy
Description: Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.
Author: Alberto Diaz-Dapena [aut, cph],
Esteban Fernandez-Vazquez [aut, cph],
Silvia Maria Franco Anaya [aut, cre, cph]
Maintainer: Silvia Maria Franco Anaya <sfrana@unileon.es>
Diff between EIEntropy versions 0.0.1.3 dated 2024-11-04 and 0.0.1.4 dated 2025-03-17
DESCRIPTION | 10 MD5 | 22 NEWS.md | 14 R/ei_gce.R | 169 +- R/ei_gme.R | 133 +- inst/doc/EIVignette.R | 18 inst/doc/EIVignette.Rmd | 164 -- inst/doc/EIVignette.html | 3000 ++++++++++++++++++++++++++--------------------- man/ei_gce.Rd | 49 man/ei_gme.Rd | 43 man/summary.kl.Rd | 2 vignettes/EIVignette.Rmd | 164 -- 12 files changed, 2043 insertions(+), 1745 deletions(-)
Title: Export Data Frames to Excel 'xlsx' Format
Description: Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'
<https://libxlsxwriter.github.io>. Fast and no Java or Excel required.
Author: Jeroen Ooms [aut, cre] ,
John McNamara [cph] )
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between writexl versions 1.5.1 dated 2024-10-04 and 1.5.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/write_xlsx.R | 5 +++-- src/Makevars | 12 ++++++++---- 5 files changed, 21 insertions(+), 13 deletions(-)
Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] ,
Kaio Dias [aut, cph] ,
Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>
Diff between ProbBreed versions 1.0.4.5 dated 2025-02-02 and 1.0.4.6 dated 2025-03-17
DESCRIPTION | 6 +- MD5 | 40 ++++++------- NEWS.md | 4 + inst/stan/IBD1.stan | 10 +-- inst/stan/IBD2.stan | 10 +-- inst/stan/IBD3.stan | 10 +-- inst/stan/IBD4.stan | 10 +-- inst/stan/IBD5.stan | 6 +- inst/stan/IBD6.stan | 6 +- inst/stan/IBD7.stan | 6 +- inst/stan/IBD8.stan | 6 +- inst/stan/RCBD1.stan | 10 +-- inst/stan/RCBD2.stan | 10 +-- inst/stan/RCBD3.stan | 10 +-- inst/stan/RCBD4.stan | 10 +-- inst/stan/RCBD5.stan | 6 +- inst/stan/RCBD6.stan | 6 +- inst/stan/RCBD7.stan | 6 +- inst/stan/RCBD8.stan | 6 +- inst/stan/entrymean1.stan | 138 +++++++++++++++++++++++----------------------- inst/stan/entrymean2.stan | 130 +++++++++++++++++++++---------------------- 21 files changed, 225 insertions(+), 221 deletions(-)
Title: Run R Scripts if Needed
Description: Automation tool to run R scripts if needed, based on last modified
time. It comes with no package dependencies, organizational overhead, or
structural requirements. In short: run an R script if underlying files have
changed, otherwise do nothing.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between makeit versions 1.0.1 dated 2023-10-27 and 1.0.2 dated 2025-03-17
DESCRIPTION | 16 - MD5 | 16 - NEWS.md | 7 R/make.R | 9 build/vignette.rds |binary inst/doc/makeit.Rmd | 16 - inst/doc/makeit.html | 469 ++++++++++++++++++++++++++++----------------------- man/make.Rd | 9 vignettes/makeit.Rmd | 16 - 9 files changed, 321 insertions(+), 237 deletions(-)
Title: Preprocessing and Feature Engineering Steps for Modeling
Description: A recipe prepares your data for modeling. We provide an
extensible framework for pipeable sequences of feature engineering
steps provides preprocessing tools to be applied to data. Statistical
parameters for the steps can be estimated from an initial data set and
then applied to other data sets. The resulting processed output can
then be used as inputs for statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
Emil Hvitfeldt [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between recipes versions 1.1.1 dated 2025-02-12 and 1.2.0 dated 2025-03-17
DESCRIPTION | 8 MD5 | 679 +++++++++++----------- NAMESPACE | 25 NEWS.md | 43 + R/BoxCox.R | 29 R/YeoJohnson.R | 39 - R/aaa.R | 63 +- R/arrange.R | 22 R/bin2factor.R | 21 R/bs.R | 46 + R/case_weights.R | 27 R/center.R | 32 - R/class.R | 95 +-- R/classdist.R | 63 +- R/classdist_shrunken.R | 226 ++++--- R/colcheck.R | 24 R/corr.R | 72 +- R/count.R | 99 ++- R/cut.R | 23 R/date.R | 75 +- R/deprec-impute_bag.R | 26 R/deprec-impute_knn.R | 26 R/deprec-impute_lower.R | 18 R/deprec-impute_median.R | 18 R/deprec-impute_mena.R | 22 R/deprec-impute_mode.R | 22 R/deprec-impute_roll.R | 24 R/deprec-terms_select.R | 2 R/depth.R | 57 + R/developer.R | 16 R/discretize.R | 80 +- R/dummy.R | 101 +-- R/dummy_extract.R | 127 +++- R/dummy_multi_choice.R | 119 ++- R/extension_check.R | 17 R/extract_parameter.R | 9 R/factor2string.R | 17 R/filter.R | 22 R/filter_missing.R | 58 + R/format.R | 6 R/geodist.R | 90 +- R/get_types_recipes.R | 7 R/harmonic.R | 80 +- R/holiday.R | 108 ++- R/hyperbolic.R | 27 R/ica.R | 64 +- R/import-standalone-obj-type.R | 107 +-- R/import-standalone-types-check.R | 293 +++++---- R/impute_bag.R | 39 - R/impute_knn.R | 60 + R/impute_linear.R | 43 - R/impute_lower.R | 26 R/impute_mean.R | 53 + R/impute_median.R | 46 + R/impute_mode.R | 40 - R/impute_roll.R | 21 R/indicate_na.R | 62 +- R/integer.R | 38 - R/interact.R | 48 - R/intercept.R | 16 R/inverse.R | 18 R/invlogit.R | 11 R/isomap.R | 57 + R/kpca.R | 62 +- R/kpca_poly.R | 67 +- R/kpca_rbf.R | 54 + R/lag.R | 59 + R/lincomb.R | 32 - R/log.R | 22 R/logit.R | 18 R/misc.R | 78 +- R/missing.R | 16 R/mutate.R | 20 R/mutate_at.R | 17 R/naomit.R | 19 R/newvalues.R | 33 - R/nnmf.R | 72 +- R/nnmf_sparse.R | 79 +- R/normalize.R | 43 - R/novel.R | 21 R/ns.R | 43 - R/num2factor.R | 22 R/nzv.R | 60 + R/ordinalscore.R | 47 - R/other.R | 88 +- R/pca.R | 87 +- R/percentile.R | 50 + R/pls.R | 129 +++- R/poly.R | 45 - R/poly_bernstein.R | 44 - R/printing.R | 39 - R/profile.R | 47 - R/ptype.R | 115 +-- R/range.R | 29 R/range_check.R | 66 +- R/ratio.R | 42 - R/recipe.R | 232 ++++--- R/recipes-package.R | 1 R/reexports.R | 5 R/regex.R | 90 ++ R/relevel.R | 22 R/relu.R | 38 - R/rename.R | 22 R/rename_at.R | 24 R/rm.R | 24 R/roles.R | 80 +- R/sample.R | 49 + R/scale.R | 50 + R/select.R | 21 R/selections.R | 36 - R/shuffle.R | 23 R/slice.R | 22 R/sparsevctrs.R | 59 + R/spatialsign.R | 30 R/spline_b.R | 45 - R/spline_convex.R | 45 - R/spline_helpers.R | 28 R/spline_monotone.R | 45 - R/spline_natural.R | 76 +- R/spline_nonnegative.R | 45 - R/sqrt.R | 27 R/steps_and_checks.R | 64 +- R/string2factor.R | 20 R/testthat_helper.R | 16 R/time.R | 45 - R/tune_args.R | 21 R/unknown.R | 21 R/unorder.R | 17 R/update-role-requirements.R | 47 - R/update.R | 5 R/window.R | 61 + R/zv.R | 33 - inst/boilerplate.R | 54 + inst/doc/Dummies.html | 5 inst/doc/Roles.html | 5 inst/doc/Selecting_Variables.html | 5 inst/doc/Skipping.html | 5 inst/doc/recipes.html | 5 inst/old-get_types.R | 10 inst/pls_test_references.R | 33 - man/dot-recipes_preserve_sparsity.Rd |only man/recipes_ptype.Rd | 2 man/reexports.Rd | 2 man/rmd/non-standard-roles.Rmd | 10 man/roles.Rd | 11 man/sparse_data.Rd | 4 man/step_arrange.Rd | 7 man/step_count.Rd | 19 man/step_dummy.Rd | 19 man/step_dummy_extract.Rd | 19 man/step_dummy_multi_choice.Rd | 19 man/step_filter.Rd | 7 man/step_filter_missing.Rd | 7 man/step_holiday.Rd | 19 man/step_impute_mean.Rd | 7 man/step_impute_median.Rd | 7 man/step_indicate_na.Rd | 19 man/step_lag.Rd | 7 man/step_naomit.Rd | 7 man/step_regex.Rd | 19 man/step_rename.Rd | 7 man/step_rename_at.Rd | 7 man/step_rm.Rd | 7 man/step_sample.Rd | 7 man/step_scale.Rd | 9 man/step_select.Rd | 7 man/step_shuffle.Rd | 7 man/step_slice.Rd | 7 man/step_sqrt.Rd | 7 man/step_zv.Rd | 7 tests/testthat/_snaps/BoxCox.md | 2 tests/testthat/_snaps/basics.md | 56 + tests/testthat/_snaps/bs.md | 4 tests/testthat/_snaps/classdist.md | 2 tests/testthat/_snaps/classdist_shrunken.md | 2 tests/testthat/_snaps/corr.md | 2 tests/testthat/_snaps/date.md | 2 tests/testthat/_snaps/depth.md | 2 tests/testthat/_snaps/discretize.md | 2 tests/testthat/_snaps/dummy.md | 14 tests/testthat/_snaps/factor2string.md | 4 tests/testthat/_snaps/filter_missing.md | 2 tests/testthat/_snaps/geodist.md | 6 tests/testthat/_snaps/hyperbolic.md | 4 tests/testthat/_snaps/ica.md | 6 tests/testthat/_snaps/impute_knn.md | 4 tests/testthat/_snaps/impute_lower.md | 4 tests/testthat/_snaps/mutate_at.md | 2 tests/testthat/_snaps/nnmf_sparse.md | 4 tests/testthat/_snaps/normalize.md | 4 tests/testthat/_snaps/ns.md | 4 tests/testthat/_snaps/nzv.md | 5 tests/testthat/_snaps/other.md | 4 tests/testthat/_snaps/pca.md | 4 tests/testthat/_snaps/percentile.md | 8 tests/testthat/_snaps/poly.md | 4 tests/testthat/_snaps/poly_bernstein.md | 4 tests/testthat/_snaps/range.md | 4 tests/testthat/_snaps/ratio.md | 2 tests/testthat/_snaps/rename_at.md | 2 tests/testthat/_snaps/scale.md | 4 tests/testthat/_snaps/spatialsign.md | 12 tests/testthat/_snaps/spline_b.md | 4 