Title: Wrap Vectors in Markdown Formatting
Description: Ease the transition between R vectors and markdown
text. With 'gluedown' and 'rmarkdown', users can create traditional
vectors in R, glue those strings together with the markdown syntax,
and print those formatted vectors directly to the document. This
package primarily uses GitHub Flavored Markdown (GFM), an offshoot of
the unambiguous CommonMark specification by John MacFarlane (2019)
<https://spec.commonmark.org/>.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between gluedown versions 1.0.4 dated 2021-05-10 and 1.0.5 dated 2022-11-04
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 R/md-convert.R | 4 README.md | 6 build/vignette.rds |binary inst/doc/github-spec.html | 831 +++++++++++++++++++++++++--------- inst/doc/literal-programming.html | 409 +++++++++++++++- tests/testthat/test-4.5-fenced-code.R | 2 9 files changed, 1020 insertions(+), 258 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Provides a common framework for optimization of black-box
functions for other packages, e.g. 'mlr3tuning' or 'mlr3fselect'. It
offers various optimization methods e.g. grid search, random search,
generalized simulated annealing and iterated racing.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 0.6.0 dated 2022-10-25 and 0.7.0 dated 2022-11-04
bbotk-0.6.0/bbotk/R/helper_irace.R |only bbotk-0.7.0/bbotk/DESCRIPTION | 27 + bbotk-0.7.0/bbotk/MD5 | 29 +- bbotk-0.7.0/bbotk/NAMESPACE | 2 bbotk-0.7.0/bbotk/NEWS.md | 13 bbotk-0.7.0/bbotk/R/ObjectiveRFunDt.R | 14 - bbotk-0.7.0/bbotk/R/ObjectiveRFunMany.R |only bbotk-0.7.0/bbotk/R/OptimizerIrace.R | 108 ++++++- bbotk-0.7.0/bbotk/R/Terminator.R | 2 bbotk-0.7.0/bbotk/R/helper.R | 24 + bbotk-0.7.0/bbotk/build/partial.rdb |binary bbotk-0.7.0/bbotk/inst/doc/bbotk.html | 238 ++++++++--------- bbotk-0.7.0/bbotk/man/ObjectiveRFunMany.Rd |only bbotk-0.7.0/bbotk/man/branin.Rd | 21 + bbotk-0.7.0/bbotk/man/mlr_optimizers_irace.Rd | 25 - bbotk-0.7.0/bbotk/tests/testthat/test_Objective.R | 56 +++- bbotk-0.7.0/bbotk/tests/testthat/test_OptimizerIrace.R | 118 +++++--- 17 files changed, 436 insertions(+), 241 deletions(-)
Title: Extending 'gt' for Beautiful HTML Tables
Description: Provides additional functions for creating beautiful tables
with 'gt'. The functions are generally wrappers around boilerplate or
adding opinionated niche capabilities and helpers functions.
Author: Thomas Mock [aut, cre, cph],
Daniel D. Sjoberg [ctb]
Maintainer: Thomas Mock <j.thomasmock@gmail.com>
Diff between gtExtras versions 0.4.2 dated 2022-09-03 and 0.4.3 dated 2022-11-04
gtExtras-0.4.2/gtExtras/man/img_circle.Rd |only gtExtras-0.4.3/gtExtras/DESCRIPTION | 8 - gtExtras-0.4.3/gtExtras/MD5 | 83 +++++----- gtExtras-0.4.3/gtExtras/NAMESPACE | 6 gtExtras-0.4.3/gtExtras/NEWS.md | 6 gtExtras-0.4.3/gtExtras/R/fontawesome-icons.R | 8 - gtExtras-0.4.3/gtExtras/R/gt_alert_icon.R |only gtExtras-0.4.3/gtExtras/R/gt_highlight_cols.R | 5 gtExtras-0.4.3/gtExtras/R/gt_highlight_rows.R | 7 gtExtras-0.4.3/gtExtras/R/gt_img_circle.R | 93 ++++++++++-- gtExtras-0.4.3/gtExtras/R/gt_plt_bar.R | 1 gtExtras-0.4.3/gtExtras/R/gt_plt_sparkline.R | 4 gtExtras-0.4.3/gtExtras/R/merge_and_stack.R | 92 +++++++++++ gtExtras-0.4.3/gtExtras/man/add_text_img.Rd | 2 gtExtras-0.4.3/gtExtras/man/fa_icon_repeat.Rd | 2 gtExtras-0.4.3/gtExtras/man/fmt_pad_num.Rd | 2 gtExtras-0.4.3/gtExtras/man/fmt_pct_extra.Rd | 2 gtExtras-0.4.3/gtExtras/man/fmt_symbol_first.Rd | 2 gtExtras-0.4.3/gtExtras/man/generate_df.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_add_divider.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_alert_icon.Rd |only gtExtras-0.4.3/gtExtras/man/gt_badge.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_double_table.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_duplicate_column.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_fa_column.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_fa_rank_change.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_fa_rating.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_fa_repeats.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_highlight_cols.Rd | 7 gtExtras-0.4.3/gtExtras/man/gt_highlight_rows.Rd | 5 gtExtras-0.4.3/gtExtras/man/gt_img_border.Rd |only gtExtras-0.4.3/gtExtras/man/gt_img_circle.Rd | 28 ++- gtExtras-0.4.3/gtExtras/man/gt_img_multi_rows.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_img_rows.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_index.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_merge_stack.Rd | 2 gtExtras-0.4.3/gtExtras/man/gt_merge_stack_color.Rd |only gtExtras-0.4.3/gtExtras/man/gt_plt_sparkline.Rd | 4 gtExtras-0.4.3/gtExtras/man/gt_two_column_layout.Rd | 2 gtExtras-0.4.3/gtExtras/man/gtsave_extra.Rd | 2 gtExtras-0.4.3/gtExtras/man/img_header.Rd | 2 gtExtras-0.4.3/gtExtras/man/pad_fn.Rd | 2 gtExtras-0.4.3/gtExtras/man/tab_style_by_grp.Rd | 2 gtExtras-0.4.3/gtExtras/tests/testthat/test-fmt_pct_extra.R | 28 +-- gtExtras-0.4.3/gtExtras/tests/testthat/test-gt_text_img.R | 6 45 files changed, 343 insertions(+), 94 deletions(-)
Title: Functional Data Analysis and Partial Differential Equations
(PDE); Statistical Analysis of Functional and Spatial Data,
Based on Regression with PDE Regularization
Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization. See Sangalli, L. M. (2021). Spatial Regression With Partial Differential Equation Regularisation. International Statistical Review, 89(3), 505-531. for an overview. The release 1.1-9 requires R (>= 4.2.0) to be installed on windows machines.
Author: Eleonora Arnone [aut, cre],
Laura M. Sangalli [aut],
Eardi Lila [aut],
Jim Ramsay [aut],
Luca Formaggia [aut],
Giovanni Ardenghi [ctb],
Michele Cavazzutti [ctb],
Aldo Clemente [ctb],
Alessandra Colli [ctb],
Alberto Colombo [ctb],
Luca Colombo [ctb],
[...truncated...]
Maintainer: Eleonora Arnone <eleonora.arnone@polimi.it>
Diff between fdaPDE versions 1.1-10 dated 2022-10-31 and 1.1-11 dated 2022-11-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/smoothing_volume_CPP.R | 2 +- R/smoothing_volume_CPP_time.R | 2 +- src/FdaPDE.h | 9 ++++++--- src/Inference/Include/Wald_imp.h | 1 - 6 files changed, 17 insertions(+), 15 deletions(-)
Title: Consensus Value Constructor
Description: An implementation of the International Bureau of Weights and Measures (BIPM) generalized consensus estimators used to assign the reference value in a key comparison exercise. This can also be applied to any interlaboratory study. Given a set of different sources, primary laboratories or measurement methods this package provides an evaluation of the variance components according to the selected statistical method for consensus building. It also implements the comparison among different consensus builders and evaluates the participating method or sources against the consensus reference value. Based on a diverse set of references, DerSimonian-Laird (1986) <doi:10.1016/0197-2456(86)90046-2>, for a complete list of references look at the reference section in the package documentation.
Author: Hugo Gasca-Aragon
Maintainer: Hugo Gasca-Aragon <hugo_gasca_aragon@hotmail.com>
Diff between gconsensus versions 0.3.1 dated 2021-09-27 and 0.3.2 dated 2022-11-04
DESCRIPTION | 14 +-- MD5 | 36 ++++----- R/comparison.gconsensus.R | 12 +-- R/doe.gconsensus.R | 36 +++++---- R/gconsensus-internal.R | 30 +++++--- R/gconsensus.R | 47 ++++++++----- R/plot.comparison.R | 37 ++++++---- R/plot.doe.R | 19 ++--- R/plot.gconsensus.R | 166 +++++++++++++++++++++++++++++++++------------- R/toString.comparison.R | 2 R/toString.doe.R | 8 +- R/toString.gconsensus.R | 4 - build/partial.rdb |binary man/doe.gconsensus.Rd | 2 man/gconsensus-package.Rd | 33 ++++++--- man/gconsensus.Rd | 14 +-- man/plot.comparison.Rd | 5 + man/plot.doe.Rd | 7 + man/plot.gconsensus.Rd | 3 19 files changed, 309 insertions(+), 166 deletions(-)
Title: Cooperative Learning for Multi-View Analysis
Description: Cooperative learning combines the usual squared error loss of predictions with an agreement penalty to encourage the predictions from different data views to agree. By varying the weight of the agreement penalty, we get a continuum of solutions that include the well-known early and late fusion approaches. Cooperative learning chooses the degree of agreement (or fusion) in an adaptive manner, using a validation set or cross-validation to estimate test set prediction error. In the setting of cooperative regularized linear regression, the method combines the lasso penalty with the agreement penalty (Ding, D., Li, S., Narasimhan, B., Tibshirani, R. (2021) <doi:10.1073/pnas.2202113119>).
