Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that
aims to provide fast, extensible implementations of cutting-edge
machine learning algorithms. See also Curtin et al. (2023)
<doi:10.21105/joss.05026>.
Author: Yashwant Singh Parihar [aut, ctb, cph],
Ryan Curtin [aut, ctb, cph, cre],
Dirk Eddelbuettel [aut, ctb, cph],
James Balamuta [aut, ctb, cph],
Bill March [ctb, cph],
Dongryeol Lee [ctb, cph],
Nishant Mehta [ctb, cph],
Parikshit Ram [ctb, cph],
James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>
Diff between mlpack versions 4.3.0 dated 2023-11-29 and 4.3.0.1 dated 2024-02-23
DESCRIPTION | 10 +-- MD5 | 9 +- R/inline.R |only R/package.R | 4 - man/mlpack.Rd | 167 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- src/Makevars.win | 2 6 files changed, 178 insertions(+), 14 deletions(-)
Title: Langevin Tour
Description: An HTML widget that randomly tours 2D projections of numerical data. A random walk through projections of the data is shown. The user can manipulate the plot to use specified axes, or turn on Guided Tour mode to find an informative projection of the data. Groups within the data can be hidden or shown, as can particular axes. Points can be brushed, and the selection can be linked to other widgets using crosstalk. The underlying method to produce the random walk and projection pursuit uses Langevin dynamics. The widget can be used from within R, or included in a self-contained R Markdown or Quarto document or presentation, or used in a Shiny app.
Author: Paul Harrison [aut, cre]
Maintainer: Paul Harrison <pfh@logarithmic.net>
Diff between langevitour versions 0.6 dated 2023-11-17 and 0.7 dated 2024-02-23
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/langevitour.R | 7 ++++--- README.md | 2 ++ inst/doc/usage.html | 8 ++++---- inst/htmlwidgets/langevitour.js | 2 +- inst/htmlwidgets/langevitour.yaml | 2 +- inst/htmlwidgets/lib/langevitour-pack.js | 2 +- man/langevitour.Rd | 4 ++-- 10 files changed, 33 insertions(+), 24 deletions(-)
Title: Process Analysis for Exponential Random Graph Models
Description: Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM).
Includes functions to conduct mediation and moderation analyses and to diagnose
multicollinearity.
URL: <https://github.com/sduxbury/ergMargins>.
BugReports: <https://github.com/sduxbury/ergMargins/issues>.
Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>.
Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>.
Mize, Trenton D. (2019) <doi:10.15195/v6.a4>.
Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>.
Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>.
Duxbury, Scott W, Jenna Wertsching (2023) <doi:10.1016/j.socnet.2023.02.003>.
Huang, Peng, Carter Butts (2023) <doi:10.1016/j.socnet.2023.07.001>.
Author: Scott Duxbury [aut, cre, cph]
Maintainer: Scott Duxbury <duxbury@email.unc.edu>
Diff between ergMargins versions 1.1 dated 2023-11-11 and 1.2 dated 2024-02-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/ergmAME.R | 18 +++++++++++------- R/ergmAME_boot.R | 2 +- R/ergmMEM.R | 6 +++--- R/ergmMEM_boot.R | 1 - 6 files changed, 23 insertions(+), 20 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre] ,
Peter Slaughter [aut] ,
Jeroen Ooms [aut] ,
Carl Boettiger [aut] ,
Scott Chamberlain [ctb] ,
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-17 dated 2023-05-23 and 1.0.17-18 dated 2024-02-23
redland-1.0.17-17/redland/inst/Makefile |only redland-1.0.17-17/redland/inst/config.log |only redland-1.0.17-17/redland/inst/config.status |only redland-1.0.17-17/redland/tools/Makefile |only redland-1.0.17-17/redland/tools/NEWS |only redland-1.0.17-17/redland/tools/README |only redland-1.0.17-17/redland/tools/aclocal.m4 |only redland-1.0.17-17/redland/tools/config.log |only redland-1.0.17-17/redland/tools/config.status |only redland-1.0.17-18/redland/DESCRIPTION | 30 +++---- redland-1.0.17-18/redland/MD5 | 61 ++++++--------- redland-1.0.17-18/redland/NAMESPACE | 40 ++++----- redland-1.0.17-18/redland/NEWS | 8 + redland-1.0.17-18/redland/R/Model.R | 8 - redland-1.0.17-18/redland/R/Node.R | 10 +- redland-1.0.17-18/redland/R/Parser.R | 8 - redland-1.0.17-18/redland/R/Query.R | 16 +-- redland-1.0.17-18/redland/R/QueryResults.R | 6 - redland-1.0.17-18/redland/R/Serializer.R | 12 +- redland-1.0.17-18/redland/R/Statement.R | 8 - redland-1.0.17-18/redland/R/Storage.R | 6 - redland-1.0.17-18/redland/R/World.R | 6 - redland-1.0.17-18/redland/README.md | 2 redland-1.0.17-18/redland/build/vignette.rds |binary redland-1.0.17-18/redland/configure | 2 redland-1.0.17-18/redland/inst/doc/redland_overview.html | 46 +++++------ redland-1.0.17-18/redland/man/Model-class.Rd | 8 - redland-1.0.17-18/redland/man/Node-class.Rd | 10 +- redland-1.0.17-18/redland/man/Parser-class.Rd | 8 - redland-1.0.17-18/redland/man/Query-class.Rd | 16 +-- redland-1.0.17-18/redland/man/QueryResults-class.Rd | 6 - redland-1.0.17-18/redland/man/Serializer-class.Rd | 12 +- redland-1.0.17-18/redland/man/Statement-class.Rd | 8 - redland-1.0.17-18/redland/man/Storage-class.Rd | 6 - redland-1.0.17-18/redland/man/World-class.Rd | 6 - redland-1.0.17-18/redland/src/Makevars.ucrt | 9 +- 36 files changed, 181 insertions(+), 177 deletions(-)
Title: The T-LARS Algorithm: Early-Terminated Forward Variable
Selection
Description: Computes the solution path of the Terminating-LARS (T-LARS) algorithm. The T-LARS algorithm
is a major building block of the T-Rex selector (see R package 'TRexSelector').
The package is based on the papers Machkour, Muma, and Palomar (2022) <arXiv:2110.06048>, Efron, Hastie, Johnstone,
and Tibshirani (2004) <doi:10.1214/009053604000000067>, and Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>.
Author: Jasin Machkour [aut, cre],
Simon Tien [aut],
Daniel P. Palomar [aut],
Michael Muma [aut]
Maintainer: Jasin Machkour <jasin.machkour@tu-darmstadt.de>
Diff between tlars versions 1.0.0 dated 2024-02-21 and 1.0.1 dated 2024-02-23
tlars-1.0.0/tlars/vignettes/the-annals-of-statistics.csl |only tlars-1.0.1/tlars/DESCRIPTION | 8 tlars-1.0.1/tlars/MD5 | 14 - tlars-1.0.1/tlars/NEWS.md | 12 - tlars-1.0.1/tlars/README.md | 168 ++++++++------- tlars-1.0.1/tlars/inst/doc/tlars_variable_selection.Rmd | 2 tlars-1.0.1/tlars/inst/doc/tlars_variable_selection.html | 18 - tlars-1.0.1/tlars/vignettes/ieee.csl |only tlars-1.0.1/tlars/vignettes/tlars_variable_selection.Rmd | 2 9 files changed, 132 insertions(+), 92 deletions(-)
Title: T-Rex Selector: High-Dimensional Variable Selection & FDR
Control
Description: Performs fast variable selection in high-dimensional settings while controlling the
false discovery rate (FDR) at a user-defined target level. The package is based on the paper
Machkour, Muma, and Palomar (2022) <arXiv:2110.06048>.
Author: Jasin Machkour [aut, cre],
Simon Tien [aut],
Daniel P. Palomar [aut],
Michael Muma [aut]
Maintainer: Jasin Machkour <jasin.machkour@tu-darmstadt.de>
Diff between TRexSelector versions 0.0.1 dated 2022-08-17 and 1.0.0 dated 2024-02-23
TRexSelector-0.0.1/TRexSelector/vignettes/the-annals-of-statistics.csl |only TRexSelector-1.0.0/TRexSelector/DESCRIPTION | 22 TRexSelector-1.0.0/TRexSelector/MD5 | 59 TRexSelector-1.0.0/TRexSelector/NAMESPACE | 6 TRexSelector-1.0.0/TRexSelector/NEWS.md | 12 TRexSelector-1.0.0/TRexSelector/R/Phi_prime_fun.R | 4 TRexSelector-1.0.0/TRexSelector/R/add_dummies_GVS.R | 22 TRexSelector-1.0.0/TRexSelector/R/fdp_hat.R | 6 TRexSelector-1.0.0/TRexSelector/R/lm_dummy.R | 54 TRexSelector-1.0.0/TRexSelector/R/random_experiments.R | 49 TRexSelector-1.0.0/TRexSelector/R/screen_trex.R |only TRexSelector-1.0.0/TRexSelector/R/select_var_fun.R | 2 TRexSelector-1.0.0/TRexSelector/R/select_var_fun_DA_BT.R |only TRexSelector-1.0.0/TRexSelector/R/trex.R | 541 ++ TRexSelector-1.0.0/TRexSelector/README.md | 124 TRexSelector-1.0.0/TRexSelector/build/partial.rdb |only TRexSelector-1.0.0/TRexSelector/build/vignette.rds |binary TRexSelector-1.0.0/TRexSelector/inst/CITATION | 46 TRexSelector-1.0.0/TRexSelector/inst/doc/TRexSelector_usage_and_simulations.R | 21 TRexSelector-1.0.0/TRexSelector/inst/doc/TRexSelector_usage_and_simulations.Rmd | 28 TRexSelector-1.0.0/TRexSelector/inst/doc/TRexSelector_usage_and_simulations.html | 1815 ++++++++-- TRexSelector-1.0.0/TRexSelector/man/Phi_prime_fun.Rd | 4 TRexSelector-1.0.0/TRexSelector/man/add_dummies_GVS.Rd | 4 TRexSelector-1.0.0/TRexSelector/man/fdp_hat.Rd | 10 TRexSelector-1.0.0/TRexSelector/man/lm_dummy.Rd | 13 TRexSelector-1.0.0/TRexSelector/man/random_experiments.Rd | 23 TRexSelector-1.0.0/TRexSelector/man/screen_trex.Rd |only TRexSelector-1.0.0/TRexSelector/man/select_var_fun.Rd | 2 TRexSelector-1.0.0/TRexSelector/man/select_var_fun_DA_BT.Rd |only TRexSelector-1.0.0/TRexSelector/man/trex.Rd | 33 TRexSelector-1.0.0/TRexSelector/tests/testthat/test-add_dummies_GVS.R | 2 TRexSelector-1.0.0/TRexSelector/vignettes/TRexSelector_usage_and_simulations.Rmd | 28 TRexSelector-1.0.0/TRexSelector/vignettes/ieee.csl |only TRexSelector-1.0.0/TRexSelector/vignettes/refs.bib | 79 34 files changed, 2505 insertions(+), 504 deletions(-)
Title: R-Based Visualization Techniques for Task-Based Applications
Description: Performance analysis workflow that combines the power of the R
language (and the tidyverse realm) and many auxiliary tools to
provide a consistent, flexible, extensible, fast, and versatile
framework for the performance analysis of task-based applications
that run on top of the StarPU runtime (with its MPI (Message
Passing Interface) layer for multi-node support). Its goal is to
provide a fruitful prototypical environment to conduct performance
analysis hypothesis-checking for task-based applications that run
on heterogeneous (multi-GPU, multi-core) multi-node HPC
(High-performance computing) platforms.
Author: Lucas Mello Schnorr [aut, ths]
,
Vinicius Garcia Pinto [aut] ,
Lucas Leandro Nesi [aut, cre] ,
Marcelo Cogo Miletto [aut] ,
Guilherme Alles [ctb],
Arnaud Legrand [ctb],
Luka Stanisic [ctb],
Remy Drouilhet [ctb]
Maintainer: Lucas Leandro Nesi <lucas.nesi@inf.ufrgs.br>
Diff between starvz versions 0.7.1 dated 2022-02-13 and 0.8.0 dated 2024-02-23
DESCRIPTION | 18 +-- MD5 | 83 +++++++-------- NAMESPACE | 9 - R/RcppExports.R | 11 -- R/phase1.R | 102 +++++++++--------- R/phase1_outlier.R | 33 ++---- R/phase1_parse_csv.R | 166 +++++++++++++++--------------- R/phase2.R | 35 ++---- R/phase2_aggregation.R | 34 +++--- R/phase2_atree.R | 218 ++++++++++++++++++++-------------------- R/phase2_config.R | 3 R/phase2_gaps.R | 12 +- R/phase2_imbalance.R | 53 +++++---- R/phase2_kchart.R | 6 - R/phase2_lackready.R | 4 R/phase2_memory.R | 122 +++++++++++----------- R/phase2_metrics.R | 58 +++++----- R/phase2_mpi.R | 16 +- R/phase2_node_summary.R | 9 - R/phase2_pmtool.R | 23 ---- R/phase2_progress.R |only R/phase2_states_chart.R | 92 ++++++++++------ R/phase2_util.R | 136 +++++++++++++++--------- R/phase2_var_chart.R | 10 - R/phase2_var_panels.R | 14 -- R/read_functions.R | 27 ++-- R/starvz_data.R | 47 ++++++++ R/write_functions.R | 10 - inst/tools/2d_map.R | 2 inst/tools/fxt2paje.sh | 2 inst/tools/phase1-workflow.R | 2 inst/tools/phase1-workflow.sh | 4 inst/tools/phase2-memsnaps.R | 2 inst/tools/phase2-workflow.R | 2 man/panel_atree.Rd | 6 - man/panel_progress.Rd |only man/panel_st_agg_node.Rd | 5 man/panel_st_raw.Rd | 3 man/starvz_assemble.Rd | 3 man/starvz_check_data.Rd | 3 man/starvz_phase1.Rd | 2 man/starvz_read.Rd | 8 + man/starvz_transform_olddata.Rd |only tests/testthat/test_lu.R | 3 44 files changed, 751 insertions(+), 647 deletions(-)
Title: Error Detection in Science
Description: Test published summary statistics for consistency
(Brown and Heathers, 2017, <doi:10.1177/1948550616673876>;
Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>;
Heathers and Brown, 2019, <https://osf.io/5vb3u/>).
The package also provides infrastructure for implementing new
error detection techniques.