tests/testthat/_snaps/spline_convex.md | 4 tests/testthat/_snaps/spline_monotone.md | 4 tests/testthat/_snaps/spline_natural.md | 4 tests/testthat/_snaps/spline_nonnegative.md | 4 tests/testthat/_snaps/sqrt.md | 4 tests/testthat/_snaps/string2factor.md | 4 tests/testthat/_snaps/unknown.md | 4 tests/testthat/_snaps/unorder.md | 2 tests/testthat/helper-case-weights.R | 1 tests/testthat/helper-extract_parameter_set.R | 7 tests/testthat/test-BoxCox.R | 138 +++- tests/testthat/test-YeoJohnson.R | 148 +++- tests/testthat/test-arrange.R | 41 - tests/testthat/test-bake.R | 2 tests/testthat/test-basics.R | 142 ++-- tests/testthat/test-bin2factor.R | 13 tests/testthat/test-bs.R | 56 + tests/testthat/test-case-weight-functions.R | 20 tests/testthat/test-center.R | 31 - tests/testthat/test-class.R | 45 - tests/testthat/test-classdist.R | 66 +- tests/testthat/test-classdist_shrunken.R | 116 ++- tests/testthat/test-colcheck.R | 49 - tests/testthat/test-column_order.R | 52 - tests/testthat/test-corr.R | 22 tests/testthat/test-count.R | 120 +++ tests/testthat/test-cut.R | 66 +- tests/testthat/test-data.frame.R | 12 tests/testthat/test-date.R | 91 +- tests/testthat/test-deprec-impute_bag.R | 7 tests/testthat/test-deprec-impute_knn.R | 7 tests/testthat/test-deprec-impute_lower.R | 5 tests/testthat/test-deprec-impute_median.R | 7 tests/testthat/test-deprec-impute_mena.R | 7 tests/testthat/test-deprec-impute_mode.R | 5 tests/testthat/test-deprec-impute_roll.R | 5 tests/testthat/test-depth.R | 34 - tests/testthat/test-discretize.R | 34 - tests/testthat/test-dummy.R | 160 +++-- tests/testthat/test-dummy_extract.R | 139 +++- tests/testthat/test-dummy_multi_choice.R | 126 +++- tests/testthat/test-extract-dials.R | 46 - tests/testthat/test-factor2string.R | 4 tests/testthat/test-filter.R | 58 + tests/testthat/test-filter_missing.R | 19 tests/testthat/test-format.R | 3 tests/testthat/test-formula.R | 13 tests/testthat/test-geodist.R | 229 ++++--- tests/testthat/test-grouped_df.R | 2 tests/testthat/test-harmonic.R | 214 ++---- tests/testthat/test-holiday.R | 78 ++ tests/testthat/test-hyperbolic.R | 3 tests/testthat/test-ica.R | 107 ++- tests/testthat/test-impute_bag.R | 56 + tests/testthat/test-impute_knn.R | 94 +-- tests/testthat/test-impute_linear.R | 31 - tests/testthat/test-impute_lower.R | 13 tests/testthat/test-impute_mean.R | 41 - tests/testthat/test-impute_median.R | 30 tests/testthat/test-impute_mode.R | 25 tests/testthat/test-impute_roll.R | 23 tests/testthat/test-indicate_na.R | 90 ++ tests/testthat/test-integer.R | 24 tests/testthat/test-interact.R | 121 ++- tests/testthat/test-intercept.R | 9 tests/testthat/test-inverse.R | 6 tests/testthat/test-invlogit.R | 2 tests/testthat/test-isomap.R | 75 +- tests/testthat/test-kpca.R | 27 tests/testthat/test-kpca_poly.R | 42 - tests/testthat/test-kpca_rbf.R | 37 - tests/testthat/test-lag.R | 25 tests/testthat/test-lincomb.R | 22 tests/testthat/test-list_cols.R | 2 tests/testthat/test-log.R | 2 tests/testthat/test-logit.R | 17 tests/testthat/test-matrix.R | 20 tests/testthat/test-misc.R | 20 tests/testthat/test-missing.R | 6 tests/testthat/test-multivariate.R | 6 tests/testthat/test-mutate.R | 58 - tests/testthat/test-mutate_at.R | 60 - tests/testthat/test-naomit.R | 19 tests/testthat/test-newvalues.R | 85 +- tests/testthat/test-nnmf_sparse.R | 21 tests/testthat/test-nomial_types.R | 77 +- tests/testthat/test-normalize.R | 36 - tests/testthat/test-novel.R | 10 tests/testthat/test-ns.R | 48 - tests/testthat/test-num2factor.R | 6 tests/testthat/test-nzv.R | 16 tests/testthat/test-ordinalscore.R | 43 - tests/testthat/test-other.R | 172 +++-- tests/testthat/test-pca.R | 139 +++- tests/testthat/test-percentile.R | 38 - tests/testthat/test-pls.R | 154 +++- tests/testthat/test-poly.R | 54 + tests/testthat/test-poly_bernstein.R | 41 - tests/testthat/test-profile.R | 42 - tests/testthat/test-ptype.R | 34 - tests/testthat/test-range.R | 144 +++- tests/testthat/test-range_check.R | 22 tests/testthat/test-ratio.R | 83 +- tests/testthat/test-regex.R | 105 ++- tests/testthat/test-relevel.R | 9 tests/testthat/test-relu.R | 16 tests/testthat/test-rename.R | 52 + tests/testthat/test-rename_at.R | 33 - tests/testthat/test-retraining.R | 3 tests/testthat/test-rm.R | 59 + tests/testthat/test-roles.R | 104 +-- tests/testthat/test-sample.R | 104 +-- tests/testthat/test-scale.R | 65 +- tests/testthat/test-select.R | 21 tests/testthat/test-selections.R | 280 +++++++-- tests/testthat/test-shuffle.R | 14 tests/testthat/test-skipping.R | 34 - tests/testthat/test-slice.R | 54 + tests/testthat/test-sparsevctrs.R | 9 tests/testthat/test-sparsity.R | 22 tests/testthat/test-spatialsign.R | 19 tests/testthat/test-spline_b.R | 44 - tests/testthat/test-spline_convex.R | 58 + tests/testthat/test-spline_monotone.R | 72 +- tests/testthat/test-spline_natural.R | 41 - tests/testthat/test-spline_nonnegative.R | 72 +- tests/testthat/test-sqrt.R | 14 tests/testthat/test-string2factor.R | 6 tests/testthat/test-stringsAsFactors.R | 17 tests/testthat/test-term_info.R | 802 ++++++++++++++++++++------ tests/testthat/test-tidy.R | 7 tests/testthat/test-time.R | 64 +- tests/testthat/test-tune_args.R | 17 tests/testthat/test-unknown.R | 16 tests/testthat/test-unorder.R | 13 tests/testthat/test-update.R | 49 + tests/testthat/test-window.R | 59 - tests/testthat/test-zv.R | 21 341 files changed, 9569 insertions(+), 5254 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.1.1 dated 2025-03-05 and 3.1.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ src/Makevars.in | 17 ++++++----------- src/Makevars.win | 8 +++----- src/osx/Makevars | 16 ++++++---------- 6 files changed, 26 insertions(+), 34 deletions(-)
Title: Minimal Examples of Using Rust Code in R
Description: Template R package with minimal setup to use Rust code in R without
hacks or frameworks. Includes basic examples of importing cargo dependencies,
spawning threads and passing numbers or strings from Rust to R. Cargo crates
are automatically 'vendored' in the R source package to support offline
installation. The GitHub repository for this package has more details and also
explains how to set up CI. This project was first presented at 'Erum2018' to
showcase R-Rust integration <https://jeroen.github.io/erum2018/>; for a real
world use-case, see the 'gifski' package on 'CRAN'.
Author: Jeroen Ooms [aut, cre] ,
Authors of the dependency Rust crates [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between hellorust versions 1.2.2 dated 2024-09-22 and 1.2.3 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ inst/AUTHORS | 4 ++-- src/Makevars | 6 +++--- src/Makevars.win | 9 +++------ src/myrustlib/vendor.tar.xz |binary 7 files changed, 20 insertions(+), 20 deletions(-)
Title: A GraphQL Query Parser
Description: Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL
<https://graphql.org> syntax and exports the AST in JSON format.
Author: Jeroen Ooms [cre, aut],
Barret Schloerke [ctb],
Scott Wolchok [ctb],
Facebook, Inc [aut, cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between graphql versions 1.5.2 dated 2024-10-04 and 1.5.3 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars | 8 +++----- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Tree-Guided Rare Feature Selection and Logic Aggregation
Description: Implementation of the tree-guided feature selection and logic aggregation approach introduced in Chen et al. (2024) <doi:10.1080/01621459.2024.2326621>. The method enables the selection and aggregation of large-scale rare binary features with a known hierarchical structure using a convex, linearly-constrained regularized regression framework. The package facilitates the application of this method to both linear regression and binary classification problems by solving the optimization problem via the smoothing proximal gradient descent algorithm (Chen et al. (2012) <doi:10.1214/11-AOAS514>).
Author: Jianmin Chen [aut, cre],
Kun Chen [aut]
Maintainer: Jianmin Chen <jianminc000@gmail.com>
Diff between TSLA versions 0.1.1 dated 2025-02-10 and 0.1.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/SPGlinear.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Sparse Vectors for Use in Data Frames
Description: Provides sparse vectors powered by ALTREP (Alternative
Representations for R Objects) that behave like regular vectors, and
can thus be used in data frames. Also provides tools to convert
between sparse matrices and data frames with sparse columns and
functions to interact with sparse vectors.