Author: Daisy Yi Ding [aut],
Robert J. Tibshirani [aut],
Balasubramanian Narasimhan [aut, cre],
Trevor Hastie [aut],
Kenneth Tay [aut],
James Yang [aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between multiview versions 0.4 dated 2022-09-02 and 0.7 dated 2022-11-04
DESCRIPTION | 10 MD5 | 59 ++-- NAMESPACE | 5 NEWS.md |only R/buildPredmat.coxnetlist.R |only R/coxpath.R |only R/cv.multiview.R | 45 ++- R/family.multiview.R | 12 R/get_start.R | 84 ------ R/multiview.R | 490 ++++++++++++++++++++++++++++------- R/multiview.path.R | 520 +++++++++++++++++--------------------- R/predict.multiview.R | 2 R/response.coxnet.R |only R/utils.R | 83 ++++++ R/view.contribution.R | 2 build/vignette.rds |binary inst/doc/multiview.R | 2 inst/doc/multiview.Rmd | 2 inst/doc/multiview.pdf |binary man/collapse_named_lists.Rd | 2 man/cox_obj_function.Rd |only man/cv.multiview.Rd | 15 - man/get_cox_lambda_max.Rd |only man/multiview.Rd | 140 ++++++++-- man/multiview.cox.fit.Rd |only man/multiview.cox.path.Rd |only man/multiview.fit.Rd | 85 +++--- man/multiview.path.Rd | 168 +++++++----- man/reshape_x_to_xlist.Rd | 2 man/response.coxnet.Rd |only man/select_matrix_list_columns.Rd | 2 man/to_nvar_index.Rd | 2 man/to_xlist_index.Rd | 2 man/view.contribution.Rd | 18 - vignettes/multiview.Rmd | 2 35 files changed, 1060 insertions(+), 694 deletions(-)
Title: Multiple Empirical Likelihood Tests
Description: Performs multiple empirical likelihood tests for linear and
generalized linear models. The package offers an easy-to-use interface
and flexibility in specifying hypotheses and calibration methods,
extending the framework to simultaneous inferences. The core
computational routines are implemented using the 'Eigen' C++ library
and 'RcppEigen' interface, with OpenMP for parallel computation.
Details of the testing procedures are given in Kim, MacEachern, and
Peruggia (2021) <arxiv:2112.09206>. This work was supported by the
U.S. National Science Foundation under Grants No. SES-1921523 and
DMS-2015552.
Author: Eunseop Kim [aut, cre],
Steven MacEachern [ctb, ths],
Mario Peruggia [ctb, ths],
Pierre Chausse [rev],
Alex Stringer [rev]
Maintainer: Eunseop Kim <kim.7302@osu.edu>
Diff between melt versions 1.8.0 dated 2022-09-20 and 1.9.0 dated 2022-11-04
melt-1.8.0/melt/R/logLik-methods.R |only melt-1.8.0/melt/tests/testthat/test-logLik.R |only melt-1.9.0/melt/DESCRIPTION | 8 melt-1.9.0/melt/MD5 | 192 ++++----- melt-1.9.0/melt/NEWS.md | 22 - melt-1.9.0/melt/R/AllClasses.R | 331 ++++++++++++--- melt-1.9.0/melt/R/AllGenerics.R | 185 +++++--- melt-1.9.0/melt/R/RcppExports.R | 4 melt-1.9.0/melt/R/calibrate.R | 7 melt-1.9.0/melt/R/chisq-methods.R | 15 melt-1.9.0/melt/R/coef-methods.R | 12 melt-1.9.0/melt/R/confint-methods.R | 48 ++ melt-1.9.0/melt/R/confreg-methods.R | 12 melt-1.9.0/melt/R/conv-methods.R | 18 melt-1.9.0/melt/R/critVal-methods.R | 12 melt-1.9.0/melt/R/data-thiamethoxam.R | 2 melt-1.9.0/melt/R/deprecated.R | 25 - melt-1.9.0/melt/R/describe_hypothesis.R | 5 melt-1.9.0/melt/R/el_control.R | 24 - melt-1.9.0/melt/R/el_glm.R | 10 melt-1.9.0/melt/R/el_lm.R | 8 melt-1.9.0/melt/R/el_mean.R | 13 melt-1.9.0/melt/R/el_sd.R | 7 melt-1.9.0/melt/R/eld-methods.R | 32 - melt-1.9.0/melt/R/elmt-methods.R | 21 melt-1.9.0/melt/R/elt-methods.R | 63 ++ melt-1.9.0/melt/R/getDF-methods.R | 10 melt-1.9.0/melt/R/getOptim-methods.R | 15 melt-1.9.0/melt/R/logL-methods.R | 15 melt-1.9.0/melt/R/logLR-methods.R | 15 melt-1.9.0/melt/R/nobs-methods.R | 10 melt-1.9.0/melt/R/pVal-methods.R | 20 melt-1.9.0/melt/R/print-methods.R | 405 +++++++++---------- melt-1.9.0/melt/R/show_convergence.R |only melt-1.9.0/melt/R/summary-methods.R | 116 +++-- melt-1.9.0/melt/data/thiamethoxam.rda |binary melt-1.9.0/melt/inst/doc/article.pdf |binary melt-1.9.0/melt/inst/doc/model.html | 12 melt-1.9.0/melt/inst/doc/performance.html | 26 - melt-1.9.0/melt/man/CEL-class.Rd | 75 +-- melt-1.9.0/melt/man/ConfregEL-class.Rd | 2 melt-1.9.0/melt/man/ControlEL-class.Rd | 5 melt-1.9.0/melt/man/EL-class.Rd | 75 +-- melt-1.9.0/melt/man/ELD-class.Rd | 2 melt-1.9.0/melt/man/ELMT-class.Rd | 16 melt-1.9.0/melt/man/ELT-class.Rd | 17 melt-1.9.0/melt/man/GLM-class.Rd | 53 +- melt-1.9.0/melt/man/LM-class.Rd | 53 +- melt-1.9.0/melt/man/QGLM-class.Rd | 53 +- melt-1.9.0/melt/man/SD-class.Rd | 17 melt-1.9.0/melt/man/SummaryEL-class.Rd |only melt-1.9.0/melt/man/SummaryELMT-class.Rd |only melt-1.9.0/melt/man/SummaryELT-class.Rd |only melt-1.9.0/melt/man/SummaryGLM-class.Rd | 59 ++ melt-1.9.0/melt/man/SummaryLM-class.Rd | 55 +- melt-1.9.0/melt/man/SummaryQGLM-class.Rd | 59 ++ melt-1.9.0/melt/man/chisq.Rd | 27 - melt-1.9.0/melt/man/clothianidin.Rd | 12 melt-1.9.0/melt/man/coef.Rd | 22 - melt-1.9.0/melt/man/confint.Rd | 34 - melt-1.9.0/melt/man/confreg.Rd | 34 - melt-1.9.0/melt/man/conv.Rd | 23 - melt-1.9.0/melt/man/critVal.Rd | 17 melt-1.9.0/melt/man/el_control.Rd | 52 +- melt-1.9.0/melt/man/el_eval.Rd | 84 ++- melt-1.9.0/melt/man/el_glm.Rd | 122 ++--- melt-1.9.0/melt/man/el_lm.Rd | 82 +-- melt-1.9.0/melt/man/el_mean.Rd | 40 + melt-1.9.0/melt/man/el_pairwise.Rd | 33 - melt-1.9.0/melt/man/el_sd.Rd | 26 - melt-1.9.0/melt/man/eld.Rd | 43 +- melt-1.9.0/melt/man/elmt.Rd | 55 +- melt-1.9.0/melt/man/elt.Rd | 85 ++- melt-1.9.0/melt/man/getDF.Rd | 18 melt-1.9.0/melt/man/getOptim.Rd | 28 - melt-1.9.0/melt/man/logL.Rd | 18 melt-1.9.0/melt/man/logLR.Rd | 18 melt-1.9.0/melt/man/logLik.Rd | 40 - melt-1.9.0/melt/man/logLikEL-class.Rd | 2 melt-1.9.0/melt/man/melt-package.Rd | 4 melt-1.9.0/melt/man/nobs.Rd | 10 melt-1.9.0/melt/man/pVal.Rd | 31 + melt-1.9.0/melt/man/plot.Rd | 11 melt-1.9.0/melt/man/print.Rd | 37 - melt-1.9.0/melt/man/sigTests.Rd | 6 melt-1.9.0/melt/man/summary.Rd | 40 + melt-1.9.0/melt/man/thiamethoxam.Rd | 10 melt-1.9.0/melt/man/weights.Rd | 8 melt-1.9.0/melt/src/RcppExports.cpp | 25 + melt-1.9.0/melt/src/compute_confidence_intervals.cpp | 99 ++++ melt-1.9.0/melt/tests/testthat/test-confint.R | 30 + melt-1.9.0/melt/tests/testthat/test-confreg.R | 1 melt-1.9.0/melt/tests/testthat/test-el_glm.R | 1 melt-1.9.0/melt/tests/testthat/test-el_lm.R | 2 melt-1.9.0/melt/tests/testthat/test-el_mean.R | 9 melt-1.9.0/melt/tests/testthat/test-el_sd.R | 2 melt-1.9.0/melt/tests/testthat/test-eld.R | 2 melt-1.9.0/melt/tests/testthat/test-elmt.R | 18 melt-1.9.0/melt/tests/testthat/test-elt.R | 7 melt-1.9.0/melt/tests/testthat/test-skip_on_cran.R | 22 - 100 files changed, 2308 insertions(+), 1243 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.1 dated 2022-06-24 and 4.1-1 dated 2022-11-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 9 +++++++++ src/emf+.h | 8 ++++---- src/emf.h | 8 ++++---- 5 files changed, 25 insertions(+), 16 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package
supports the static site generator 'Hugo' (<https://gohugo.io>) best,
and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo'
(<https://hexo.io>).
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Alison Presmanes Hill [aut] ,
Amber Thomas [ctb],
Beilei Bian [ctb],
Brandon Greenwell [ctb],
Brian Barkley [ctb],
Deependra Dhakal [ctb],
Eric Nantz [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 1.13 dated 2022-09-24 and 1.14 dated 2022-11-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/hugo.R | 3 ++- R/render.R | 2 +- R/serve.R | 12 +++++++++--- R/utils.R | 2 +- inst/resources/Rprofile | 4 ++-- 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that
cannot be directly estimated from the data). These tools can be used
to define objects for creating, simulating, or validating values for
such parameters.