Author: Lukas Jung [aut, cre],
Aurelien Allard [ctb]
Maintainer: Lukas Jung <jung-lukas@gmx.net>
Diff between scrutiny versions 0.3.0 dated 2023-08-08 and 0.4.0 dated 2024-02-23
scrutiny-0.3.0/scrutiny/R/grim-explain.R |only scrutiny-0.3.0/scrutiny/inst/doc/consistency-tests.R |only scrutiny-0.3.0/scrutiny/inst/doc/consistency-tests.Rmd |only scrutiny-0.3.0/scrutiny/inst/doc/consistency-tests.html |only scrutiny-0.3.0/scrutiny/inst/doc/infrastructure.R |only scrutiny-0.3.0/scrutiny/inst/doc/infrastructure.Rmd |only scrutiny-0.3.0/scrutiny/inst/doc/infrastructure.html |only scrutiny-0.3.0/scrutiny/inst/doc/rounding.R |only scrutiny-0.3.0/scrutiny/inst/doc/rounding.Rmd |only scrutiny-0.3.0/scrutiny/inst/doc/rounding.html |only scrutiny-0.3.0/scrutiny/vignettes/consistency-tests.Rmd |only scrutiny-0.3.0/scrutiny/vignettes/infrastructure.Rmd |only scrutiny-0.3.0/scrutiny/vignettes/rounding.Rmd |only scrutiny-0.4.0/scrutiny/DESCRIPTION | 31 scrutiny-0.4.0/scrutiny/MD5 | 390 +++++----- scrutiny-0.4.0/scrutiny/NAMESPACE | 1 scrutiny-0.4.0/scrutiny/NEWS.md | 28 scrutiny-0.4.0/scrutiny/R/audit-cols-minimal.R | 11 scrutiny-0.4.0/scrutiny/R/audit.R | 89 +- scrutiny-0.4.0/scrutiny/R/before-inside-parens.R | 37 scrutiny-0.4.0/scrutiny/R/data-doc.R | 40 - scrutiny-0.4.0/scrutiny/R/data-frame-predicates.R | 26 scrutiny-0.4.0/scrutiny/R/debit-map-seq.R | 19 scrutiny-0.4.0/scrutiny/R/debit-map-total-n.R | 16 scrutiny-0.4.0/scrutiny/R/debit-map.R | 49 - scrutiny-0.4.0/scrutiny/R/debit-plot.R | 21 scrutiny-0.4.0/scrutiny/R/debit-table.R | 5 scrutiny-0.4.0/scrutiny/R/debit.R | 15 scrutiny-0.4.0/scrutiny/R/decimal-places.R | 25 scrutiny-0.4.0/scrutiny/R/disperse.R | 41 - scrutiny-0.4.0/scrutiny/R/duplicate-count-colpair.R | 20 scrutiny-0.4.0/scrutiny/R/duplicate-count.R | 57 - scrutiny-0.4.0/scrutiny/R/duplicate-detect.R | 66 + scrutiny-0.4.0/scrutiny/R/function-factory-helpers.R | 96 +- scrutiny-0.4.0/scrutiny/R/function-map-seq.R | 251 +++--- scrutiny-0.4.0/scrutiny/R/function-map-total-n.R | 362 +-------- scrutiny-0.4.0/scrutiny/R/function-map.R | 220 +++-- scrutiny-0.4.0/scrutiny/R/grim-map-debug.R |only scrutiny-0.4.0/scrutiny/R/grim-map-seq.R | 10 scrutiny-0.4.0/scrutiny/R/grim-map-total-n.R | 16 scrutiny-0.4.0/scrutiny/R/grim-map.R | 93 +- scrutiny-0.4.0/scrutiny/R/grim-plot.R | 109 +- scrutiny-0.4.0/scrutiny/R/grim-stats.R | 14 scrutiny-0.4.0/scrutiny/R/grim.R | 102 -- scrutiny-0.4.0/scrutiny/R/grimmer-map-seq.R | 29 scrutiny-0.4.0/scrutiny/R/grimmer-map-total-n.R | 14 scrutiny-0.4.0/scrutiny/R/grimmer-map.R | 54 - scrutiny-0.4.0/scrutiny/R/grimmer.R | 25 scrutiny-0.4.0/scrutiny/R/import-reexport.R | 1 scrutiny-0.4.0/scrutiny/R/is-numeric-like.R | 31 scrutiny-0.4.0/scrutiny/R/manage-extra-cols.R | 15 scrutiny-0.4.0/scrutiny/R/mapper-function-helpers.R | 44 - scrutiny-0.4.0/scrutiny/R/metadata.R | 58 + scrutiny-0.4.0/scrutiny/R/method-audit-seq.R | 3 scrutiny-0.4.0/scrutiny/R/method-audit-total-n.R | 2 scrutiny-0.4.0/scrutiny/R/method-debit-map.R | 1 scrutiny-0.4.0/scrutiny/R/method-detect.R | 7 scrutiny-0.4.0/scrutiny/R/method-dup-count-colpair.R | 2 scrutiny-0.4.0/scrutiny/R/method-dup-count.R | 4 scrutiny-0.4.0/scrutiny/R/method-grim-map.R | 6 scrutiny-0.4.0/scrutiny/R/method-grim-sequence.R | 23 scrutiny-0.4.0/scrutiny/R/method-grimmer-map.R | 4 scrutiny-0.4.0/scrutiny/R/method-tally.R | 12 scrutiny-0.4.0/scrutiny/R/reround-to-fraction.R | 16 scrutiny-0.4.0/scrutiny/R/reround.R | 206 +---- scrutiny-0.4.0/scrutiny/R/restore-zeros.R | 25 scrutiny-0.4.0/scrutiny/R/reverse-map-seq.R | 51 - scrutiny-0.4.0/scrutiny/R/reverse-map-total-n.R | 13 scrutiny-0.4.0/scrutiny/R/rivets-plot-cols.R | 20 scrutiny-0.4.0/scrutiny/R/rivets-plot-lines.R | 10 scrutiny-0.4.0/scrutiny/R/rivets-t-test.R | 24 scrutiny-0.4.0/scrutiny/R/rivets_new.R | 2 scrutiny-0.4.0/scrutiny/R/round-ceil-floor.R | 26 scrutiny-0.4.0/scrutiny/R/round.R | 55 - scrutiny-0.4.0/scrutiny/R/rounding-bias.R | 11 scrutiny-0.4.0/scrutiny/R/row-to-colnames.R | 11 scrutiny-0.4.0/scrutiny/R/sd-binary.R | 10 scrutiny-0.4.0/scrutiny/R/seq-decimal.R | 19 scrutiny-0.4.0/scrutiny/R/seq-disperse.R | 190 +++- scrutiny-0.4.0/scrutiny/R/seq-length.R | 6 scrutiny-0.4.0/scrutiny/R/seq-predicates.R | 50 - scrutiny-0.4.0/scrutiny/R/split-by-parens.R | 25 scrutiny-0.4.0/scrutiny/R/subset-superset.R | 5 scrutiny-0.4.0/scrutiny/R/sysdata.rda |binary scrutiny-0.4.0/scrutiny/R/unround.R | 48 - scrutiny-0.4.0/scrutiny/R/utils.R | 367 ++++++--- scrutiny-0.4.0/scrutiny/R/write-doc-audit.R | 144 ++- scrutiny-0.4.0/scrutiny/README.md | 204 ++--- scrutiny-0.4.0/scrutiny/build/vignette.rds |binary scrutiny-0.4.0/scrutiny/inst/doc/consistency-tests-in-depth.R |only scrutiny-0.4.0/scrutiny/inst/doc/consistency-tests-in-depth.Rmd |only scrutiny-0.4.0/scrutiny/inst/doc/consistency-tests-in-depth.html |only scrutiny-0.4.0/scrutiny/inst/doc/consistency-tests-simple.R |only scrutiny-0.4.0/scrutiny/inst/doc/consistency-tests-simple.Rmd |only scrutiny-0.4.0/scrutiny/inst/doc/consistency-tests-simple.html |only scrutiny-0.4.0/scrutiny/inst/doc/debit.R | 19 scrutiny-0.4.0/scrutiny/inst/doc/debit.Rmd | 36 scrutiny-0.4.0/scrutiny/inst/doc/debit.html | 281 ++----- scrutiny-0.4.0/scrutiny/inst/doc/devtools.R |only scrutiny-0.4.0/scrutiny/inst/doc/devtools.Rmd |only scrutiny-0.4.0/scrutiny/inst/doc/devtools.html |only scrutiny-0.4.0/scrutiny/inst/doc/duplicates.R | 6 scrutiny-0.4.0/scrutiny/inst/doc/duplicates.Rmd | 27 scrutiny-0.4.0/scrutiny/inst/doc/duplicates.html | 106 +- scrutiny-0.4.0/scrutiny/inst/doc/grim.R | 56 - 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scrutiny-0.4.0/scrutiny/man/rounding-uncommon.Rd | 19 scrutiny-0.4.0/scrutiny/man/rounding_bias.Rd | 8 scrutiny-0.4.0/scrutiny/man/row_to_colnames.Rd | 6 scrutiny-0.4.0/scrutiny/man/sd-binary.Rd | 4 scrutiny-0.4.0/scrutiny/man/seq-decimal.Rd | 14 scrutiny-0.4.0/scrutiny/man/seq-predicates.Rd | 8 scrutiny-0.4.0/scrutiny/man/seq_disperse.Rd | 37 scrutiny-0.4.0/scrutiny/man/split_by_parens.Rd | 18 scrutiny-0.4.0/scrutiny/man/subset-superset.Rd | 2 scrutiny-0.4.0/scrutiny/man/unnest_consistency_cols.Rd | 4 scrutiny-0.4.0/scrutiny/man/unround.Rd | 4 scrutiny-0.4.0/scrutiny/man/write_doc_audit.Rd | 16 scrutiny-0.4.0/scrutiny/man/write_doc_audit_seq.Rd | 12 scrutiny-0.4.0/scrutiny/man/write_doc_audit_total_n.Rd | 14 scrutiny-0.4.0/scrutiny/man/write_doc_factory_map_conventions.Rd | 21 scrutiny-0.4.0/scrutiny/tests/testthat/test-audit.R | 51 + scrutiny-0.4.0/scrutiny/tests/testthat/test-debit-map.R | 4 scrutiny-0.4.0/scrutiny/tests/testthat/test-debit-plot.R | 2 scrutiny-0.4.0/scrutiny/tests/testthat/test-disperse.R | 5 scrutiny-0.4.0/scrutiny/tests/testthat/test-duplicate-count.R | 10 scrutiny-0.4.0/scrutiny/tests/testthat/test-function-map.R | 52 + scrutiny-0.4.0/scrutiny/tests/testthat/test-grim-granularity.R | 8 scrutiny-0.4.0/scrutiny/tests/testthat/test-grim-map-seq.R | 133 ++- scrutiny-0.4.0/scrutiny/tests/testthat/test-grim-map-total-n.R | 44 - scrutiny-0.4.0/scrutiny/tests/testthat/test-grim-map.R | 24 scrutiny-0.4.0/scrutiny/tests/testthat/test-grim-plot.R | 2 scrutiny-0.4.0/scrutiny/tests/testthat/test-grim.R | 12 scrutiny-0.4.0/scrutiny/tests/testthat/test-grimmer-map.R |only scrutiny-0.4.0/scrutiny/tests/testthat/test-method-dup-count.R | 6 scrutiny-0.4.0/scrutiny/tests/testthat/test-method-grim-map.R | 10 scrutiny-0.4.0/scrutiny/tests/testthat/test-method-grim-sequence.R | 2 scrutiny-0.4.0/scrutiny/tests/testthat/test-method-tally.R | 6 scrutiny-0.4.0/scrutiny/tests/testthat/test-restore-zeros.R | 28 scrutiny-0.4.0/scrutiny/tests/testthat/test-seq-disperse.R |only scrutiny-0.4.0/scrutiny/tests/testthat/test-split-by-parens.R | 15 scrutiny-0.4.0/scrutiny/tests/testthat/test-unround.R | 6 scrutiny-0.4.0/scrutiny/tests/testthat/test-utils.R | 14 scrutiny-0.4.0/scrutiny/vignettes/consistency-tests-in-depth.Rmd |only scrutiny-0.4.0/scrutiny/vignettes/consistency-tests-simple.Rmd |only scrutiny-0.4.0/scrutiny/vignettes/debit.Rmd | 36 scrutiny-0.4.0/scrutiny/vignettes/devtools.Rmd |only scrutiny-0.4.0/scrutiny/vignettes/duplicates.Rmd | 27 scrutiny-0.4.0/scrutiny/vignettes/grim.Rmd | 60 - scrutiny-0.4.0/scrutiny/vignettes/grimmer.Rmd | 39 - scrutiny-0.4.0/scrutiny/vignettes/references.bib | 54 + scrutiny-0.4.0/scrutiny/vignettes/rounding-in-depth.Rmd |only scrutiny-0.4.0/scrutiny/vignettes/rounding-options.Rmd |only scrutiny-0.4.0/scrutiny/vignettes/wrangling.Rmd | 14 214 files changed, 3358 insertions(+), 3685 deletions(-)
Title: Text Analysis Through the 'Receptiviti' API
Description: Send text to the <https://www.receptiviti.com> API to be scored
by all available frameworks.
Author: Receptiviti Inc. [fnd, cph],
Kent English [cre],
Micah Iserman [aut, ctr]
Maintainer: Kent English <kenglish@receptiviti.com>
Diff between receptiviti versions 0.1.6 dated 2023-11-27 and 0.1.7 dated 2024-02-23
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ NAMESPACE | 13 ------------- NEWS.md | 5 +++++ R/receptiviti.R | 15 +++++++++------ README.md | 4 ++-- tests/testthat/test-receptiviti.R | 12 +++++------- 7 files changed, 35 insertions(+), 41 deletions(-)
Title: Tools for Identifying Important Nodes in Networks
Description: Includes assorted tools for network analysis. Bridge centrality; goldbricker; MDS, PCA, & eigenmodel network plotting.
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <paytonjjones@gmail.com>
Diff between networktools versions 1.5.1 dated 2023-08-22 and 1.5.2 dated 2024-02-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/goldbricker.R | 7 +++++-- 4 files changed, 16 insertions(+), 9 deletions(-)
Title: Access and Analyze eBird Status and Trends Data Products
Description: Tools for accessing and analyzing eBird Status and
Trends Data Products
(<https://science.ebird.org/en/status-and-trends>). eBird
(<https://ebird.org/home>) is a global database of bird observations
collected by member of the public. eBird Status and Trends uses these
data to model global bird distributions, abundances, and population trends
at a high spatial and temporal resolution.
Author: Matthew Strimas-Mackey [aut, cre]
,
Shawn Ligocki [aut],
Tom Auer [aut] ,
Daniel Fink [aut] ,
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between ebirdst versions 3.2022.1 dated 2023-12-08 and 3.2022.2 dated 2024-02-23
DESCRIPTION | 17 - MD5 | 32 - NEWS.md | 6 R/data.R | 2 R/ebirdst-package.R | 2 R/load.R | 4 R/sample.R | 10 R/trends.R | 11 build/vignette.rds |binary inst/doc/applications.R | 432 ++++++++++++++++---------- inst/doc/applications.Rmd | 564 +++++++++++++++++++++-------------- inst/doc/applications.html | 724 ++++++++++++++++++++++++++++----------------- man/assign_to_grid.Rd | 2 man/ebirdst-package.Rd | 2 man/ebirdst_runs.Rd | 2 man/grid_sample.Rd | 2 vignettes/applications.Rmd | 564 +++++++++++++++++++++-------------- 17 files changed, 1486 insertions(+), 890 deletions(-)
Title: Clinical Pharmacokinetics Toolkit
Description: Provides equations commonly used in clinical
pharmacokinetics and clinical pharmacology, such as equations
for dose individualization, compartmental pharmacokinetics,
drug exposure, anthropomorphic calculations, clinical
chemistry, and conversion of common clinical parameters. Where
possible and relevant, it provides multiple published and
peer-reviewed equations within the respective R function.
Author: Ron Keizer [aut, cre],
Jasmine Hughes [aut],
Dominic Tong [aut],
Kara Woo [aut],
InsightRX [cph, fnd]
Maintainer: Ron Keizer <ron@insight-rx.com>
Diff between clinPK versions 0.11.1 dated 2022-05-10 and 0.13.0 dated 2024-02-23
clinPK-0.11.1/clinPK/man/ibw_devine.Rd |only clinPK-0.11.1/clinPK/man/ibw_standard.Rd |only clinPK-0.13.0/clinPK/DESCRIPTION | 26 - clinPK-0.13.0/clinPK/MD5 | 114 ++++--- clinPK-0.13.0/clinPK/NAMESPACE | 4 clinPK-0.13.0/clinPK/NEWS.md | 15 clinPK-0.13.0/clinPK/R/calc_aki_stage.R | 2 clinPK-0.13.0/clinPK/R/calc_carboplatin_calvert.R |only clinPK-0.13.0/clinPK/R/calc_creat_neo.R | 4 clinPK-0.13.0/clinPK/R/calc_egfr.R | 12 clinPK-0.13.0/clinPK/R/calc_egfr_cystatin.R | 32 +- clinPK-0.13.0/clinPK/R/calc_ffm.R | 7 clinPK-0.13.0/clinPK/R/calc_ibw.R | 4 clinPK-0.13.0/clinPK/R/calc_neutropenia_grade.R |only clinPK-0.13.0/clinPK/R/check_covs_available.R | 3 clinPK-0.13.0/clinPK/R/clinPK-package.R | 2 clinPK-0.13.0/clinPK/R/convert_albumin_unit.R |only clinPK-0.13.0/clinPK/R/convert_bilirubin_unit.R |only clinPK-0.13.0/clinPK/R/convert_conc_unit.R |only clinPK-0.13.0/clinPK/R/convert_creat_unit.R | 38 -- clinPK-0.13.0/clinPK/R/convert_flow_unit.R | 1 clinPK-0.13.0/clinPK/R/misc.R | 10 clinPK-0.13.0/clinPK/R/nca.R | 20 - clinPK-0.13.0/clinPK/R/nca_linear.R |only clinPK-0.13.0/clinPK/R/nca_trapezoid.R | 2 clinPK-0.13.0/clinPK/R/pct_for_age_generic.R | 1 clinPK-0.13.0/clinPK/R/print.nca_output.R | 1 clinPK-0.13.0/clinPK/R/utils.R | 16 + clinPK-0.13.0/clinPK/R/valid_units.R | 15 clinPK-0.13.0/clinPK/R/weight2kg.R | 23 - clinPK-0.13.0/clinPK/README.md | 152 +++------- clinPK-0.13.0/clinPK/man/as.num.Rd | 3 clinPK-0.13.0/clinPK/man/calc_carboplatin_calvert.Rd |only clinPK-0.13.0/clinPK/man/calc_creat_neo.Rd | 4 clinPK-0.13.0/clinPK/man/calc_egfr.Rd | 40 -- clinPK-0.13.0/clinPK/man/calc_egfr_cystatin.Rd | 6 clinPK-0.13.0/clinPK/man/calc_ffm.Rd | 21 - clinPK-0.13.0/clinPK/man/calc_ibw.Rd | 6 clinPK-0.13.0/clinPK/man/calc_neutropenia_grade.Rd |only clinPK-0.13.0/clinPK/man/check_covs_available.Rd | 2 clinPK-0.13.0/clinPK/man/clinPK-package.Rd | 1 clinPK-0.13.0/clinPK/man/convert_albumin_unit.Rd |only clinPK-0.13.0/clinPK/man/convert_bilirubin_unit.Rd |only clinPK-0.13.0/clinPK/man/convert_conc_unit.Rd |only clinPK-0.13.0/clinPK/man/convert_creat_unit.Rd | 12 clinPK-0.13.0/clinPK/man/figures |only clinPK-0.13.0/clinPK/man/find_factor.Rd | 1 clinPK-0.13.0/clinPK/man/grapes-greater-than-equals-grapes.Rd | 1 clinPK-0.13.0/clinPK/man/grapes-less-than-equals-grapes.Rd | 1 clinPK-0.13.0/clinPK/man/is.nil.Rd | 3 clinPK-0.13.0/clinPK/man/kdigo_stage.Rd | 1 clinPK-0.13.0/clinPK/man/mean_step.Rd |only clinPK-0.13.0/clinPK/man/nca_linear.Rd |only clinPK-0.13.0/clinPK/man/nca_trapezoid.Rd | 1 clinPK-0.13.0/clinPK/man/pct_for_age_generic.Rd | 1 clinPK-0.13.0/clinPK/man/print.nca_output.Rd | 1 clinPK-0.13.0/clinPK/man/remove_lt_gt.Rd | 1 clinPK-0.13.0/clinPK/man/valid_units.Rd | 9 clinPK-0.13.0/clinPK/tests/testthat/test_calc_carboplatin_calvert.R |only clinPK-0.13.0/clinPK/tests/testthat/test_calc_egfr_cystatin.R | 9 clinPK-0.13.0/clinPK/tests/testthat/test_calc_neutropenia_grade.R |only clinPK-0.13.0/clinPK/tests/testthat/test_convert_albumin_unit.R |only clinPK-0.13.0/clinPK/tests/testthat/test_convert_bilirubin_units.R |only clinPK-0.13.0/clinPK/tests/testthat/test_convert_conc_unit.R |only clinPK-0.13.0/clinPK/tests/testthat/test_convert_creat_unit.R | 57 +++ clinPK-0.13.0/clinPK/tests/testthat/test_mean_step.R |only clinPK-0.13.0/clinPK/tests/testthat/test_nca.R | 46 +++ clinPK-0.13.0/clinPK/tests/testthat/test_valid_units.R | 44 ++ clinPK-0.13.0/clinPK/tests/testthat/test_weight2kg.R | 22 + 69 files changed, 456 insertions(+), 341 deletions(-)
Title: Download Data from Brazil's Population Census
Description: Download data from Brazil's population census. The package is built
on top of the 'Arrow' platform <https://arrow.apache.org/docs/r/>,
which allows users to work with larger-than-memory census data using
'dplyr' familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.