Author: Emil Hvitfeldt [aut, cre] ,
Davis Vaughan [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between sparsevctrs versions 0.3.0 dated 2025-03-10 and 0.3.1 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/sparse-arithmatic.c | 21 ++++++++++++++------- 4 files changed, 24 insertions(+), 13 deletions(-)
More information about pacta.loanbook at CRAN
Permanent link
Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie [aut, cre] ,
Jeffrey Horner [ctb],
Beilei Bian [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between mime versions 0.12 dated 2021-09-28 and 0.13 dated 2025-03-17
DESCRIPTION | 13 MD5 | 17 R/mime.R | 94 -- R/mimeextra.R |only R/mimemap.R | 1965 +++++++++++++++++++++++++++++++++++++------------ R/parse.R | 6 README.md | 12 man/guess_type.Rd | 21 man/mimemap.Rd | 10 man/parse_multipart.Rd | 8 10 files changed, 1551 insertions(+), 595 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-0 dated 2025-03-01 and 0.9-1 dated 2025-03-17
DESCRIPTION | 8 MD5 | 58 NEWS.md | 23 R/blrm_exnex.R | 94 R/example_single_agent.R | 16 R/posterior.R | 2 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.R | 14 inst/doc/introduction.html | 314 - inst/doc/map_approach.R |only inst/doc/map_approach.Rmd |only inst/doc/map_approach.html |only inst/sbc/calibration.md5 | 6 inst/sbc/sbc_example_models.R | 34 inst/sbc/sbc_report.html | 1488 ++++----- inst/stan/blrm_exnex.stan | 58 man/blrm_exnex.Rd | 10 man/example-single-agent.Rd | 34 man/hist_SA.Rd | 18 src/stanExports_blrm_exnex.h | 2963 +++++++++--------- tests/testthat/helper-sampling.R | 3 tests/testthat/test-blrm_exnex.R | 353 +- tests/testthat/test-blrm_trial.R | 6 tests/testthat/test-plot_toxicity_curve.R | 9 tests/testthat/test-plot_toxicity_intervals.R | 21 tests/testthat/test-plot_toxicity_intervals_stacked.R | 11 tests/testthat/test-posterior.R | 29 vignettes/map_approach.Rmd |only vignettes/settings-knitr.txt | 4 vignettes/settings-sampling.txt | 10 32 files changed, 2949 insertions(+), 2637 deletions(-)
Title: Gaussian Processes on Graphs and Lattices in 'Stan'
Description: Gaussian processes are flexible distributions to model functional data. Whilst
theoretically appealing, they are computationally cumbersome except for small datasets.
This package implements two methods for scaling Gaussian process inference in 'Stan'. First, a
sparse approximation of the likelihood that is generally applicable and, second, an exact method
for regularly spaced data modeled by stationary kernels using fast Fourier methods. Utility
functions are provided to compile and fit 'Stan' models using the 'cmdstanr' interface.
References: Hoffmann and Onnela (2025) <doi:10.18637/jss.v112.i02>.
Author: Till Hoffmann [aut, cre] ,
Jukka-Pekka Onnela [ctb]
Maintainer: Till Hoffmann <thoffmann@hsph.harvard.edu>
Diff between gptoolsStan versions 0.2.0 dated 2024-12-12 and 1.0.0 dated 2025-03-17
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- README.md | 2 +- inst/CITATION |only inst/doc/getting_started.html | 20 +++++++++++++++++--- 5 files changed, 26 insertions(+), 11 deletions(-)
Title: Automatic Processing of Terrestrial-Based Technologies Point
Cloud Data for Forestry Purposes
Description: Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
Adela Martinez-Calvo [aut, com],
Maria Jose Ginzo Villamayor [aut, com],
Manuel Antonio Novo Perez [aut, com],
Juan Gabriel Alvarez-Gonzalez [aut, ths],
Fernando Montes [aut],
Cesar Perez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <jamolinavalero@gmail.com>
Diff between FORTLS versions 1.4.0 dated 2024-01-21 and 1.5.0 dated 2025-03-17
FORTLS-1.4.0/FORTLS/R/PythonFunctions.R |only FORTLS-1.4.0/FORTLS/inst/python/my_python_script.py |only FORTLS-1.4.0/FORTLS/man/ncr_point_cloud_double.Rd |only FORTLS-1.4.0/FORTLS/man/ver_point_cloud_double.Rd |only FORTLS-1.4.0/FORTLS/src/simulations_1.5.cpp |only FORTLS-1.4.0/FORTLS/src/surface_variation_1.3.cpp |only FORTLS-1.5.0/FORTLS/DESCRIPTION | 33 FORTLS-1.5.0/FORTLS/MD5 | 103 + FORTLS-1.5.0/FORTLS/NAMESPACE | 1 FORTLS-1.5.0/FORTLS/R/RcppExports.R | 40 FORTLS-1.5.0/FORTLS/R/auxiliary.functions.R | 674 +++++-------- FORTLS-1.5.0/FORTLS/R/correlations.R | 3 FORTLS-1.5.0/FORTLS/R/geometric.features.R |only FORTLS-1.5.0/FORTLS/R/globals.R |only FORTLS-1.5.0/FORTLS/R/normalize.R | 153 ++ FORTLS-1.5.0/FORTLS/R/optimize.plot.design.R | 20 FORTLS-1.5.0/FORTLS/R/python.functions.R |only FORTLS-1.5.0/FORTLS/R/relative.bias.R | 8 FORTLS-1.5.0/FORTLS/R/section.functions.R | 73 - FORTLS-1.5.0/FORTLS/R/species.classification.R |only FORTLS-1.5.0/FORTLS/R/stem.analysis.R | 16 FORTLS-1.5.0/FORTLS/R/tree.detection.multi.scan.R | 419 +++++--- FORTLS-1.5.0/FORTLS/R/tree.detection.several.plots.R | 23 FORTLS-1.5.0/FORTLS/R/tree.detection.single.scan.R | 405 +++++-- FORTLS-1.5.0/FORTLS/build/partial.rdb |binary FORTLS-1.5.0/FORTLS/build/vignette.rds |binary FORTLS-1.5.0/FORTLS/inst/CITATION | 2 FORTLS-1.5.0/FORTLS/inst/doc/plot_design_optimization.R | 30 FORTLS-1.5.0/FORTLS/inst/doc/plot_design_optimization.html | 14 FORTLS-1.5.0/FORTLS/inst/doc/stand_level.R | 18 FORTLS-1.5.0/FORTLS/inst/doc/stand_level.html | 4 FORTLS-1.5.0/FORTLS/inst/doc/tree_level.R | 96 - FORTLS-1.5.0/FORTLS/inst/doc/tree_level.Rmd | 2 FORTLS-1.5.0/FORTLS/inst/doc/tree_level.html | 10 FORTLS-1.5.0/FORTLS/inst/python/random_forest_fit.py |only FORTLS-1.5.0/FORTLS/inst/python/random_forest_sp.py |only FORTLS-1.5.0/FORTLS/inst/python/voxel_grid_downsampling.py |only FORTLS-1.5.0/FORTLS/man/RANSAC_cpp.Rd |only FORTLS-1.5.0/FORTLS/man/VoxR_vox_update.Rd |only FORTLS-1.5.0/FORTLS/man/chunk_size_from_area.Rd |only FORTLS-1.5.0/FORTLS/man/correlations.Rd | 4 FORTLS-1.5.0/FORTLS/man/datatable_grid.Rd |only FORTLS-1.5.0/FORTLS/man/distance.sampling.Rd | 8 FORTLS-1.5.0/FORTLS/man/fit_circle_cpp_modified.Rd |only FORTLS-1.5.0/FORTLS/man/geometric.features.Rd |only FORTLS-1.5.0/FORTLS/man/geometric_features.Rd |only FORTLS-1.5.0/FORTLS/man/geometric_features_point.Rd |only FORTLS-1.5.0/FORTLS/man/internal_ransac.Rd |only FORTLS-1.5.0/FORTLS/man/is_one_row_all_na.Rd |only FORTLS-1.5.0/FORTLS/man/iterations_RANSAC.Rd |only FORTLS-1.5.0/FORTLS/man/normalize.Rd | 29 FORTLS-1.5.0/FORTLS/man/optimize.plot.design.Rd | 4 FORTLS-1.5.0/FORTLS/man/random.forest.fit.Rd |only FORTLS-1.5.0/FORTLS/man/random.forest.sp.Rd |only FORTLS-1.5.0/FORTLS/man/relative.bias.Rd | 4 FORTLS-1.5.0/FORTLS/man/sample_indices.Rd |only FORTLS-1.5.0/FORTLS/man/save_file_as_laz.Rd |only FORTLS-1.5.0/FORTLS/man/save_to_tiles.Rd |only FORTLS-1.5.0/FORTLS/man/simulations.Rd | 2 FORTLS-1.5.0/FORTLS/man/sort_sublists.Rd |only FORTLS-1.5.0/FORTLS/man/species.classification.Rd |only FORTLS-1.5.0/FORTLS/man/tree.detection.multi.scan.Rd | 11 FORTLS-1.5.0/FORTLS/man/tree.detection.several.plots.Rd | 16 FORTLS-1.5.0/FORTLS/man/tree.detection.single.scan.Rd | 16 FORTLS-1.5.0/FORTLS/man/voxel_grid_downsampling.Rd |only FORTLS-1.5.0/FORTLS/src/RcppExports.cpp | 167 ++- FORTLS-1.5.0/FORTLS/src/geometric.features.cpp |only FORTLS-1.5.0/FORTLS/src/ransac_and_util.cpp |only FORTLS-1.5.0/FORTLS/src/simulations.cpp |only FORTLS-1.5.0/FORTLS/vignettes/tree_level.Rmd | 2 70 files changed, 1446 insertions(+), 964 deletions(-)
Title: Get Basic Information from Chinese ID Number
Description: The Chinese ID number contains a lot of information,
this package helps you get the region, date of birth, age,
age based on year, gender, zodiac, constellation information from
the Chinese ID number.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between CNID versions 2.0.2 dated 2025-02-28 and 2.1.0 dated 2025-03-17
DESCRIPTION | 10 - MD5 | 46 ++--- NAMESPACE | 1 R/age.R | 56 +++--- R/age_by_year.R | 56 +++--- R/birth_date.R | 56 +++--- R/check_id.R | 56 +++--- R/cnid_info.R | 453 +++++++++++++++++++++++++++-------------------------- R/convert18.R |only R/cstl.R | 56 +++--- R/gender.R | 56 +++--- R/region.R | 56 +++--- R/sysdata.rda |binary R/zodiac.R | 56 +++--- README.md | 6 man/age.Rd | 12 - man/age_by_year.Rd | 12 - man/birth_date.Rd | 12 - man/check_id.Rd | 12 - man/cnid_info.Rd | 14 - man/convert18.Rd |only man/cstl.Rd | 12 - man/gender.Rd | 12 - man/region.Rd | 12 - man/zodiac.Rd | 12 - 25 files changed, 549 insertions(+), 525 deletions(-)
Title: Data Collection from the Central Bank of Brazil
Description: Provides tools to facilitate the access and processing of data
from the Central Bank of Brazil API. The package allows users
to retrieve economic and financial data, transforming them into usable
tabular formats for further analysis. The data is obtained from the
Central Bank of Brazil API: <https://api.bcb.gov.br/dados/serie/bcdata.sgs.{series_code}/dados?formato=json&dataInicial={start_date}&dataFinal={end_date}>.
