Title: Bayesian Generalized Linear Models with Time-Varying
Coefficients
Description: Efficient Bayesian generalized linear models with time-varying coefficients
as in Helske (2022, <doi:10.1016/j.softx.2022.101016>). Gaussian, Poisson, and binomial
observations are supported. The Markov chain Monte Carlo (MCMC) computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, the package uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2020, <doi:10.1111/sjos.12492>).
Author: Jouni Helske [aut, cre]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 1.0.6-1 dated 2022-10-16 and 1.0.7 dated 2023-08-08
walker-1.0.6-1/walker/src/Makevars |only walker-1.0.7/walker/DESCRIPTION | 10 walker-1.0.7/walker/MD5 | 27 +- walker-1.0.7/walker/R/walker.R | 5 walker-1.0.7/walker/README.md | 7 walker-1.0.7/walker/build/vignette.rds |binary walker-1.0.7/walker/configure | 6 walker-1.0.7/walker/configure.win | 8 walker-1.0.7/walker/inst/doc/walker.html | 218 ++++++++---------- walker-1.0.7/walker/man/walker.Rd | 5 walker-1.0.7/walker/src/Makevars.win | 8 walker-1.0.7/walker/src/stanExports_rw1_model.h | 4 walker-1.0.7/walker/src/stanExports_rw1_model_naive.h | 4 walker-1.0.7/walker/src/stanExports_walker_glm.h | 4 walker-1.0.7/walker/src/stanExports_walker_lm.h | 4 15 files changed, 156 insertions(+), 154 deletions(-)
Title: Create Geographic and Non-Geographic Map Tiles
Description: Creates geographic map tiles from geospatial map files or
non-geographic map tiles from simple image files. This package provides a
tile generator function for creating map tile sets for use with packages
such as 'leaflet'. In addition to generating map tiles based on a common
raster layer source, it also handles the non-geographic edge case, producing
map tiles from arbitrary images. These map tiles, which have a
non-geographic, simple coordinate reference system (CRS), can also be used
with 'leaflet' when applying the simple CRS option. Map tiles can be created
from an input file with any of the following extensions: tif, grd and nc for
spatial maps and png, jpg and bmp for basic images. This package requires
'Python' and the 'gdal' library for 'Python'. 'Windows' users are
recommended to install 'OSGeo4W' (<https://trac.osgeo.org/osgeo4w/>) as an
easy way to obtain the required 'gdal' support for 'Python'.
Author: Matthew Leonawicz [aut, cre] ,
Alex M Chubaty [ctb]
Maintainer: Matthew Leonawicz <mfleonawicz@gmail.com>
Diff between tiler versions 0.2.5 dated 2021-02-20 and 0.3.0 dated 2023-08-08
tiler-0.2.5/tiler/vignettes/precompile.R |only tiler-0.3.0/tiler/DESCRIPTION | 48 + tiler-0.3.0/tiler/MD5 | 49 - tiler-0.3.0/tiler/NAMESPACE | 2 tiler-0.3.0/tiler/NEWS.md | 12 tiler-0.3.0/tiler/R/options.R | 27 tiler-0.3.0/tiler/R/tile.R | 138 ++-- tiler-0.3.0/tiler/R/tiler.R | 23 tiler-0.3.0/tiler/R/viewer.R | 70 +- tiler-0.3.0/tiler/R/zzz.R | 22 tiler-0.3.0/tiler/README.md | 47 - tiler-0.3.0/tiler/build/vignette.rds |binary tiler-0.3.0/tiler/inst/WORDLIST | 32 - tiler-0.3.0/tiler/inst/doc/tiler-intro.Rmd | 56 - tiler-0.3.0/tiler/inst/doc/tiler-intro.html | 725 +++++++++++++++---------- tiler-0.3.0/tiler/inst/python/gdal2tilesIMG.py | 8 tiler-0.3.0/tiler/man/tile.Rd | 268 ++++----- tiler-0.3.0/tiler/man/tile_viewer.Rd | 117 +--- tiler-0.3.0/tiler/man/tiler.Rd | 55 - tiler-0.3.0/tiler/man/tiler_options.Rd | 99 +-- tiler-0.3.0/tiler/man/view_tiles.Rd | 62 +- tiler-0.3.0/tiler/tests/testthat/test-opts.R | 2 tiler-0.3.0/tiler/tests/testthat/test-tile.R | 41 + tiler-0.3.0/tiler/tests/testthat/test-viewer.R | 37 - tiler-0.3.0/tiler/vignettes/tiler-intro.Rmd | 56 - tiler-0.3.0/tiler/vignettes/vignette-ex6-1.png |binary 26 files changed, 1115 insertions(+), 881 deletions(-)
Title: Southwest Fisheries Science Center Aerial DAS Data Processing
Description: Process and summarize aerial survey 'DAS' data (AirDAS)
<https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-185.PDF>
collected using an aerial survey program from the
Southwest Fisheries Science Center (SWFSC)
<https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>.
PDF files detailing the relevant AirDAS data formats are included in this package.
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between swfscAirDAS versions 0.2.3 dated 2022-06-01 and 0.3.0 dated 2023-08-08
DESCRIPTION | 12 +-- MD5 | 36 ++++----- NAMESPACE | 3 NEWS.md | 7 + R/airdas_chop_equallength.R | 11 +- R/airdas_effort.R | 32 ++++---- R/airdas_read.R | 7 + R/airdas_sight.R | 93 +++++++++++++++++------ R/swfscAirDAS-package.R | 8 +- README.md | 12 +-- build/vignette.rds |binary inst/doc/swfscAirDAS.R | 2 inst/doc/swfscAirDAS.Rmd | 2 inst/doc/swfscAirDAS.html | 172 ++++++++++++++++++++++--------------------- man/airdas_effort.Rd | 22 +++-- man/airdas_read.Rd | 7 + man/airdas_sight.Rd | 31 +++++-- tests/testthat/test-output.R | 6 + vignettes/swfscAirDAS.Rmd | 2 19 files changed, 279 insertions(+), 186 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://wikis.ec.europa.eu/pages/viewpage.action?pageId=44165555>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.20.6 dated 2023-03-09 and 0.21.2 dated 2023-08-08
DESCRIPTION | 14 +-- MD5 | 26 +++-- NAMESPACE | 1 NEWS.md | 23 ++++- R/extract_data.R | 2 R/get_eurostat_codelist.R |only R/get_eurostat_data.R | 188 ++++++++++++++++++++++++++--------------- R/get_eurostat_dsd.R | 17 ++- R/get_eurostat_raw.R | 72 +++++++++++++-- inst/tinytest/test_restatapi.R | 76 +++++++++++----- man/extract_data.Rd | 2 man/get_eurostat_codelist.Rd |only man/get_eurostat_data.Rd | 4 man/get_eurostat_dsd.Rd | 4 man/get_eurostat_raw.Rd | 10 +- 15 files changed, 308 insertions(+), 131 deletions(-)
Title: Logic Regression
Description: Routines for fitting Logic Regression models. Logic Regression is described
in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte
Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005)
<DOI:10.1002/gepi.20042>.
Author: Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski <ingo@jhu.edu>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between LogicReg versions 1.6.5 dated 2022-10-31 and 1.6.6 dated 2023-08-08
DESCRIPTION | 8 - MD5 | 10 +- src/external.f | 2 src/sextra.f | 10 +- src/slogic.f | 274 ++++++++++++++++++++++++++++----------------------------- src/trioLR.f | 12 +- 6 files changed, 158 insertions(+), 158 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Demirhan (2020)(<doi:10.1371/journal.pone.0228812>) and Baltagi (2011)(<doi:10.1007/978-3-642-20059-5>) for more information.