Author: Max Kuhn [aut],
Hannah Frick [aut, cre],
RStudio [cph, fnd]
Maintainer: Hannah Frick <hannah@rstudio.com>
Diff between dials versions 1.0.0 dated 2022-06-14 and 1.1.0 dated 2022-11-04
DESCRIPTION | 10 +-- MD5 | 82 +++++++++++++------------- NAMESPACE | 26 +++++++- NEWS.md | 25 +++++++ R/aaa_ranges.R | 3 R/aaa_values.R | 49 +++++---------- R/compat-vctrs-helpers-parameters.R | 4 - R/constructors.R | 28 +++++--- R/dials-package.R | 5 + R/grids.R | 4 - R/param_Laplace.R | 1 R/param_adjust_reg_free.R | 1 R/param_bart.R | 7 -- R/param_class_weights.R | 1 R/param_degree.R | 2 R/param_engine_c50.R | 2 R/param_engine_cubist.R | 2 R/param_engine_earth.R | 1 R/param_engine_lightgbm.R |only R/param_engine_ranger.R | 3 R/param_engine_xgboost.R | 1 R/param_min_unique.R | 1 R/param_num_breaks.R | 1 R/param_num_clusters.R |only R/param_nzv.R | 2 R/param_over_ratio.R | 2 R/param_prune_method.R | 1 R/param_schedulers.R |only R/param_sparse_bayes_pca.R | 2 R/param_threshold.R | 1 inst/doc/dials.html | 31 +++++---- man/bart-param.Rd | 2 man/lightgbm_parameters.Rd |only man/new-param.Rd | 9 +- man/num_clusters.Rd |only man/scheduler-param.Rd |only man/value_validate.Rd | 3 tests/testthat/_snaps/constructors.md | 24 ++++++- tests/testthat/_snaps/encode_unit.md | 39 ++++++++---- tests/testthat/_snaps/pull_dials_object.md | 2 tests/testthat/_snaps/values.md | 7 ++ tests/testthat/test-compat-dplyr-parameters.R | 4 - tests/testthat/test-constructors.R | 23 +++++++ tests/testthat/test-params.R | 9 ++ tests/testthat/test-values.R | 77 ++++++------------------ 45 files changed, 281 insertions(+), 216 deletions(-)
Title: Testing for Partial Copulas and the Simplifying Assumption in
Vine Copulas
Description: Routines for two different test types, the Constant Conditional Correlation (CCC) test and the Vectorial Independence (VI) test are provided (Kurz and Spanhel (2022) <doi:10.1214/22-EJS2051>). The tests can be applied to check whether a conditional copula coincides with its partial copula. Functions to test whether a regular vine copula satisfies the so-called simplifying assumption or to test a single copula within a regular vine copula to be a (j-1)-th order partial copula are available. The CCC test comes with a decision tree approach to allow testing in high-dimensional settings.
Author: Malte S. Kurz [aut, cre]
Maintainer: Malte S. Kurz <mkurz-software@gmx.de>
Diff between pacotest versions 0.4.1 dated 2021-11-08 and 0.4.2 dated 2022-11-04
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ README.md | 2 +- inst/CITATION | 12 ++++++++---- man/pacotest-package.Rd | 4 ++-- man/pacotest.Rd | 4 ++-- man/pacotestRvineSeq.Rd | 4 ++-- man/pacotestRvineSingleCopula.Rd | 4 ++-- man/pacotestset.Rd | 2 +- 10 files changed, 38 insertions(+), 29 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
David Cooley [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Shane Saunders [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.2.16 dated 2022-09-19 and 0.2.17 dated 2022-11-04
DESCRIPTION | 6 MD5 | 69 +++---- NEWS.md | 15 + R/cache.R | 17 + R/centrality.R | 4 R/compound-junctions.R | 6 R/dists-categorical.R | 4 R/dists.R | 201 ++++++++-------------- R/flows.R | 220 +++++++++++-------------- R/from-to-params.R |only R/fund-cycles.R | 2 R/graph-contraction.R | 87 ++++++++- R/graph-conversion.R | 5 R/graph-functions-misc.R | 14 + R/graph-functions.R | 10 - R/graph-merge.R | 2 R/iso.R | 51 ----- R/save_load_streetnet.R | 2 R/weight-streetnet-times.R | 140 ++++++++++----- R/weight-streetnet.R | 10 - README.md | 79 +++++---- inst/doc/dists-categorical.html | 187 +++++++++------------ inst/doc/dodgr.html | 289 ++++++++++++++------------------- inst/doc/flows.html | 177 ++++++++------------ inst/doc/parallel.html | 177 ++++++++------------ inst/doc/times.html | 177 ++++++++------------ man/dodgr_contract_graph.Rd | 6 man/dodgr_distances.Rd | 6 man/dodgr_dists.Rd | 6 man/dodgr_times.Rd | 6 man/dodgr_uncontract_graph.Rd | 6 tests/testthat/test-cache.R | 12 - tests/testthat/test-flows.R | 21 +- tests/testthat/test-graph-conversion.R | 5 tests/testthat/test-save-load.R | 4 tests/testthat/test-sc.R | 6 36 files changed, 975 insertions(+), 1054 deletions(-)
Title: Benchmark and Frontier Analysis Using DEA and SFA
Description: Methods for frontier
analysis, Data Envelopment Analysis (DEA), under different
technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+),
and using different efficiency measures (input based, output based,
hyperbolic graph, additive, super, and directional efficiency). Peers
and slacks are available, partial price information can be included,
and optimal cost, revenue and profit can be calculated. Evaluation of
mergers is also supported. Methods for graphing the technology sets
are also included. There is also support for comparative methods based
on Stochastic Frontier Analyses (SFA) and for convex nonparametric
least squares of convex functions (STONED). In general, the methods
can be used to solve not only standard models, but also many other
model variants. It complements the book, Bogetoft and Otto,
Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of
course also be used as a stand-alone package.
Author: Peter Bogetoft and Lars Otto
Maintainer: Lars Otto <larsot23@gmail.com>
Diff between Benchmarking versions 0.30 dated 2022-05-05 and 0.31 dated 2022-11-04
Benchmarking-0.30/Benchmarking/R/Benchmarking.R |only Benchmarking-0.31/Benchmarking/DESCRIPTION | 8 - Benchmarking-0.31/Benchmarking/MD5 | 21 ++--- Benchmarking-0.31/Benchmarking/NEWS | 17 +++- Benchmarking-0.31/Benchmarking/R/dea.plot.R | 4 Benchmarking-0.31/Benchmarking/R/deaUtil.R | 3 Benchmarking-0.31/Benchmarking/R/malmq.R | 62 +++++++++----- Benchmarking-0.31/Benchmarking/R/malmquist.R | 47 +++++------ Benchmarking-0.31/Benchmarking/man/malmq.Rd | 96 ++++++++++++----------- Benchmarking-0.31/Benchmarking/man/malmquist.Rd | 19 ++-- Benchmarking-0.31/Benchmarking/src/chol_down.cpp | 16 +-- Benchmarking-0.31/Benchmarking/src/outlier.cpp | 4 12 files changed, 169 insertions(+), 128 deletions(-)
Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Diff between dsfa versions 1.0.0 dated 2022-09-26 and 1.0.1 dated 2022-11-04
DESCRIPTION | 6 MD5 | 64 +++--- NAMESPACE | 9 NEWS.md | 33 +++ R/OwenT.R | 39 ++-- R/chainrule.R | 258 +++++++++++++++++++-------- R/check_arguments.R |only R/comperr.R | 27 +- R/comperr_mv.R | 49 ++--- R/comperr_mv_mgcv.R | 26 +- R/cop.R | 463 +++++++++++++++++++++++++++++-------------------- R/cop_mgcv.R | 30 +-- R/elasticity.R | 2 R/erf.R | 50 +++-- R/normexp.R | 139 ++++++-------- R/normexp_mgcv.R | 29 ++- R/normhnorm.R | 199 ++++++++------------- R/normhnorm_mgcv.R | 30 ++- R/reparametrize.R | 82 +------- R/rsp.R |only R/utility_functions.R | 28 ++ R/zeta.R | 24 -- build/partial.rdb |binary man/OwenT.Rd | 10 - man/chainrule.Rd | 49 +---- man/check_arguments.Rd |only man/cop.Rd | 17 - man/dcomperr.Rd | 23 +- man/dcomperr_mv.Rd | 37 ++- man/dnormexp.Rd | 19 +- man/dnormhnorm.Rd | 15 + man/erf.Rd | 37 ++- man/pos_eigen.Rd | 17 + man/reparametrize.Rd | 33 --- man/rsp.Rd |only 35 files changed, 1032 insertions(+), 812 deletions(-)
Title: Efficient Manipulation of Date-Times
Description: Efficient routines for manipulation of date-time objects while
accounting for time-zones and daylight saving times. The package includes
utilities for updating of date-time components (year, month, day etc.),
modification of time-zones, rounding of date-times, period addition and
subtraction etc. Parts of the 'CCTZ' source code, released under the Apache
2.0 License, are included in this package. See
<https://github.com/google/cctz> for more details.