Author: Paulo Icaro [aut],
Lissandro Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Sousa <lisandrosousa54@gmail.com>
Diff between BacenAPI versions 0.1.0 dated 2025-03-07 and 0.1.1 dated 2025-03-17
DESCRIPTION | 14 +++++-- MD5 | 16 ++++---- R/bacen_api.R | 103 +++++++++++++++++++++------------------------------- R/bacen_series.R | 6 ++- R/bacen_url.R | 4 +- README.md | 53 ++++++++++---------------- man/bacen_api.Rd | 4 -- man/bacen_series.Rd | 6 ++- man/bacen_url.Rd | 4 +- 9 files changed, 98 insertions(+), 112 deletions(-)
Title: Fast Tidy Tools for Date and Date-Time Manipulation
Description: A set of fast tidy functions for wrangling, completing and
summarising date and date-time data. It combines 'tidyverse' syntax
with the efficiency of 'data.table' and speed of 'collapse'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between timeplyr versions 1.0.0 dated 2025-02-03 and 1.1.0 dated 2025-03-17
timeplyr-1.0.0/timeplyr/R/GRP_utils.R |only timeplyr-1.0.0/timeplyr/R/utils.R |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-12-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-14-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-15-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-15-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-16-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-17-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-2-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-22-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-22-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-23-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-23-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-25-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-26-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-26-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-27-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-27-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-28-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-28-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-29-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-3-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-30-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-30-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-31-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-31-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-34-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-34-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-35-1.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-35-2.png |only timeplyr-1.0.0/timeplyr/man/figures/README-unnamed-chunk-4-1.png |only timeplyr-1.0.0/timeplyr/src/utils.cpp |only timeplyr-1.1.0/timeplyr/DESCRIPTION | 14 timeplyr-1.1.0/timeplyr/MD5 | 220 +-- timeplyr-1.1.0/timeplyr/NAMESPACE | 18 timeplyr-1.1.0/timeplyr/NEWS.md | 22 timeplyr-1.1.0/timeplyr/R/abc.R |only timeplyr-1.1.0/timeplyr/R/age_years.R | 66 timeplyr-1.1.0/timeplyr/R/calendar.R | 2 timeplyr-1.1.0/timeplyr/R/collapse_utils.R |only timeplyr-1.1.0/timeplyr/R/cpp11.R | 20 timeplyr-1.1.0/timeplyr/R/df_utils.R | 4 timeplyr-1.1.0/timeplyr/R/get_time_delay.R | 2 timeplyr-1.1.0/timeplyr/R/growth.R | 2 timeplyr-1.1.0/timeplyr/R/growth_rate.R | 2 timeplyr-1.1.0/timeplyr/R/is_whole_number.R | 15 timeplyr-1.1.0/timeplyr/R/iso_week.R | 2 timeplyr-1.1.0/timeplyr/R/legacy_time_utils.R | 2 timeplyr-1.1.0/timeplyr/R/reset.R | 4 timeplyr-1.1.0/timeplyr/R/resolution.R | 27 timeplyr-1.1.0/timeplyr/R/roll.R | 2 timeplyr-1.1.0/timeplyr/R/roll_apply.R | 2 timeplyr-1.1.0/timeplyr/R/roll_lag.R | 2 timeplyr-1.1.0/timeplyr/R/roll_na_fill.R | 3 timeplyr-1.1.0/timeplyr/R/scales.R | 22 timeplyr-1.1.0/timeplyr/R/time_arithmetic.R |only timeplyr-1.1.0/timeplyr/R/time_core.R | 5 timeplyr-1.1.0/timeplyr/R/time_cut.R | 30 timeplyr-1.1.0/timeplyr/R/time_diff.R | 24 timeplyr-1.1.0/timeplyr/R/time_elapsed.R | 2 timeplyr-1.1.0/timeplyr/R/time_episodes.R | 2 timeplyr-1.1.0/timeplyr/R/time_expand.R | 132 - timeplyr-1.1.0/timeplyr/R/time_ggplot.R | 2 timeplyr-1.1.0/timeplyr/R/time_id.R | 3 timeplyr-1.1.0/timeplyr/R/time_interval.R | 28 timeplyr-1.1.0/timeplyr/R/time_is_regular.R | 2 timeplyr-1.1.0/timeplyr/R/time_roll.R | 4 timeplyr-1.1.0/timeplyr/R/time_seq.R | 220 +-- timeplyr-1.1.0/timeplyr/R/time_seq_fill.R | 28 timeplyr-1.1.0/timeplyr/R/time_seq_id.R | 4 timeplyr-1.1.0/timeplyr/R/time_utils.R | 207 +-- timeplyr-1.1.0/timeplyr/R/timeplyr-package.R | 32 timeplyr-1.1.0/timeplyr/R/timespan.R | 25 timeplyr-1.1.0/timeplyr/R/ts_as_tbl.R | 2 timeplyr-1.1.0/timeplyr/R/utils-pipe.R |only timeplyr-1.1.0/timeplyr/R/year_month.R | 8 timeplyr-1.1.0/timeplyr/R/zzz.R | 4 timeplyr-1.1.0/timeplyr/README.md | 530 ++++++- timeplyr-1.1.0/timeplyr/man/calendar.Rd | 2 timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-21-1.png |only timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-29-1.png |binary timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-44-1.png |only timeplyr-1.1.0/timeplyr/man/figures/README-unnamed-chunk-44-2.png |only timeplyr-1.1.0/timeplyr/man/get_time_delay.Rd | 2 timeplyr-1.1.0/timeplyr/man/growth.Rd | 2 timeplyr-1.1.0/timeplyr/man/growth_rate.Rd | 2 timeplyr-1.1.0/timeplyr/man/is_whole_number.Rd | 11 timeplyr-1.1.0/timeplyr/man/iso_week.Rd | 2 timeplyr-1.1.0/timeplyr/man/pipe.Rd |only timeplyr-1.1.0/timeplyr/man/roll_lag.Rd | 2 timeplyr-1.1.0/timeplyr/man/roll_sum.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_add.Rd |only timeplyr-1.1.0/timeplyr/man/time_cut.Rd | 21 timeplyr-1.1.0/timeplyr/man/time_elapsed.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_episodes.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_expand.Rd | 7 timeplyr-1.1.0/timeplyr/man/time_ggplot.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_is_regular.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_roll.Rd | 2 timeplyr-1.1.0/timeplyr/man/time_seq.Rd | 22 timeplyr-1.1.0/timeplyr/man/time_seq_id.Rd | 2 timeplyr-1.1.0/timeplyr/man/timeplyr-package.Rd | 23 timeplyr-1.1.0/timeplyr/man/ts_as_tbl.Rd | 2 timeplyr-1.1.0/timeplyr/src/cpp11.cpp | 44 timeplyr-1.1.0/timeplyr/src/diff.cpp | 11 timeplyr-1.1.0/timeplyr/src/is_whole_num.cpp | 85 - timeplyr-1.1.0/timeplyr/src/roll.cpp | 107 + timeplyr-1.1.0/timeplyr/src/time_arithmetic.cpp |only timeplyr-1.1.0/timeplyr/src/timeplyr.h | 15 timeplyr-1.1.0/timeplyr/tests/testthat/test-age_years.R | 11 timeplyr-1.1.0/timeplyr/tests/testthat/test-calendar.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-get_time_delay.R | 90 - timeplyr-1.1.0/timeplyr/tests/testthat/test-growth.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-growth_rate.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-is_whole_number.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-iso_week.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-roll_lag.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-roll_mean.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-roll_na_fill.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_by.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_core.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_cut.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_diff.R | 171 ++ timeplyr-1.1.0/timeplyr/tests/testthat/test-time_elapsed.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_episodes.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_expand.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_gaps.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_is_regular.R | 6 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_roll.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-time_seq.R | 666 ++++------ timeplyr-1.1.0/timeplyr/tests/testthat/test-time_seq_id.R | 2 timeplyr-1.1.0/timeplyr/tests/testthat/test-ts_as_tbl.R | 2 132 files changed, 1737 insertions(+), 1376 deletions(-)
Title: Measure Memory and CPU Usage for Parallel R Code
Description: Measures memory and CPU usage of R code by regularly taking
snapshots of calls to the system command 'ps'. The package provides an entry
point (albeit coarse) to profile usage of system resources by R code run
in parallel.
Author: Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between syrup versions 0.1.1 dated 2024-07-18 and 0.1.2 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/syrup.R | 3 +-- R/utils.R | 14 ++++++++++++++ 5 files changed, 26 insertions(+), 9 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>,
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>,
Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>,
Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>,
Centofanti et al. (2022) <doi:10.48550/arXiv.2205.06256>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Antonio Lepore [aut],
Biagio Palumbo [aut],
Alessandra Menafoglio [ctb],
Simone Vantini [ctb]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.6.0 dated 2024-12-11 and 1.7.0 dated 2025-03-17
DESCRIPTION | 6 ++-- MD5 | 55 ++++++++++++++++++++++++-------------------- NAMESPACE | 4 +++ NEWS.md | 30 +++++++++++++++++------- R/02_fof_pc.R | 2 - R/03_phaseI_training.R | 2 - R/04_phaseII.R | 2 - R/AMFCC.R |only R/FRTM.R | 2 - R/amfewma.R | 10 ++++---- R/funcharts-package.R | 11 ++++---- R/rmfcc.R | 14 +++++------ R/simulate.R | 4 +-- man/AMFCC_PhaseI.Rd |only man/AMFCC_PhaseII.Rd |only man/AMFEWMA_PhaseI.Rd | 5 ++-- man/AMFEWMA_PhaseII.Rd | 5 ++-- man/RoMFCC_PhaseI.Rd | 2 - man/RoMFCC_PhaseII.Rd | 2 - man/RoMFDI.Rd | 2 - man/funcharts-package.Rd | 13 +++++----- man/functional_filter.Rd | 6 ++-- man/mFPCA.Rd | 2 - man/plot.AMFCC_PhaseI.Rd |only man/predict_fof_pc.Rd | 2 - man/regr_cc_fof.Rd | 2 - man/rpca_mfd.Rd | 2 - man/sim_funcharts.Rd | 2 - man/simulate_mfd.Rd | 2 - tests/testthat/Rplots.pdf |binary tests/testthat/test_AMFCC.R |only 31 files changed, 109 insertions(+), 80 deletions(-)
Title: Bayesian State-Space Modeling of Mouse-Tracking Experiments via
Stan
Description: Estimates previously compiled state-space modeling for mouse-tracking experiments using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.