Author: Rafael H. M. Pereira [aut, cre]
,
Rogerio J. Barbosa [aut] ,
Diego Rabatone Oliveira [ctb],
Neal Richardson [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between censobr versions 0.3.0 dated 2024-01-09 and 0.3.1 dated 2024-02-23
DESCRIPTION | 25 +- MD5 | 85 ++++----- NEWS.md | 9 R/read_emigration.R | 3 R/read_families.R | 3 R/read_households.R | 4 R/read_mortality.R | 3 R/read_population.R | 3 R/read_tracts.R | 3 R/utils.R | 38 ++-- inst/doc/censobr.html | 60 +----- inst/doc/census_tracts_data.html | 254 ++++++++-------------------- inst/doc/documentation.html | 4 man/arrow_open_dataset.Rd |only man/cache_message.Rd | 46 ++--- man/censobr.Rd | 3 man/data_dictionary.Rd | 3 man/interview_manual.Rd | 3 man/questionnaire.Rd | 3 man/read_emigration.Rd | 3 man/read_households.Rd | 3 man/read_mortality.Rd | 3 man/read_population.Rd | 3 man/read_tracts.Rd | 3 man/roxygen/templates/year.R | 3 tests/tests_rafa/add_labels_2000.R |only tests/tests_rafa/merge_household.R | 208 ++++++---------------- tests/tests_rafa/merge_household_notes.R |only tests/tests_rafa/test_rafa.R | 113 ++++++++++++ tests/testthat.R | 3 tests/testthat/test_docs_interview_manual.R | 2 tests/testthat/test_docs_questionnaire.R | 2 tests/testthat/test_labels_emigration.R | 1 tests/testthat/test_labels_families.R | 1 tests/testthat/test_labels_households.R | 1 tests/testthat/test_labels_mortality.R | 1 tests/testthat/test_labels_population.R | 1 tests/testthat/test_read_emigration.R | 3 tests/testthat/test_read_families.R | 3 tests/testthat/test_read_households.R | 5 tests/testthat/test_read_mortality.R | 12 + tests/testthat/test_read_population.R | 3 tests/testthat/test_read_tracts.R | 1 tests/testthat/test_set_censobr_cache_dir.R | 3 tests/testthat/test_z_censobr_cache.R | 7 45 files changed, 433 insertions(+), 507 deletions(-)
Title: Semi-Parametric Gene-Environment Interaction via Bayesian
Variable Selection
Description: Many complex diseases are known to be affected by the interactions between
genetic variants and environmental exposures beyond the main genetic and environmental
effects. Existing Bayesian methods for gene-environment (G×E) interaction studies are
challenged by the high-dimensional nature of the study and the complexity of environmental
influences. We have developed a novel and powerful semi-parametric Bayesian variable
selection method that can accommodate linear and nonlinear G×E interactions simultaneously
(Ren et al. (2020) <doi:10.1002/sim.8434>). Furthermore, the proposed method can conduct
structural identification by distinguishing nonlinear interactions from main effects only
case within Bayesian framework. Spike-and-slab priors are incorporated on both individual
and group level to shrink coefficients corresponding to irrelevant main and interaction
effects to zero exactly. The Markov chain Monte Carlo algorithms of the proposed and
alternative methods are efficiently [...truncated...]
Author: Jie Ren, Fei Zhou, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Jie Ren <jieren@ksu.edu>
Diff between spinBayes versions 0.1.0 dated 2019-06-06 and 0.2.0 dated 2024-02-23
DESCRIPTION | 17 +-- MD5 | 61 ++++++----- NAMESPACE | 3 R/BVCFit.R | 41 ++++--- R/BVSelection.R | 51 ++++----- R/RcppExports.R | 22 ++-- R/Utilities.R | 1 R/catch-routine-registration.R |only R/data.R | 2 R/plot.BVCfit.R |only R/print.BVCfit.R | 4 R/spinBayes-package.R | 51 +++++---- README.md | 118 +++++++++++---------- build |only data/gExp.L.rda |binary man/BVCfit.Rd | 223 +++++++++++++++++++++-------------------- man/BVSelection.Rd | 131 ++++++++++++------------ man/data.Rd | 108 ++++++++++--------- man/plot.BVCfit.Rd |only man/predict.BVCfit.Rd | 122 ++++++++++------------ man/spinBayes-package.Rd | 128 +++++++++++++---------- src/BVC.cpp | 8 + src/BVCPM.cpp | 2 src/BVCPM_NS.cpp | 2 src/BVCUtilities.cpp | 36 ------ src/BVC_NS.cpp | 2 src/BayesRefit.cpp |only src/Makevars | 6 - src/Makevars.win | 6 - src/RcppExports.cpp | 36 ++++++ src/test-runner.cpp |only src/test-utilities.cpp |only tests |only 33 files changed, 643 insertions(+), 538 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects.
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.2.2 dated 2023-06-13 and 0.2.3 dated 2024-02-23
DESCRIPTION | 6 MD5 | 14 R/gprofiler2.R | 704 +++++++++++----------------- build/vignette.rds |binary inst/doc/gprofiler2.R | 10 inst/doc/gprofiler2.Rmd | 8 inst/doc/gprofiler2.html | 1150 +++++++++++++++++++++++------------------------ vignettes/gprofiler2.Rmd | 8 8 files changed, 871 insertions(+), 1029 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 5.2.0 dated 2023-11-09 and 6.0.0 dated 2024-02-23
ggblanket-5.2.0/ggblanket/R/gg_blank.R |only ggblanket-5.2.0/ggblanket/R/pal.R |only ggblanket-5.2.0/ggblanket/R/str_keep_seq.R |only ggblanket-5.2.0/ggblanket/man/dark_mode.Rd |only ggblanket-5.2.0/ggblanket/man/gg_blank.Rd |only ggblanket-5.2.0/ggblanket/man/guardian.Rd |only ggblanket-5.2.0/ggblanket/man/light_mode.Rd |only ggblanket-5.2.0/ggblanket/man/na_if_inf.Rd |only ggblanket-5.2.0/ggblanket/man/pal_dark_mode.Rd |only ggblanket-5.2.0/ggblanket/man/pal_light_mode.Rd |only ggblanket-5.2.0/ggblanket/man/str_keep_seq.Rd |only ggblanket-6.0.0/ggblanket/DESCRIPTION | 50 ggblanket-6.0.0/ggblanket/MD5 | 324 + ggblanket-6.0.0/ggblanket/NAMESPACE | 33 ggblanket-6.0.0/ggblanket/NEWS.md | 52 ggblanket-6.0.0/ggblanket/R/aes_contrast.R |only ggblanket-6.0.0/ggblanket/R/base_mode.R |only ggblanket-6.0.0/ggblanket/R/col_pals.R |only ggblanket-6.0.0/ggblanket/R/dark_mode.R | 282 - ggblanket-6.0.0/ggblanket/R/gg_area.R | 1654 --------- ggblanket-6.0.0/ggblanket/R/gg_bar.R | 1655 --------- ggblanket-6.0.0/ggblanket/R/gg_bin_2d.R | 1682 --------- ggblanket-6.0.0/ggblanket/R/gg_blanket.R |only ggblanket-6.0.0/ggblanket/R/gg_boxplot.R | 1660 --------- ggblanket-6.0.0/ggblanket/R/gg_col.R | 1658 --------- ggblanket-6.0.0/ggblanket/R/gg_contour.R | 1751 ---------- ggblanket-6.0.0/ggblanket/R/gg_contour_filled.R | 1748 --------- ggblanket-6.0.0/ggblanket/R/gg_crossbar.R | 1726 --------- ggblanket-6.0.0/ggblanket/R/gg_density.R | 1656 --------- ggblanket-6.0.0/ggblanket/R/gg_density_2d.R | 1706 --------- ggblanket-6.0.0/ggblanket/R/gg_density_2d_filled.R | 1692 --------- ggblanket-6.0.0/ggblanket/R/gg_errorbar.R | 1725 --------- ggblanket-6.0.0/ggblanket/R/gg_freqpoly.R | 1657 --------- ggblanket-6.0.0/ggblanket/R/gg_function.R |only ggblanket-6.0.0/ggblanket/R/gg_hex.R | 1679 --------- ggblanket-6.0.0/ggblanket/R/gg_histogram.R | 1653 --------- ggblanket-6.0.0/ggblanket/R/gg_jitter.R | 1658 --------- ggblanket-6.0.0/ggblanket/R/gg_label.R | 1669 --------- ggblanket-6.0.0/ggblanket/R/gg_line.R | 1656 --------- ggblanket-6.0.0/ggblanket/R/gg_linerange.R | 1730 --------- ggblanket-6.0.0/ggblanket/R/gg_path.R | 1653 --------- ggblanket-6.0.0/ggblanket/R/gg_point.R | 1652 --------- ggblanket-6.0.0/ggblanket/R/gg_pointrange.R | 1730 --------- ggblanket-6.0.0/ggblanket/R/gg_polygon.R | 1659 --------- ggblanket-6.0.0/ggblanket/R/gg_qq.R | 1702 --------- ggblanket-6.0.0/ggblanket/R/gg_quantile.R |only ggblanket-6.0.0/ggblanket/R/gg_raster.R | 1662 --------- ggblanket-6.0.0/ggblanket/R/gg_rect.R | 1721 --------- ggblanket-6.0.0/ggblanket/R/gg_ribbon.R | 1737 --------- ggblanket-6.0.0/ggblanket/R/gg_rug.R |only ggblanket-6.0.0/ggblanket/R/gg_segment.R | 1706 --------- ggblanket-6.0.0/ggblanket/R/gg_sf.R | 1575 -------- ggblanket-6.0.0/ggblanket/R/gg_smooth.R | 1652 --------- ggblanket-6.0.0/ggblanket/R/gg_step.R | 1659 --------- ggblanket-6.0.0/ggblanket/R/gg_text.R | 1668 --------- ggblanket-6.0.0/ggblanket/R/gg_tile.R | 1669 --------- ggblanket-6.0.0/ggblanket/R/gg_violin.R | 1653 --------- ggblanket-6.0.0/ggblanket/R/grey_mode.R |only ggblanket-6.0.0/ggblanket/R/light_mode.R | 282 - ggblanket-6.0.0/ggblanket/R/mode_set.R |only ggblanket-6.0.0/ggblanket/R/replace_seq.R |only ggblanket-6.0.0/ggblanket/R/utils.R | 111 ggblanket-6.0.0/ggblanket/README.md | 22 ggblanket-6.0.0/ggblanket/build/vignette.rds |binary ggblanket-6.0.0/ggblanket/inst/doc/ggblanket.R | 701 +--- ggblanket-6.0.0/ggblanket/inst/doc/ggblanket.Rmd | 922 ++--- ggblanket-6.0.0/ggblanket/inst/doc/ggblanket.html | 1127 ++---- ggblanket-6.0.0/ggblanket/man/aes_contrast.Rd |only ggblanket-6.0.0/ggblanket/man/base_mode.Rd |only ggblanket-6.0.0/ggblanket/man/base_mode_b.Rd |only ggblanket-6.0.0/ggblanket/man/base_mode_n.Rd |only ggblanket-6.0.0/ggblanket/man/base_mode_r.Rd |only ggblanket-6.0.0/ggblanket/man/base_mode_t.Rd |only ggblanket-6.0.0/ggblanket/man/blue.Rd |only ggblanket-6.0.0/ggblanket/man/dark_mode_b.Rd |only ggblanket-6.0.0/ggblanket/man/dark_mode_n.Rd |only ggblanket-6.0.0/ggblanket/man/dark_mode_r.Rd |only ggblanket-6.0.0/ggblanket/man/dark_mode_t.Rd |only ggblanket-6.0.0/ggblanket/man/darkness.Rd |only ggblanket-6.0.0/ggblanket/man/figures/README-unnamed-chunk-2-1.png |binary ggblanket-6.0.0/ggblanket/man/figures/logo.png |binary ggblanket-6.0.0/ggblanket/man/gg_area.Rd | 227 - ggblanket-6.0.0/ggblanket/man/gg_bar.Rd | 229 - ggblanket-6.0.0/ggblanket/man/gg_bin_2d.Rd | 228 - ggblanket-6.0.0/ggblanket/man/gg_blanket.Rd |only ggblanket-6.0.0/ggblanket/man/gg_boxplot.Rd | 234 - ggblanket-6.0.0/ggblanket/man/gg_col.Rd | 231 - ggblanket-6.0.0/ggblanket/man/gg_contour.Rd | 250 - ggblanket-6.0.0/ggblanket/man/gg_contour_filled.Rd | 247 - ggblanket-6.0.0/ggblanket/man/gg_crossbar.Rd | 223 - ggblanket-6.0.0/ggblanket/man/gg_density.Rd | 229 - ggblanket-6.0.0/ggblanket/man/gg_density_2d.Rd | 246 - ggblanket-6.0.0/ggblanket/man/gg_density_2d_filled.Rd | 236 - ggblanket-6.0.0/ggblanket/man/gg_errorbar.Rd | 222 - ggblanket-6.0.0/ggblanket/man/gg_freqpoly.Rd | 229 - ggblanket-6.0.0/ggblanket/man/gg_function.Rd |only ggblanket-6.0.0/ggblanket/man/gg_hex.Rd | 226 - ggblanket-6.0.0/ggblanket/man/gg_histogram.Rd | 227 - ggblanket-6.0.0/ggblanket/man/gg_jitter.Rd | 233 - ggblanket-6.0.0/ggblanket/man/gg_label.Rd | 232 - ggblanket-6.0.0/ggblanket/man/gg_line.Rd | 229 - ggblanket-6.0.0/ggblanket/man/gg_linerange.Rd | 227 - ggblanket-6.0.0/ggblanket/man/gg_path.Rd | 228 - ggblanket-6.0.0/ggblanket/man/gg_point.Rd | 227 - ggblanket-6.0.0/ggblanket/man/gg_pointrange.Rd | 228 - ggblanket-6.0.0/ggblanket/man/gg_polygon.Rd | 224 - ggblanket-6.0.0/ggblanket/man/gg_qq.Rd | 254 - ggblanket-6.0.0/ggblanket/man/gg_quantile.Rd |only ggblanket-6.0.0/ggblanket/man/gg_raster.Rd | 236 - ggblanket-6.0.0/ggblanket/man/gg_rect.Rd | 231 - ggblanket-6.0.0/ggblanket/man/gg_ribbon.Rd | 236 - ggblanket-6.0.0/ggblanket/man/gg_rug.Rd |only ggblanket-6.0.0/ggblanket/man/gg_segment.Rd | 223 - ggblanket-6.0.0/ggblanket/man/gg_sf.Rd | 230 - ggblanket-6.0.0/ggblanket/man/gg_smooth.Rd | 227 - ggblanket-6.0.0/ggblanket/man/gg_step.Rd | 233 - ggblanket-6.0.0/ggblanket/man/gg_text.Rd | 232 - ggblanket-6.0.0/ggblanket/man/gg_tile.Rd | 242 - ggblanket-6.0.0/ggblanket/man/gg_violin.Rd | 228 - ggblanket-6.0.0/ggblanket/man/ggblanket-package.Rd | 8 ggblanket-6.0.0/ggblanket/man/grey_mode_b.Rd |only ggblanket-6.0.0/ggblanket/man/grey_mode_n.Rd |only ggblanket-6.0.0/ggblanket/man/grey_mode_r.Rd |only ggblanket-6.0.0/ggblanket/man/grey_mode_t.Rd |only ggblanket-6.0.0/ggblanket/man/greyness.Rd |only ggblanket-6.0.0/ggblanket/man/greys.Rd |only ggblanket-6.0.0/ggblanket/man/light_mode_b.Rd |only ggblanket-6.0.0/ggblanket/man/light_mode_n.Rd |only ggblanket-6.0.0/ggblanket/man/light_mode_r.Rd |only ggblanket-6.0.0/ggblanket/man/light_mode_t.Rd |only ggblanket-6.0.0/ggblanket/man/lightness.Rd |only ggblanket-6.0.0/ggblanket/man/mode_set.Rd |only ggblanket-6.0.0/ggblanket/man/navy.Rd |only ggblanket-6.0.0/ggblanket/man/orange.Rd |only ggblanket-6.0.0/ggblanket/man/plum.Rd |only ggblanket-6.0.0/ggblanket/man/replace_seq.Rd |only ggblanket-6.0.0/ggblanket/man/teal.Rd |only ggblanket-6.0.0/ggblanket/tests |only ggblanket-6.0.0/ggblanket/vignettes/autocomplete_y.png |binary ggblanket-6.0.0/ggblanket/vignettes/ggblanket.Rmd | 922 ++--- 140 files changed, 11666 insertions(+), 58167 deletions(-)
Title: Mining Rigs for Problems in the Subset Sum Family
Description: Specialized solvers for combinatorial optimization problems in the Subset Sum family. The solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value multisets with predefined subset sum errors, (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) option of mapping floating-point instance to [...truncated...]