Author: Haydar Demirhan [aut, cre, cph]
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.1.8 dated 2022-05-10 and 1.1.12 dated 2023-08-08
DESCRIPTION | 10 +++++----- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 5 +++++ NEWS.md | 4 ++++ R/ardlDlm.R | 2 +- R/ardlDlm.default.R | 2 +- R/ardlDlm.main.R | 1 + R/ardlDlmForecast.main.R | 2 +- R/dlm.R | 2 +- R/dlm.default.R | 2 +- R/dlm.main.R | 6 ++++-- R/dlmForecast.main.R | 13 +++++++++++-- R/finiteDLMauto.R | 2 +- R/finiteDLMauto.default.R | 2 +- R/finiteDLMauto.main.R | 1 + R/koyckDlm.main.R | 1 + R/polyDlm.main.R | 1 + README.md | 2 ++ inst/CITATION | 2 +- man/ardlDlm.Rd | 5 ++++- man/dLagM-package.Rd | 4 ++-- man/dlm.Rd | 5 ++++- man/finiteDLMauto.Rd | 6 ++++-- 23 files changed, 79 insertions(+), 45 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] ,
Marcel Ramos [aut, cre]
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.21.1 dated 2023-07-18 and 1.30.22 dated 2023-08-08
DESCRIPTION | 6 - MD5 | 20 +++--- NEWS | 13 +++- R/install.R | 4 - R/repositories.R | 23 ++++--- R/valid.R | 2 build/vignette.rds |binary inst/doc/BiocManager.Rmd | 4 - inst/doc/BiocManager.html | 18 ++--- tests/testthat/test_repositories.R | 118 +++++++++++++++++++++++++------------ vignettes/BiocManager.Rmd | 4 - 11 files changed, 135 insertions(+), 77 deletions(-)
Title: Aggregation Trees
Description: Nonparametric data-driven approach to discovering heterogeneous subgroups in a selection-on-observables framework.
Aggregation trees allow researchers to assess whether there is relevant heterogeneity in treatment effects. The approach
generates a sequence of optimal groupings, one for each level of granularity. For each grouping, we obtain point estimation
and inference about the Group Average Treatment Effects. Please reference the use as Di Francesco (2022) <doi:10.2139/ssrn.4304256>.
Author: Riccardo Di Francesco [aut, cre]
Maintainer: Riccardo Di Francesco <difrancesco.riccardo96@gmail.com>
Diff between aggTrees versions 2.0.0 dated 2023-02-21 and 2.0.1 dated 2023-08-08
DESCRIPTION | 12 - LICENSE | 4 MD5 | 66 +++--- NAMESPACE | 56 ++--- NEWS.md | 14 - R/aggregation-trees.R | 35 ++- R/balance-measures.R | 12 - R/generic-s3.R | 21 +- R/rpart-functions.R | 106 ++++++++-- R/utils.R | 39 ++- README.md | 105 ++-------- build/vignette.rds |only inst |only man/avg_characteristics_rpart.Rd | 122 +++++------ man/balance_measures.Rd | 110 +++++----- man/build_aggtree.Rd | 409 +++++++++++++++++++-------------------- man/causal_ols_rpart.Rd | 257 +++++++++++++----------- man/descriptive_arm.Rd | 45 ++-- man/dr_scores.Rd | 58 ++--- man/estimate_rpart.Rd | 180 ++++++++--------- man/expand_df.Rd | 61 +++-- man/figures |only man/get_leaves.Rd | 88 ++++---- man/leaf_membership.Rd | 94 ++++---- man/log_ratio_sd.Rd | 47 ++-- man/node_membership.Rd | 98 ++++----- man/normalized_diff.Rd | 49 ++-- man/plot.aggTrees.Rd | 128 ++++++------ man/print.aggTrees.Rd | 60 ++--- man/print.aggTrees.inference.Rd | 136 ++++++------ man/rename_latex.Rd | 35 +-- man/sample_split.Rd | 44 ++-- man/subtree.Rd | 96 ++++----- man/summary.aggTrees.Rd | 60 ++--- vignettes |only 35 files changed, 1381 insertions(+), 1266 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear
programming (MILP). It provides a flexible interface for building and
solving conservation planning problems. Once built, conservation planning
problems can be solved using a variety of commercial and open-source exact
algorithm solvers. By using exact algorithm solvers, solutions can be
generated that are guaranteed to be optimal (or within a pre-specified
optimality gap). Furthermore, conservation problems can be constructed to
optimize the spatial allocation of different management actions or zones,
meaning that conservation practitioners can identify solutions that benefit
multiple stakeholders. To solve large-scale or complex conservation
planning problems, users should install the Gurobi optimization software
(available from <https://www.gurobi.com/>) and the 'gurobi' R package (see
Gurobi Installation Guide vignette for details). Users can also install the
IBM CPLEX software (<https://www.ibm.com/products [...truncated...]
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Brandon P M Edwards [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 8.0.2 dated 2023-05-01 and 8.0.3 dated 2023-08-08
DESCRIPTION | 16 MD5 | 823 +-- NAMESPACE | 481 +- NEWS.md | 3029 ++++++------- R/ConservationModifier-class.R | 230 R/ConservationProblem-class.R | 1984 ++++---- R/Constraint-class.R | 64 R/Decision-class.R | 64 R/Objective-class.R | 80 R/OptimizationProblem-class.R | 408 - R/OptimizationProblem-methods.R | 542 +- R/Penalty-class.R | 64 R/Portfolio-class.R | 66 R/RcppExports.R | 406 - R/Solver-class.R | 166 R/Target-class.R | 62 R/add_absolute_targets.R | 648 +- R/add_asym_connectivity_penalties.R | 778 +-- R/add_binary_decisions.R | 192 R/add_boundary_penalties.R | 896 +-- R/add_cbc_solver.R | 568 +- R/add_compile_solver.R | 112 R/add_connectivity_penalties.R | 1195 ++--- R/add_contiguity_constraints.R | 760 +-- R/add_cplex_solver.R | 650 +- R/add_cuts_portfolio.R | 280 - R/add_default_solver.R | 230 R/add_extra_portfolio.R | 270 - R/add_feature_contiguity_constraints.R | 902 +-- R/add_feature_weights.R | 710 +-- R/add_gap_portfolio.R | 360 - R/add_gurobi_solver.R | 666 +- R/add_highs_solver.R | 418 - R/add_linear_constraints.R | 882 +-- R/add_linear_penalties.R | 860 +-- R/add_locked_in_constraints.R | 978 ++-- R/add_locked_out_constraints.R | 840 +-- R/add_loglinear_targets.R | 352 - R/add_lpsymphony_solver.R | 462 - R/add_mandatory_allocation_constraints.R | 206 R/add_manual_bounded_constraints.R | 520 +- R/add_manual_locked_constraints.R | 540 +- R/add_manual_targets.R | 750 +-- R/add_max_cover_objective.R | 396 - R/add_max_features_objective.R | 330 - R/add_max_phylo_div_objective.R | 548 +- R/add_max_phylo_end_objective.R | 634 +- R/add_max_utility_objective.R | 322 - R/add_min_largest_shortfall_objective.R | 326 - R/add_min_set_objective.R | 256 - R/add_min_shortfall_objective.R | 338 - R/add_neighbor_constraints.R | 870 +-- R/add_proportion_decisions.R | 178 R/add_relative_targets.R | 460 - R/add_rsymphony_solver.R | 430 - R/add_semicontinuous_decisions.R | 210 R/add_shuffle_portfolio.R | 380 - R/add_top_portfolio.R | 292 - R/adjacency_matrix.R | 386 - R/all_binary.R | 148 R/all_columns_any_finite.R | 122 R/all_columns_inherit.R | 122 R/all_finite.R | 176 R/all_positive.R | 170 R/all_proportion.R | 124 R/any_nonNA.R | 212 R/any_nonzero.R | 172 R/as.R | 84 R/as_Matrix.R | 124 R/assertions.R | 406 - R/assertions_class.R | 400 - R/assertions_misc.R | 182 R/assertions_raster.R | 170 R/assertions_sf.R | 56 R/assertions_vector.R | 238 - R/binary_stack.R | 154 R/boundary_matrix.R | 460 - R/branch_matrix.R | 122 R/category_layer.R | 138 R/category_vector.R | 170 R/cli.R | 388 - R/compile.R | 406 - R/connectivity_matrix.R | 670 +- R/constraints.R | 224 R/data.R | 652 +- R/decisions.R | 166 R/deprecated.R | 418 - R/eval_asym_connectivity_summary.R | 664 +- R/eval_boundary_summary.R | 550 +- R/eval_connectivity_summary.R | 656 +- R/eval_cost_summary.R | 372 - R/eval_feature_representation_summary.R | 570 +- R/eval_ferrier_importance.R | 958 ++-- R/eval_n_summary.R | 316 - R/eval_rare_richness_importance.R | 774 +-- R/eval_replacement_importance.R | 1314 ++--- R/eval_target_coverage_summary.R | 648 +- R/external-classes.R | 54 R/fast_extract.R | 384 - R/feature_abundances.R | 384 - R/feature_names.R | 142 R/get_crs.R | 104 R/importance.R | 246 - R/internal.R | 212 R/intersecting_units.R | 480 +- R/is_numeric_values.R | 118 R/is_same_crs.R | 96 R/is_spatial_extents_overlap.R | 124 R/knit_print.R | 102 R/list_text.R | 68 R/loglinear_interpolation.R | 228 R/marxan_boundary_data_to_matrix.R | 144 R/marxan_connectivity_data_to_matrix.R | 436 - R/marxan_problem.R | 906 +-- R/number_of_features.R | 140 R/number_of_planning_units.R | 114 R/number_of_total_units.R | 138 R/number_of_zones.R | 146 R/objectives.R | 226 R/optimization_problem.R | 296 - R/package.R | 188 R/penalties.R | 200 R/planning_unit_solution_status.R | 1154 ++-- R/portfolios.R | 220 R/presolve_check.R | 1206 ++--- R/print.R | 68 R/problem-deprecated.R | 818 +-- R/problem.R | 2363 +++++----- R/proximity_matrix.R | 382 - R/reexports.R | 70 R/repr.R | 476 +- R/rescale_matrix.R |only R/rij_matrix.R | 398 - R/run_calculations.R | 190 R/show.R | 104 R/simulate.R | 494 +- R/solve.R | 837 +-- R/solvers.R | 316 - R/st_geometry_classes.R | 32 R/summaries.R | 204 R/summary.R | 14 R/targets.R | 148 R/tbl_df.R | 140 R/test-helpers.R | 296 - R/waiver.R | 94 R/write_problem.R | 224 R/zone_names.R | 140 R/zones.R | 542 +- R/zzz.R | 120 README.md | 1140 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/calibrating_trade-offs_tutorial.Rmd | 1423 +++--- inst/doc/calibrating_trade-offs_tutorial.html | 162 inst/doc/connectivity_tutorial.Rmd | 1021 ++-- inst/doc/connectivity_tutorial.html | 45 inst/doc/gurobi_installation_guide.Rmd | 366 - inst/doc/management_zones_tutorial.Rmd | 788 +-- inst/doc/package_overview.Rmd | 2088 ++++---- inst/doc/package_overview.html | 6 inst/doc/prioritizr.Rmd | 635 +- inst/doc/prioritizr.html | 2 inst/doc/publication_record.Rmd | 235 - inst/doc/publication_record.html | 34 inst/doc/solver_benchmarks.Rmd | 1158 ++-- inst/extdata/marxan/input.dat | 110 inst/extdata/sim_phylogeny.txt | 46 inst/knitr/print.Rmd | 18 man/ConservationModifier-class.Rd | 466 +- man/ConservationProblem-class.Rd | 1246 ++--- man/Constraint-class.Rd | 170 man/Decision-class.Rd | 170 man/Objective-class.Rd | 212 man/OptimizationProblem-class.Rd | 720 +-- man/OptimizationProblem-methods.Rd | 268 - man/Penalty-class.Rd | 170 man/Portfolio-class.Rd | 174 man/Solver-class.Rd | 344 - man/Target-class.Rd | 156 man/add_absolute_targets.Rd | 362 - man/add_asym_connectivity_penalties.Rd | 610 +- man/add_binary_decisions.Rd | 166 man/add_boundary_penalties.Rd | 540 +- man/add_cbc_solver.Rd | 438 - man/add_connectivity_penalties.Rd | 855 +-- man/add_contiguity_constraints.Rd | 478 +- man/add_cplex_solver.Rd | 258 - man/add_cuts_portfolio.Rd | 208 man/add_default_solver.Rd | 90 man/add_extra_portfolio.Rd | 180 man/add_feature_contiguity_constraints.Rd | 508 +- man/add_feature_weights.Rd | 504 +- man/add_gap_portfolio.Rd | 218 man/add_gurobi_solver.Rd | 490 +- man/add_highs_solver.Rd | 192 man/add_linear_constraints.Rd | 590 +- man/add_linear_penalties.Rd | 498 +- man/add_locked_in_constraints.Rd | 552 +- man/add_locked_out_constraints.Rd | 558 +- man/add_loglinear_targets.Rd | 264 - man/add_lsymphony_solver.Rd | 250 - man/add_mandatory_allocation_constraints.Rd | 174 man/add_manual_bounded_constraints.Rd | 338 - man/add_manual_locked_constraints.Rd | 334 - man/add_manual_targets.Rd | 550 +- man/add_max_cover_objective.Rd | 354 - man/add_max_features_objective.Rd | 288 - man/add_max_phylo_div_objective.Rd | 480 +- man/add_max_phylo_end_objective.Rd | 486 +- man/add_max_utility_objective.Rd | 274 - man/add_min_largest_shortfall_objective.Rd | 286 - man/add_min_set_objective.Rd | 226 man/add_min_shortfall_objective.Rd | 280 - man/add_neighbor_constraints.Rd | 437 - man/add_proportion_decisions.Rd | 164 man/add_relative_targets.Rd | 346 - man/add_rsymphony_solver.Rd | 218 man/add_semicontinuous_decisions.Rd | 178 man/add_shuffle_portfolio.Rd | 210 man/add_top_portfolio.Rd | 186 man/adjacency_matrix.Rd | 200 man/binary_stack.Rd | 106 man/boundary_matrix.Rd | 206 man/branch_matrix.Rd | 88 man/category_layer.Rd | 112 