Author: Antonio Calcagnì [aut, cre],
Massimiliano Pastore [ctb]
Maintainer: Antonio Calcagnì <ant.calcagni@gmail.com>
Diff between ssMousetrack versions 1.1.6 dated 2023-04-05 and 1.1.7 dated 2025-03-17
ssMousetrack-1.1.6/ssMousetrack/src/Makevars.win |only ssMousetrack-1.1.7/ssMousetrack/DESCRIPTION | 15 ssMousetrack-1.1.7/ssMousetrack/MD5 | 51 ssMousetrack-1.1.7/ssMousetrack/NEWS | 17 ssMousetrack-1.1.7/ssMousetrack/R/ssMousetrack-package.R | 2 ssMousetrack-1.1.7/ssMousetrack/R/stanmodels.R | 2 ssMousetrack-1.1.7/ssMousetrack/inst/stan/fit_model.stan | 16 ssMousetrack-1.1.7/ssMousetrack/inst/stan/fit_model_gomp.stan | 24 ssMousetrack-1.1.7/ssMousetrack/inst/stan/fit_model_log.stan | 24 ssMousetrack-1.1.7/ssMousetrack/inst/stan/simulate_data.stan | 16 ssMousetrack-1.1.7/ssMousetrack/inst/stan/simulate_data_gomp.stan | 16 ssMousetrack-1.1.7/ssMousetrack/inst/stan/simulate_data_log.stan | 16 ssMousetrack-1.1.7/ssMousetrack/man/ssMousetrack-package.Rd | 10 ssMousetrack-1.1.7/ssMousetrack/src/Makevars | 5 ssMousetrack-1.1.7/ssMousetrack/src/RcppExports.cpp | 5 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model.h | 2896 ++++--- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_gomp.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_gomp.h | 3727 +++++----- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_log.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_fit_model_log.h | 3365 +++++---- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data.h | 2347 +++--- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_gomp.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_gomp.h | 2729 ++++--- ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_log.cc | 2 ssMousetrack-1.1.7/ssMousetrack/src/stanExports_simulate_data_log.h | 2362 +++--- 27 files changed, 10204 insertions(+), 7453 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification <https://github.github.com/gfm/> defines
a rationalized version of markdown syntax. This package uses the 'cmark'
reference implementation for converting markdown text into various formats
including html, latex and groff man. In addition it exposes the markdown
parse tree in xml format. Also includes opt-in support for GFM extensions
including tables, autolinks, and strikethrough text.
Author: Jeroen Ooms [aut, cre] ,
John MacFarlane [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between commonmark versions 1.9.4 dated 2025-03-17 and 1.9.5 dated 2025-03-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.5 dated 2024-11-08 and 1.0.6 dated 2025-03-17
DESCRIPTION | 6 MD5 | 45 +++- NAMESPACE | 13 + NEWS.md | 5 R/FitCoupledGrowth_class.R |only R/data.R | 346 ++++++++++++++++++---------------- R/fit_coupled_growth.R |only R/initial_guesses.R | 14 - R/top_fit.R | 2 build/vignette.rds |binary data/example_coupled_onestep.rda |only data/example_coupled_twosteps.rda |only inst/doc/v01_growth_predictions.html | 2 inst/doc/v02_growth_fitting.html | 12 - inst/doc/v03_growth_uncertainty.html | 14 - inst/doc/v04_model_comparison.html | 6 inst/doc/v06_coupledmodels.R |only inst/doc/v06_coupledmodels.Rmd |only inst/doc/v06_coupledmodels.html |only inst/doc/v24_publication_figures.html | 6 inst/doc/v99_deprecated.html | 14 - man/FitCoupledGrowth.Rd |only man/cost_coupled_onestep.Rd |only man/cost_coupled_twosteps.Rd |only man/example_coupled_onestep.Rd |only man/example_coupled_twosteps.Rd |only man/fit_coupled_growth.Rd |only man/pred_coupled_baranyi.Rd |only man/pred_lambda.Rd |only man/pred_sqmu.Rd |only man/residuals_lambda.Rd |only man/residuals_sqmu.Rd |only vignettes/v06_coupledmodels.Rmd |only 33 files changed, 273 insertions(+), 212 deletions(-)
Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>,
including storage, database, and compute services, such as 'Simple
Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda'
functions-as-a-service.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws versions 0.8.0 dated 2025-02-10 and 0.9.0 dated 2025-03-17
paws-0.8.0/paws/man/elasticinference.Rd |only paws-0.9.0/paws/DESCRIPTION | 22 paws-0.9.0/paws/MD5 | 44 paws-0.9.0/paws/NAMESPACE | 2 paws-0.9.0/paws/R/paws.R | 5167 +++++++++++--------------------- paws-0.9.0/paws/man/accessanalyzer.Rd | 1 paws-0.9.0/paws/man/cloudformation.Rd | 5 paws-0.9.0/paws/man/cloudtrail.Rd | 1 paws-0.9.0/paws/man/connect.Rd | 3 paws-0.9.0/paws/man/connectcases.Rd | 12 paws-0.9.0/paws/man/ec2.Rd | 10 paws-0.9.0/paws/man/ecr.Rd | 2 paws-0.9.0/paws/man/iam.Rd | 2 paws-0.9.0/paws/man/lightsail.Rd | 4 paws-0.9.0/paws/man/networkfirewall.Rd | 7 paws-0.9.0/paws/man/opsworks.Rd | 2 paws-0.9.0/paws/man/rds.Rd | 2 paws-0.9.0/paws/man/s3tables.Rd |only paws-0.9.0/paws/man/sesv2.Rd | 1 paws-0.9.0/paws/man/ssm.Rd | 18 paws-0.9.0/paws/man/ssooidc.Rd | 7 paws-0.9.0/paws/man/storagegateway.Rd | 7 paws-0.9.0/paws/man/swf.Rd | 2 paws-0.9.0/paws/man/wafv2.Rd | 31 24 files changed, 2018 insertions(+), 3334 deletions(-)
Title: Tailored Knowledge Catalog
Description: Facilitate the management of data from knowledge
resources that are frequently used alone or together
in research environments.
In 'TKCat', knowledge resources are manipulated as modeled database (MDB)
objects. These objects provide access to the data tables along with a general
description of the resource and a detail data model documenting the
tables, their fields and their relationships.
These MDBs are then gathered in catalogs that can be easily
explored an shared.
Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and
create new catalogs suited for specific needs.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between TKCat versions 1.1.11 dated 2024-07-03 and 1.1.12 dated 2025-03-17
DESCRIPTION | 6 +- MD5 | 26 ++++----- NAMESPACE | 6 +- R/chMDB.R | 22 +++++++ R/fileMDB.R | 22 +++++++ R/namespace.R | 3 - build/vignette.rds |binary inst/doc/TKCat-KMR-POK.R | 4 - inst/doc/TKCat-KMR-POK.html | 6 +- inst/doc/TKCat.R | 112 +++++++++++++++++++-------------------- inst/doc/TKCat.html | 125 +++++++++++++++++++++++--------------------- inst/pkgdown.yml | 7 +- man/chMDB.Rd | 10 ++- man/fileMDB.Rd | 10 ++- 14 files changed, 215 insertions(+), 144 deletions(-)
Title: Easy Interface to the Statistical Disclosure Control Package
'sdcTable' Extended with Own Implementation of
'GaussSuppression'
Description: The main function, ProtectTable(), performs table suppression according to a
frequency rule with a data set as the only required input. Within this function,
protectTable(), protect_linked_tables() or runArgusBatchFile() in package 'sdcTable' is called.
Lists of level-hierarchy (parameter 'dimList') and other required input to these functions
are created automatically.
The suppression method Gauss (default) is implemented independently of 'sdcTable'.
The function, PTgui(), starts a graphical user interface based on the 'shiny' package.
Author: Oeyvind Langsrud [aut, cre]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between easySdcTable versions 1.0.7 dated 2022-12-22 and 1.1.1 dated 2025-03-17
DESCRIPTION | 15 - MD5 | 37 +- NEWS.md | 16 + R/EasyData.R | 2 R/PTwrap.R | 12 R/ProtectTable.R | 40 +- R/ProtectTable1.R | 14 - build/vignette.rds |binary inst/doc/easySdcTableVignette.R | 10 inst/doc/easySdcTableVignette.Rmd | 12 inst/doc/easySdcTableVignette.html | 506 +++++++++++++++++++++++++++---------- inst/doc/singletonsAndZeros.Rmd | 10 inst/doc/singletonsAndZeros.html | 433 +++++++++++++++++++++++++------ man/EasyData.Rd | 2 man/PTwrap.Rd | 10 man/ProtectTable.Rd | 40 +- man/ProtectTable1.Rd | 14 - man/figures |only vignettes/easySdcTableVignette.Rmd | 12 vignettes/singletonsAndZeros.Rmd | 10 20 files changed, 882 insertions(+), 313 deletions(-)
Title: Connect to the 'nettskjema.no' API of the University of Oslo
Description: Enables users to retrieve data, meta-data, and codebooks from
<https://nettskjema.no/>. The data from the API is richer than from
the online data portal. Mowinckel (2021) <doi:10.5281/zenodo.4745481>.