Author: Vitalie Spinu [aut, cre],
Google Inc. [ctb, cph]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between timechange versions 0.1.0 dated 2022-10-30 and 0.1.1 dated 2022-11-04
timechange-0.1.0/timechange/R/RcppExports.R |only timechange-0.1.0/timechange/src/RcppExports.cpp |only timechange-0.1.1/timechange/DESCRIPTION | 11 timechange-0.1.1/timechange/MD5 | 52 +- timechange-0.1.1/timechange/NAMESPACE | 2 timechange-0.1.1/timechange/NEWS.md | 9 timechange-0.1.1/timechange/R/addition.R | 133 ++++--- timechange-0.1.1/timechange/R/cpp11.R |only timechange-0.1.1/timechange/R/get.R | 56 +-- timechange-0.1.1/timechange/R/package.R | 2 timechange-0.1.1/timechange/R/round.R | 139 ++++--- timechange-0.1.1/timechange/R/update.R | 48 +- timechange-0.1.1/timechange/R/utils.R | 38 -- timechange-0.1.1/timechange/man/time_add.Rd | 106 +++-- timechange-0.1.1/timechange/man/time_round.Rd | 107 +++-- timechange-0.1.1/timechange/man/time_update.Rd | 8 timechange-0.1.1/timechange/src/common.cpp | 70 +++ timechange-0.1.1/timechange/src/common.h | 38 +- timechange-0.1.1/timechange/src/cpp11.cpp |only timechange-0.1.1/timechange/src/get.cpp | 36 - timechange-0.1.1/timechange/src/parse.c | 13 timechange-0.1.1/timechange/src/round.cpp | 240 +++++++++---- timechange-0.1.1/timechange/src/tzone.cpp | 26 - timechange-0.1.1/timechange/src/tzone.h | 9 timechange-0.1.1/timechange/src/update.cpp | 211 ++++++----- timechange-0.1.1/timechange/tests/testthat/test-addition.R | 62 ++- timechange-0.1.1/timechange/tests/testthat/test-get.R | 1 timechange-0.1.1/timechange/tests/testthat/test-round.R | 153 +++++++- timechange-0.1.1/timechange/tests/testthat/test-update.R | 101 +++-- 29 files changed, 1076 insertions(+), 595 deletions(-)
Title: Syllable Counting and Readability Measurements
Description: An English language syllable counter, plus readability score
measure-er. For readability, we support 'Flesch' Reading Ease and
'Flesch-Kincaid' Grade Level ('Kincaid' 'et al'. 1975)
<https://stars.library.ucf.edu/cgi/viewcontent.cgi?article=1055&context=istlibrary>,
Automated Readability Index ('Senter' and Smith 1967)
<https://apps.dtic.mil/sti/citations/AD0667273>,
Simple Measure of Gobbledygook (McLaughlin 1969)
<https://www.semanticscholar.org/paper/SMOG-Grading-A-New-Readability-Formula.-Laughlin/5fccb74c14769762b3de010c5e8a1a7ce700d17a>,
and 'Coleman-Liau' (Coleman and 'Liau' 1975) <doi:10.1037/h0076540>. The
package has been carefully optimized and should be very efficient, both in
terms of run time performance and memory consumption. The main methods are
'vectorized' by document, and scores for multiple documents are computed in
parallel via 'OpenMP'.
Author: Drew Schmidt [aut, cre]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between sylcount versions 0.2-4 dated 2022-03-11 and 0.2-5 dated 2022-11-04
ChangeLog | 3 +++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 2 +- src/sylcount_native.c | 2 +- src/sylcount_nthreads.c | 4 ++-- 6 files changed, 15 insertions(+), 12 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre] ,
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb],
Romain Lesur [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.24 dated 2021-11-16 and 0.25 dated 2022-11-04
DESCRIPTION | 8 ++++---- MD5 | 17 ++++++++++------- NAMESPACE | 2 ++ R/dynamic.R | 10 ++-------- R/redirect.R |only R/static.R | 51 ++++++++++++++++++++++++++++++++++++++++++--------- R/utils.R | 8 ++++++-- man/create_server.Rd |only man/httd.Rd | 7 +++---- man/random_port.Rd | 9 ++++++++- man/redirect.Rd |only 11 files changed, 77 insertions(+), 35 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 3.3.1 dated 2022-08-24 and 3.3.2 dated 2022-11-04
DESCRIPTION | 19 MD5 | 484 +++++----- NEWS.md | 9 R/RcppExports.R | 4 R/class_analysis_dataset.R | 118 +- R/class_analysis_results.R | 48 R/class_analysis_stage_results.R | 108 +- R/class_core_parameter_set.R | 12 R/class_design.R | 152 ++- R/class_design_plan.R | 22 R/class_design_power_and_asn.R | 9 R/class_design_set.R | 20 R/class_simulation_results.R | 62 - R/class_summary.R | 25 R/class_time.R | 32 R/data.R | 54 - R/f_analysis_base.R | 239 +++- R/f_analysis_base_means.R | 458 ++++----- R/f_analysis_base_rates.R | 181 +-- R/f_analysis_base_survival.R | 160 +-- R/f_analysis_enrichment_means.R | 20 R/f_analysis_enrichment_rates.R | 10 R/f_analysis_enrichment_survival.R | 8 R/f_analysis_multiarm.R | 6 R/f_analysis_multiarm_means.R | 15 R/f_analysis_utilities.R | 53 - R/f_core_assertions.R | 40 R/f_core_constants.R | 6 R/f_core_output_formats.R | 8 R/f_core_plot.R | 10 R/f_core_utilities.R | 32 R/f_design_fisher_combination_test.R | 10 R/f_design_group_sequential.R | 28 R/f_design_sample_size_calculator.R | 48 R/f_design_utilities.R | 16 R/f_logger.R | 18 R/f_quality_assurance.R | 19 R/f_simulation_base_means.R | 414 +++++--- R/f_simulation_base_rates.R | 205 ++-- R/f_simulation_base_survival.R | 14 R/f_simulation_utilities.R | 58 + R/parameter_descriptions.R | 91 - inst/doc/rpact_getting_started.html | 4 man/AnalysisResultsConditionalDunnett.Rd | 2 man/AnalysisResultsEnrichmentInverseNormal.Rd | 2 man/AnalysisResultsFisher.Rd | 2 man/AnalysisResultsGroupSequential.Rd | 2 man/AnalysisResultsInverseNormal.Rd | 2 man/AnalysisResultsMultiArmFisher.Rd | 4 man/AnalysisResultsMultiArmInverseNormal.Rd | 2 man/ClosedCombinationTestResults.Rd | 2 man/ConditionalPowerResults.Rd | 25 man/Dataset.Rd | 4 man/DatasetMeans.Rd | 13 man/DatasetRates.Rd | 15 man/DatasetSurvival.Rd | 6 man/PowerAndAverageSampleNumberResult.Rd | 10 man/SimulationResults.Rd | 8 man/SimulationResultsEnrichmentMeans.Rd | 2 man/SimulationResultsEnrichmentRates.Rd | 2 man/SimulationResultsEnrichmentSurvival.Rd | 2 man/SimulationResultsMeans.Rd | 15 man/SimulationResultsMultiArmMeans.Rd | 2 man/SimulationResultsMultiArmRates.Rd | 2 man/SimulationResultsMultiArmSurvival.Rd | 2 man/SimulationResultsRates.Rd | 15 man/SimulationResultsSurvival.Rd | 2 man/StageResults.Rd | 16 man/StageResultsMeans.Rd | 28 man/StageResultsRates.Rd | 25 man/StageResultsSurvival.Rd | 25 man/TrialDesign.Rd | 31 man/TrialDesignCharacteristics.Rd | 4 man/TrialDesignConditionalDunnett.Rd | 50 - man/TrialDesignFisher.Rd | 56 + man/TrialDesignGroupSequential.Rd | 104 ++ man/TrialDesignInverseNormal.Rd | 104 ++ man/TrialDesignPlanMeans.Rd | 2 man/TrialDesignPlanRates.Rd | 2 man/TrialDesignPlanSurvival.Rd | 2 man/TrialDesignSet.Rd | 4 man/as.data.frame.AnalysisResults.Rd | 2 man/as.data.frame.TrialDesignSet.Rd | 2 man/dataEnrichmentMeans.Rd | 4 man/dataEnrichmentMeansStratified.Rd | 4 man/dataEnrichmentRates.Rd | 4 man/dataEnrichmentRatesStratified.Rd | 4 man/dataEnrichmentSurvival.Rd | 4 man/dataEnrichmentSurvivalStratified.Rd | 4 man/dataMeans.Rd | 4 man/dataMultiArmMeans.Rd | 4 man/dataMultiArmRates.Rd | 4 man/dataMultiArmSurvival.Rd | 4 man/dataRates.Rd | 4 man/dataSurvival.Rd | 4 man/getAccrualTime.Rd | 20 man/getAnalysisResults.Rd | 19 man/getAvailablePlotTypes.Rd | 6 man/getClosedCombinationTestResults.Rd | 14 man/getClosedConditionalDunnettTestResults.Rd | 16 man/getConditionalPower.Rd | 17 man/getConditionalRejectionProbabilities.Rd | 2 man/getData.Rd | 12 man/getDataset.Rd | 16 man/getDesignCharacteristics.Rd | 12 man/getDesignConditionalDunnett.Rd | 17 man/getDesignFisher.Rd | 23 man/getDesignGroupSequential.Rd | 29 man/getDesignInverseNormal.Rd | 27 man/getDesignSet.Rd | 10 man/getEventProbabilities.Rd | 28 man/getFinalConfidenceInterval.Rd | 8 man/getFinalPValue.Rd | 2 man/getLogLevel.Rd | 4 man/getLongFormat.Rd | 2 man/getNumberOfSubjects.Rd | 20 man/getObjectRCode.Rd | 2 man/getObservedInformationRates.Rd | 3 man/getOutputFormat.Rd | 2 man/getParameterCaption.Rd | 2 man/getParameterName.Rd | 2 man/getPiecewiseSurvivalTime.Rd | 20 man/getPowerAndAverageSampleNumber.Rd | 14 man/getPowerMeans.Rd | 16 man/getPowerRates.Rd | 14 man/getPowerSurvival.Rd | 32 man/getRawData.Rd | 8 man/getRepeatedConfidenceIntervals.Rd | 8 man/getRepeatedPValues.Rd | 4 man/getSampleSizeMeans.Rd | 14 man/getSampleSizeRates.Rd | 12 man/getSampleSizeSurvival.Rd | 28 