man/category_vector.Rd | 106 man/compile.Rd | 130 man/connectivity_matrix.Rd | 380 - man/constraints.Rd | 246 - man/decisions.Rd | 186 man/eval_asym_connectivity_summary.Rd | 614 +- man/eval_boundary_summary.Rd | 644 +- man/eval_connectivity_summary.Rd | 608 +- man/eval_cost_summary.Rd | 460 - man/eval_feature_representation_summary.Rd | 628 +- man/eval_ferrier_importance.Rd | 422 - man/eval_n_summary.Rd | 430 - man/eval_rare_richness_importance.Rd | 440 - man/eval_replacement_importance.Rd | 598 +- man/eval_target_coverage_summary.Rd | 624 +- man/fast_extract.Rd | 144 man/feature_abundances.Rd | 332 - man/feature_names.Rd | 96 man/figures/README-boundary_penalties-1.png |binary man/figures/README-importance-1.png |binary man/figures/README-locked_in_constraints-1.png |binary man/figures/README-locked_in_constraints-2.png |binary man/figures/README-locked_out_constraints-1.png |binary man/figures/README-locked_out_constraints-2.png |binary man/figures/README-minimal_solution-1.png |binary man/importance.Rd | 264 - man/intersecting_units.Rd | 186 man/knit_print.Rd | 58 man/loglinear_interpolation.Rd | 192 man/marxan_boundary_data_to_matrix.Rd | 96 man/marxan_connectivity_data_to_matrix.Rd | 184 man/marxan_problem.Rd | 432 - man/new_waiver.Rd | 58 man/number_of_features.Rd | 102 man/number_of_planning_units.Rd | 100 man/number_of_total_units.Rd | 128 man/number_of_zones.Rd | 106 man/objectives.Rd | 246 - man/optimization_problem.Rd | 192 man/penalties.Rd | 222 man/portfolios.Rd | 238 - man/presolve_check.Rd | 382 - man/prioritizr-deprecated.Rd | 236 - man/prioritizr.Rd | 166 man/problem.Rd | 1088 ++-- man/proximity_matrix.Rd | 218 man/reexports.Rd | 34 man/rescale_matrix.Rd |only man/rij_matrix.Rd | 186 man/run_calculations.Rd | 178 man/show.Rd | 62 man/sim_data.Rd | 470 +- man/simulate_cost.Rd | 114 man/simulate_data.Rd | 148 man/simulate_species.Rd | 102 man/solve.Rd | 446 - man/solvers.Rd | 336 - man/summaries.Rd | 222 man/targets.Rd | 170 man/tibble-methods.Rd | 104 man/write_problem.Rd | 116 man/zone_names.Rd | 100 man/zones.Rd | 268 - src/RcppExports.cpp | 4 src/rcpp_apply_neighbor_constraints.cpp | 10 tests/testthat.R | 54 tests/testthat/_snaps/assertions.md | 504 +- tests/testthat/helper_asym_connectivity.R | 126 tests/testthat/helper_boundary.R | 168 tests/testthat/helper_connectivity.R | 116 tests/testthat/helper_ferrier_scores.R | 456 - tests/testthat/helper_raster.R | 140 tests/testthat/helper_sf.R | 32 tests/testthat/helper_skip.R | 160 tests/testthat/setup.R | 8 tests/testthat/test_ConservationModifier.R | 40 tests/testthat/test_OptimizationProblem.R | 278 - tests/testthat/test_Waiver.R | 16 tests/testthat/test_add_absolute_targets.R | 608 +- tests/testthat/test_add_asym_connectivity_penalties.R | 1154 ++-- tests/testthat/test_add_boundary_penalties.R | 1136 ++-- tests/testthat/test_add_cbc_solver.R | 576 +- tests/testthat/test_add_connectivity_penalties.R | 686 +- tests/testthat/test_add_contiguity_constraints.R | 606 +- tests/testthat/test_add_cplex_solver.R | 378 - tests/testthat/test_add_cuts_portfolio.R | 266 - tests/testthat/test_add_default_solver.R | 36 tests/testthat/test_add_extra_portfolio.R | 184 tests/testthat/test_add_feature_contiguity_constraints.R | 1024 ++-- tests/testthat/test_add_feature_weights.R | 1076 ++-- tests/testthat/test_add_gap_portfolio.R | 192 tests/testthat/test_add_gurobi_solver.R | 576 +- tests/testthat/test_add_highs_solver.R | 524 +- tests/testthat/test_add_linear_constraints.R | 1260 ++--- tests/testthat/test_add_linear_penalties.R | 1134 ++-- tests/testthat/test_add_locked_in_constraints.R | 1506 +++--- tests/testthat/test_add_locked_out_constraints.R | 1250 ++--- tests/testthat/test_add_loglinear_targets.R | 212 tests/testthat/test_add_lpsymphony_solver.R | 400 - tests/testthat/test_add_mandatory_allocation_constraints.R | 416 - tests/testthat/test_add_manual_bounded_constraints.R | 623 +- tests/testthat/test_add_manual_locked_constraints.R | 618 +- tests/testthat/test_add_manual_targets.R | 576 +- tests/testthat/test_add_max_cover_objective.R | 1268 ++--- tests/testthat/test_add_max_features_objective.R | 1510 +++--- tests/testthat/test_add_max_phylo_div_objective.R | 1992 ++++---- tests/testthat/test_add_max_phylo_end_objective.R | 2110 ++++----- tests/testthat/test_add_max_utility_objective.R | 1334 ++--- tests/testthat/test_add_min_largest_shortfall_objective.R | 1360 ++--- tests/testthat/test_add_min_set_objective.R | 766 +-- tests/testthat/test_add_min_shortfall_objective.R | 1536 +++--- tests/testthat/test_add_neighbor_constraints.R | 685 +- tests/testthat/test_add_relative_targets.R | 516 +- tests/testthat/test_add_rsymphony_solver.R | 400 - tests/testthat/test_add_shuffle_portfolio.R | 334 - tests/testthat/test_add_top_portfolio.R | 188 tests/testthat/test_adjacency_matrix.R | 290 - tests/testthat/test_all_binary.R | 222 tests/testthat/test_all_columns_any_finite.R | 154 tests/testthat/test_all_columns_inherit.R | 128 tests/testthat/test_all_finite.R | 212 tests/testthat/test_all_positive.R | 256 - tests/testthat/test_all_proportion.R | 148 tests/testthat/test_any_nonNA.R | 310 - tests/testthat/test_any_nonzero.R | 272 - tests/testthat/test_as_Matrix.R | 56 tests/testthat/test_assertions.R | 512 +- tests/testthat/test_assertions_class.R | 78 tests/testthat/test_assertions_misc.R | 74 tests/testthat/test_assertions_raster.R | 150 tests/testthat/test_assertions_sf.R | 24 tests/testthat/test_assertions_vector.R | 80 tests/testthat/test_binary_stack.R | 60 tests/testthat/test_boundary_matrix.R | 718 +-- tests/testthat/test_branch_matrix.R | 80 tests/testthat/test_category_layer.R | 70 tests/testthat/test_category_vector.R | 112 tests/testthat/test_compile.R | 304 - tests/testthat/test_connectivity_matrix.R | 362 - tests/testthat/test_cplex.R | 298 - tests/testthat/test_decisions.R | 542 +- tests/testthat/test_documentation.R | 14 tests/testthat/test_eval_asym_connectivity_summary.R | 612 +- tests/testthat/test_eval_boundary_summary.R | 732 +-- tests/testthat/test_eval_connectivity_summary.R | 616 +- tests/testthat/test_eval_cost_summary.R | 254 - tests/testthat/test_eval_feature_representation_summary.R | 1272 ++--- tests/testthat/test_eval_ferrier_importance.R | 696 +- tests/testthat/test_eval_n_summary.R | 206 tests/testthat/test_eval_rare_richness_importance.R | 788 +-- tests/testthat/test_eval_replacement_importance.R | 1350 ++--- tests/testthat/test_eval_target_coverage_summary.R | 666 +- tests/testthat/test_fast_extract.R | 470 +- tests/testthat/test_feature_abundances.R | 668 +- tests/testthat/test_get_crs.R | 94 tests/testthat/test_helper_raster.R | 134 tests/testthat/test_internal.R | 46 tests/testthat/test_intersecting_units.R | 326 - tests/testthat/test_is_numeric_values.R | 116 tests/testthat/test_is_spatial_extents_overlap.R | 312 - tests/testthat/test_marxan_boundary_data_to_matrix.R | 96 tests/testthat/test_marxan_connectivity_data_to_matrix.R | 374 - tests/testthat/test_marxan_problem.R | 870 +-- tests/testthat/test_planning_unit_solution_status.R | 820 +-- tests/testthat/test_presolve_check.R | 642 +- tests/testthat/test_prioritizrdata.R | 138 tests/testthat/test_problem-deprecated.R | 1592 +++--- tests/testthat/test_problem.R | 2724 ++++++----- tests/testthat/test_problem_negative.R | 2338 +++++----- tests/testthat/test_proximity_matrix.R | 748 +-- tests/testthat/test_repr.R | 184 tests/testthat/test_rescale_matrix.R |only tests/testthat/test_rij_matrix.R | 564 +- tests/testthat/test_run_calculations.R | 50 tests/testthat/test_simulate.R | 228 tests/testthat/test_solve.R | 1208 ++--- tests/testthat/test_st_geometry_classes.R | 76 tests/testthat/test_write_problem.R | 172 tests/testthat/test_zones.R | 178 vignettes/calibrating_trade-offs_tutorial.Rmd | 1423 +++--- vignettes/connectivity_tutorial.Rmd | 1021 ++-- vignettes/gurobi_installation_guide.Rmd | 366 - vignettes/management_zones_tutorial.Rmd | 788 +-- vignettes/package_overview.Rmd | 2088 ++++---- vignettes/prioritizr.Rmd | 635 +- vignettes/publication_record.Rmd | 235 - vignettes/reference-style.csl | 402 - vignettes/references.bib | 1366 ++--- vignettes/solver_benchmarks.Rmd | 1158 ++-- 414 files changed, 88058 insertions(+), 87467 deletions(-)
Title: Analyze Dependency Heaviness of R Packages
Description: A new metric named 'dependency heaviness' is proposed that measures the number
of additional dependency packages that a parent package brings to its child package
and are unique to the dependency packages imported by all other parents.
The dependency heaviness analysis is visualized by a customized heatmap.
The package is described in <doi:10.1093/bioinformatics/btac449>.
We have also performed the dependency heaviness analysis on the CRAN/Bioconductor
package ecosystem and the results are implemented as a web-based database
which provides comprehensive tools for querying dependencies of individual R packages.
The systematic analysis on the CRAN/Bioconductor ecosystem is described in
<doi:10.1016/j.jss.2023.111610>. From 'pkgndep' version 2.0.0, the heaviness
database includes snapshots of the CRAN/Bioconductor ecosystems for many old R versions.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between pkgndep versions 1.2.1 dated 2022-11-15 and 1.99.2 dated 2023-08-08
pkgndep-1.2.1/pkgndep/R/stat.R |only pkgndep-1.2.1/pkgndep/R/version.R |only pkgndep-1.2.1/pkgndep/man/heaviness_db.Rd |only pkgndep-1.2.1/pkgndep/man/load_from_pkgndep_db.Rd |only pkgndep-1.2.1/pkgndep/man/pkgndep.Rd |only pkgndep-1.2.1/pkgndep/man/print.heaviness_db_info.Rd |only pkgndep-1.99.2/pkgndep/DESCRIPTION | 19 pkgndep-1.99.2/pkgndep/LICENSE | 2 pkgndep-1.99.2/pkgndep/MD5 | 151 ++-- pkgndep-1.99.2/pkgndep/NAMESPACE | 12 pkgndep-1.99.2/pkgndep/NEWS | 6 pkgndep-1.99.2/pkgndep/R/db.R | 113 ++- pkgndep-1.99.2/pkgndep/R/dependency.R | 87 +- pkgndep-1.99.2/pkgndep/R/global.R | 92 ++ pkgndep-1.99.2/pkgndep/R/heaviness.R |only pkgndep-1.99.2/pkgndep/R/load_data.R | 228 +++++- pkgndep-1.99.2/pkgndep/R/load_pkg.R | 4 pkgndep-1.99.2/pkgndep/R/pkgndep.R | 224 ++++-- pkgndep-1.99.2/pkgndep/R/plot.R | 140 ++- pkgndep-1.99.2/pkgndep/R/report.R | 19 pkgndep-1.99.2/pkgndep/R/utils.R |only pkgndep-1.99.2/pkgndep/R/website.R | 48 - pkgndep-1.99.2/pkgndep/R/zzz.R | 9 pkgndep-1.99.2/pkgndep/inst/CITATION | 24 pkgndep-1.99.2/pkgndep/inst/doc/co_heaviness.R | 3 pkgndep-1.99.2/pkgndep/inst/doc/co_heaviness.Rmd | 5 pkgndep-1.99.2/pkgndep/inst/doc/co_heaviness.html | 15 pkgndep-1.99.2/pkgndep/inst/doc/database.Rmd | 2 pkgndep-1.99.2/pkgndep/inst/doc/database.html | 2 pkgndep-1.99.2/pkgndep/inst/doc/pkgndep.R | 7 pkgndep-1.99.2/pkgndep/inst/doc/pkgndep.Rmd | 14 pkgndep-1.99.2/pkgndep/inst/doc/pkgndep.html | 105 +- pkgndep-1.99.2/pkgndep/inst/doc/suggestions.Rmd | 2 pkgndep-1.99.2/pkgndep/inst/doc/suggestions.html | 15 pkgndep-1.99.2/pkgndep/inst/extdata/DESeq2_dep.rds |only pkgndep-1.99.2/pkgndep/inst/extdata/analysis.R | 361 ++++++---- pkgndep-1.99.2/pkgndep/inst/extdata/lt_history.R |only pkgndep-1.99.2/pkgndep/inst/extdata/timeline.R |only pkgndep-1.99.2/pkgndep/inst/website/app.R | 248 ++++++ pkgndep-1.99.2/pkgndep/inst/website/lib.R | 305 ++++++-- pkgndep-1.99.2/pkgndep/inst/website/template/child_dependency.html | 31 pkgndep-1.99.2/pkgndep/inst/website/template/dependency_table.html | 107 ++ pkgndep-1.99.2/pkgndep/inst/website/template/downstream_dependency.html | 9 pkgndep-1.99.2/pkgndep/inst/website/template/footer.html | 5 pkgndep-1.99.2/pkgndep/inst/website/template/global_heaviness_analysis.html | 103 -- pkgndep-1.99.2/pkgndep/inst/website/template/header.html | 27 pkgndep-1.99.2/pkgndep/inst/website/template/package.html | 16 pkgndep-1.99.2/pkgndep/inst/website/template/parent_dependency.html | 27 pkgndep-1.99.2/pkgndep/inst/website/template/timeline.html |only pkgndep-1.99.2/pkgndep/inst/website/template/upstream_dependency.html | 7 pkgndep-1.99.2/pkgndep/inst/www/_css/pkgndep.css | 95 ++ pkgndep-1.99.2/pkgndep/inst/www/_image |only pkgndep-1.99.2/pkgndep/inst/www/_js/pkgndep.js | 36 pkgndep-1.99.2/pkgndep/man/ALL_BIOC_RELEASES.Rd |only pkgndep-1.99.2/pkgndep/man/all_pkg_stat_snapshot.Rd | 2 pkgndep-1.99.2/pkgndep/man/child_dependency.Rd | 10 pkgndep-1.99.2/pkgndep/man/co_heaviness.Rd | 3 pkgndep-1.99.2/pkgndep/man/dependency_database.Rd | 12 pkgndep-1.99.2/pkgndep/man/dependency_report.Rd | 20 pkgndep-1.99.2/pkgndep/man/dependency_website.Rd | 12 pkgndep-1.99.2/pkgndep/man/downstream_dependency.Rd | 4 pkgndep-1.99.2/pkgndep/man/get_all_functions_imported_to_children.Rd | 15 pkgndep-1.99.2/pkgndep/man/heaviness_database.Rd |only pkgndep-1.99.2/pkgndep/man/heaviness_from_upstream.Rd | 3 pkgndep-1.99.2/pkgndep/man/heaviness_on_children.Rd | 6 pkgndep-1.99.2/pkgndep/man/heaviness_on_downstream.Rd | 8 pkgndep-1.99.2/pkgndep/man/heaviness_report.Rd |only pkgndep-1.99.2/pkgndep/man/is_upstream.Rd | 4 pkgndep-1.99.2/pkgndep/man/load_all_pkg_dep.Rd | 6 pkgndep-1.99.2/pkgndep/man/load_from_heaviness_db.Rd |only pkgndep-1.99.2/pkgndep/man/load_heaviness_timeline.Rd |only pkgndep-1.99.2/pkgndep/man/load_pkg_db.Rd | 8 pkgndep-1.99.2/pkgndep/man/load_pkg_description.Rd |only pkgndep-1.99.2/pkgndep/man/load_pkg_downstream_dependency_path_snapshot.Rd | 2 pkgndep-1.99.2/pkgndep/man/load_pkg_namespace.Rd |only pkgndep-1.99.2/pkgndep/man/load_pkg_stat_snapshot.Rd | 4 pkgndep-1.99.2/pkgndep/man/parent_dependency.Rd | 10 pkgndep-1.99.2/pkgndep/man/pkgndep.rd |only pkgndep-1.99.2/pkgndep/man/pkgndep_opt.Rd | 3 pkgndep-1.99.2/pkgndep/man/plot.pkgndep.Rd | 7 pkgndep-1.99.2/pkgndep/man/reformat_db.Rd | 5 pkgndep-1.99.2/pkgndep/man/upstream_dependency.Rd | 4 pkgndep-1.99.2/pkgndep/tests/testthat/test_pkgndep.R | 2 pkgndep-1.99.2/pkgndep/vignettes/co_heaviness.Rmd | 5 pkgndep-1.99.2/pkgndep/vignettes/database.Rmd | 2 pkgndep-1.99.2/pkgndep/vignettes/pkgndep.Rmd | 14 pkgndep-1.99.2/pkgndep/vignettes/suggestions.Rmd | 2 87 files changed, 2061 insertions(+), 837 deletions(-)
Title: Neo-Normal Distributions Family for Markov Chain Monte Carlo
(MCMC) Models in 'JAGS'
Description: A 'JAGS' extension module provides neo-normal distributions
family including MSNBurr, MSNBurr-IIa, GMSNBurr, Lunetta Exponential Power,
Fernandez-Steel Skew t, Fernandez-Steel Skew Normal, Fernandez-Osiewalski-Steel
Skew Exponential Power, Jones Skew Exponential Power.
References:
Choir, A. S. (2020). "The New Neo-Normal Distributions and Their Properties".Unpublished Dissertation.
Denwood, M.J. (2016) <doi:10.18637/jss.v071.i09>.
Fernandez, C., Osiewalski, J., & Steel, M. F. (1995) <doi:10.1080/01621459.1995.10476637>.
Fernandez, C., & Steel, M. F. (1998) <doi:10.1080/01621459.1998.10474117>.
Iriawan, N. (2000). "Computationally Intensive Approaches to Inference in NeoNormal Linear Models".Unpublished Dissertation.
Mineo, A., & Ruggieri, M. (2005) <doi:10.18637/jss.v012.i04>.
Rigby, R. A., & Stasinopoulos, D. M. (2005) <doi:10.1111/j.1467-9876.2005.00510.x>.
Lunetta, G. (1963). "Di una Generalizzazione dello Schema della Curva Normale".
Ri [...truncated...]
Author: Achmad Syahrul Choir [aut, cre],
Resi Ramadani [aut],
Nur Iriawan [aut],
S Sifa'ul Khusna Malikhatul Mutmainah [ctb],
Matthew Denwood [cph],
Martyn Plummer [cph]
Maintainer: Achmad Syahrul Choir <madsyair@stis.ac.id>
Diff between neojags versions 0.1.3 dated 2023-07-05 and 0.1.4 dated 2023-08-08
CHANGELOG | 3 +++ DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ R/load.module.neojags.R | 2 +- R/utilities.invisible.R | 2 +- README.md |only inst/doc/vignettes.html | 18 +++++++++--------- man/load.neojagsmodule.Rd | 2 +- 8 files changed, 25 insertions(+), 21 deletions(-)
Title: Implementation of Remez Algorithm for Polynomial and Rational
Function Approximation
Description: Implements the algorithm of Remez (1962) for polynomial minimax
approximation and of Cody et al. (1968) <doi:10.1007/BF02162506> for
rational minimax approximation.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between minimaxApprox versions 0.0.2 dated 2023-07-20 and 0.1.0 dated 2023-08-08
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 35 +++++++++++++++++++---------------- R/MiniMaxApprox.R | 16 +++++++++------- R/RemezPolynomial.R | 5 ++--- R/RemezRational.R | 8 +++----- R/compensatedHorner.R |only R/methods.R | 11 +++++++---- R/shared.R | 37 +++++++++++++++++++++++-------------- README.md | 14 +++++++------- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 33 ++++++++++++++++++++++++++++++--- inst/tinytest/test_MiniMaxApprox.R | 24 ++++++++++++++++-------- inst/tinytest/test_horner.R |only inst/tinytest/test_shared.R | 23 ++++++++++++++++++----- inst/tinytest/test_version.R | 4 ++-- man/MiniMaxApprox.Rd | 37 +++++++++++++++++++++++++++++++------ man/minimaxApprox-internal.Rd | 7 +++++++ man/minimaxEval.Rd | 3 ++- 20 files changed, 182 insertions(+), 87 deletions(-)
Title: Liquid Chromatography/Mass Spectrometry (LC/MS) Quality
Assessment
Description: The goal of 'LCMSQA' is to make it easy to check the quality of
liquid chromatograph/mass spectrometry (LC/MS) experiments using a
'shiny' application. This package provides interactive data
visualizations for quality control (QC) samples, including total
ion current chromatogram (TIC), base peak chromatogram (BPC), mass
spectrum, extracted ion chromatogram (XIC), and feature detection
results from internal standards or known metabolites.