Author: Athanasia Mo Mowinckel [aut, cre]
,
Trym Nohr Fjoertoft [ctb]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between nettskjemar versions 0.1.4 dated 2021-05-20 and 1.0.0 dated 2025-03-17
nettskjemar-0.1.4/nettskjemar/R/api-funcs.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-codebook.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-data_sorters.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-elements.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema-meta.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema_auth.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema_get_form.R |only nettskjemar-0.1.4/nettskjemar/R/nettskjema_write.R |only nettskjemar-0.1.4/nettskjemar/inst/background_docs |only nettskjemar-0.1.4/nettskjemar/inst/doc/auth_setup.R |only nettskjemar-0.1.4/nettskjemar/inst/doc/auth_setup.Rmd |only nettskjemar-0.1.4/nettskjemar/inst/doc/auth_setup.html |only nettskjemar-0.1.4/nettskjemar/inst/doc/nettskjemar.R |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_codebook.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_data.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_extra.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_get_meta.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_renviron_edit.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_token2renviron.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_token_expiry.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_user_create.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_write_codebook.Rd |only nettskjemar-0.1.4/nettskjemar/man/nettskjema_write_meta.Rd |only nettskjemar-0.1.4/nettskjemar/tests/testthat/test-data_sorters.R |only nettskjemar-0.1.4/nettskjemar/tests/testthat/test-nettskjema_auth.R |only nettskjemar-0.1.4/nettskjemar/tests/testthat/test-nettskjema_get.R |only nettskjemar-0.1.4/nettskjemar/vignettes/auth_setup.Rmd |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_api_create.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_api_create2.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_api_user.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_create_token.png |only nettskjemar-0.1.4/nettskjemar/vignettes/static/nettskjema_create_token2.png |only nettskjemar-1.0.0/nettskjemar/DESCRIPTION | 45 nettskjemar-1.0.0/nettskjemar/MD5 | 156 +- nettskjemar-1.0.0/nettskjemar/NAMESPACE | 89 - nettskjemar-1.0.0/nettskjemar/NEWS.md | 22 nettskjemar-1.0.0/nettskjemar/R/nettskjemar-package.R |only nettskjemar-1.0.0/nettskjemar/R/ns-attachment.R |only nettskjemar-1.0.0/nettskjemar/R/ns-auth.R |only nettskjemar-1.0.0/nettskjemar/R/ns-browser.R |only nettskjemar-1.0.0/nettskjemar/R/ns-checkbox.R |only nettskjemar-1.0.0/nettskjemar/R/ns-codebook.R |only nettskjemar-1.0.0/nettskjemar/R/ns-data.R |only nettskjemar-1.0.0/nettskjemar/R/ns-data_labels.R |only nettskjemar-1.0.0/nettskjemar/R/ns-form.R |only nettskjemar-1.0.0/nettskjemar/R/ns-me.R |only nettskjemar-1.0.0/nettskjemar/R/ns-meta.R |only nettskjemar-1.0.0/nettskjemar/R/ns-submission.R |only nettskjemar-1.0.0/nettskjemar/R/utils.R | 94 - nettskjemar-1.0.0/nettskjemar/README.md | 65 - nettskjemar-1.0.0/nettskjemar/build/partial.rdb |only nettskjemar-1.0.0/nettskjemar/build/vignette.rds |binary nettskjemar-1.0.0/nettskjemar/inst/WORDLIST | 47 nettskjemar-1.0.0/nettskjemar/inst/doc/attachments.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/attachments.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/authentication.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/authentication.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/forms.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/forms.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/labelled_data.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/labelled_data.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/metadata.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/metadata.html |only nettskjemar-1.0.0/nettskjemar/inst/doc/nettskjemar.Rmd | 297 ++++ nettskjemar-1.0.0/nettskjemar/inst/doc/nettskjemar.html | 607 ++++++++-- nettskjemar-1.0.0/nettskjemar/inst/doc/submissions.Rmd |only nettskjemar-1.0.0/nettskjemar/inst/doc/submissions.html |only nettskjemar-1.0.0/nettskjemar/man/codebook.Rd | 10 nettskjemar-1.0.0/nettskjemar/man/get_raw_codebook.Rd | 12 nettskjemar-1.0.0/nettskjemar/man/has_codebook.Rd |only nettskjemar-1.0.0/nettskjemar/man/nettskjemar-package.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_add_labels.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_alter_checkbox.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_api_docs.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_auth_token.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_create_client.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_attachment.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_codebook.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_data.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_form_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_form_reports.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_forms.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_me.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_meta.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_submission.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_submission_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_get_submission_pdf.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_list_form_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_list_submission_attachments.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_req.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_write_codebook.Rd |only nettskjemar-1.0.0/nettskjemar/man/ns_write_meta.Rd |only nettskjemar-1.0.0/nettskjemar/tests/fixtures |only nettskjemar-1.0.0/nettskjemar/tests/spelling.R | 9 nettskjemar-1.0.0/nettskjemar/tests/testthat.R | 6 nettskjemar-1.0.0/nettskjemar/tests/testthat/helper-vcr.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/helpers.R | 8 nettskjemar-1.0.0/nettskjemar/tests/testthat/test-data_labels.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-attachment.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-auth.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-codebook.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-form.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-me.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-meta.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns-submission.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-ns_checkbox.R |only nettskjemar-1.0.0/nettskjemar/tests/testthat/test-utils.R | 85 - nettskjemar-1.0.0/nettskjemar/vignettes/attachments.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/attachments.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/authentication.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/authentication.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/forms.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/forms.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/labelled_data.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/labelled_data.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/metadata.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/metadata.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/nettskjemar.Rmd | 297 ++++ nettskjemar-1.0.0/nettskjemar/vignettes/nettskjemar.Rmd.orig |only nettskjemar-1.0.0/nettskjemar/vignettes/static/lab-overview-1.png |only nettskjemar-1.0.0/nettskjemar/vignettes/static/ns_vidat-1.png |only nettskjemar-1.0.0/nettskjemar/vignettes/submissions.Rmd |only nettskjemar-1.0.0/nettskjemar/vignettes/submissions.Rmd.orig |only 123 files changed, 1462 insertions(+), 387 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.18 dated 2024-12-14 and 2.19.1 dated 2025-03-17
DESCRIPTION | 22 - MD5 | 108 +++-- NAMESPACE | 11 NEWS.md | 17 R/Design.R | 23 + R/PBA.R | 69 ++- R/SimCheck.R | 8 R/SimCollect.R | 8 R/SimDesign.R | 2 R/SimFunctions.R | 8 R/SimSolve.R | 16 R/analysis.R | 35 + R/functions.R | 30 + R/notifications.R |only R/reSummarise.R | 24 + R/runArraySimulation.R | 16 R/runSimulation.R | 135 ++++--- R/summary_functions.R | 6 R/util.R | 62 +-- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Catch_errors.R | 14 inst/doc/Catch_errors.html | 342 +++++++++++------- inst/doc/Fixed_obj_fun.R | 14 inst/doc/Fixed_obj_fun.html | 241 +++++++----- inst/doc/HPC-computing.R | 225 ++++++----- inst/doc/HPC-computing.Rmd | 15 inst/doc/HPC-computing.html | 733 ++++++++++++++++++++++++++++----------- inst/doc/MultipleAnalyses.R | 194 +++++----- inst/doc/MultipleAnalyses.html | 318 ++++++++++------ inst/doc/Parallel-computing.R | 74 +-- inst/doc/Parallel-computing.html | 315 ++++++++++------ inst/doc/Saving-results.R | 18 inst/doc/Saving-results.html | 311 ++++++++++------ inst/doc/SimDesign-intro.R | 4 inst/doc/SimDesign-intro.html | 453 ++++++++++++++++-------- man/PBA.Rd | 8 man/SimCheck.Rd | 3 man/SimCollect.Rd | 8 man/SimFunctions.Rd | 8 man/SimSolve.Rd | 9 man/bias.Rd | 2 man/clusterSetRNGSubStream.Rd | 2 man/createDesign.Rd | 13 man/listAvailableNotifiers.Rd |only man/new_PushbulletNotifier.Rd |only man/new_TelegramNotifier.Rd |only man/notify.PushbulletNotifier.Rd |only man/notify.Rd |only man/notify.TelegramNotifier.Rd |only man/reSummarise.Rd | 8 man/runSimulation.Rd | 79 ++-- man/timeFormater.Rd | 14 tests/tests/archive |only tests/tests/test-01-core.R | 11 tests/tests/test-02-aggregate.R | 2 tests/tests/test-03-array.R | 16 vignettes/HPC-computing.Rmd | 15 59 files changed, 2575 insertions(+), 1498 deletions(-)
Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration
The 'Rcpp' package contains a C++ library that facilitates the integration of
R and C++ in various ways. This package provides some usage examples.
Note that the documentation in this package currently does not cover all the
features in the package. The site <https://gallery.rcpp.org> regroups a large
number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppExamples versions 0.1.9 dated 2019-08-24 and 0.1.10 dated 2025-03-17
ChangeLog | 94 +++++++++++++++++++++++++++++++++++++++++++- DESCRIPTION | 24 +++++++---- MD5 | 26 ++++++------ NAMESPACE | 6 +- R/RcppExports.R | 26 ++++++++++++ README.md | 15 ++++--- inst/NEWS.Rd | 19 +++++++- man/RcppExamples-package.Rd | 2 man/RcppRNGsExample.Rd | 8 +-- man/factor2char.Rd |only src/DateExample.cpp | 23 ---------- src/FactorExample.cpp |only src/Makevars | 7 +-- src/Makevars.win | 8 +-- src/RcppExports.cpp | 29 +++++++++++++ 15 files changed, 217 insertions(+), 70 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 1.0.1 dated 2023-09-18 and 1.0.2 dated 2025-03-17
DESCRIPTION | 11 +- MD5 | 80 +++++++++--------- NEWS.md | 41 +++++++++ R/assign_to_R_env.R | 2 R/check_digit.R |only R/check_if_unique_rows.R | 2 R/clean_path_name.R | 2 R/clear.R | 2 R/close_all_connections.R | 2 R/dot_helper.R | 2 R/dt_row_to_string.R | 2 R/equals2.R | 2 R/feedback.R | 2 R/file_lines_to_list.R | 4 R/firstup.R | 2 R/format_POSIXct.R | 2 R/get_config.R | 2 R/get_current_timestamp.R | 2 R/is.empty.R | 4 R/is_date_format.R | 2 R/notin.R | 2 R/number_to_position.R | 2 R/paste2.R | 2 R/paste_pct_sum.R | 2 R/pretty_timestamp.R | 2 R/rep2.R | 2 R/robust_round.R | 2 R/setdiff_all.R | 2 R/setenv2.R | 2 R/setenv_file.R | 2 R/string_replacements.R | 2 R/time_diff_print.R | 6 - R/trim.space.R | 16 +-- R/vgsub.R | 2 R/zzz.R | 2 README.md | 167 ++++++++++++++++++++------------------ man/dt_row_to_string.Rd | 3 man/paste2.Rd | 11 +- man/time_diff_print.Rd | 4 tests/testthat/test-check_digit.R |only tests/testthat/test-feedback.R | 2 tests/testthat/test-lints.R | 2 42 files changed, 229 insertions(+), 176 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification <https://github.github.com/gfm/> defines
a rationalized version of markdown syntax. This package uses the 'cmark'
reference implementation for converting markdown text into various formats
including html, latex and groff man. In addition it exposes the markdown
parse tree in xml format. Also includes opt-in support for GFM extensions
including tables, autolinks, and strikethrough text.