man/getSimulationEnrichmentMeans.Rd | 32 man/getSimulationEnrichmentRates.Rd | 30 man/getSimulationEnrichmentSurvival.Rd | 32 man/getSimulationMeans.Rd | 32 man/getSimulationMultiArmMeans.Rd | 32 man/getSimulationMultiArmRates.Rd | 28 man/getSimulationMultiArmSurvival.Rd | 30 man/getSimulationRates.Rd | 26 man/getSimulationSurvival.Rd | 52 - man/getStageResults.Rd | 14 man/getTestActions.Rd | 2 man/getWideFormat.Rd | 2 man/names.AnalysisResults.Rd | 2 man/names.SimulationResults.Rd | 3 man/param_accrualIntensity.Rd | 4 man/param_accrualTime.Rd | 2 man/param_adaptations.Rd | 2 man/param_alpha.Rd | 2 man/param_beta.Rd | 4 man/param_bindingFutility.Rd | 2 man/param_conditionalPower.Rd | 2 man/param_dataInput.Rd | 4 man/param_digits.Rd | 2 man/param_directionUpper.Rd | 2 man/param_epsilonValue.Rd | 2 man/param_hazardRatio.Rd | 2 man/param_kMax.Rd | 3 man/param_lambda1.Rd | 2 man/param_lambda2.Rd | 2 man/param_maxNumberOfEventsPerStage.Rd | 2 man/param_maxNumberOfIterations.Rd | 2 man/param_maxNumberOfSubjectsPerStage.Rd | 2 man/param_maxNumberOfSubjects_survival.Rd | 2 man/param_median2.Rd | 2 man/param_minNumberOfEventsPerStage.Rd | 2 man/param_minNumberOfSubjectsPerStage.Rd | 2 man/param_nMax.Rd | 2 man/param_piecewiseSurvivalTime.Rd | 2 man/param_plannedEvents.Rd | 2 man/param_plannedSubjects.Rd | 2 man/param_plotPointsEnabled.Rd | 2 man/param_plotSettings.Rd | 2 man/param_populations.Rd | 2 man/param_showSource.Rd | 2 man/param_showStatistics.Rd | 2 man/param_sided.Rd | 2 man/param_stDev.Rd | 2 man/param_stDevH1.Rd | 2 man/param_stDevSimulation.Rd | 2 man/param_stageResults.Rd | 2 man/param_stratifiedAnalysis.Rd | 2 man/param_thetaH1.Rd | 2 man/param_tolerance.Rd | 2 man/plot.AnalysisResults.Rd | 8 man/plot.Dataset.Rd | 4 man/plot.EventProbabilities.Rd | 6 man/plot.NumberOfSubjects.Rd | 6 man/plot.ParameterSet.Rd | 4 man/plot.SimulationResults.Rd | 8 man/plot.StageResults.Rd | 11 man/plot.TrialDesign.Rd | 22 man/plot.TrialDesignPlan.Rd | 18 man/plot.TrialDesignSet.Rd | 10 man/rawDataTwoArmNormal.Rd | 2 man/readDataset.Rd | 22 man/readDatasets.Rd | 8 man/resetLogLevel.Rd | 4 man/setLogLevel.Rd | 6 man/setOutputFormat.Rd | 2 man/summary.AnalysisResults.Rd | 6 man/summary.Dataset.Rd | 6 man/summary.ParameterSet.Rd | 6 man/summary.TrialDesignSet.Rd | 6 man/utilitiesForPiecewiseExponentialDistribution.Rd | 6 man/utilitiesForSurvivalTrials.Rd | 2 man/writeDataset.Rd | 8 man/writeDatasets.Rd | 8 src/RcppExports.cpp | 34 src/f_design_fisher_combination_test.cpp | 25 src/f_design_group_sequential.cpp | 9 src/f_simulation_base_means.cpp |only src/f_simulation_base_survival.cpp | 7 src/f_simulation_survival_utilities.cpp | 8 src/f_simulation_survival_utilities.h | 3 src/f_utilities.cpp | 122 -- src/f_utilities.h | 12 src/rpact_types.h |only tests/testthat/test-class_analysis_dataset.R | 55 - tests/testthat/test-class_time.R | 20 tests/testthat/test-f_analysis_base_means.R | 17 tests/testthat/test-f_analysis_base_rates.R | 9 tests/testthat/test-f_analysis_base_survival.R | 15 tests/testthat/test-f_analysis_enrichment_means.R | 16 tests/testthat/test-f_analysis_enrichment_rates.R | 11 tests/testthat/test-f_analysis_enrichment_survival.R | 9 tests/testthat/test-f_analysis_input_validation.R | 5 tests/testthat/test-f_analysis_multiarm_means.R | 7 tests/testthat/test-f_analysis_multiarm_rates.R | 7 tests/testthat/test-f_analysis_multiarm_survival.R | 7 tests/testthat/test-f_analysis_utilities.R | 19 tests/testthat/test-f_core_utilities.R | 49 - tests/testthat/test-f_design_group_sequential.R | 39 tests/testthat/test-f_design_group_sequential_beta_spending.R | 3 tests/testthat/test-f_design_power_calculator.R | 55 - tests/testthat/test-f_design_sample_size_calculator.R | 31 tests/testthat/test-f_design_utilities.R | 45 tests/testthat/test-f_simulation_enrichment_means.R | 5 tests/testthat/test-f_simulation_enrichment_rates.R | 17 tests/testthat/test-f_simulation_enrichment_survival.R | 5 tests/testthat/test-f_simulation_multiarm_means.R | 14 tests/testthat/test-f_simulation_multiarm_rates.R | 14 tests/testthat/test-f_simulation_multiarm_survival.R | 11 244 files changed, 3454 insertions(+), 2324 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>
Diff between QTLRel versions 1.11 dated 2022-06-17 and 1.12 dated 2022-11-04
ChangeLog | 2 + DESCRIPTION | 8 ++--- MD5 | 18 ++++++------- R/estVC.R | 58 +++++++++++++++++++++++++++++++++++-------- data/miscEx.RData |binary inst/doc/QTLRel_Tutorial.pdf |binary man/estVC.Rd | 9 ++++-- src/ibsFn.c | 6 ++-- src/idcoef.c | 20 +++++++------- src/rgdat.c | 4 +- 10 files changed, 84 insertions(+), 41 deletions(-)
Title: Named Entity Recognition in Texts using 'NameTag'
Description: Wraps the 'nametag' library <https://github.com/ufal/nametag>, allowing users to find and extract entities (names, persons, locations, addresses, ...) in raw text and build your own entity recognition models.
Based on a maximum entropy Markov model which is described in Strakova J., Straka M. and Hajic J. (2013) <https://ufal.mff.cuni.cz/~straka/papers/2013-tsd_ner.pdf>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between nametagger versions 0.1.1 dated 2020-10-11 and 0.1.2 dated 2022-11-04
nametagger-0.1.1/nametagger/data/datalist |only nametagger-0.1.2/nametagger/DESCRIPTION | 10 - nametagger-0.1.2/nametagger/MD5 | 17 +-- nametagger-0.1.2/nametagger/NEWS.md | 5 nametagger-0.1.2/nametagger/R/nametagger.R | 8 - nametagger-0.1.2/nametagger/README.md | 56 +++++++++- nametagger-0.1.2/nametagger/man/nametagger.Rd | 2 nametagger-0.1.2/nametagger/man/nametagger_download_model.Rd | 2 nametagger-0.1.2/nametagger/man/nametagger_options.Rd | 4 nametagger-0.1.2/nametagger/src/nametag/src/morphodita/morpho/czech_lemma_addinfo.h | 2 10 files changed, 80 insertions(+), 26 deletions(-)
Title: Tools to Process the Munich ChronoType Questionnaire (MCTQ)
Description: A complete toolkit to process the Munich ChronoType
Questionnaire (MCTQ) for its three versions (standard, micro, and shift).
MCTQ is a quantitative and validated tool to assess chronotypes using
peoples' sleep behavior, originally presented by Till Roenneberg, Anna
Wirz-Justice, and Martha Merrow (2003, <doi:10.1177/0748730402239679>).
Author: Daniel Vartanian [aut, cre, ccp, cph]
,
Ana Amelia Benedito-Silva [aut, sad]
,
Mario Pedrazzoli [aut, sad] ,
Jonathan Keane [rev] ,
Mario Andre Leocadio-Miguel [rev]
,
Interdisciplinary Sleep Research Group [fnd],
University of Sao Paulo [fnd]
Maintainer: Daniel Vartanian <danvartan@gmail.com>
Diff between mctq versions 0.3.0 dated 2022-08-22 and 0.3.1 dated 2022-11-04
DESCRIPTION | 18 ++++++------- MD5 | 24 +++++++++--------- NEWS.md | 51 ++++++++++++++++++++++----------------- README.md | 6 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 +-- inst/doc/mctq.Rmd | 6 ++-- inst/doc/mctq.html | 12 ++++----- tests/testthat.R | 7 +++++ tests/testthat/Rplots.pdf |binary tests/testthat/test-round_time.R | 4 +-- vignettes/mctq.Rmd | 6 ++-- 13 files changed, 76 insertions(+), 62 deletions(-)
Title: Greedy Experimental Design Construction
Description: Computes experimental designs for a
two-arm experiment with covariates via a number of methods:
(0) complete randomization and randomization with forced-balance,
(1) Greedily optimizing a
balance objective function via pairwise switching. This optimization
provides lower variance for the treatment effect estimator (and higher
power) while preserving a design that is close to complete randomization.
We return all iterations of the designs for use in a permutation test,
(2) The second is via numerical optimization
(via 'gurobi' which must be installed, see <https://www.gurobi.com/documentation/9.1/quickstart_windows/r_ins_the_r_package.html>)
a la Bertsimas and Kallus,
(3) rerandomization,
(4) Karp's method for one covariate,
(5) exhaustive enumeration to find the
optimal solution (only for small sample sizes),
(6) Binary pair matching using the 'nbpMatching' library,
(7) Binary pair matching plus design number (1) to further optimize balance,
(8) Binary pair matching plus design n [...truncated...]