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between FLSSS versions 9.1.1 dated 2022-05-17 and 9.1.3 dated 2024-02-23
DESCRIPTION | 6 MD5 | 21 +- man/mFLSSSparImposeBounds.Rd | 311 +++++++++++++++++++++---------------------- src/Makevars.in | 2 src/Makevars.win | 2 src/findBoundInterface.cpp | 4 src/header/dnyTasking.hpp | 12 + src/legacy/Makevars |only src/legacy/mflsssComo.cpp | 3 src/legacy/multiDstack.hpp | 16 +- src/legacy/multiDstack02.hpp | 16 +- src/mflsssVariableTree.cpp | 9 - 12 files changed, 204 insertions(+), 198 deletions(-)
Title: Scale Bar, North Arrow, and Pretty Margins in R
Description: Automates the process of creating a scale bar and north arrow in
any package that uses base graphics to plot in R. Bounding box tools help find
and manipulate extents. Finally, there is a function to automate the process
of setting margins, plotting the map, scale bar, and north arrow, and resetting
graphic parameters upon completion.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between prettymapr versions 0.2.4 dated 2022-06-09 and 0.2.5 dated 2024-02-23
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NAMESPACE | 15 +++++++++++++++ R/caches.R | 44 ++++++++++++++++++++++++++++++++++++-------- R/northarrow.R | 6 ------ R/prettymap.R | 11 ----------- R/scalebar.R | 18 ------------------ man/addnortharrow.Rd | 6 ------ man/addscalebar.Rd | 11 ----------- man/prettymap.Rd | 11 ----------- man/scalebarparams.Rd | 6 ------ man/set_cached.Rd |only 12 files changed, 67 insertions(+), 92 deletions(-)
More information about teal.modules.clinical at CRAN
Permanent link
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 2.0.1 dated 2023-11-17 and 2.1.0 dated 2024-02-23
scCustomize-2.0.1/scCustomize/man/Add_Cell_Complexity_LIGER.Rd |only scCustomize-2.0.1/scCustomize/man/Add_Cell_Complexity_Seurat.Rd |only scCustomize-2.0.1/scCustomize/man/Add_Mito_Ribo_LIGER.Rd |only scCustomize-2.0.1/scCustomize/man/Add_Mito_Ribo_Seurat.Rd |only scCustomize-2.0.1/scCustomize/man/Meta_Present_LIGER.Rd |only scCustomize-2.0.1/scCustomize/man/Split_FeatureScatter.Rd |only scCustomize-2.1.0/scCustomize/DESCRIPTION | 18 scCustomize-2.1.0/scCustomize/MD5 | 116 - scCustomize-2.1.0/scCustomize/NAMESPACE | 38 scCustomize-2.1.0/scCustomize/NEWS.md | 52 scCustomize-2.1.0/scCustomize/R/Color_Palettes.R | 6 scCustomize-2.1.0/scCustomize/R/Deprecated.R |only scCustomize-2.1.0/scCustomize/R/Generics.R |only scCustomize-2.1.0/scCustomize/R/Internal_Utilities.R | 415 +++- scCustomize-2.1.0/scCustomize/R/LIGER_Plotting.R | 41 scCustomize-2.1.0/scCustomize/R/LIGER_Utilities.R | 395 +--- scCustomize-2.1.0/scCustomize/R/Object_Conversion.R |only scCustomize-2.1.0/scCustomize/R/Object_Utilities.R | 671 ++++-- scCustomize-2.1.0/scCustomize/R/Plotting_Utilities.R | 985 +++++++++- scCustomize-2.1.0/scCustomize/R/QC_Plotting_Seurat.R | 23 scCustomize-2.1.0/scCustomize/R/Reexports.R |only scCustomize-2.1.0/scCustomize/R/Seurat_Iterative_Plotting.R | 264 ++ scCustomize-2.1.0/scCustomize/R/Seurat_Plotting.R | 738 +------ scCustomize-2.1.0/scCustomize/R/Statistics.R | 18 scCustomize-2.1.0/scCustomize/R/Statistics_Plotting.R | 24 scCustomize-2.1.0/scCustomize/R/Utilities.R | 504 ++++- scCustomize-2.1.0/scCustomize/man/Add_Alt_Feature_ID.Rd |only scCustomize-2.1.0/scCustomize/man/Add_CellBender_Diff.Rd | 2 scCustomize-2.1.0/scCustomize/man/Add_Cell_Complexity.Rd |only scCustomize-2.1.0/scCustomize/man/Add_Cell_QC_Metrics.Rd | 2 scCustomize-2.1.0/scCustomize/man/Add_Mito_Ribo.Rd |only scCustomize-2.1.0/scCustomize/man/Add_Sample_Meta.Rd | 2 scCustomize-2.1.0/scCustomize/man/Add_Top_Gene_Pct_Seurat.Rd | 2 scCustomize-2.1.0/scCustomize/man/Case_Check.Rd | 2 scCustomize-2.1.0/scCustomize/man/Change_Delim_All.Rd | 2 scCustomize-2.1.0/scCustomize/man/Change_Delim_Prefix.Rd | 2 scCustomize-2.1.0/scCustomize/man/Change_Delim_Suffix.Rd | 2 scCustomize-2.1.0/scCustomize/man/CheckMatrix_scCustom.Rd | 4 scCustomize-2.1.0/scCustomize/man/Clustered_DotPlot.Rd | 23 scCustomize-2.1.0/scCustomize/man/Convert_Assay.Rd |only scCustomize-2.1.0/scCustomize/man/Extract_Modality.Rd | 2 scCustomize-2.1.0/scCustomize/man/Extract_Sample_Meta.Rd | 2 scCustomize-2.1.0/scCustomize/man/Feature_Present.Rd |only scCustomize-2.1.0/scCustomize/man/Fetch_Meta.Rd | 5 scCustomize-2.1.0/scCustomize/man/Gene_Present.Rd | 6 scCustomize-2.1.0/scCustomize/man/Iterate_DimPlot_bySample.Rd | 12 scCustomize-2.1.0/scCustomize/man/Iterate_FeaturePlot_scCustom.Rd | 13 scCustomize-2.1.0/scCustomize/man/LIGER_Features.Rd |only scCustomize-2.1.0/scCustomize/man/Liger_to_Seurat.Rd | 25 scCustomize-2.1.0/scCustomize/man/Merge_Seurat_List.Rd | 2 scCustomize-2.1.0/scCustomize/man/Merge_Sparse_Data_All.Rd | 2 scCustomize-2.1.0/scCustomize/man/Merge_Sparse_Multimodal_All.Rd | 2 scCustomize-2.1.0/scCustomize/man/Meta_Numeric.Rd | 2 scCustomize-2.1.0/scCustomize/man/Meta_Present.Rd | 11 scCustomize-2.1.0/scCustomize/man/Meta_Remove_Seurat.Rd | 2 scCustomize-2.1.0/scCustomize/man/QC_Plots_Complexity.Rd | 2 scCustomize-2.1.0/scCustomize/man/Reduction_Loading_Present.Rd | 2 scCustomize-2.1.0/scCustomize/man/Rename_Clusters.Rd | 2 scCustomize-2.1.0/scCustomize/man/Replace_Suffix.Rd | 2 scCustomize-2.1.0/scCustomize/man/Split_Layers.Rd |only scCustomize-2.1.0/scCustomize/man/Split_Vector.Rd |only scCustomize-2.1.0/scCustomize/man/Store_Misc_Info_Seurat.Rd | 2 scCustomize-2.1.0/scCustomize/man/Store_Palette_Seurat.Rd | 3 scCustomize-2.1.0/scCustomize/man/Updated_HGNC_Symbols.Rd |only scCustomize-2.1.0/scCustomize/man/as.LIGER.Rd |only scCustomize-2.1.0/scCustomize/man/as.Seurat.Rd |only scCustomize-2.1.0/scCustomize/man/as.anndata.Rd |only scCustomize-2.1.0/scCustomize/man/deprecated.Rd |only scCustomize-2.1.0/scCustomize/man/plotFactors_scCustom.Rd | 4 scCustomize-2.1.0/scCustomize/man/reexports.Rd |only scCustomize-2.1.0/scCustomize/man/scCustomize_Palette.Rd | 1 71 files changed, 2972 insertions(+), 1483 deletions(-)
Title: Connect to Your 'Zoom' Data
Description: Facilitates making a connection to the 'Zoom' API and executing
various queries. You can use it to get data on 'Zoom' webinars and 'Zoom'
meetings. The 'Zoom' documentation is available at
<https://developers.zoom.us/docs/api/>. This package is
not supported by 'Zoom' (owner of the software).
Author: Chris Umphlett [aut, cre]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between zoomr versions 0.2.0 dated 2023-04-25 and 0.3.0 dated 2024-02-23
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 1 + R/get_tracking_sources.R |only R/utils.R | 1 + man/get_tracking_sources.Rd |only 6 files changed, 11 insertions(+), 7 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Author: Elizabeth Chun [aut],
Steve Broll [aut],
David Buchanan [aut],
John Muschelli [aut] ,
Nathaniel Fernandes [aut],
Jung Hoon Seo [ctb],
Johnathan Shih [ctb],
Jacek Urbanek [ctb],
John Schwenck [ctb],
Marielle Hicban [ctb],
Mary Martin [ctb],
Pratik Pat [...truncated...]
Maintainer: Irina Gaynanova <irinagn@umich.edu>
Diff between iglu versions 3.5.0 dated 2023-10-20 and 4.0.0 dated 2024-02-23
iglu-3.5.0/iglu/data/example_meal.rda |only iglu-3.5.0/iglu/man/example_meal.Rd |only iglu-3.5.0/iglu/vignettes/mage_figures/Figure3_heatmap_percent_error.png |only iglu-4.0.0/iglu/DESCRIPTION | 43 iglu-4.0.0/iglu/MD5 | 112 - iglu-4.0.0/iglu/NAMESPACE | 1 iglu-4.0.0/iglu/NEWS.md | 25 iglu-4.0.0/iglu/R/all_metrics.R | 123 + iglu-4.0.0/iglu/R/data.R | 51 iglu-4.0.0/iglu/R/epicalc_profile.R | 46 iglu-4.0.0/iglu/R/episode_calculation.R | 95 - iglu-4.0.0/iglu/R/gri.R | 2 iglu-4.0.0/iglu/R/heatmap.R | 27 iglu-4.0.0/iglu/R/mage.R | 51 iglu-4.0.0/iglu/R/mage_ma_single.R | 676 +++++--- iglu-4.0.0/iglu/R/meal_metrics.R | 70 iglu-4.0.0/iglu/R/optimized_iglu_functions.R | 88 - iglu-4.0.0/iglu/R/pgs.R |only iglu-4.0.0/iglu/R/read_raw_data.r | 75 iglu-4.0.0/iglu/R/utils.R | 62 iglu-4.0.0/iglu/README.md | 29 iglu-4.0.0/iglu/data/example_data_hall.rda |only iglu-4.0.0/iglu/data/example_meals_hall.rda |only iglu-4.0.0/iglu/inst/doc/AGP_and_Episodes.html | 20 iglu-4.0.0/iglu/inst/doc/MAGE.R | 13 iglu-4.0.0/iglu/inst/doc/MAGE.Rmd | 757 +++++++--- iglu-4.0.0/iglu/inst/doc/MAGE.html | 550 ++++--- iglu-4.0.0/iglu/inst/doc/metrics_list.Rmd | 101 - iglu-4.0.0/iglu/inst/doc/metrics_list.html | 61 iglu-4.0.0/iglu/inst/shiny_iglu/rsconnect/shinyapps.io/irinagain |only iglu-4.0.0/iglu/inst/shiny_iglu/server.R | 211 +- iglu-4.0.0/iglu/inst/shiny_iglu/ui.R | 5 iglu-4.0.0/iglu/man/CGMS2DayByDay.Rd | 2 iglu-4.0.0/iglu/man/agp.Rd | 2 iglu-4.0.0/iglu/man/all_metrics.Rd | 27 iglu-4.0.0/iglu/man/cv_measures.Rd | 2 iglu-4.0.0/iglu/man/epicalc_profile.Rd | 9 iglu-4.0.0/iglu/man/episode_calculation.Rd | 28 iglu-4.0.0/iglu/man/example_data_hall.Rd |only iglu-4.0.0/iglu/man/example_meals_hall.Rd |only iglu-4.0.0/iglu/man/figures/README-unnamed-chunk-3-1.png |binary iglu-4.0.0/iglu/man/figures/README-unnamed-chunk-3-2.png |binary iglu-4.0.0/iglu/man/gri.Rd | 3 iglu-4.0.0/iglu/man/mage.Rd | 45 iglu-4.0.0/iglu/man/mage_ma_single.Rd | 46 iglu-4.0.0/iglu/man/meal_metrics.Rd | 12 iglu-4.0.0/iglu/man/metrics_heatmap.Rd | 7 iglu-4.0.0/iglu/man/pgs.Rd |only iglu-4.0.0/iglu/man/plot_agp.Rd | 2 iglu-4.0.0/iglu/man/plot_ranges.Rd | 2 iglu-4.0.0/iglu/tests |only iglu-4.0.0/iglu/vignettes/MAGE.Rmd | 757 +++++++--- iglu-4.0.0/iglu/vignettes/mage_figures/boxplot-of-errors.png |only iglu-4.0.0/iglu/vignettes/mage_figures/hyper-param-tuning.png |only iglu-4.0.0/iglu/vignettes/mage_figures/whiplash1.png |only iglu-4.0.0/iglu/vignettes/mage_figures/whiplash2.png |only iglu-4.0.0/iglu/vignettes/metrics_list.Rmd | 101 - 57 files changed, 3045 insertions(+), 1294 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). See Zhou, Hanson and Zhang (2020) <doi:10.18637/jss.v092.i09>.
Author: Haiming Zhou [aut, cre, cph],
Timothy Hanson [aut]
Maintainer: Haiming Zhou <haiming2019@gmail.com>
Diff between spBayesSurv versions 1.1.7 dated 2023-05-17 and 1.1.8 dated 2024-02-23
DESCRIPTION | 8 MD5 | 20 R/SpatDensReg.R | 942 +++++++++----------- R/SuperSurvRegBayes.R | 1258 +++++++++++++------------- R/anovaDDP.R | 634 ++++++------- R/frailtyGAFT.R | 1348 ++++++++++++++-------------- R/indeptCoxph.R | 774 ++++++++-------- R/spCopulaCoxph.R | 976 ++++++++++---------- R/spCopulaDDP.R | 790 ++++++++-------- R/survregbayes.R | 2330 ++++++++++++++++++++++++-------------------------- R/survregbayes2.R | 1410 ++++++++++++++---------------- 11 files changed, 5126 insertions(+), 5364 deletions(-)
Title: Helper Functions for Simulation Studies
Description: Calculates performance criteria measures and associated Monte Carlo standard errors for simulation results. Includes functions to help run simulation studies. Our derivation and explanation of formulas and our general simulation workflow is closely aligned with the approach described by Morris, White, and Crowther (2019) <DOI:10.1002/sim.8086>.