Author: Jeroen Ooms [aut, cre] ,
John MacFarlane [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between commonmark versions 1.9.2 dated 2024-10-04 and 1.9.4 dated 2025-03-17
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NEWS | 4 ++++ R/extensions.R | 2 +- man/extensions.Rd | 2 +- src/Makevars | 6 +++--- src/cmark/node.c | 4 ++++ src/cmark/xml.c | 19 +++++++++++++++++++ src/patches |only src/wrapper.c | 1 + tests/testthat/test-extensions.R | 18 +++++++++--------- 11 files changed, 57 insertions(+), 27 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.15.5 dated 2025-03-01 and 0.15.7 dated 2025-03-17
DESCRIPTION | 6 MD5 | 75 ++++---- NEWS.md | 14 + R/nix_build.R | 62 +++---- R/rix.R | 19 ++ R/rix_helpers.R | 102 ++++++++++-- README.md | 21 ++ inst/doc/d1-installing-r-packages-in-a-nix-environment.R | 11 + inst/doc/d1-installing-r-packages-in-a-nix-environment.Rmd | 25 ++ inst/doc/d1-installing-r-packages-in-a-nix-environment.html | 68 +++++--- inst/extdata/available_df.csv | 2 inst/extdata/default.nix | 30 +-- man/nix_build.Rd | 35 ++-- man/renv2nix.Rd | 4 man/rix.Rd | 6 tests/testthat/_snaps/renv_helpers/default_datathin.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix | 20 +- tests/testthat/_snaps/renv_helpers/default_v1-0-7.nix | 20 +- tests/testthat/_snaps/rix-python |only tests/testthat/_snaps/rix/bioc-devel_default.nix | 20 +- tests/testthat/_snaps/rix/bleeding-edge_default.nix | 20 +- tests/testthat/_snaps/rix/code_default.nix | 20 +- tests/testthat/_snaps/rix/codium_default.nix | 20 +- tests/testthat/_snaps/rix/date_default.nix | 20 +- tests/testthat/_snaps/rix/frozen-edge_default.nix | 20 +- tests/testthat/_snaps/rix/no_quarto_default.nix | 20 +- tests/testthat/_snaps/rix/one_git_default.nix | 20 +- tests/testthat/_snaps/rix/other_default.nix | 20 +- tests/testthat/_snaps/rix/positron_default.nix | 20 +- tests/testthat/_snaps/rix/r-devel-bioc-devel_default.nix | 20 +- tests/testthat/_snaps/rix/r-devel_default.nix | 20 +- tests/testthat/_snaps/rix/rstudio_default.nix | 20 +- tests/testthat/_snaps/rix/yes_quarto_default.nix | 20 +- tests/testthat/test-rix-python.R |only tests/testthat/testdata/remote-pkgs/gen_envs.R |only tests/testthat/testdata/remote-pkgs/mlr3_default.nix | 20 +- tests/testthat/testdata/remote-pkgs/mlr3_dups_default.nix | 20 +- vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd | 25 ++ 40 files changed, 588 insertions(+), 337 deletions(-)
Title: Single Tree Simulator
Description: Framework to build an individual tree simulator.
Author: Clara Anton Fernandez [aut] ,
Ignacio Sevillano [cre]
Maintainer: Ignacio Sevillano <ignacio.sevillano@nibio.no>
Diff between sitree versions 0.1-14 dated 2024-02-07 and 0.1-15 dated 2025-03-17
DESCRIPTION | 22 ++++++++----- MD5 | 8 ++-- build/vignette.rds |binary inst/doc/SiTree.html | 72 ++++++++++++++++++++++---------------------- inst/doc/TestEquations.html | 6 +-- 5 files changed, 57 insertions(+), 51 deletions(-)
Title: Power Analysis for Research Experiments
Description: Provides tools for calculating statistical power for experiments
analyzed using linear mixed models. It supports standard designs, including
randomized block, split-plot, and Latin Square designs, while offering flexibility
to accommodate a variety of other complex study designs.
Author: Kai Wang [aut, cre, cph] ,
Mutian Niu [aut, cph]
Maintainer: Kai Wang <kai.wang@usys.ethz.ch>
Diff between pwr4exp versions 0.1.0 dated 2024-10-11 and 1.0.0 dated 2025-03-17
pwr4exp-0.1.0/pwr4exp/LICENSE |only pwr4exp-0.1.0/pwr4exp/R/data.R |only pwr4exp-0.1.0/pwr4exp/R/design-generating.R |only pwr4exp-0.1.0/pwr4exp/R/power-calculation.R |only pwr4exp-0.1.0/pwr4exp/R/sample-size.R |only pwr4exp-0.1.0/pwr4exp/R/utils_df.R |only pwr4exp-0.1.0/pwr4exp/man/calc.theta.Rd |only pwr4exp-0.1.0/pwr4exp/man/customLmerMod-class.Rd |only pwr4exp-0.1.0/pwr4exp/man/find_sample_size.Rd |only pwr4exp-0.1.0/pwr4exp/man/fit.pseu.model.Rd |only pwr4exp-0.1.0/pwr4exp/man/theta.names.Rd |only pwr4exp-1.0.0/pwr4exp/DESCRIPTION | 36 pwr4exp-1.0.0/pwr4exp/MD5 | 66 pwr4exp-1.0.0/pwr4exp/NAMESPACE | 28 pwr4exp-1.0.0/pwr4exp/NEWS.md | 2 pwr4exp-1.0.0/pwr4exp/R/data_documentation.R |only pwr4exp-1.0.0/pwr4exp/R/df_utils.R |only pwr4exp-1.0.0/pwr4exp/R/mkdesign.R |only pwr4exp-1.0.0/pwr4exp/R/power_calculation.R |only pwr4exp-1.0.0/pwr4exp/R/standard_designs.R |only pwr4exp-1.0.0/pwr4exp/R/utils.R | 1737 ++++++++++++++++++++-- pwr4exp-1.0.0/pwr4exp/README.md | 147 + pwr4exp-1.0.0/pwr4exp/build/vignette.rds |binary pwr4exp-1.0.0/pwr4exp/inst/doc/pwr4exp.R | 189 +- pwr4exp-1.0.0/pwr4exp/inst/doc/pwr4exp.Rmd | 1288 ++++++++-------- pwr4exp-1.0.0/pwr4exp/inst/doc/pwr4exp.html | 1756 +++++++++++++---------- pwr4exp-1.0.0/pwr4exp/man/contrast1D.Rd |only pwr4exp-1.0.0/pwr4exp/man/contrastMD.Rd |only pwr4exp-1.0.0/pwr4exp/man/create_designs.Rd | 260 +-- pwr4exp-1.0.0/pwr4exp/man/df.cod.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.crd.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.lsd.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.rcbd.Rd | 35 pwr4exp-1.0.0/pwr4exp/man/df.spd.Rd | 22 pwr4exp-1.0.0/pwr4exp/man/expandDoubleVerts.Rd |only pwr4exp-1.0.0/pwr4exp/man/factorize.Rd |only pwr4exp-1.0.0/pwr4exp/man/findbars.Rd |only pwr4exp-1.0.0/pwr4exp/man/milk.Rd | 2 pwr4exp-1.0.0/pwr4exp/man/mkRTrms.Rd |only pwr4exp-1.0.0/pwr4exp/man/mkReTrms.Rd |only pwr4exp-1.0.0/pwr4exp/man/mkStruct.Rd |only pwr4exp-1.0.0/pwr4exp/man/mkdesign.Rd |only pwr4exp-1.0.0/pwr4exp/man/nobars.Rd |only pwr4exp-1.0.0/pwr4exp/man/pwr.anova.Rd | 42 pwr4exp-1.0.0/pwr4exp/man/pwr.contrast.Rd | 75 pwr4exp-1.0.0/pwr4exp/man/pwr.summary.Rd |only pwr4exp-1.0.0/pwr4exp/man/subbars.Rd |only pwr4exp-1.0.0/pwr4exp/vignettes/pwr4exp.Rmd | 1288 ++++++++-------- 48 files changed, 4500 insertions(+), 2578 deletions(-)
Title: Periodically Correlated and Periodically Integrated Time Series
Description: Classes and methods for modelling and simulation of
periodically correlated (PC) and periodically integrated time
series. Compute theoretical periodic autocovariances and related
properties of PC autoregressive moving average models. Some original
methods including Boshnakov & Iqelan (2009)
<doi:10.1111/j.1467-9892.2009.00617.x>, Boshnakov (1996)
<doi:10.1111/j.1467-9892.1996.tb00281.x>.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between pcts versions 0.15.7 dated 2023-11-25 and 0.15.8 dated 2025-03-17
pcts-0.15.7/pcts/data/ex1f.rda |only pcts-0.15.8/pcts/DESCRIPTION | 10 pcts-0.15.8/pcts/MD5 | 62 pcts-0.15.8/pcts/NAMESPACE | 838 +-- pcts-0.15.8/pcts/NEWS.md | 880 ++-- pcts-0.15.8/pcts/R/classCycle.R | 2138 +++++----- pcts-0.15.8/pcts/build/partial.rdb |binary pcts-0.15.8/pcts/build/vignette.rds |binary pcts-0.15.8/pcts/data/ex1f.R |only pcts-0.15.8/pcts/inst/REFERENCES.bib | 1 pcts-0.15.8/pcts/inst/auto/REFERENCES.el | 52 pcts-0.15.8/pcts/inst/doc/pcts_data.R | 128 pcts-0.15.8/pcts/inst/doc/pcts_data.html | 1014 ++-- pcts-0.15.8/pcts/man/FittedPeriodicArmaModel-class.Rd | 6 pcts-0.15.8/pcts/man/PartialPeriodicAutocorrelations-class.Rd | 4 pcts-0.15.8/pcts/man/Pctime.Rd | 326 - pcts-0.15.8/pcts/man/PeriodicArmaFilter-class.Rd | 4 pcts-0.15.8/pcts/man/PeriodicAutocorrelations-class.Rd | 4 pcts-0.15.8/pcts/man/PeriodicAutocovariances-class.Rd | 4 pcts-0.15.8/pcts/man/PeriodicBJFilter-class.Rd | 6 pcts-0.15.8/pcts/man/PeriodicInterceptSpec-class.Rd | 8 pcts-0.15.8/pcts/man/PeriodicMTS-class.Rd | 2 pcts-0.15.8/pcts/man/PeriodicSPFilter-class.Rd | 6 pcts-0.15.8/pcts/man/PeriodicTS-class.Rd | 8 pcts-0.15.8/pcts/man/PeriodicVector-class.Rd | 8 pcts-0.15.8/pcts/man/SamplePeriodicAutocorrelations-class.Rd | 6 pcts-0.15.8/pcts/man/SamplePeriodicAutocovariances-class.Rd | 6 pcts-0.15.8/pcts/man/fit_trigPAR_optim.Rd | 170 pcts-0.15.8/pcts/man/partialAutocovariances-methods.Rd | 1 pcts-0.15.8/pcts/man/pcTest-methods.Rd | 210 pcts-0.15.8/pcts/man/pcacfMat.Rd | 4 pcts-0.15.8/pcts/man/pcarma_solve.Rd | 514 +- pcts-0.15.8/pcts/man/sim_parCoef.Rd | 4 33 files changed, 3220 insertions(+), 3204 deletions(-)
Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a
pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4
class system. This package allows the user to read/write a
pharmacometric model from/to files and adapt it further on the fly in
the R environment. For this purpose, this package provides an
intuitive API to add, modify or delete equations, ordinary
differential equations (ODE's), model parameters or compartment
properties (like infusion duration or rate, bioavailability and
initial values). Finally, this package also provides a useful export
of the model for use with simulation packages 'rxode2' and 'mrgsolve'.