Author: Adam Kapelner [aut, cre] ,
David Azriel [aut],
Abba Krieger [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between GreedyExperimentalDesign versions 1.4 dated 2020-12-07 and 1.5 dated 2022-11-04
GreedyExperimentalDesign-1.4/GreedyExperimentalDesign/man/binaryMatchExperimentalDesignSearch.Rd |only GreedyExperimentalDesign-1.4/GreedyExperimentalDesign/man/binaryMatchFollowedByGreedyExperimentalDesignSearch.Rd |only GreedyExperimentalDesign-1.4/GreedyExperimentalDesign/man/binaryMatchFollowedByRerandomizationDesignSearch.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/CHANGELOG | 6 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/DESCRIPTION | 56 ++++--- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/MD5 | 64 ++++---- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/NAMESPACE | 18 +- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/GreedyExperimentalDesign.R | 8 - GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/binary_match_followed_by_greedy_search.R | 67 +++++---- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/binary_match_followed_by_rerandomization_search.R | 8 - GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/binary_match_search.R | 73 +++++++--- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/complete_randomization.R | 6 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/greedy_multiple_kernel_search.R |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/greedy_search.R | 62 ++++---- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/hadamard_search.R | 3 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/optimal_search.R | 5 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/rerandomization_search.R | 16 +- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/R/shared.R | 2 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/inst/java/GreedyExperimentalDesign.jar |binary GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/GreedyExperimentalDesign.Rd | 2 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/complete_randomization.Rd | 3 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/complete_randomization_with_forced_balanced.Rd | 3 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/hadamardExperimentalDesign.Rd | 3 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initBinaryMatchExperimentalDesignSearch.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initBinaryMatchFollowedByGreedyExperimentalDesignSearch.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initBinaryMatchFollowedByRerandomizationDesignSearch.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initGreedyExperimentalDesignObject.Rd | 17 +- GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initGreedyMultipleKernelExperimentalDesignObject.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initOptimalExperimentalDesignObject.Rd | 3 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/initRerandomizationExperimentalDesignObject.Rd | 9 - GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/plot.greedy_experimental_design_search.Rd | 6 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/plot.greedy_multiple_kernel_experimental_design.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/plot_obj_val_order_statistic.Rd | 2 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/print.greedy_multiple_kernel_experimental_design.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/resultsBinaryMatchSearch.Rd | 10 - GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/resultsMultipleKernelGreedySearch.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/resultsOptimalSearch.Rd | 2 GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/man/summary.greedy_multiple_kernel_experimental_design.Rd |only GreedyExperimentalDesign-1.5/GreedyExperimentalDesign/src/RcppExports.cpp | 5 39 files changed, 296 insertions(+), 163 deletions(-)
More information about GreedyExperimentalDesign at CRAN
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Title: A 'ggplot2' Extension Inspired by 'GraphPad Prism'
Description: Provides various themes, palettes, and other functions
that are used to customise ggplots to look like they were made in 'GraphPad
Prism'. The 'Prism'-look is achieved with theme_prism() and
scale_fill|colour_prism(), axes can be changed with custom guides like
guide_prism_minor(), and significance indicators added with add_pvalue().
Author: Charlotte Dawson [aut, cre]
Maintainer: Charlotte Dawson <csdaw@outlook.com>
Diff between ggprism versions 1.0.3 dated 2021-06-08 and 1.0.4 dated 2022-11-04
DESCRIPTION | 8 MD5 | 74 +-- NAMESPACE | 35 - NEWS.md | 9 R/add_pvalue.R | 40 - R/geom_bracket.R | 11 R/ggprism-package.R | 10 R/guide_prism_bracket.R | 8 R/guide_prism_minor.R | 12 R/guide_prism_offset.R | 8 R/guide_prism_offset_minor.R | 12 R/utils.R | 159 ++++++- README.md | 13 build/partial.rdb |binary build/vignette.rds |binary inst/doc/axes.html | 443 +++++++++++++++++--- inst/doc/colours.html | 297 ++++++++++++- inst/doc/ggprism.html | 279 +++++++++++-- inst/doc/pvalues.R | 49 +- inst/doc/pvalues.Rmd | 57 ++ inst/doc/pvalues.html | 835 ++++++++++++++++++++++++++------------- inst/doc/themes.html | 298 ++++++++++++- inst/tinytest/test-add_pvalue.R | 22 - inst/tinytest/test-utils.R | 5 man/add_pvalue.Rd | 4 man/figures/README-ex-1.png |binary man/figures/README-ex-2.png |binary man/figures/README-ex2-2.png |binary man/ggprism-package.Rd | 6 man/guide_prism_bracket.Rd | 2 man/guide_prism_minor.Rd | 2 man/guide_prism_offset.Rd | 2 man/guide_prism_offset_minor.Rd | 2 man/scale_colour_prism.Rd | 10 man/scale_fill_prism.Rd | 10 man/scale_shape_prism.Rd | 10 vignettes/pvalues.Rmd | 57 ++ vignettes/web-only/ex2-wings.Rmd | 8 38 files changed, 2158 insertions(+), 639 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre]
,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
RStudio [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between ggplot2 versions 3.3.6 dated 2022-05-03 and 3.4.0 dated 2022-11-04
ggplot2-3.3.6/ggplot2/R/ggplot2.r |only ggplot2-3.3.6/ggplot2/R/translate-qplot-ggplot.r |only ggplot2-3.3.6/ggplot2/R/translate-qplot-lattice.r |only ggplot2-3.3.6/ggplot2/man/translate_qplot_ggplot.Rd |only ggplot2-3.3.6/ggplot2/man/translate_qplot_lattice.Rd |only ggplot2-3.3.6/ggplot2/tests/testthat/test-rbind-dfs.R |only ggplot2-3.3.6/ggplot2/tests/testthat/test-sanitise-dim.r |only ggplot2-3.4.0/ggplot2/DESCRIPTION | 98 ggplot2-3.4.0/ggplot2/MD5 | 1072 +++++----- ggplot2-3.4.0/ggplot2/NAMESPACE | 30 ggplot2-3.4.0/ggplot2/NEWS.md | 193 + ggplot2-3.4.0/ggplot2/R/aes-colour-fill-alpha.r | 1 ggplot2-3.4.0/ggplot2/R/aes-evaluation.r | 38 ggplot2-3.4.0/ggplot2/R/aes-position.r | 1 ggplot2-3.4.0/ggplot2/R/aes.r | 120 - ggplot2-3.4.0/ggplot2/R/annotation-custom.r | 8 ggplot2-3.4.0/ggplot2/R/annotation-logticks.r | 9 ggplot2-3.4.0/ggplot2/R/annotation-map.r | 16 ggplot2-3.4.0/ggplot2/R/annotation-raster.r | 8 ggplot2-3.4.0/ggplot2/R/annotation.r | 24 ggplot2-3.4.0/ggplot2/R/autolayer.r | 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ggplot2-3.4.0/ggplot2/R/position-jitterdodge.R | 5 ggplot2-3.4.0/ggplot2/R/position-stack.r | 22 ggplot2-3.4.0/ggplot2/R/quick-plot.r | 24 ggplot2-3.4.0/ggplot2/R/reshape-add-margins.R | 4 ggplot2-3.4.0/ggplot2/R/save.r | 39 ggplot2-3.4.0/ggplot2/R/scale-.r | 124 - ggplot2-3.4.0/ggplot2/R/scale-alpha.r | 4 ggplot2-3.4.0/ggplot2/R/scale-binned.R | 6 ggplot2-3.4.0/ggplot2/R/scale-brewer.r | 29 ggplot2-3.4.0/ggplot2/R/scale-colour.r | 37 ggplot2-3.4.0/ggplot2/R/scale-continuous.r | 1 ggplot2-3.4.0/ggplot2/R/scale-date.r | 1 ggplot2-3.4.0/ggplot2/R/scale-discrete-.r | 62 ggplot2-3.4.0/ggplot2/R/scale-expansion.r | 6 ggplot2-3.4.0/ggplot2/R/scale-gradient.r | 1 ggplot2-3.4.0/ggplot2/R/scale-hue.r | 3 ggplot2-3.4.0/ggplot2/R/scale-identity.r | 2 ggplot2-3.4.0/ggplot2/R/scale-linetype.r | 7 ggplot2-3.4.0/ggplot2/R/scale-linewidth.R |only ggplot2-3.4.0/ggplot2/R/scale-manual.r | 7 ggplot2-3.4.0/ggplot2/R/scale-shape.r | 8 ggplot2-3.4.0/ggplot2/R/scale-size.r | 11 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Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic-process movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced and detailed in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
Fleming et al (2019) <doi:10.1111/2041-21 [...truncated...]
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Bjoern Reineking [ctb],
Guillaume Peron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [...truncated...]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 1.0.0 dated 2022-07-12 and 1.1.0 dated 2022-11-04
DESCRIPTION | 18 - MD5 | 143 +++++----- NAMESPACE | 11 NEWS.md | 45 +++ R/1.R | 2 R/QP.R | 227 ++++++++++------- R/acf.R | 4 R/bandwidth.R |only R/cluster.R | 24 - R/covm.R | 24 + R/ctmm.R | 26 + R/diff.R |only R/encounter.R | 4 R/export.R | 10 R/fit.R | 8 R/generic.R | 20 + R/kde.R | 604 +++++++++++++--------------------------------- R/krige.R | 12 R/likelihood.R | 3 R/log.R |only R/matrix.R | 16 - R/mean.UD.R | 9 R/mean.ctmm.R | 188 ++++++++++---- R/meta.chisq.R | 74 ++++- R/meta.normal.R | 1 R/nsv.R |only R/occurrence.R | 4 R/outlier.R | 156 +++++++---- R/overlap.R | 1 R/plot.telemetry.R | 63 +++- R/population.R |only R/rsf.R | 246 +++++++++++++----- R/sdm.R |only R/series.R | 27 +- R/sigfig.R |only R/speed.R | 12 R/speeds.R | 99 ++++--- R/stats.R | 71 +++-- R/summary.ctmm.R | 63 ++++ R/telemetry.R | 9 R/ts.plot.R |only R/units.R | 13 R/variogram.R | 37 +- README.md | 17 + TODO | 21 + build/partial.rdb |binary build/vignette.rds |binary data/datalist | 14 - inst/doc/akde.R | 18 - inst/doc/akde.Rmd | 24 - inst/doc/akde.html | 72 ++--- inst/doc/error.R | 13 inst/doc/error.Rmd | 13 inst/doc/error.html | 105 ++++--- inst/doc/periodogram.html | 81 +++--- inst/doc/variogram.html | 53 ++-- man/akde.Rd | 13 man/bandwidth.Rd | 15 - man/cluster.Rd | 4 man/ctmm-package.Rd | 45 +-- man/ctmm.boot.Rd | 4 man/ctmm.fit.Rd | 1 man/difference.Rd |only man/encounter.Rd | 3 man/log.Rd |only man/mean.Rd | 5 man/meta.Rd | 4 man/outlie.Rd | 4 man/overlap.Rd | 2 man/residuals.Rd | 3 man/sigfig.Rd |only man/simulate.ctmm.Rd | 4 man/speed.Rd | 13 man/uere.Rd | 6 man/unit.Rd | 4 man/variogram.Rd | 3 vignettes/akde.Rmd | 24 - vignettes/error.Rmd | 13 78 files changed, 1668 insertions(+), 1207 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Sta [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut],
Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.2.0 dated 2022-05-24 and 1.2.1 dated 2022-11-04
DESCRIPTION | 11 MD5 | 85 +++---- NEWS.md | 20 + R/RcppExports.R | 8 R/data.R | 2 R/misc.R | 7 R/smc_mallows_deprecated.R | 5 R/smc_post_processing_functions.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/SMC-Mallows.html | 146 ++++++------- inst/examples/obs_freq_example.R | 3 inst/examples/sample_mallows_example.R | 15 - man/metropolis_hastings_aug_ranking.Rd | 4 man/obs_freq.Rd | 3 man/rank_conversion.Rd | 6 man/sample_dataset.Rd | 13 - man/sample_mallows.Rd | 15 - man/smc_mallows_new_item_rank.Rd | 12 - man/smc_mallows_new_users.Rd | 8 src/RcppExports.cpp | 11 src/distances.cpp | 3 src/importance_sampling.cpp | 1 src/leapandshift.cpp | 1 src/missing_data.cpp | 4 src/mixtures.cpp | 2 src/pairwise_comparisons.cpp | 25 -- src/parameterupdates.cpp | 6 src/partitionfuns.cpp | 11 src/rmallows.cpp | 4 src/run_mcmc.cpp | 11 src/smc.h | 1 src/smc_calculate_probability.cpp | 4 src/smc_correction_kernel_pseudo.cpp | 2 src/smc_get_sample_probabilities.cpp | 1 src/smc_leap_and_shift_probs.cpp | 1 src/smc_mallows_new_item_rank.cpp | 269 +++++++++++------------- src/smc_mallows_new_users_funs.cpp | 3 src/subset.cpp | 4 tests/testthat.R | 4 tests/testthat/test-distance_function.R | 64 +++-- tests/testthat/test-partition_function.R | 11 tests/testthat/test-smc_mallows_new_item_rank.R | 40 ++- tests/testthat/test-smc_updated_new_item_rank.R |only 44 files changed, 398 insertions(+), 456 deletions(-)
Title: Run Allometric Trophic Networks Models
Description: Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.