Author: Megha Joshi [aut, cre] ,
James Pustejovsky [aut]
Maintainer: Megha Joshi <megha.j456@gmail.com>
Diff between simhelpers versions 0.1.2 dated 2022-05-03 and 0.2.0 dated 2024-02-23
simhelpers-0.1.2/simhelpers/R/globals.R |only simhelpers-0.2.0/simhelpers/DESCRIPTION | 13 simhelpers-0.2.0/simhelpers/MD5 | 70 simhelpers-0.2.0/simhelpers/NAMESPACE | 3 simhelpers-0.2.0/simhelpers/NEWS.md | 10 simhelpers-0.2.0/simhelpers/R/bundle_sim.R |only simhelpers-0.2.0/simhelpers/R/calc_absolute.R | 77 simhelpers-0.2.0/simhelpers/R/calc_coverage.R | 62 simhelpers-0.2.0/simhelpers/R/calc_rejection.R | 73 simhelpers-0.2.0/simhelpers/R/calc_relative.R | 87 simhelpers-0.2.0/simhelpers/R/calc_relative_var.R | 88 simhelpers-0.2.0/simhelpers/R/evaluate_by_row.R | 9 simhelpers-0.2.0/simhelpers/build/partial.rdb |binary simhelpers-0.2.0/simhelpers/build/vignette.rds |binary simhelpers-0.2.0/simhelpers/inst/doc/MCSE.Rmd | 2 simhelpers-0.2.0/simhelpers/inst/doc/MCSE.html | 1162 +++++++--- simhelpers-0.2.0/simhelpers/inst/doc/simulation_workflow.R | 14 simhelpers-0.2.0/simhelpers/inst/doc/simulation_workflow.Rmd | 17 simhelpers-0.2.0/simhelpers/inst/doc/simulation_workflow.html | 1157 ++++++--- simhelpers-0.2.0/simhelpers/inst/doc/visualization.html | 608 ++++- simhelpers-0.2.0/simhelpers/inst/skel_temp |only simhelpers-0.2.0/simhelpers/inst/templates/simulation_skeleton.R | 8 simhelpers-0.2.0/simhelpers/man/bundle_sim.Rd |only simhelpers-0.2.0/simhelpers/man/calc_absolute.Rd | 14 simhelpers-0.2.0/simhelpers/man/calc_coverage.Rd | 16 simhelpers-0.2.0/simhelpers/man/calc_rejection.Rd | 25 simhelpers-0.2.0/simhelpers/man/calc_relative.Rd | 14 simhelpers-0.2.0/simhelpers/man/calc_relative_var.Rd | 14 simhelpers-0.2.0/simhelpers/man/evaluate_by_row.Rd | 3 simhelpers-0.2.0/simhelpers/tests/testthat/test_bundle_sim.R |only simhelpers-0.2.0/simhelpers/tests/testthat/test_bundle_sim_with_ebr.R |only simhelpers-0.2.0/simhelpers/tests/testthat/test_calc_combinations.R |only simhelpers-0.2.0/simhelpers/tests/testthat/test_ebr.R | 28 simhelpers-0.2.0/simhelpers/tests/testthat/test_perfm_conv.R | 137 - simhelpers-0.2.0/simhelpers/tests/testthat/test_perfm_mcse.R | 65 simhelpers-0.2.0/simhelpers/vignettes/MCSE.Rmd | 2 simhelpers-0.2.0/simhelpers/vignettes/simulation_workflow.Rmd | 17 37 files changed, 2615 insertions(+), 1180 deletions(-)
Title: Nonparametric Bootstrap Test with Pooled Resampling
Description: Addressing crucial research questions often necessitates a small
sample size due to factors such as distinctive target populations, rarity
of the event under study, time and cost constraints, ethical concerns, or
group-level unit of analysis. Many readily available analytic methods,
however, do not accommodate small sample sizes, and the choice of the best
method can be unclear. The 'npboottprm' package enables the execution of
nonparametric bootstrap tests with pooled resampling to help fill this gap.
Grounded in the statistical methods for small sample size studies detailed
in Dwivedi, Mallawaarachchi, and Alvarado (2017) <doi:10.1002/sim.7263>, the
package facilitates a range of statistical tests, encompassing independent
t-tests, paired t-tests, and one-way Analysis of Variance (ANOVA) F-tests.
The nonparboot() function undertakes essential computations, yielding
detailed outputs which include test statistics, effect sizes, confidence
intervals, and bootstrap distributions. F [...truncated...]
Author: Mackson Ncube [aut, cre],
mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Diff between npboottprm versions 0.2.0 dated 2023-11-25 and 0.2.1 dated 2024-02-23
DESCRIPTION | 8 MD5 | 22 NEWS.md | 2 R/replext_helpers.R | 1842 ++++++++++++++++++++++++++-------------------------- R/replext_t2.R | 796 +++++++++++----------- R/replext_t3.R | 858 ++++++++++++------------ R/replext_t4.R | 1008 ++++++++++++++-------------- R/replext_t5.R | 644 +++++++++--------- R/replext_t6.R | 504 +++++++------- R/replext_ts1.R | 344 ++++----- R/replext_ts2.R | 974 +++++++++++++-------------- R/replext_ts3.R | 810 +++++++++++----------- 12 files changed, 3907 insertions(+), 3905 deletions(-)
Title: A Modular Approach to Dose-Finding Clinical Trials
Description: Methods for working with dose-finding clinical trials. We provide
implementations of many dose-finding clinical trial designs, including the
continual reassessment method (CRM) by O'Quigley et al. (1990)
<doi:10.2307/2531628>, the toxicity probability interval (TPI) design by Ji
et al. (2007) <doi:10.1177/1740774507079442>, the modified TPI (mTPI) design
by Ji et al. (2010) <doi:10.1177/1740774510382799>, the Bayesian optimal
interval design (BOIN) by Liu & Yuan (2015) <doi:10.1111/rssc.12089>, EffTox
by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the design of
Wages & Tait (2015) <doi:10.1080/10543406.2014.920873>, and the 3+3
described by Korn et al. (1994) <doi:10.1002/sim.4780131802>. All designs
are implemented with a common interface. We also offer optional additional
classes to tailor the behaviour of all designs, including avoiding skipping
doses, stopping after n patients have been treated at the recommended [...truncated...]
Author: Kristian Brock [aut, cre] ,
Daniel Slade [aut] ,
Michael Sweeting [aut]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between escalation versions 0.1.5 dated 2023-05-29 and 0.1.8 dated 2024-02-23
DESCRIPTION | 31 MD5 | 159 ++-- NAMESPACE | 93 ++ NEWS.md | 6 R/boin12_logic.R |only R/boin12_selector.R |only R/convergence_plot.R |only R/correlated_patient_sample.R |only R/derived_dose_selector.R | 45 + R/dfcrm_selector.R | 11 R/dose_paths.R | 1 R/expit.R |only R/get_empiric_crm_skeleton_weights.R | 3 R/get_potential_outcomes.R |only R/helpers.R | 1 R/interface.R | 34 - R/mtpi_selector.R | 10 R/patient_sample.R |only R/phase1_2_sim.R | 37 - R/phase1_sim.R | 15 R/select_boin12_obd.R |only R/select_boin_mtd.R | 40 - R/select_mtpi2_mtd.R |only R/select_mtpi_mtd.R |only R/select_tpi_mtd.R |only R/selector.R | 65 + R/simulate_compare.R |only R/simulate_trials.R | 113 +-- R/simulations.R | 3 R/simulations_collection.R |only R/stack_sims_vert.R |only R/stop_when_too_toxic.R | 42 - R/three_plus_three_selector.R | 8 R/trialr_crm_selector.R | 11 R/trialr_efftox_selector.R | 6 R/trialr_nbg_selector.R | 11 README.md | 272 ++++++-- build/vignette.rds |binary inst/doc/A100-DoseSelectors.html | 237 +++---- inst/doc/A205-CRM.html | 522 +++++++-------- inst/doc/A207-NBG.html | 309 ++++----- inst/doc/A210-TPI.html | 272 ++++---- inst/doc/A220-mTPI.html | 272 ++++---- inst/doc/A230-BOIN.html | 144 ++-- inst/doc/A600-DosePaths.html | 532 ++++++++------- inst/doc/A700-Simulation.R | 2 inst/doc/A700-Simulation.Rmd | 24 inst/doc/A700-Simulation.html | 621 +++++++++--------- inst/doc/A710-SimulationComparison.R |only inst/doc/A710-SimulationComparison.Rmd |only inst/doc/A710-SimulationComparison.html |only man/CorrelatedPatientSample.Rd |only man/PatientSample.Rd |only man/as_tibble.derived_dose_selector.Rd |only man/as_tibble.simulations_collection.Rd |only man/convergence_plot.Rd |only man/get_boin12.Rd |only man/get_empiric_crm_skeleton_weights.Rd | 3 man/get_potential_outcomes.Rd |only man/select_boin12_obd.Rd |only man/select_boin_mtd.Rd | 23 man/select_mtpi2_mtd.Rd |only man/select_mtpi_mtd.Rd |only man/select_tpi_mtd.Rd |only man/simulate_compare.Rd |only man/simulate_trials.Rd | 105 +-- man/simulations_collection.Rd |only man/stack_sims_vert.Rd |only man/utility.Rd |only tests/testthat/test_boin.R | 113 +++ tests/testthat/test_boin12.R |only tests/testthat/test_correlated_patient_sample.R |only tests/testthat/test_crystallised_dose_paths.R | 49 - tests/testthat/test_demand_n_at_dose.R | 36 + tests/testthat/test_dfcrm.R | 14 tests/testthat/test_dont_skip_doses.R | 85 +- tests/testthat/test_follow_path.R | 32 tests/testthat/test_mtpi.R | 806 +++++++++++++++++++++++- tests/testthat/test_mtpi2.R | 423 ++++++++++++ tests/testthat/test_patient_sample.R |only tests/testthat/test_random_selector.R | 1 tests/testthat/test_select_boin_mtd.R | 31 tests/testthat/test_select_dose_by_cibp.R | 6 tests/testthat/test_select_mtpi2_mtd.R |only tests/testthat/test_select_mtpi_mtd.R |only tests/testthat/test_select_tpi_mtd.R |only tests/testthat/test_simulate_trials.R | 134 +++ tests/testthat/test_stop_at_n.R | 45 + tests/testthat/test_stop_when_n_at_dose.R | 25 tests/testthat/test_stop_when_too_toxic.R | 82 ++ tests/testthat/test_stop_when_tox_ci_covered.R | 22 tests/testthat/test_three_plus_three.R | 208 ++++++ tests/testthat/test_tpi.R | 429 ++++++++++++ tests/testthat/test_trialr_crm.R | 1 tests/testthat/test_trialr_nbg.R | 8 tests/testthat/test_try_rescue_dose.R | 16 tests/testthat/test_wages_tait.R | 1 vignettes/A700-Simulation.Rmd | 24 vignettes/A710-SimulationComparison.Rmd |only vignettes/library.bib | 49 + 100 files changed, 4895 insertions(+), 1828 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut, cre],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [...truncated...]
Maintainer: Nic Crane <thisisnic@gmail.com>
Diff between arrow versions 14.0.0.2 dated 2023-12-01 and 14.0.2.1 dated 2024-02-23
DESCRIPTION | 9 MD5 | 95 ++-- NEWS.md | 25 + R/duckdb.R | 19 configure | 2 configure.win | 202 ++++++++- inst/build_arrow_static.sh | 3 src/altrep.cpp | 56 +- src/array.cpp | 18 src/array_to_vector.cpp | 14 src/arraydata.cpp | 12 src/arrowExports.cpp | 76 +-- src/arrow_cpp11.h | 14 src/arrow_types.h | 4 src/chunkedarray.cpp | 5 src/compression.cpp | 2 src/compute.cpp | 15 src/dataset.cpp | 4 src/datatype.cpp | 2 src/io.cpp | 11 src/message.cpp | 4 src/r_to_arrow.cpp | 32 + src/recordbatch.cpp | 14 src/schema.cpp | 4 src/table.cpp | 16 tests/testthat/test-dplyr-summarize.R | 44 -- tests/testthat/test-duckdb.R | 10 tools/check-versions.R | 35 + tools/checksums/darwin-arm64-openssl-1.1/arrow-14.0.2.zip.sha512 |only tools/checksums/darwin-arm64-openssl-3.0/arrow-14.0.2.zip.sha512 |only tools/checksums/darwin-x86_64-openssl-1.1/arrow-14.0.2.zip.sha512 |only tools/checksums/darwin-x86_64-openssl-3.0/arrow-14.0.2.zip.sha512 |only tools/checksums/linux-openssl-1.0/arrow-14.0.2.zip.sha512 |only tools/checksums/linux-openssl-1.1/arrow-14.0.2.zip.sha512 |only tools/checksums/linux-openssl-3.0/arrow-14.0.2.zip.sha512 |only tools/checksums/windows/arrow-13.0.0.zip.sha512 |only tools/cpp/CMakeLists.txt | 2 tools/cpp/build-support/__pycache__ |only tools/cpp/cmake_modules/ThirdpartyToolchain.cmake | 17 tools/cpp/src/arrow/CMakeLists.txt | 2 tools/cpp/src/arrow/csv/reader.cc | 21 - tools/cpp/src/arrow/dataset/file_parquet.cc | 5 tools/cpp/src/arrow/filesystem/s3fs.cc | 11 tools/cpp/src/arrow/filesystem/util_internal.cc | 1 tools/cpp/src/arrow/util/bit_util.h | 9 tools/cpp/src/arrow/util/bitmap_generate.h | 7 tools/cpp/src/parquet/arrow/reader.cc | 6 tools/cpp/src/parquet/encoding.cc | 36 + tools/cpp/vcpkg.json | 2 tools/nixlibs-allowlist.txt | 1 tools/nixlibs.R | 209 ++++++---- tools/test-check-versions.R | 40 + tools/update-checksums.R | 9 53 files changed, 779 insertions(+), 346 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-18 0.1.0
Title: Read and Modify 'STICS' Input/Output Files
Description: Manipulating input and output files of the 'STICS' crop
model. Files are either 'JavaSTICS' XML files or text files used by
the model 'fortran' executable. Most basic functionalities are reading
or writing parameter names and values in both XML or text input files,
and getting data from output files. Advanced functionalities include
XML files generation from XML templates and/or spreadsheets, or text
files generation from XML files by using 'xslt' transformation.
Author: Patrice Lecharpentier [aut, cre]
,
Remi Vezy [aut] ,
Samuel Buis [aut] ,
Michel Giner [aut] ,
Thomas Robine [ctb],
Amine Barkaoui [ctb],
Patrick Chabrier [ctb],
Julie Constantin [rev],
Dominique Ripoche [rev],
Marie Launay [rev],
Alain Mollier [rev], [...truncated...]
Maintainer: Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Diff between SticsRFiles versions 1.1.3 dated 2023-07-11 and 1.2.0 dated 2024-02-23
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Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for
drawing probability-proportional-to-size samples with a given number of
units, and is commonly used for price-index surveys. This package gives
functions to draw stratified sequential Poisson samples according to the
method by Ohlsson (1998, ISSN:0282-423X), as well as other order sample
designs by Rosén (1997, <doi:10.1016/S0378-3758(96)00186-3>), and generate
appropriate bootstrap replicate weights according to the generalized
bootstrap method by Beaumont and Patak
(2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between sps versions 0.5.3 dated 2023-10-16 and 0.5.4 dated 2024-02-23
DESCRIPTION | 25 +- MD5 | 41 +-- NAMESPACE | 21 + NEWS.md | 9 R/inclusion_prob.R | 47 +++ R/prop_allocation.R | 4 R/sps-package.R | 4 R/sps.R | 71 ----- R/sps_repweights.R | 8 R/sps_sample-class.R |only README.md | 55 +++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/sps.R | 32 ++ inst/doc/sps.Rmd | 37 ++- inst/doc/sps.html | 416 ++++++++++++++++++----------------- man/figures |only man/inclusion_prob.Rd | 23 + man/sps-package.Rd | 5 man/sps.Rd | 6 tests/testthat/test-inclusion_prob.R | 51 +++- vignettes/sps.Rmd | 37 ++- 23 files changed, 528 insertions(+), 364 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim [aut, cre],
Daniel T. Kaplan [aut],
Nicholas J. Horton [aut]
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 1.9.0 dated 2023-11-09 and 1.9.1 dated 2024-02-23
DESCRIPTION | 8 +-- MD5 | 26 ++++++------ NEWS.md | 6 ++ R/dpqrdist.R | 5 +- inst/doc/MinimalRgg.pdf |binary inst/doc/Resampling.html | 8 +-- inst/doc/mosaic-resources.html | 4 - man/mosaic-package.Rd | 9 ++++ tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/clustering/clustering1.svg | 48 +++++++++++------------ tests/testthat/_snaps/clustering/clustering2.svg | 48 +++++++++++------------ tests/testthat/_snaps/clustering/clustering3.svg | 24 +++++------ tests/testthat/_snaps/clustering/clustering4.svg | 24 +++++------ tests/testthat/test-clustering.R | 12 ++--- 14 files changed, 119 insertions(+), 103 deletions(-)
Title: Processing Force-Plate Data
Description: Process raw force-plate data (txt-files) by segmenting them into trials and, if needed, calculating (user-defined) descriptive
statistics of variables for user-defined time bins (relative to trigger onsets) for each trial. When segmenting the data a baseline
correction, a filter, and a data imputation can be applied if needed. Experimental data can also be processed and combined with the
segmented force-plate data. This procedure is suggested by Johannsen et al. (2023) <doi:10.6084/m9.figshare.22190155> and some of the
options (e.g., choice of low-pass filter) are also suggested by Winter (2009) <doi:10.1002/9780470549148>.