Author: Jaehyun Joo [aut, cre],
Blanca Himes [aut]
Maintainer: Jaehyun Joo <jaehyunjoo@outlook.com>
Diff between LCMSQA versions 1.0.0 dated 2023-03-16 and 1.0.1 dated 2023-08-08
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- NAMESPACE | 15 ++------------- R/LCMSQA-package.R | 10 +++------- R/feature_detection.R | 2 +- R/global.R | 14 ++++++++++++-- R/runQA.R | 2 ++ R/server.R | 32 ++++++++++++++++---------------- R/zzz.R | 17 ++++++++++++++++- build/vignette.rds |binary inst/doc/LCMSQA.Rmd | 2 +- inst/doc/LCMSQA.html | 2 +- man/LCMSQA-package.Rd | 4 ++-- vignettes/LCMSQA.Rmd | 2 +- 14 files changed, 76 insertions(+), 64 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 3.4.1 dated 2023-05-08 and 3.5.1 dated 2023-08-08
DESCRIPTION | 14 MD5 | 103 +- NEWS.md | 21 R/Olink_anova.R | 2 R/Olink_bridgeselector.R | 40 R/Olink_normalization.R | 46 R/Olink_one_non_parametric.R | 2 R/Olink_ordinalRegression.R | 2 R/Olink_plate_randomizer.R | 392 ++++++-- R/Olink_ttest.R | 2 R/Olink_wilcox.R | 3 R/Read_NPX_data.R | 419 ++++---- R/dist_plot.R | 18 R/globals.R | 6 R/npxProcessing.R | 19 R/olink_qc_plot.R | 30 R/pca_plot.R | 2 R/read_flex.R |only R/read_npx_csv.R |only R/read_npx_parquet.R |only R/read_npx_zip.R |only data/npx_data1.rda |binary data/npx_data2.rda |binary inst/doc/OutlierExclusion.R | 2 inst/doc/OutlierExclusion.Rmd | 2 inst/doc/OutlierExclusion.html | 186 +-- inst/doc/Vignett.R | 31 inst/doc/Vignett.Rmd | 31 inst/doc/Vignett.html | 564 +++++------ inst/doc/bridging_introduction.R | 113 +- inst/doc/bridging_introduction.Rmd | 177 ++- inst/doc/bridging_introduction.html | 1290 ++++++++++++++++++++------- inst/doc/plate_randomizer.R | 70 + inst/doc/plate_randomizer.Rmd | 81 + inst/doc/plate_randomizer.html | 366 +++++++ inst/extdata/npx_data1.xlsx |binary inst/extdata/npx_data_ext.parquet |only man/olink_displayPlateLayout.Rd | 9 man/olink_pca_plot.Rd | 2 man/olink_plate_randomizer.Rd | 9 man/olink_qc_plot.Rd | 2 man/read_flex.Rd |only man/read_npx_csv.Rd |only man/read_npx_parquet.Rd |only man/read_npx_zip.Rd |only tests/data/refResults.R | 13 tests/data/refResults.RData |binary tests/testthat/Rplots.pdf |only tests/testthat/_snaps/Olink_plate_randomizer |only tests/testthat/test-Olink_bridgeselector.R | 25 tests/testthat/test-Olink_normalization.R | 42 tests/testthat/test-Olink_plate_randomizer.R | 44 tests/testthat/test-Read_NPX_data.R | 16 tests/testthat/test-npxProcessing.R | 25 vignettes/OutlierExclusion.Rmd | 2 vignettes/Vignett.Rmd | 31 vignettes/bridging_introduction.Rmd | 177 ++- vignettes/plate_randomizer.Rmd | 81 + 58 files changed, 3156 insertions(+), 1356 deletions(-)
Title: Multiscale Inference for Nonparametric Time Trend(s)
Description: Performs a multiscale analysis of a nonparametric
regression or nonparametric regressions with time series errors. In case
of one regression, with the help of this package it is possible to detect
the regions where the trend function is increasing or decreasing.
In case of multiple regressions, the test identifies regions where
the trend functions are different from each other. See
Khismatullina and Vogt (2020) <doi:10.1111/rssb.12347>,
Khismatullina and Vogt (2022) <doi:10.48550/arXiv.2209.10841> and
Khismatullina and Vogt (2023) <doi:10.1016/j.jeconom.2021.04.010>
for more details on theory and applications.
Author: Marina Khismatullina [aut, cre],
Michael Vogt [aut]
Maintainer: Marina Khismatullina <khismatullina@ese.eur.nl>
Diff between MSinference versions 0.0.9 dated 2023-01-23 and 0.1.0 dated 2023-08-08
MSinference-0.0.9/MSinference/man/msinference-package.Rd |only MSinference-0.1.0/MSinference/DESCRIPTION | 8 +- MSinference-0.1.0/MSinference/MD5 | 27 +++++---- MSinference-0.1.0/MSinference/R/estimate_lrv.R | 6 +- MSinference-0.1.0/MSinference/R/msinference-package.R | 2 MSinference-0.1.0/MSinference/R/multiscale_test.R | 2 MSinference-0.1.0/MSinference/build/partial.rdb |binary MSinference-0.1.0/MSinference/build/vignette.rds |binary MSinference-0.1.0/MSinference/inst/doc/MSinference.R | 11 +-- MSinference-0.1.0/MSinference/inst/doc/MSinference.Rnw | 28 +++++----- MSinference-0.1.0/MSinference/inst/doc/MSinference.pdf |binary MSinference-0.1.0/MSinference/man/MSinference-package.Rd |only MSinference-0.1.0/MSinference/man/ar_coef.Rd | 2 MSinference-0.1.0/MSinference/man/corrections.Rd | 6 +- MSinference-0.1.0/MSinference/vignettes/MSinference-concordance.tex |only MSinference-0.1.0/MSinference/vignettes/MSinference.Rnw | 28 +++++----- 16 files changed, 60 insertions(+), 60 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R.
The corpus analysis platform 'KorAP' has been developed as a scientific tool to make
potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo'
or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify
hypotheses and to find interesting patterns in real language use.
The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code,
as a programmatic alternative to the 'KorAP' web user-interface.
You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 0.7.6 dated 2023-04-19 and 0.7.7 dated 2023-08-08
RKorAPClient-0.7.6/RKorAPClient/demo/Rmd/ca_files |only RKorAPClient-0.7.7/RKorAPClient/DESCRIPTION | 6 RKorAPClient-0.7.7/RKorAPClient/MD5 | 99 ------------ RKorAPClient-0.7.7/RKorAPClient/NEWS.md | 6 RKorAPClient-0.7.7/RKorAPClient/R/collocationAnalysis.R | 2 RKorAPClient-0.7.7/RKorAPClient/demo/00Index | 4 RKorAPClient-0.7.7/RKorAPClient/demo/adjectiveCollocates.R |only RKorAPClient-0.7.7/RKorAPClient/demo/displayKwics.R | 95 ++--------- RKorAPClient-0.7.7/RKorAPClient/demo/mosaicplot.R | 2 RKorAPClient-0.7.7/RKorAPClient/demo/pluralGenderVariants.R |only 10 files changed, 42 insertions(+), 172 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>
Diff between QTLRel versions 1.12 dated 2022-11-04 and 1.14 dated 2023-08-08
ChangeLog | 2 DESCRIPTION | 8 MD5 | 24 NAMESPACE | 2 R/hapSim.R | 28 - R/lodci.R | 130 ++-- R/pedRecode.R | 2 R/plots.R | 106 ++- R/scan.R | 1192 +++++++++++++++++++++---------------------- data/miscEx.RData |binary inst/CITATION | 26 inst/doc/QTLRel_Tutorial.R | 28 - inst/doc/QTLRel_Tutorial.pdf |binary 13 files changed, 795 insertions(+), 753 deletions(-)
Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharche [...truncated...]