Author: Benoit Gauzens [cre, aut],
Emilio Berti [aut]
Maintainer: Benoit Gauzens <benoit.gauzens@gmail.com>
Diff between ATNr versions 1.0.1 dated 2022-02-07 and 1.0.2 dated 2022-11-04
ATNr-1.0.1/ATNr/man/Joacobian.Rd |only ATNr-1.0.2/ATNr/DESCRIPTION | 8 ATNr-1.0.2/ATNr/MD5 | 72 +++---- ATNr-1.0.2/ATNr/NAMESPACE | 2 ATNr-1.0.2/ATNr/NEWS.md | 13 + ATNr-1.0.2/ATNr/R/RcppExports.R | 4 ATNr-1.0.2/ATNr/R/connected_component.R | 3 ATNr-1.0.2/ATNr/R/create_model.R | 2 ATNr-1.0.2/ATNr/R/default_initialisations.R | 35 +++ ATNr-1.0.2/ATNr/R/fw_generative_models.R | 21 -- ATNr-1.0.2/ATNr/R/jacobian.R | 4 ATNr-1.0.2/ATNr/R/plot_odeweb.R | 1 ATNr-1.0.2/ATNr/R/wrap_solvers.R | 1 ATNr-1.0.2/ATNr/README.md | 11 - ATNr-1.0.2/ATNr/inst/doc/ATNr.R | 24 -- ATNr-1.0.2/ATNr/inst/doc/ATNr.Rmd | 35 --- ATNr-1.0.2/ATNr/inst/doc/ATNr.html | 158 ++++++---------- ATNr-1.0.2/ATNr/inst/doc/model_descriptions.ltx | 52 ++--- ATNr-1.0.2/ATNr/inst/doc/model_descriptions.pdf |binary ATNr-1.0.2/ATNr/man/Unscaled.Rd | 2 ATNr-1.0.2/ATNr/man/Unscaled_nuts.Rd | 2 ATNr-1.0.2/ATNr/man/create_Lmatrix.Rd | 2 ATNr-1.0.2/ATNr/man/create_model_Unscaled.Rd | 4 ATNr-1.0.2/ATNr/man/initialise_default_Scaled.Rd | 10 + ATNr-1.0.2/ATNr/man/initialise_default_Unscaled_nuts.Rd | 10 + ATNr-1.0.2/ATNr/man/jacobian.Rd |only ATNr-1.0.2/ATNr/man/plot_odeweb.Rd | 1 ATNr-1.0.2/ATNr/src/Scaled.cpp | 9 ATNr-1.0.2/ATNr/src/Scaled_loops.cpp | 2 ATNr-1.0.2/ATNr/src/Unscaled.cpp | 6 ATNr-1.0.2/ATNr/src/Unscaled_loops.cpp | 4 ATNr-1.0.2/ATNr/src/Unscaled_nuts.cpp | 5 ATNr-1.0.2/ATNr/src/Unscaled_nuts_loops.cpp | 2 ATNr-1.0.2/ATNr/tests/testthat/test-Binzer.R | 5 ATNr-1.0.2/ATNr/tests/testthat/test-Delmas.R | 5 ATNr-1.0.2/ATNr/tests/testthat/test-Schneider.R | 5 ATNr-1.0.2/ATNr/vignettes/ATNr.Rmd | 35 --- ATNr-1.0.2/ATNr/vignettes/model_descriptions.ltx | 52 ++--- 38 files changed, 281 insertions(+), 326 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-15 0.2.0
2022-04-20 0.1.0
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr'
R package for matching 'HTTP' requests by various rules ('HTTP' method,
'URL', query parameters, headers, body, etc.), and then caching
real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests
matching any previous requests in the same 'cassette' use a cached
'HTTP' response.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [ctb] ,
Maelle Salmon [ctb] ,
rOpenSci [fnd]
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between vcr versions 1.0.2 dated 2021-05-31 and 1.1.0 dated 2022-11-04
DESCRIPTION | 10 LICENSE | 2 MD5 | 115 ++-- NEWS.md | 16 R/cassette_class.R | 2 R/cpp11.R | 2 R/error_suggestions.R | 2 R/http_interaction_list.R | 4 R/request_class.R | 27 R/request_matcher_registry.R | 8 R/response_class.R | 11 R/serializer.R | 12 R/vcr_test_path.R | 11 R/write.R | 11 build/vignette.rds |binary inst/doc/cassette-manual-editing.html | 491 +++++++++--------- inst/doc/configuration.html | 310 ++++++----- inst/doc/debugging.html | 270 +++++---- inst/doc/design.html | 163 ++++- inst/doc/internals.html | 190 +++--- inst/doc/lightswitch.html | 271 +++++---- inst/doc/record-modes.html | 230 ++++---- inst/doc/request_matching.html | 250 +++++---- inst/doc/vcr.html | 426 +++++++++------ inst/doc/write-to-disk.html | 229 ++++---- man/Cassette.Rd | 174 +++--- man/FileSystem.Rd | 30 - man/HTTPInteraction.Rd | 24 man/HTTPInteractionList.Rd | 42 - man/Hooks.Rd | 24 man/JSON.Rd | 30 - man/Persisters.Rd | 12 man/Request.Rd | 24 man/RequestHandler.Rd | 18 man/RequestHandlerCrul.Rd | 22 man/RequestHandlerHttr.Rd | 26 man/RequestIgnorer.Rd | 42 - man/RequestMatcherRegistry.Rd | 30 - man/Serializer.Rd | 24 man/Serializers.Rd | 12 man/UnhandledHTTPRequestError.Rd | 126 ++-- man/VcrResponse.Rd | 80 +- man/YAML.Rd | 30 - man/check_cassette_names.Rd | 15 man/insert_cassette.Rd | 15 man/lightswitch.Rd | 68 +- man/request-matching.Rd | 30 - man/rmdhunks/vcr-design.Rmd | 4 man/vcr_configure.Rd | 6 man/vcr_test_path.Rd | 3 src/cpp11.cpp | 7 tests/testthat/test-ause_cassette_match_query.R |only tests/testthat/test-httr.R | 2 tests/testthat/test-quiet.R | 13 tests/testthat/test-response_summary.R | 11 tests/testthat/test-utils.R | 23 tests/testthat/test-vcr_last_error.R | 2 tests/testthat/test-vcr_test_path.R | 46 + tests/testthat/test-write_disk_path_package_context.R | 4 59 files changed, 2322 insertions(+), 1760 deletions(-)
Title: Create Custom Plots for Viewing Genetic Association Results
Description: A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.
Author: Genuity Science [cph],
Thorhildur Juliusdottir [aut, cre],
Andri Stefansson [aut]
Maintainer: Thorhildur Juliusdottir <thorhildur@genuitysci.com>
Diff between topr versions 1.1.0 dated 2022-10-25 and 1.1.1 dated 2022-11-04
topr-1.1.0/topr/tests/testthat/test-dummy.R |only topr-1.1.1/topr/DESCRIPTION | 6 +++--- topr-1.1.1/topr/MD5 | 18 +++++++++++------- topr-1.1.1/topr/NEWS.md | 5 +++++ topr-1.1.1/topr/R/get_plots.R | 8 ++++++-- topr-1.1.1/topr/R/manhattan.R | 15 ++++++++++++++- topr-1.1.1/topr/R/plot_functions.R | 8 ++++---- topr-1.1.1/topr/man/manhattan.Rd | 5 ++++- topr-1.1.1/topr/tests/testthat/test-locuszoom.R |only topr-1.1.1/topr/tests/testthat/test-manhattan.R |only topr-1.1.1/topr/tests/testthat/test-regionplot.R |only topr-1.1.1/topr/tests/testthat/test-test-datasets.R |only topr-1.1.1/topr/tests/testthat/test-utils.R |only 13 files changed, 47 insertions(+), 18 deletions(-)
Title: Functional Data Clustering Using Adaptive Density Peak Detection
Description: An implementation of a clustering algorithm for functional data based on adaptive density peak detection technique, in which the density is estimated by functional k-nearest neighbor density estimation based on a proposed semi-metric between functions. The proposed functional data clustering algorithm is computationally fast since it does not need iterative process. (Alex Rodriguez and Alessandro Laio (2014) <doi:10.1126/science.1242072>; Xiao-Feng Wang and Yifan Xu (2016) <doi:10.1177/0962280215609948>).