Author: Raphae Hartmann [aut, cre] ,
Anton Koger [aut, ctb] ,
Leif Johannsen [ctb]
Maintainer: Raphae Hartmann <raphael.hartmann@protonmail.com>
Diff between forceplate versions 1.1-0 dated 2024-01-31 and 1.1-1 dated 2024-02-23
forceplate-1.1-0/forceplate/R/prep_bw_data.R |only forceplate-1.1-0/forceplate/R/time_lock_bioware.R |only forceplate-1.1-1/forceplate/DESCRIPTION | 6 forceplate-1.1-1/forceplate/MD5 | 18 - forceplate-1.1-1/forceplate/R/checks.R | 2 forceplate-1.1-1/forceplate/R/segment_fp_data.R |only forceplate-1.1-1/forceplate/R/time_lock_stats.R |only forceplate-1.1-1/forceplate/R/tools.R | 46 +-- forceplate-1.1-1/forceplate/README.md | 2 forceplate-1.1-1/forceplate/man/figures/forceplate_logo.svg | 156 ++++++------ forceplate-1.1-1/forceplate/man/segment_fp_data.Rd | 12 forceplate-1.1-1/forceplate/man/time_lock_stats.Rd | 2 12 files changed, 122 insertions(+), 122 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.17.0 dated 2023-11-28 and 2.18.0 dated 2024-02-23
DESCRIPTION | 8 - MD5 | 40 ++++----- NEWS.md | 6 + R/dicom_reader.R | 2 R/fit_display.R | 19 +++- R/mrs_data_display.R | 49 ++++++++--- R/mrs_data_io.R | 32 +++---- R/mrs_data_proc.R | 14 +++ R/mrs_read_dicom.R | 88 +++++++++++++++------ R/mrs_read_ima.R | 7 + R/mrs_read_twix.R | 24 +++++ R/mrs_write_nifti.R | 5 + R/svs_batch_fit.R | 157 ++++++++++++++++++++------------------ inst/doc/spant-intro.html | 126 +++++++++++++++--------------- inst/doc/spant-preprocessing.html | 4 man/image.mrs_data.Rd | 4 man/plot.fit_result.Rd | 3 man/scale_spec.Rd | 2 man/stackplot.fit_result.Rd | 3 man/stackplot.mrs_data.Rd | 6 - man/svs_1h_brain_analysis_dev.Rd | 27 ++++-- 21 files changed, 388 insertions(+), 238 deletions(-)
Title: Left-Truncated Mixtures of Gamma, Weibull, and Lognormal
Distributions
Description: Mixture modelling of one-dimensional data using combinations of left-truncated Gamma, Weibull, and Lognormal Distributions. Blostein, Martin & Miljkovic, Tatjana. (2019) <doi:10.1016/j.insmatheco.2018.12.001>.
Author: Martin Blostein <martin.blostein@gmail.com> and Tatjana Miljkovic <miljkot@miamioh.edu>
Maintainer: Martin Blostein <martin.blostein@gmail.com>
Diff between ltmix versions 0.2.1 dated 2021-07-05 and 0.2.2 dated 2024-02-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/data_docs.R | 1 - R/distributions.R | 3 ++- R/ltmix-package.R | 2 +- man/ltmix.Rd | 2 +- man/secura.Rd | 2 -- 7 files changed, 14 insertions(+), 16 deletions(-)
Title: Balanced and Spatially Balanced Sampling
Description: Select balanced and spatially balanced probability samples in multi-dimensional spaces
with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of
the included sampling methods. The local pivotal method by Grafström, Lundström and Schelin (2012)
<doi:10.1111/j.1541-0420.2011.01699.x> and spatially correlated Poisson sampling by Grafström (2012)
<doi:10.1016/j.jspi.2011.07.003> are included. Also the cube method (for balanced sampling) and
the local cube method (for doubly balanced sampling) are included, see Grafström and Tillé (2013)
<doi:10.1002/env.2194>.
Author: Anton Grafstroem, Jonathan Lisic, Wilmer Prentius
Maintainer: Anton Grafstroem <anton.grafstrom@gmail.com>
Diff between BalancedSampling versions 1.6.3 dated 2022-06-29 and 2.0.5 dated 2024-02-23
BalancedSampling-1.6.3/BalancedSampling/R/hlpm.R |only BalancedSampling-1.6.3/BalancedSampling/R/probabilities.R |only BalancedSampling-1.6.3/BalancedSampling/man/BalancedSampling-package.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/cubestratified.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/flightphase.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/hlpm.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/landingphase.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/lcps.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/lcubeflightphase.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/lcubelandingphase.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/lcubestratified.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/lpm1.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/lpm2.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/probabilities.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/rpm.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/scps_coord.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/scps_getrand.Rd |only BalancedSampling-1.6.3/BalancedSampling/man/spm.Rd |only BalancedSampling-1.6.3/BalancedSampling/src/cube.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/lcps.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/lpm.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/lpm1.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/lpm2.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/rpm.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/sb.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/scps.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/spm.cpp |only BalancedSampling-1.6.3/BalancedSampling/src/vsb.cpp |only BalancedSampling-2.0.5/BalancedSampling/DESCRIPTION | 28 BalancedSampling-2.0.5/BalancedSampling/MD5 | 94 +- BalancedSampling-2.0.5/BalancedSampling/NAMESPACE | 10 BalancedSampling-2.0.5/BalancedSampling/R/BalancedSampling-package.R |only BalancedSampling-2.0.5/BalancedSampling/R/RcppExports.R | 76 +- BalancedSampling-2.0.5/BalancedSampling/R/cube.R |only BalancedSampling-2.0.5/BalancedSampling/R/getPips.R |only BalancedSampling-2.0.5/BalancedSampling/R/hlpm2.R |only BalancedSampling-2.0.5/BalancedSampling/R/lcube.R |only BalancedSampling-2.0.5/BalancedSampling/R/lpm.R |only BalancedSampling-2.0.5/BalancedSampling/R/populations.R |only BalancedSampling-2.0.5/BalancedSampling/R/sb.R |only BalancedSampling-2.0.5/BalancedSampling/R/scps.R |only BalancedSampling-2.0.5/BalancedSampling/R/utils.R |only BalancedSampling-2.0.5/BalancedSampling/R/vsb.R |only BalancedSampling-2.0.5/BalancedSampling/man/BalancedSampling.Rd |only BalancedSampling-2.0.5/BalancedSampling/man/cube.Rd | 126 ++- BalancedSampling-2.0.5/BalancedSampling/man/genpopUniform.Rd |only BalancedSampling-2.0.5/BalancedSampling/man/getPips.Rd |only BalancedSampling-2.0.5/BalancedSampling/man/hlpm2.Rd |only BalancedSampling-2.0.5/BalancedSampling/man/lcube.Rd | 152 +++- BalancedSampling-2.0.5/BalancedSampling/man/lpm.Rd | 183 ++++- BalancedSampling-2.0.5/BalancedSampling/man/sb.Rd | 95 ++ BalancedSampling-2.0.5/BalancedSampling/man/scps.Rd | 147 +++- BalancedSampling-2.0.5/BalancedSampling/man/vsb.Rd | 76 +- BalancedSampling-2.0.5/BalancedSampling/src/CpsClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/CpsClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/CubeClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/CubeClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/CubeStratifiedClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/CubeStratifiedClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/IndexListClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/IndexListClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/KDNodeClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/KDNodeClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/KDStoreClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/KDStoreClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/KDTreeClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/KDTreeClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/LpmClass.cc |only BalancedSampling-2.0.5/BalancedSampling/src/LpmClass.h |only BalancedSampling-2.0.5/BalancedSampling/src/Makevars |only BalancedSampling-2.0.5/BalancedSampling/src/Makevars.win |only BalancedSampling-2.0.5/BalancedSampling/src/RcppExports.cpp | 320 +++++----- BalancedSampling-2.0.5/BalancedSampling/src/ReducedRowEchelonForm.cc |only BalancedSampling-2.0.5/BalancedSampling/src/ReducedRowEchelonForm.h |only BalancedSampling-2.0.5/BalancedSampling/src/cps.cc |only BalancedSampling-2.0.5/BalancedSampling/src/cube.cc |only BalancedSampling-2.0.5/BalancedSampling/src/cube_stratified.cc |only BalancedSampling-2.0.5/BalancedSampling/src/getPips.cc |only BalancedSampling-2.0.5/BalancedSampling/src/hlpm2.cc |only BalancedSampling-2.0.5/BalancedSampling/src/lpm.cc |only BalancedSampling-2.0.5/BalancedSampling/src/sb-localbalance.cc |only BalancedSampling-2.0.5/BalancedSampling/src/sb-voronoi.cc |only BalancedSampling-2.0.5/BalancedSampling/src/uniform.h |only BalancedSampling-2.0.5/BalancedSampling/src/utils.h |only BalancedSampling-2.0.5/BalancedSampling/src/vsb.cc |only 85 files changed, 872 insertions(+), 435 deletions(-)
More information about BalancedSampling at CRAN
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Title: Functions for Plotting Graphical Shapes, Colors
Description: Functions for plotting graphical shapes
such as ellipses, circles, cylinders, arrows, ...
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between shape versions 1.4.6 dated 2021-05-19 and 1.4.6.1 dated 2024-02-23
DESCRIPTION | 6 +++--- MD5 | 7 +++++-- build |only inst/doc/shape.R |only inst/doc/shape.Rnw |only inst/doc/shape.pdf |binary 6 files changed, 8 insertions(+), 5 deletions(-)
Title: One-Step Estimation
Description: Provide principally an eponymic function that numerically computes
the Le Cam's one-step estimator for an independent and identically distributed sample.
One-step estimation is asymptotically
efficient (see L. Le Cam (1956) <https://projecteuclid.org/euclid.bsmsp/1200501652>)
and can be computed faster than the maximum likelihood estimator for large observation
samples, see e.g. Brouste et al. (2021) <doi:10.32614/RJ-2021-044>.
Author: Alexandre Brouste [aut] ,
Christophe Dutang [aut, cre] ,
Darel Noutsa Mieniedou [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between OneStep versions 0.9.2 dated 2021-01-15 and 0.9.3 dated 2024-02-23
OneStep-0.9.2/OneStep/inst/NEWS |only OneStep-0.9.3/OneStep/DESCRIPTION | 29 OneStep-0.9.3/OneStep/MD5 | 31 OneStep-0.9.3/OneStep/NAMESPACE | 11 OneStep-0.9.3/OneStep/R/onestep-closedform.R | 572 +++++++--- OneStep-0.9.3/OneStep/R/onestep-generic.R | 82 - OneStep-0.9.3/OneStep/R/onestep.R | 108 + OneStep-0.9.3/OneStep/build/partial.rdb |binary OneStep-0.9.3/OneStep/inst/CITATION | 34 OneStep-0.9.3/OneStep/inst/NEWS.md |only OneStep-0.9.3/OneStep/man/onestep.Rd | 29 OneStep-0.9.3/OneStep/tests/t-Beta.R | 121 +- OneStep-0.9.3/OneStep/tests/t-Pareto.R | 2 OneStep-0.9.3/OneStep/tests/t-cauchy.R |only OneStep-0.9.3/OneStep/tests/t-location-scaled-student.R |only OneStep-0.9.3/OneStep/tests/t-onestep-4-closedform-defensive.R | 3 OneStep-0.9.3/OneStep/tests/t-onestep-4-control-arg.R |only OneStep-0.9.3/OneStep/tests/t-student.R |only OneStep-0.9.3/OneStep/tests/t-weibull(2).R | 16 OneStep-0.9.3/OneStep/tests/t-weibull.R |only 20 files changed, 724 insertions(+), 314 deletions(-)
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.2.0 dated 2024-02-14 and 2.2.1 dated 2024-02-23
DESCRIPTION | 6 ++-- MD5 | 56 ++++++++++++++++++++-------------------- NEWS.md | 7 +++++ R/fbam.R | 8 ++--- R/get_est.R | 4 +- R/hbam.R | 14 +++++----- R/inits.R | 6 ++-- R/plot_by_group.R | 5 +-- inst/doc/hbamr.R | 2 - inst/doc/hbamr.Rmd | 6 ++-- inst/doc/hbamr.html | 10 +++---- inst/stan/BAM.stan | 2 - inst/stan/HBAM.stan | 8 ++--- inst/stan/HBAM_MINI.stan | 6 ++-- inst/stan/HBAM_MULTI.stan | 8 ++--- inst/stan/HBAM_MULTI_NF.stan | 8 ++--- inst/stan/HBAM_NF.stan | 8 ++--- inst/stan/HBAM_R_MINI.stan | 6 ++-- man/fbam.Rd | 6 ++-- man/hbam.Rd | 10 +++---- man/plot_by_group.Rd | 2 - src/stanExports_BAM.h | 4 +- src/stanExports_HBAM.h | 12 ++++---- src/stanExports_HBAM_MINI.h | 8 ++--- src/stanExports_HBAM_MULTI.h | 12 ++++---- src/stanExports_HBAM_MULTI_NF.h | 12 ++++---- src/stanExports_HBAM_NF.h | 12 ++++---- src/stanExports_HBAM_R_MINI.h | 8 ++--- vignettes/hbamr.Rmd | 6 ++-- 29 files changed, 134 insertions(+), 128 deletions(-)
Title: Create Dendrograms and Tree Diagrams Using 'ggplot2'
Description: This is a set of tools for dendrograms and
tree plots using 'ggplot2'. The 'ggplot2' philosophy is to
clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots
directly to a plot device without exposing the data.
The 'ggdendro' package resolves this by making available
functions that extract the dendrogram plot data. The package
provides implementations for 'tree', 'rpart', as well as diana and agnes
(from 'cluster') diagrams.
Author: Andrie de Vries [aut, cre],
Brian D. Ripley [aut]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between ggdendro versions 0.1.23 dated 2022-02-16 and 0.2.0 dated 2024-02-23
ggdendro-0.1.23/ggdendro/NEWS |only ggdendro-0.1.23/ggdendro/man/labels.rpart.Rd |only ggdendro-0.2.0/ggdendro/DESCRIPTION | 11 ggdendro-0.2.0/ggdendro/MD5 | 56 +- ggdendro-0.2.0/ggdendro/NEWS.md |only ggdendro-0.2.0/ggdendro/R/dendro_data.R | 19 ggdendro-0.2.0/ggdendro/R/dendro_rpart.R | 5 ggdendro-0.2.0/ggdendro/R/dendrogram.R | 257 +---------- ggdendro-0.2.0/ggdendro/R/ggdendro-package.R | 27 - ggdendro-0.2.0/ggdendro/R/ggdendrogram.R | 4 ggdendro-0.2.0/ggdendro/R/plotNode.R |only ggdendro-0.2.0/ggdendro/R/rpart.R | 3 ggdendro-0.2.0/ggdendro/R/stats_functions.R |only ggdendro-0.2.0/ggdendro/build/vignette.rds |binary ggdendro-0.2.0/ggdendro/inst/WORDLIST | 13 ggdendro-0.2.0/ggdendro/inst/doc/ggdendro.R | 2 ggdendro-0.2.0/ggdendro/inst/doc/ggdendro.Rmd | 12 ggdendro-0.2.0/ggdendro/inst/doc/ggdendro.html | 273 ++++++------ ggdendro-0.2.0/ggdendro/inst/doc/modify_output.R |only ggdendro-0.2.0/ggdendro/inst/doc/modify_output.Rmd |only ggdendro-0.2.0/ggdendro/inst/doc/modify_output.html |only ggdendro-0.2.0/ggdendro/inst/examples/example_dendro_tree.R | 2 ggdendro-0.2.0/ggdendro/man/dendro_data.Rd | 28 - ggdendro-0.2.0/ggdendro/man/dendro_data.rpart.Rd | 2 ggdendro-0.2.0/ggdendro/man/dendro_data.tree.Rd | 4 ggdendro-0.2.0/ggdendro/man/dendrogram_data.Rd | 7 ggdendro-0.2.0/ggdendro/man/figures/logo.png |only ggdendro-0.2.0/ggdendro/man/figures/logo.svg |only ggdendro-0.2.0/ggdendro/man/ggdendro-package.Rd | 16 ggdendro-0.2.0/ggdendro/man/rpart_labels.Rd | 7 ggdendro-0.2.0/ggdendro/man/rpart_segments.Rd | 2 ggdendro-0.2.0/ggdendro/tests/testthat/Rplots.pdf |only ggdendro-0.2.0/ggdendro/tests/testthat/data |only ggdendro-0.2.0/ggdendro/tests/testthat/test-7-recursion.R |only ggdendro-0.2.0/ggdendro/vignettes/ggdendro.Rmd | 12 ggdendro-0.2.0/ggdendro/vignettes/modify_output.Rmd |only 36 files changed, 294 insertions(+), 468 deletions(-)
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions. Methodology described in Murphy (2019)
<doi:10.1016/j.envsoft.2019.03.027>.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 2.0.9 dated 2023-05-25 and 2.0.11 dated 2024-02-23
baytrends-2.0.11/baytrends/DESCRIPTION | 11 baytrends-2.0.11/baytrends/MD5 | 18 baytrends-2.0.11/baytrends/NEWS | 43 baytrends-2.0.11/baytrends/NEWS.md | 43 baytrends-2.0.11/baytrends/R/analysisOrganizeData.R | 24 baytrends-2.0.11/baytrends/R/baytrends.R | 3 baytrends-2.0.11/baytrends/build/vignette.rds |binary baytrends-2.0.11/baytrends/inst/doc/Detrending_Flow_and_Salinity_Data.html | 112 +- baytrends-2.0.11/baytrends/inst/doc/Processing_Censored_Data.html | 504 +++++----- baytrends-2.0.11/baytrends/man/baytrends-package.Rd |only baytrends-2.0.9/baytrends/man/baytrends.Rd |only 11 files changed, 411 insertions(+), 347 deletions(-)
Title: A Class of Mixture Models for Ordinal Data
Description: For ordinal rating data, estimate and test models within the family of CUB models and their extensions (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions); Simulation routines, plotting facilities and fitting measures are also provided.