This package is designed and intended to be used with package
'campsis', a PK/PD simulation platform built on top of 'rxode2' and
'mrgsolve'.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsismod versions 1.2.0 dated 2025-02-07 and 1.2.1 dated 2025-03-17
campsismod-1.2.0/campsismod/man/extractModelParametersFromNames.Rd |only campsismod-1.2.1/campsismod/DESCRIPTION | 10 campsismod-1.2.1/campsismod/MD5 | 31 +- campsismod-1.2.1/campsismod/NAMESPACE | 10 campsismod-1.2.1/campsismod/NEWS.md | 6 campsismod-1.2.1/campsismod/R/campsis_model.R | 8 campsismod-1.2.1/campsismod/R/omega_block.R | 9 campsismod-1.2.1/campsismod/R/parameter_uncertainty_utils.R | 76 +++-- campsismod-1.2.1/campsismod/R/replicated_campsis_model.R | 131 +++++++--- campsismod-1.2.1/campsismod/R/replication_settings.R | 19 - campsismod-1.2.1/campsismod/R/rxode_conversion.R | 65 +--- campsismod-1.2.1/campsismod/man/AutoReplicationSettings.Rd | 6 campsismod-1.2.1/campsismod/man/add.Rd | 3 campsismod-1.2.1/campsismod/man/auto_replication_settings-class.Rd | 6 campsismod-1.2.1/campsismod/man/sampleFromInverseWishartCore.Rd | 4 campsismod-1.2.1/campsismod/tests/testthat/testMiscellaneous.R | 48 +++ campsismod-1.2.1/campsismod/tests/testthat/testReplicatedCampsisModel.R | 92 ++++--- 17 files changed, 345 insertions(+), 179 deletions(-)
Title: Generate and Simulate Deterministic Discrete-Time Compartmental
Models
Description: R package to build and simulate deterministic discrete-time compartmental models that can be non-Markov. Length of stay in each compartment can be defined to follow a parametric distribution (d_exponential(), d_gamma(), d_weibull(), d_lognormal()) or a non-parametric distribution (nonparametric()). Other supported types of transition from one compartment to another includes fixed transition (constant()), multinomial (multinomial()), fixed transition probability (transprob()).
Author: Thinh Ong [aut, cph] ,
Anh Phan [aut, cre] ,
Marc Choisy [aut] ,
Niels Lohman [ctb],
Bjoern Hoehrmann [ctb],
Florian Loitsch [ctb],
Ingo Berg [ctb]
Maintainer: Anh Phan <anhptq@oucru.org>
Diff between denim versions 1.0.0 dated 2024-06-05 and 1.0.1 dated 2025-03-17
denim-1.0.0/denim/inst/doc/denim_vs_deSolve.R |only denim-1.0.0/denim/inst/doc/denim_vs_deSolve.Rmd |only denim-1.0.0/denim/inst/doc/denim_vs_deSolve.html |only denim-1.0.0/denim/man/figures/logo.png |only denim-1.0.0/denim/vignettes/denim_vs_deSolve.Rmd |only denim-1.0.1/denim/DESCRIPTION | 17 denim-1.0.1/denim/MD5 | 35 denim-1.0.1/denim/NEWS.md | 2 denim-1.0.1/denim/R/simulators.R | 9 denim-1.0.1/denim/README.md | 2 denim-1.0.1/denim/build/vignette.rds |binary denim-1.0.1/denim/inst/doc/deSolve_to_denim.R |only denim-1.0.1/denim/inst/doc/deSolve_to_denim.Rmd |only denim-1.0.1/denim/inst/doc/deSolve_to_denim.html |only denim-1.0.1/denim/inst/doc/denim.R | 26 denim-1.0.1/denim/inst/doc/denim.Rmd | 29 denim-1.0.1/denim/inst/doc/denim.html | 1263 ++++++++++++++++++++--- denim-1.0.1/denim/man/figures/logo.svg |only denim-1.0.1/denim/src/ModelJSON.cpp | 3 denim-1.0.1/denim/src/json.h | 4 denim-1.0.1/denim/tests/testthat/test-result.R | 2 denim-1.0.1/denim/vignettes/deSolve_to_denim.Rmd |only denim-1.0.1/denim/vignettes/denim.Rmd | 29 denim-1.0.1/denim/vignettes/references.bib |only 24 files changed, 1260 insertions(+), 161 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-12 0.2.1
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Description: Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
Author: Zheng Ren [aut, cre, cph] ,
Andrew Chen [aut, cph] ,
Elizabeth Horwath [ctb]
Maintainer: Zheng Ren <zren1422@gmail.com>
Diff between ComBatFamQC versions 1.0.4 dated 2025-01-25 and 1.0.5 dated 2025-03-17
DESCRIPTION | 8 - MD5 | 8 - NEWS.md | 4 tests/testthat/test-age_shiny.R | 79 ++------------ tests/testthat/test-comfam_shiny.R | 206 +++++++++++-------------------------- 5 files changed, 88 insertions(+), 217 deletions(-)
Title: Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies
Description: DNA methylation is an epigenetic modification involved in genomic stability,
gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl group to cytosines,
for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
Tissue-specific methylation patterns lead to genomic regions with different characteristic
methylation levels.
E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
expressed genes tend to be unmethylated.
'MethEvolSIM' is a model-based simulation software for the generation and modification
of cytosine methylation patterns along a given tree, which can be a genealogy of
cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
The simulations are based on an extension of the model of
Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
the met [...truncated...]
Author: Sara Castillo Vicente [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Diff between MethEvolSIM versions 0.1.7 dated 2024-09-22 and 0.2 dated 2025-03-17
DESCRIPTION | 8 MD5 | 94 NAMESPACE | 26 R/multiRegion_SIM.R | 1090 ++++++++--- R/summaryStatistics.R |only R/user_functions.R | 73 build/vignette.rds |binary inst/doc/CFTP_method-vignette.R |only inst/doc/CFTP_method-vignette.Rmd |only inst/doc/CFTP_method-vignette.html |only inst/doc/intro-vignette.R | 16 inst/doc/intro-vignette.Rmd | 4 inst/doc/intro-vignette.html | 250 +- inst/doc/sumstats-vignette.R |only inst/doc/sumstats-vignette.Rmd |only inst/doc/sumstats-vignette.html |only man/MeanSiteFChange_cherry.Rd |only man/categorize_islandGlbSt.Rd |only man/categorize_siteMethSt.Rd |only man/cftpStepGenerator.Rd |only man/combiStructureGenerator.Rd | 196 + man/compare_CherryFreqs.Rd |only man/computeFitch_islandGlbSt.Rd |only man/compute_fitch.Rd |only man/compute_meanCor_i.Rd |only man/compute_meanCor_ni.Rd |only man/countSites_cherryMethDiff.Rd |only man/count_upm.Rd |only man/freqSites_cherryMethDiff.Rd |only man/get_cherryDist.Rd |only man/get_islandMeanFreqM.Rd |only man/get_islandMeanFreqP.Rd |only man/get_islandSDFreqM.Rd |only man/get_islandSDFreqP.Rd |only man/get_meanMeth_islands.Rd |only man/get_nonislandMeanFreqM.Rd |only man/get_nonislandMeanFreqP.Rd |only man/get_nonislandSDFreqM.Rd |only man/get_nonislandSDFreqP.Rd |only man/get_siteFChange_cherry.Rd |only man/mean_CherryFreqsChange_i.Rd |only man/mean_TreeFreqsChange_i.Rd |only man/pValue_CherryFreqsChange_i.Rd |only man/simulate_evolData.Rd | 9 man/simulate_initialData.Rd | 14 man/singleStructureGenerator.Rd | 188 + man/treeMultiRegionSimulator.Rd | 13 man/validate_dataAcrossTips.Rd |only man/validate_data_cherryDist.Rd |only man/validate_structureIndices.Rd |only man/validate_tree.Rd |only tests/testthat/test-multiRegion_SIM.R | 3144 +++++++++++++++++++++++++------- tests/testthat/test-summaryStatistics.R |only tests/testthat/test-user_functions.R | 94 vignettes/CFTP_method-vignette.Rmd |only vignettes/Figures |only vignettes/intro-vignette.Rmd | 4 vignettes/references.bib | 170 + vignettes/sumstats-vignette.Rmd |only 59 files changed, 4318 insertions(+), 1075 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-13 1.0.0
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 1.1.1 dated 2025-02-26 and 1.1.2 dated 2025-03-17
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 6 +++++ R/args_validation.R | 12 +++++++++- R/ctable.R | 50 +++++++++++++++++++++++++++++++++++++-------- R/helpers.R | 5 ++++ inst/doc/introduction.html | 14 ++++++------ inst/doc/rmarkdown.html | 42 ++++++++++++++++++------------------- man/ctable.Rd | 32 ++++++++++++++++++++++++---- 9 files changed, 130 insertions(+), 53 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
[...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 3.1-4 dated 2024-11-15 and 3.1-6 dated 2025-03-17
DESCRIPTION | 16 +++-- MD5 | 138 ++++++++++++++++++++++----------------------- NEWS | 23 +++++++ data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/btb.rda |binary data/cells.rda |binary data/cetaceans.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/concrete.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/meningitis.rda |only data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwood3.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/shelling.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/stonetools.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 3 man/macros/defns.Rd | 4 - man/meningitis.Rd |only man/paracou.Rd | 2 man/shelling.Rd | 4 + man/spruces.Rd | 2 71 files changed, 116 insertions(+), 78 deletions(-)
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
in a Bayesian Framework
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
Author: Abigail G. Keller [aut, cre],
Ryan P. Kelly [ctb],
Chitra M. Saraswati [rev],
Saras M. Windecker [rev]
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Diff between eDNAjoint versions 0.3.1 dated 2025-01-25 and 0.3.2 dated 2025-03-17
DESCRIPTION | 6 - MD5 | 20 ++--- R/goby_data.R | 2 inst/stan/functions/calc_loglik.stan | 118 +++++++++++++++++----------------- inst/stan/functions/calc_mu.stan | 8 +- inst/stan/functions/calc_p11.stan | 2 inst/stan/joint_continuous.stan | 4 - inst/stan/joint_count.stan | 6 - inst/stan/traditional_continuous.stan | 4 - inst/stan/traditional_count.stan | 6 - man/goby_data.Rd | 2 11 files changed, 89 insertions(+), 89 deletions(-)