Author: Rui Ren [aut, cre],
Kuangnan Fang [aut],
Qingzhao Zhang [aut],
Xiaofeng Wang [aut]
Maintainer: Rui Ren <xmurr@stu.xmu.edu.cn>
Diff between FADPclust versions 0.1.0 dated 2021-10-08 and 1.1.0 dated 2022-11-04
DESCRIPTION | 18 ++- MD5 | 16 +-- NAMESPACE | 1 R/FADPclust.R | 281 +++++++++++++++++++++++++++-------------------------- R/FADPplot.R | 25 ++-- R/FADPsummary.R | 23 ++-- man/FADPclust.Rd | 33 +++--- man/FADPplot.Rd | 23 ++-- man/FADPsummary.Rd | 23 ++-- 9 files changed, 244 insertions(+), 199 deletions(-)
Title: Partialised Functions
Description: Provides a 'partialised' class that extends the partialising
function of 'purrr' by making it easier to change the arguments. This is
similar to the function-like object in 'Julia'
(<https://docs.julialang.org/en/v1/manual/methods/#Function-like-objects>).
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between partialised versions 0.1.0 dated 2022-05-04 and 0.1.1 dated 2022-11-04
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 12 - R/partialised-package.R | 8 R/partialised.R | 385 ++++++++++++++++++-------------------- R/utils.R | 16 - README.md | 144 +++++++------- tests/testthat/test-partialised.R | 34 +-- 8 files changed, 305 insertions(+), 316 deletions(-)
Title: Event Detection Using Confidence Bounds
Description: Detects sustained change in digital bio-marker data using
simultaneous confidence bands. Accounts for noise using an auto-regressive
model. Based on Buehlmann (1998) "Sieve bootstrap for smoothing in
nonstationary time series" <doi:10.1214/aos/1030563978>.
Author: Zheng Chen Man [aut, cre]
Maintainer: Zheng Chen Man <zheng.chen.man@alumni.ethz.ch>
Diff between edecob versions 1.2.1 dated 2022-10-25 and 1.2.2 dated 2022-11-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/edecob.R | 15 ++++++--------- R/plot.R | 2 +- man/edecob.Rd | 15 ++++++--------- 5 files changed, 20 insertions(+), 26 deletions(-)
Title: Siena - Simulation Investigation for Empirical Network Analysis
Description: The main purpose of this package is to perform simulation-based
estimation of stochastic actor-oriented models for longitudinal network
data collected as panel data. Dependent variables can be single or
multivariate networks, which can be directed, non-directed, or two-mode;
and associated actor variables.
There are also functions for testing parameters and checking goodness of fit.
An overview of these models is given in Tom A.B. Snijders (2017), Stochastic
Actor-Oriented Models for Network Dynamics, Annual Review of Statistics and
Its Application, 4, 343-363 <doi: 10.1146/annurev-statistics-060116-054035>.
An extensive manual, scripts, and much further information is at the Siena
website <http://www.stats.ox.ac.uk/~snijders/siena/>.
Author: Tom A.B. Snijders [cre, aut] ,
Ruth Ripley [aut],
Krists Boitmanis [aut, ctb],
Christian Steglich [aut, ctb] ,
Johan Koskinen [aut, ctb] ,
Nynke Niezink [aut, ctb] ,
Viviana Amati [aut, ctb] ,
Christoph Stadtfeld [ctb] ,
James Hollway [ctb] ,
Per Blo [...truncated...]
Maintainer: Tom A.B. Snijders <tom.snijders@nuffield.ox.ac.uk>
Diff between RSiena versions 1.3.13 dated 2022-10-07 and 1.3.14 dated 2022-11-04
DESCRIPTION | 6 MD5 | 6 configure | 2056 +++++++++++++++++++++++++++++++---------------------------- configure.ac | 2 4 files changed, 1098 insertions(+), 972 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C++ code. More explicit use via 'LinkingTo:' is also supported.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.8 dated 2022-04-04 and 0.0.9 dated 2022-11-04
ChangeLog | 45 DESCRIPTION | 12 MD5 | 113 R/RcppExports.R | 91 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 inst/doc/introduction.html | 39 inst/doc/introduction.md | 101 inst/include/RcppSpdlog.h |only inst/include/RcppSpdlog_RcppExports.h |only inst/include/spdl.h |only inst/include/spdlog/common-inl.h | 2 inst/include/spdlog/common.h | 32 inst/include/spdlog/details/circular_q.h | 5 inst/include/spdlog/details/fmt_helper.h | 2 inst/include/spdlog/details/mpmc_blocking_q.h | 6 inst/include/spdlog/details/null_mutex.h | 4 inst/include/spdlog/details/os-inl.h | 6 inst/include/spdlog/details/periodic_worker-inl.h | 21 inst/include/spdlog/details/periodic_worker.h | 22 inst/include/spdlog/details/registry-inl.h | 7 inst/include/spdlog/details/registry.h | 10 inst/include/spdlog/details/thread_pool-inl.h | 5 inst/include/spdlog/details/thread_pool.h | 1 inst/include/spdlog/fmt/bin_to_hex.h | 8 inst/include/spdlog/fmt/bundled/args.h | 8 inst/include/spdlog/fmt/bundled/chrono.h | 124 - inst/include/spdlog/fmt/bundled/color.h | 213 - inst/include/spdlog/fmt/bundled/compile.h | 111 inst/include/spdlog/fmt/bundled/core.h | 875 ++++--- inst/include/spdlog/fmt/bundled/format-inl.h | 2540 +++++++--------------- inst/include/spdlog/fmt/bundled/format.h | 1955 +++++++++++++--- inst/include/spdlog/fmt/bundled/os.h | 101 inst/include/spdlog/fmt/bundled/ostream.h | 146 + inst/include/spdlog/fmt/bundled/printf.h | 31 inst/include/spdlog/fmt/bundled/ranges.h | 655 ++--- inst/include/spdlog/fmt/bundled/xchar.h | 59 inst/include/spdlog/fmt/fmt.h | 4 inst/include/spdlog/logger.h | 22 inst/include/spdlog/pattern_formatter-inl.h | 13 inst/include/spdlog/pattern_formatter.h | 1 inst/include/spdlog/sinks/android_sink.h | 33 inst/include/spdlog/sinks/daily_file_sink.h | 11 inst/include/spdlog/sinks/dist_sink.h | 14 inst/include/spdlog/sinks/hourly_file_sink.h | 8 inst/include/spdlog/sinks/mongo_sink.h | 26 inst/include/spdlog/sinks/msvc_sink.h | 19 inst/include/spdlog/sinks/ringbuffer_sink.h | 6 inst/include/spdlog/sinks/win_eventlog_sink.h | 8 inst/include/spdlog/sinks/wincolor_sink-inl.h | 4 inst/include/spdlog/spdlog-inl.h | 5 inst/include/spdlog/spdlog.h | 13 inst/include/spdlog/stopwatch.h | 1 inst/include/spdlog/tweakme.h | 7 inst/include/spdlog/version.h | 2 man/log_setup.Rd |only src/RcppExports.cpp | 384 +++ src/interface.cpp |only vignettes/introduction.md | 101 60 files changed, 4561 insertions(+), 3480 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Ef [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut]
,
Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 2.5-0 dated 2022-07-11 and 2.6-0 dated 2022-11-04
DESCRIPTION | 10 - MD5 | 42 ++--- NEWS.md | 55 +++++++ R/forest.netbind.R | 4 R/forest.netsplit.R | 40 +++-- R/netgraph.R | 6 R/netgraph.discomb.R | 10 - R/netgraph.netconnection.R | 11 - R/netgraph.netimpact.R | 25 ++- R/netgraph.netmeta.R | 309 ++++++++++++++++++++++++++---------------- R/netleague.R | 4 R/netmatrix.R | 12 - R/netsplit.R | 4 R/plot.rankogram.R | 14 - R/rankogram.R | 8 - man/netgraph.Rd | 7 man/netgraph.discomb.Rd | 9 - man/netgraph.netconnection.Rd | 8 - man/netgraph.netimpact.Rd | 25 ++- man/netgraph.netmeta.Rd | 85 ++++++++--- man/netleague.Rd | 4 man/netmatrix.Rd | 12 - 22 files changed, 462 insertions(+), 242 deletions(-)
Title: R6 Class for Structural Causal Models
Description: The implemented R6 class 'SCM' aims to simplify working with structural causal models. The missing data mechanism can be defined as a part of the structural model. The class contains methods for 1) defining a structural causal model via functions, text or conditional probability tables, 2) printing basic information on the model, 3) plotting the graph for the model using packages 'igraph' or 'qgraph', 4) simulating data from the model, 5) applying an intervention, 6) checking the identifiability of a query using the R packages 'causaleffect' and 'dosearch', 7) defining the missing data mechanism, 8) simulating incomplete data from the model according to the specified missing data mechanism and 9) checking the identifiability in a missing data problem using the R package 'dosearch'. In addition, there are functions for running experiments and doing counterfactual inference using simulation.
Author: Juha Karvanen [aut, cre]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>
Diff between R6causal versions 0.6.1 dated 2022-08-06 and 0.7.0 dated 2022-11-04
DESCRIPTION | 8 MD5 | 33 +-- NAMESPACE | 1 NEWS.md | 5 R/R6causal.R | 393 ++++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/using_R6causal.R | 45 ++++ inst/doc/using_R6causal.Rmd | 63 ++++++ inst/doc/using_R6causal.pdf |binary man/ParallelWorld.Rd |only man/SCM.Rd | 83 ++++++--- man/backdoor.Rd | 2 man/backdoor_md.Rd | 2 man/counterfactual.Rd | 55 +++--- man/frontdoor.Rd | 2 man/run_experiment.Rd | 64 +++---- man/trapdoor.Rd | 2 vignettes/using_R6causal.Rmd | 63 ++++++ 18 files changed, 668 insertions(+), 153 deletions(-)