Author: Maria Iannario [aut],
Domenico Piccolo [aut],
Rosaria Simone [aut, cre]
Maintainer: Rosaria Simone <rosaria.simone@unina.it>
Diff between CUB versions 1.1.4 dated 2020-03-31 and 1.1.5 dated 2024-02-23
DESCRIPTION | 22 +-- MD5 | 238 ++++++++++++++++++++--------------------- NAMESPACE | 146 ++++++++++++------------- R/CUB_package.R | 16 +- R/chi2cub1cov.R | 2 R/chi2cub2cov.R | 3 R/cubpq.R | 1 R/cubshe.R | 3 R/kkk.R | 2 R/relgoods.R | 1 R/univer.R | 1 build/vignette.rds |binary inst/doc/CUBvignette-knitr.pdf |binary man/CUB.Rd | 26 ++-- man/CUBE.Rd | 38 +++--- man/CUB_package.Rd | 69 +++++------ man/CUSH.Rd | 18 +-- man/GEM.Rd | 88 +++++++-------- man/Hadprod.Rd | 12 +- man/IHG.Rd | 24 ++-- man/Qdue.Rd | 6 - man/Quno.Rd | 8 - man/auxmat.Rd | 6 - man/betabinomial.Rd | 14 +- man/betabinomialcsi.Rd | 14 +- man/betar.Rd | 2 man/bitcsi.Rd | 4 man/bitgama.Rd | 6 - man/chi2cub.Rd | 10 - man/chi2cub1cov.Rd | 10 - man/chi2cub2cov.Rd | 14 +- man/cormat.Rd | 2 man/cub0q.Rd | 8 - man/cube000.Rd | 6 - man/cubecov.Rd | 10 - man/cubecsi.Rd | 6 - man/cubevisual.Rd | 6 - man/cubp0.Rd | 8 - man/cubpq.Rd | 6 - man/cubshe.Rd | 7 - man/cubshevisual.Rd | 6 - man/cubvisual.Rd | 6 - man/cushcov.Rd | 2 man/deltaprob.Rd | 2 man/dissim.Rd | 2 man/effe01.Rd | 4 man/effe10.Rd | 6 - man/effecube.Rd | 8 - man/effecubecsi.Rd | 4 man/effecush.Rd | 2 man/effeihgcov.Rd | 2 man/ellecub.Rd | 4 man/expcub00.Rd | 2 man/expcube.Rd | 4 man/fitted.GEM.Rd | 2 man/gecubpqs.Rd | 8 - man/gini.Rd | 2 man/ihg00.Rd | 2 man/ihgcov.Rd | 4 man/inibest.Rd | 10 - man/inibestcube.Rd | 2 man/inibestcubecov.Rd | 10 - man/inibestcubecsi.Rd | 10 - man/inibestgama.Rd | 8 - man/inigrid.Rd | 2 man/iniihg.Rd | 6 - man/kkk.Rd | 6 - man/laakso.Rd | 4 man/logis.Rd | 2 man/loglikCUB.Rd | 24 ++-- man/loglikCUSH.Rd | 8 - man/loglikcub00.Rd | 2 man/loglikcub0q.Rd | 4 man/loglikcube.Rd | 18 +-- man/loglikcubecov.Rd | 6 - man/loglikcubecsi.Rd | 4 man/loglikcuben.Rd | 6 - man/loglikcubp0.Rd | 4 man/loglikcubpq.Rd | 4 man/loglikcush00.Rd | 2 man/loglikcushcov.Rd | 4 man/loglikihg.Rd | 6 - man/loglikihgcov.Rd | 2 man/logscore.Rd | 10 - man/makeplot.Rd | 6 - man/multicub.Rd | 10 - man/multicube.Rd | 14 +- man/plotloglikihg.Rd | 2 man/print.GEM.Rd | 2 man/probcub00.Rd | 2 man/probcub0q.Rd | 14 +- man/probcube.Rd | 2 man/probcubp0.Rd | 14 +- man/probcubpq.Rd | 16 +- man/probcubshe1.Rd | 8 - man/probcubshe2.Rd | 8 - man/probcubshe3.Rd | 10 - man/probcush.Rd | 6 - man/probgecub.Rd | 14 +- man/probihg.Rd | 2 man/probihgcovn.Rd | 8 - man/relgoods.Rd | 55 ++++----- man/simcube.Rd | 2 man/simcubshe.Rd | 2 man/simcush.Rd | 2 man/summary.GEM.Rd | 2 man/univer.Rd | 15 +- man/varcovcub00.Rd | 4 man/varcovcub0q.Rd | 8 - man/varcovcubecov.Rd | 10 - man/varcovcubeexp.Rd | 6 - man/varcovcubeobs.Rd | 6 - man/varcovcubp0.Rd | 6 - man/varcovcubpq.Rd | 4 man/varcovcubshe.Rd | 4 man/varcovgecub.Rd | 8 - man/varcub00.Rd | 2 man/varcube.Rd | 4 man/varmatCUB.Rd | 20 +-- man/varmatCUBE.Rd | 16 +- 120 files changed, 700 insertions(+), 713 deletions(-)
Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] ,
Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalSL versions 0.92 dated 2024-02-15 and 0.93 dated 2024-02-23
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 4 ++-- R/LIB_SNN.R | 2 +- R/summary.sltime.R | 15 ++++++++++++++- R/tuneSNN.R | 2 +- man/LIB_SNN.Rd | 6 +++++- man/tuneSNN.Rd | 4 +++- 8 files changed, 39 insertions(+), 20 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.5.0 dated 2023-11-24 and 0.6.0 dated 2024-02-23
DESCRIPTION | 26 MD5 | 143 +- NAMESPACE | 22 NEWS.md | 14 R/AllClasses.R | 4 R/AllGenerics.R | 21 R/biplot.R | 250 ++-- R/ca.R | 8 R/dimensio-defunct.R |only R/dimensio-deprecated.R | 459 ------- R/dimensio-internal.R | 87 - R/dimensio-package.R | 2 R/loadings.R | 18 R/mca.R | 20 R/mutators.R | 9 R/pca.R | 23 R/predict.R | 36 R/screeplot.R | 172 +- R/show.R | 27 R/summary.R | 139 +- R/viz_contributions.R | 11 R/viz_coordinates.R | 30 R/viz_labels.R | 48 README.md | 12 inst/CITATION | 2 inst/doc/pca.R | 2 inst/doc/pca.Rmd | 20 inst/doc/pca.html | 843 +++++--------- inst/examples/ex-biplot.R | 10 inst/examples/ex-contributions.R | 2 inst/examples/ex-plot.R | 2 inst/tinytest/_snaps/mca_col_augment.rds |only inst/tinytest/_snaps/mca_col_distances.rds |only inst/tinytest/_snaps/mca_col_inertia.rds |only inst/tinytest/_snaps/mca_col_principal.rds |only inst/tinytest/_snaps/mca_col_standard.rds |only inst/tinytest/_snaps/mca_col_tidy.rds |only inst/tinytest/_snaps/mca_eigenvalues.rds |only inst/tinytest/_snaps/mca_row_augment.rds |only inst/tinytest/_snaps/mca_row_distances.rds |only inst/tinytest/_snaps/mca_row_inertia.rds |only inst/tinytest/_snaps/mca_row_principal.rds |only inst/tinytest/_snaps/mca_row_standard.rds |only inst/tinytest/_snaps/mca_row_tidy.rds |only inst/tinytest/_tinysnapshot/CA_boot_col.svg | 256 ++-- inst/tinytest/_tinysnapshot/CA_boot_row.svg | 256 ++-- inst/tinytest/_tinysnapshot/CA_ind_contrib.svg | 8 inst/tinytest/_tinysnapshot/CA_var_contrib.svg | 8 inst/tinytest/_tinysnapshot/PCA_boot_col.svg | 256 ++-- inst/tinytest/_tinysnapshot/PCA_ind_contrib.svg | 8 inst/tinytest/_tinysnapshot/PCA_ind_highlight_cos2.svg | 306 ++--- inst/tinytest/_tinysnapshot/PCA_var_contrib.svg | 8 inst/tinytest/_tinysnapshot/PCA_var_highlight_contrib.svg | 308 ++--- inst/tinytest/test_factominer_ca.R | 12 inst/tinytest/test_factominer_mca.R | 3 inst/tinytest/test_factominer_pca.R | 17 inst/tinytest/test_mca.R |only inst/tinytest/test_plot_pca.R | 3 inst/tinytest/test_scale.R | 60 man/MultivariateAnalysis.Rd | 2 man/biplot.Rd | 10 man/dimensio-defunct.Rd |only man/dimensio-deprecated.Rd | 140 -- man/dimensio-package.Rd | 5 man/figures/README-biplot-1.png |binary man/figures/README-plot-var-1.png |binary man/loadings.Rd | 7 man/mca.Rd | 2 man/pca.Rd | 4 man/predict.Rd | 3 man/prepare.Rd | 2 man/summary.Rd | 6 man/tidy.Rd | 2 man/viz_contributions.Rd | 7 man/viz_individuals.Rd | 2 man/viz_labels.Rd |only man/viz_points.Rd | 6 man/viz_variables.Rd | 12 man/viz_wrap.Rd | 2 man/wrap.Rd | 2 vignettes/pca.Rmd | 20 81 files changed, 1744 insertions(+), 2461 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-15 dated 2024-01-25 and 1.2-16 dated 2024-02-23
ChangeLog | 13 ++ DESCRIPTION | 29 +++--- MD5 | 44 ++++----- R/bivar.smooth.const-ti.R | 37 ++++---- R/bivar.smooth.const.R | 32 ++++++- R/derivative.scam.r | 130 +++++++++++++++++++++++++++-- R/plot.r | 57 +++++++----- R/predict.scam.R | 15 +-- R/uni.smooth.const-with-po.r | 42 +++++---- R/vis.scam.r | 3 build/partial.rdb |binary man/predict.scam.Rd | 50 +++++++---- man/scam-package.Rd | 28 ++++-- man/scam.Rd | 25 ++--- man/scam.check.Rd | 3 man/scam.control.Rd | 2 man/shape.constrained.smooth.terms.Rd | 9 +- man/smooth.construct.tesmd1.smooth.spec.Rd | 13 +- man/smooth.construct.tesmd2.smooth.spec.Rd | 14 +-- man/smooth.construct.tesmi1.smooth.spec.Rd | 14 +-- man/smooth.construct.tesmi2.smooth.spec.Rd | 13 +- man/smooth.construct.tismd.smooth.spec.Rd | 9 -- man/smooth.construct.tismi.smooth.spec.Rd | 9 -- 23 files changed, 402 insertions(+), 189 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 0.0.2 dated 2024-01-30 and 0.0.3 dated 2024-02-23
omopgenerics-0.0.2/omopgenerics/man/suppress.compared_result.Rd |only omopgenerics-0.0.2/omopgenerics/man/suppress.summarised_result.Rd |only omopgenerics-0.0.3/omopgenerics/DESCRIPTION | 8 omopgenerics-0.0.3/omopgenerics/MD5 | 93 - omopgenerics-0.0.3/omopgenerics/NAMESPACE | 14 omopgenerics-0.0.3/omopgenerics/R/cdmFromTables.R | 9 omopgenerics-0.0.3/omopgenerics/R/classAchillesTable.R | 27 omopgenerics-0.0.3/omopgenerics/R/classCdmReference.R | 78 omopgenerics-0.0.3/omopgenerics/R/classCdmSource.R | 17 omopgenerics-0.0.3/omopgenerics/R/classCdmTable.R | 34 omopgenerics-0.0.3/omopgenerics/R/classCohortTable.R | 76 omopgenerics-0.0.3/omopgenerics/R/classOmopTable.R | 24 omopgenerics-0.0.3/omopgenerics/R/compute.R | 23 omopgenerics-0.0.3/omopgenerics/R/methodBind.R | 15 omopgenerics-0.0.3/omopgenerics/R/methodDropTable.R | 96 - omopgenerics-0.0.3/omopgenerics/R/methodInsertFromSource.R | 4 omopgenerics-0.0.3/omopgenerics/R/methodInsertTable.R | 5 omopgenerics-0.0.3/omopgenerics/R/methodSummary.R | 24 omopgenerics-0.0.3/omopgenerics/R/methodSuppress.R | 185 -- omopgenerics-0.0.3/omopgenerics/R/overwriteClasses.R | 11 omopgenerics-0.0.3/omopgenerics/R/recordCohortAttrition.R | 6 omopgenerics-0.0.3/omopgenerics/R/sysdata.rda |binary omopgenerics-0.0.3/omopgenerics/R/utilities.R | 857 ++++------ omopgenerics-0.0.3/omopgenerics/build/vignette.rds |binary omopgenerics-0.0.3/omopgenerics/inst/doc/a03_cohort_table.R | 26 omopgenerics-0.0.3/omopgenerics/inst/doc/a03_cohort_table.Rmd | 108 + omopgenerics-0.0.3/omopgenerics/inst/doc/a03_cohort_table.html | 125 + omopgenerics-0.0.3/omopgenerics/inst/doc/reexport.R |only omopgenerics-0.0.3/omopgenerics/inst/doc/reexport.Rmd |only omopgenerics-0.0.3/omopgenerics/inst/doc/reexport.html |only omopgenerics-0.0.3/omopgenerics/man/cdmFromTables.Rd | 46 omopgenerics-0.0.3/omopgenerics/man/cdmName.Rd | 4 omopgenerics-0.0.3/omopgenerics/man/cdmReference.Rd | 9 omopgenerics-0.0.3/omopgenerics/man/cdmSource.Rd |only omopgenerics-0.0.3/omopgenerics/man/cdmVersion.Rd | 4 omopgenerics-0.0.3/omopgenerics/man/emptyAchillesTable.Rd |only omopgenerics-0.0.3/omopgenerics/man/emptyCdmReference.Rd |only omopgenerics-0.0.3/omopgenerics/man/emptyCohortTable.Rd |only omopgenerics-0.0.3/omopgenerics/man/emptyOmopTable.Rd |only omopgenerics-0.0.3/omopgenerics/man/sourceType.Rd |only omopgenerics-0.0.3/omopgenerics/man/tableName.Rd |only omopgenerics-0.0.3/omopgenerics/man/tableSource.Rd |only omopgenerics-0.0.3/omopgenerics/man/tmpPrefix.Rd |only omopgenerics-0.0.3/omopgenerics/man/uniqueTableName.Rd | 9 omopgenerics-0.0.3/omopgenerics/tests/testthat/_snaps/cdmFromTables.md | 24 omopgenerics-0.0.3/omopgenerics/tests/testthat/_snaps/classCdmReference.md | 24 omopgenerics-0.0.3/omopgenerics/tests/testthat/test-classCdmReference.R | 2 omopgenerics-0.0.3/omopgenerics/tests/testthat/test-emptyObjects.R |only omopgenerics-0.0.3/omopgenerics/tests/testthat/test-methodInsertTable.R | 13 omopgenerics-0.0.3/omopgenerics/tests/testthat/test-methodSummary.R | 220 +- omopgenerics-0.0.3/omopgenerics/tests/testthat/test-methodSuppress.R | 99 - omopgenerics-0.0.3/omopgenerics/tests/testthat/test-overwriteClasses.R | 2 omopgenerics-0.0.3/omopgenerics/tests/testthat/test-prefix.R |only omopgenerics-0.0.3/omopgenerics/tests/testthat/test-recordCohortAttrition.R | 299 +-- omopgenerics-0.0.3/omopgenerics/vignettes/a03_cohort_table.Rmd | 108 + omopgenerics-0.0.3/omopgenerics/vignettes/reexport.Rmd |only 56 files changed, 1614 insertions(+), 1114 deletions(-)
Title: NFL Logo Plots in 'ggplot2' and 'gt'
Description: A set of functions to visualize National Football League
analysis in 'ggplot2' plots and 'gt' tables.
Author: Sebastian Carl [aut, cre]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflplotR versions 1.2.0 dated 2023-09-18 and 1.3.0 dated 2024-02-23
DESCRIPTION | 24 LICENSE | 4 MD5 | 141 +- NAMESPACE | 98 + NEWS.md | 20 R/build_grobs.R | 185 +-- R/geom_from_path.R | 112 +- R/geom_lines.R | 48 R/geom_nfl_headshots.R | 268 ++--- R/geom_nfl_logos.R | 275 ++--- R/geom_nfl_wordmarks.R | 270 ++--- R/ggpreview.R | 134 +- R/gt_nfl.R | 588 ++++++----- R/nfl_team_factors.R | 184 +-- R/nfl_team_tiers.R | 320 +++--- R/nflplotR-package.R | 31 R/scale_nfl.R | 623 ++++++------ R/sysdata.rda |binary R/theme-elements.R | 744 +++++++-------- R/theme_nfl.R | 145 +- R/utils.R | 184 +-- R/zzz.R | 134 +- README.md | 173 +-- man/dot-nflplotR_clear_cache.Rd | 34 man/element.Rd | 382 +++---- man/figures/cols_label.png |only man/figures/lifecycle-deprecated.svg |only man/geom_from_path.Rd | 268 ++--- man/geom_lines.Rd | 216 ++-- man/geom_nfl_headshots.Rd | 314 +++--- man/geom_nfl_logos.Rd | 317 +++--- man/geom_nfl_wordmarks.Rd | 312 +++--- man/ggpreview.Rd | 172 +-- man/gt_nfl_cols_label.Rd |only man/gt_nfl_headshots.Rd | 150 +-- man/gt_nfl_logos.Rd | 133 +- man/gt_render_image.Rd | 76 - man/nfl_team_factor.Rd | 152 +-- man/nfl_team_tiers.Rd | 219 ++-- man/nflplotR-package.Rd | 89 - man/nflverse_sitrep.Rd | 22 man/scale_axes_nfl.Rd | 420 ++++---- man/scale_nfl.Rd | 285 ++--- man/theme_nfl.Rd | 111 +- man/valid_team_names.Rd | 52 - tests/testthat.R | 8 tests/testthat/_snaps/geom_from_path/p1.svg | 66 - tests/testthat/_snaps/geom_lines/p1.svg | 198 ++-- tests/testthat/_snaps/geom_lines/p2.svg | 194 +-- tests/testthat/_snaps/geom_lines/p3.svg | 194 +-- tests/testthat/_snaps/geom_lines/p4.svg | 198 ++-- tests/testthat/_snaps/geom_nfl_logos/p1.svg | 130 +- tests/testthat/_snaps/geom_nfl_logos/p2.svg | 136 +- tests/testthat/_snaps/geom_nfl_logos/p3.svg | 130 +- tests/testthat/_snaps/geom_nfl_wordmarks/p1.svg | 160 +-- tests/testthat/_snaps/geom_nfl_wordmarks/p2.svg | 160 +-- tests/testthat/_snaps/nfl_team_factors/p1.svg | 1186 ++++++++++++------------ tests/testthat/_snaps/nfl_team_factors/p2.svg | 1186 ++++++++++++------------ tests/testthat/_snaps/nfl_team_tiers/p1.svg | 149 +-- tests/testthat/_snaps/scale_nfl/p1.svg | 288 ++--- tests/testthat/_snaps/theme-elements/p1.svg | 72 - tests/testthat/_snaps/theme-elements/p2.svg | 72 - tests/testthat/setup.R | 56 - tests/testthat/test-geom_from_path.R | 46 tests/testthat/test-geom_lines.R | 72 - tests/testthat/test-geom_nfl_logos.R | 116 +- tests/testthat/test-geom_nfl_wordmarks.R | 102 +- tests/testthat/test-nfl_team_factors.R | 80 - tests/testthat/test-nfl_team_tiers.R | 58 - tests/testthat/test-scale_nfl.R | 44 tests/testthat/test-theme-elements.R | 58 - tests/testthat/test-utils.R | 24 tools/check.env | 18 73 files changed, 6899 insertions(+), 6731 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52) <doi:10.1177/1094428115584005>.
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or [...truncated...]
Author: Jan Dul <jdul@rsm.nl>
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 4.0.0 dated 2024-02-16 and 4.0.1 dated 2024-02-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/nca_outliers.R | 6 ++---- build/partial.rdb |binary man/NCA-package.Rd | 4 ++-- 6 files changed, 17 insertions(+), 15 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.4.0 dated 2024-02-01 and 0.4.0.1 dated 2024-02-23
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/buffer.R | 2 +- R/type.R | 2 +- inst/include/nanoarrow/r.h | 4 ++-- man/na_type.Rd | 2 +- src/array_stream.c | 4 ++-- src/pointers.c | 2 +- tests/testthat/_snaps/array-stream.md | 4 ++-- tests/testthat/test-array-stream.R | 4 ++-- 10 files changed, 24 insertions(+), 24 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] ,
Luca Scrucca [aut, cre] ,
Thomas Brendan Murphy [ctb] ,
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 6.0.1 dated 2023-11-15 and 6.1 dated 2024-02-23
mclust-6.0.1/mclust/R/mclustaddson.R |only mclust-6.1/mclust/DESCRIPTION | 8 mclust-6.1/mclust/MD5 | 57 +- mclust-6.1/mclust/NAMESPACE | 2 mclust-6.1/mclust/NEWS.md | 336 +++++++++----- mclust-6.1/mclust/R/bootstrap.R | 16 mclust-6.1/mclust/R/densityMclust.R | 21 mclust-6.1/mclust/R/graphics.R | 11 mclust-6.1/mclust/R/mclust.R | 8 mclust-6.1/mclust/R/mclust2.R |only mclust-6.1/mclust/R/mclustda.R | 116 +--- mclust-6.1/mclust/R/mclustdr.R | 36 - mclust-6.1/mclust/R/mclustssc.R | 8 mclust-6.1/mclust/R/util.R | 38 + mclust-6.1/mclust/R/weights.R | 32 - mclust-6.1/mclust/build/vignette.rds |binary mclust-6.1/mclust/data/Baudry_etal_2010_JCGS_examples.rda |binary mclust-6.1/mclust/data/EuroUnemployment.rda |binary mclust-6.1/mclust/data/GvHD.rda |binary mclust-6.1/mclust/data/acidity.rda |binary mclust-6.1/mclust/data/chevron.rda |binary mclust-6.1/mclust/data/cross.rda |binary mclust-6.1/mclust/data/diabetes.rda |binary mclust-6.1/mclust/data/thyroid.rda |binary mclust-6.1/mclust/data/wreath.rda |binary mclust-6.1/mclust/inst/doc/mclust.html | 22 mclust-6.1/mclust/man/diabetes.Rd | 2 mclust-6.1/mclust/man/logsumexp.Rd |only mclust-6.1/mclust/man/me.weighted.Rd | 27 - mclust-6.1/mclust/man/softmax.Rd |only mclust-6.1/mclust/src/init.c | 8 mclust-6.1/mclust/src/logsumexp.f |only 32 files changed, 445 insertions(+), 303 deletions(-)
Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework
(add-on to the 'lava' package). The package contains three main functionalities:
Wald tests/F-tests with improved control of the type 1 error in small samples,
adjustment for multiple comparisons when searching for local dependencies,
and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between lavaSearch2 versions 2.0.2 dated 2024-01-23 and 2.0.3 dated 2024-02-23
DESCRIPTION | 8 ++--- MD5 | 6 +-- inst/doc/overview.pdf |binary tests/testthat/test1b-sCorrect-conditionalMoment.R | 32 ++++++++++----------- 4 files changed, 23 insertions(+), 23 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] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 3.4.4 dated 2023-10-12 and 3.5.0 dated 2024-02-23
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ggplot2-3.5.0/ggplot2/R/aes-evaluation.R | 3 ggplot2-3.5.0/ggplot2/R/aes-group-order.R | 11 ggplot2-3.5.0/ggplot2/R/aes-linetype-size-shape.R | 46 ggplot2-3.5.0/ggplot2/R/aes-position.R | 12 ggplot2-3.5.0/ggplot2/R/aes.R | 9 ggplot2-3.5.0/ggplot2/R/annotation-custom.R | 2 ggplot2-3.5.0/ggplot2/R/annotation-logticks.R | 40 ggplot2-3.5.0/ggplot2/R/annotation-map.R | 4 ggplot2-3.5.0/ggplot2/R/annotation-raster.R | 2 ggplot2-3.5.0/ggplot2/R/annotation.R | 4 ggplot2-3.5.0/ggplot2/R/autolayer.R | 2 ggplot2-3.5.0/ggplot2/R/autoplot.R | 2 ggplot2-3.5.0/ggplot2/R/axis-secondary.R | 64 ggplot2-3.5.0/ggplot2/R/backports.R | 59 ggplot2-3.5.0/ggplot2/R/bin.R | 10 ggplot2-3.5.0/ggplot2/R/compat-plyr.R | 10 ggplot2-3.5.0/ggplot2/R/coord-.R | 160 - ggplot2-3.5.0/ggplot2/R/coord-cartesian-.R | 53 ggplot2-3.5.0/ggplot2/R/coord-fixed.R | 2 ggplot2-3.5.0/ggplot2/R/coord-flip.R | 52 ggplot2-3.5.0/ggplot2/R/coord-map.R | 5 ggplot2-3.5.0/ggplot2/R/coord-munch.R | 36 ggplot2-3.5.0/ggplot2/R/coord-polar.R | 56 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Title: Genesys PGR Client
Description: Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>).
Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.
Author: Global Crop Diversity Trust [cph],
Matija Obreza [aut, cre],
Nora Castaneda [ctb]
Maintainer: Matija Obreza <matija.obreza@croptrust.org>
Diff between genesysr versions 2.1.0 dated 2023-10-13 and 2.1.1 dated 2024-02-23
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/api-client.R | 18 ++++++++++++------ inst/doc/tutorial.html | 4 ++-- inst/doc/validation.html | 4 ++-- man/user_login.Rd | 10 +++++++++- 7 files changed, 40 insertions(+), 21 deletions(-)
Title: Inference with Extreme Value Inflated Count Data
Description: Allows users to model and draw inferences from extreme value inflated count data, and to evaluate these models and compare to non extreme-value inflated counterparts. The package is built to be compatible with standard presentation tools such as 'broom', 'tidy', and 'modelsummary'.
Author: David Randahl [cre, aut],
Johan Vegelius [aut]
Maintainer: David Randahl <david.randahl@pcr.uu.se>
Diff between evinf versions 0.8.7 dated 2023-09-20 and 0.8.8 dated 2024-02-23
evinf-0.8.7/evinf/man/lr_test_evzinb.Rd |only evinf-0.8.8/evinf/DESCRIPTION | 6 - evinf-0.8.8/evinf/MD5 | 14 +- evinf-0.8.8/evinf/NAMESPACE | 4 evinf-0.8.8/evinf/R/evinf-package.R | 2 evinf-0.8.8/evinf/R/lr_tests.R | 160 ++++++++++++++++++++++++++++++-- evinf-0.8.8/evinf/R/zinb_comparison.R | 6 + evinf-0.8.8/evinf/build/partial.rdb |binary evinf-0.8.8/evinf/man/lr_test.Rd |only 9 files changed, 172 insertions(+), 20 deletions(-)
Title: Distance Metrics for Trees Generated by Congreve and Lamsdell
Description: Includes the 100 datasets simulated by Congreve and Lamsdell (2016)
<doi:10.1111/pala.12236>, and analyses of the partition and quartet distance of
reconstructed trees from the generative tree, as analysed by Smith (2019)
<doi:10.1098/rsbl.2018.0632>.
Author: Martin R. Smith [aut, cre, cph]
,
Curtis R. Congreve [cph, dtc],
James C. Lamsdell [cph, dtc]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between CongreveLamsdell2016 versions 1.0.2 dated 2020-01-07 and 1.0.3 dated 2024-02-23
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More information about CongreveLamsdell2016 at CRAN
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Title: Haplotype-Aware CNV Analysis from scRNA-Seq
Description: A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
Author: Teng Gao [cre, aut],
Ruslan Soldatov [aut],
Hirak Sarkar [aut],
Evan Biederstedt [aut],
Peter Kharchenko [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Diff between numbat versions 1.3.2-1 dated 2023-06-17 and 1.4.0 dated 2024-02-23
numbat-1.3.2-1/numbat/man/calc_trans_mat.Rd |only numbat-1.3.2-1/numbat/man/dbbinom.Rd |only numbat-1.3.2-1/numbat/man/dgpois.Rd |only numbat-1.3.2-1/numbat/man/dpoilog.Rd |only numbat-1.3.2-1/numbat/man/fit_gpois.Rd |only numbat-1.3.2-1/numbat/man/forward_back_allele.Rd |only numbat-1.3.2-1/numbat/man/get_trans_probs.Rd |only numbat-1.3.2-1/numbat/man/l_bbinom.Rd |only numbat-1.3.2-1/numbat/man/l_gpois.Rd |only numbat-1.3.2-1/numbat/man/l_lnpois.Rd |only numbat-1.3.2-1/numbat/man/likelihood_allele.Rd |only numbat-1.3.2-1/numbat/man/run_allele_hmm.Rd |only numbat-1.3.2-1/numbat/man/run_joint_hmm.Rd |only numbat-1.3.2-1/numbat/man/viterbi_allele.Rd |only numbat-1.3.2-1/numbat/man/viterbi_joint.Rd |only numbat-1.3.2-1/numbat/src/bbinom.cpp |only numbat-1.3.2-1/numbat/src/hmm.cpp |only numbat-1.3.2-1/numbat/src/mle.cpp |only numbat-1.3.2-1/numbat/src/poilog.cpp |only numbat-1.4.0/numbat/DESCRIPTION | 12 numbat-1.4.0/numbat/MD5 | 59 -- numbat-1.4.0/numbat/NAMESPACE | 12 numbat-1.4.0/numbat/NEWS.md | 16 numbat-1.4.0/numbat/R/RcppExports.R | 38 - numbat-1.4.0/numbat/R/diagnostics.R | 7 numbat-1.4.0/numbat/R/genotyping.R | 3 numbat-1.4.0/numbat/R/hmm.R | 464 -------------------- numbat-1.4.0/numbat/R/main.R | 77 +-- numbat-1.4.0/numbat/R/trees.R | 4 numbat-1.4.0/numbat/R/utils.R | 72 --- numbat-1.4.0/numbat/R/vis.R | 7 numbat-1.4.0/numbat/README.md | 1 numbat-1.4.0/numbat/data/mut_graph_example.rda |binary numbat-1.4.0/numbat/data/phylogeny_example.rda |binary numbat-1.4.0/numbat/inst/bin/pileup_and_phase.R | 57 ++ numbat-1.4.0/numbat/man/exp_hclust.Rd | 2 numbat-1.4.0/numbat/man/get_exp_likelihoods.Rd | 2 numbat-1.4.0/numbat/man/log_mem.Rd | 3 numbat-1.4.0/numbat/src/RcppExports.cpp | 138 ----- numbat-1.4.0/numbat/tests/testthat/test_functions.R | 67 -- 40 files changed, 161 insertions(+), 880 deletions(-)
Title: Import and Handling for Plain and Formatted Text Files
Description: Functions for importing and handling text files and formatted text
files with additional meta-data, such including '.csv', '.tab', '.json', '.xml',
'.html', '.pdf', '.doc', '.docx', '.rtf', '.xls', '.xlsx', and others.
Author: Kenneth Benoit [aut, cre, cph],
Adam Obeng [aut],
Kohei Watanabe [ctb],
Akitaka Matsuo [ctb],
Paul Nulty [ctb],
Stefan Mueller [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between readtext versions 0.90 dated 2023-06-03 and 0.91 dated 2024-02-23
DESCRIPTION | 8 MD5 | 28 - NEWS.md | 4 R/quanteda-methods.R | 2 R/readtext-package.R | 3 R/utils.R | 3 README.md | 11 build/vignette.rds |binary inst/doc/readtext_vignette.R | 2 inst/doc/readtext_vignette.html | 682 ++++++++++++++++++++-------------------- man/add_docid.Rd | 2 man/get_temp.Rd | 2 man/readtext-package.Rd | 8 man/texts.Rd | 3 tests/testthat/test-readtext.R | 71 ++-- 15 files changed, 415 insertions(+), 414 deletions(-)