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Rasmus Rydbirk [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between pagoda2 versions 1.0.10 dated 2022-04-19 and 1.0.11 dated 2023-08-08
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/Pagoda2.R | 2 +- README.md | 6 +++--- src/Makevars | 1 - src/Makevars.win | 2 -- 6 files changed, 14 insertions(+), 16 deletions(-)
Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization
analyses with summarized data. Summarized data on genetic associations with the
exposure and with the outcome can be obtained from large consortia. These data
can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <olena.yavorska@ludwig.ox.ac.uk>
James Staley <james.staley@bristol.ac.uk>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>
Diff between MendelianRandomization versions 0.8.0 dated 2023-07-04 and 0.9.0 dated 2023-08-08
DESCRIPTION | 10 +- MD5 | 56 +++++++++------ NAMESPACE | 7 + NEWS | 6 + R/AllClasses.R | 133 ++++++++++++++++++++++++++++++++++++ R/AllData.R | 2 R/AllGenerics.R | 162 +++++++++++++++++++++++++++++++++++++++++++-- R/RcppExports.R | 146 ++++++++++++++++++++-------------------- R/getter-methods.R | 14 +++ R/mr_egger-methods.R | 4 - R/mr_ivw-methods.R | 14 +++ R/mr_mvgmm-methods.R |only R/mr_mvivw-methods.R | 127 +++++++++++++++++++++++++++++++++-- R/mr_mvpcgmm-methods.R |only R/mr_pcgmm-methods.R |only R/show-methods.R | 126 ++++++++++++++++++++++++++++++++++- man/IVW-class.Rd | 2 man/MVGMM-class.Rd |only man/MVIVW-class.Rd | 2 man/MVPCGMM-class.Rd |only man/PCGMM-class.Rd |only man/condFstat.Rd |only man/egger.bounds.Rd | 8 +- man/getter.Rd | 9 ++ man/ldlc.Rd | 2 man/mr_ivw.Rd | 1 man/mr_mvegger.Rd | 2 man/mr_mvgmm.Rd |only man/mr_mvivw.Rd | 11 +++ man/mr_mvpcgmm.Rd |only man/mr_pcgmm.Rd |only man/mr_pivw.Rd | 2 src/RcppExports.cpp | 5 + vignettes/Vignette_MR.html | 9 +- 34 files changed, 728 insertions(+), 132 deletions(-)
More information about MendelianRandomization at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-07 0.1.2
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 2.6.1 dated 2022-12-20 and 2.6.2 dated 2023-08-08
noctua-2.6.1/noctua/tests/testthat/test-base-write.R |only noctua-2.6.2/noctua/DESCRIPTION | 14 noctua-2.6.2/noctua/MD5 | 97 - noctua-2.6.2/noctua/NAMESPACE | 7 noctua-2.6.2/noctua/NEWS.md | 13 noctua-2.6.2/noctua/R/Connection.R | 247 ++- noctua-2.6.2/noctua/R/Driver.R | 5 noctua-2.6.2/noctua/R/File_Parser.R | 3 noctua-2.6.2/noctua/R/Result.R | 2 noctua-2.6.2/noctua/R/Table.R | 653 +++++----- noctua-2.6.2/noctua/R/View.R | 160 +- noctua-2.6.2/noctua/R/athena_low_api.R | 308 ++-- noctua-2.6.2/noctua/R/dplyr_integration.R | 322 +++- noctua-2.6.2/noctua/R/fetch_utils.R | 15 noctua-2.6.2/noctua/R/utils.R | 111 - noctua-2.6.2/noctua/R/zzz.R | 14 noctua-2.6.2/noctua/build/vignette.rds |binary noctua-2.6.2/noctua/inst/doc/aws_athena_query_caching.html | 122 - noctua-2.6.2/noctua/inst/doc/aws_athena_unload.html | 226 +-- noctua-2.6.2/noctua/inst/doc/aws_s3_backend.html | 12 noctua-2.6.2/noctua/inst/doc/changing_backend_file_parser.html | 52 noctua-2.6.2/noctua/inst/doc/convert_and_save_cost.html | 116 - noctua-2.6.2/noctua/inst/doc/getting_started.Rmd | 2 noctua-2.6.2/noctua/inst/doc/getting_started.html | 192 +- noctua-2.6.2/noctua/inst/doc/how_to_retry.html | 36 noctua-2.6.2/noctua/man/AthenaConnection.Rd | 14 noctua-2.6.2/noctua/man/AthenaWriteTables.Rd | 27 noctua-2.6.2/noctua/man/assume_role.Rd | 16 noctua-2.6.2/noctua/man/backend_dbplyr_v1.Rd | 2 noctua-2.6.2/noctua/man/backend_dbplyr_v2.Rd | 2 noctua-2.6.2/noctua/man/dbConnect-AthenaDriver-method.Rd | 3 noctua-2.6.2/noctua/man/dbExistsTable.Rd | 3 noctua-2.6.2/noctua/man/dbGetTables.Rd | 4 noctua-2.6.2/noctua/man/dbListTables.Rd | 4 noctua-2.6.2/noctua/man/dbRemoveTable.Rd | 6 noctua-2.6.2/noctua/man/db_compute.Rd | 72 - noctua-2.6.2/noctua/man/db_copy_to.Rd | 62 noctua-2.6.2/noctua/man/session_token.Rd | 17 noctua-2.6.2/noctua/man/sqlCreateTable.Rd | 32 noctua-2.6.2/noctua/man/work_group.Rd | 36 noctua-2.6.2/noctua/tests/testthat/helper.R | 37 noctua-2.6.2/noctua/tests/testthat/test-datatransfer-datatable.R | 21 noctua-2.6.2/noctua/tests/testthat/test-datatransfer-vroom.R | 10 noctua-2.6.2/noctua/tests/testthat/test-dplyr-compute.R | 27 noctua-2.6.2/noctua/tests/testthat/test-dplyr-copy_to.R | 4 noctua-2.6.2/noctua/tests/testthat/test-file-parser.R | 2 noctua-2.6.2/noctua/tests/testthat/test-metadata.R | 15 noctua-2.6.2/noctua/tests/testthat/test-onload-functions.R | 7 noctua-2.6.2/noctua/tests/testthat/test-view.R | 36 noctua-2.6.2/noctua/vignettes/getting_started.Rmd | 2 50 files changed, 1851 insertions(+), 1339 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-02 3.0
2014-11-26 2.9
2012-09-28 2.01
2012-07-12 1.0
Title: Word Pools Used in Studies of Learning and Memory
Description: Collects several classical word pools used most often
to provide lists of words in psychological studies of learning and memory. It
provides a simple function, 'pickList' for selecting random samples of words
within given ranges.
Author: Michael Friendly [aut, cre] ,
Matthew Dubins [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between WordPools versions 1.1-1 dated 2018-12-15 and 1.2.0 dated 2023-08-08
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 20 ++++++++++++-------- NAMESPACE | 1 + NEWS.md | 11 ++++++++++- R/pickList.R | 3 ++- inst |only man/CatProp.Rd | 2 +- man/TWP.Rd | 10 +++++----- man/WordPools-package.Rd | 11 +++-------- man/figures |only man/plotDensity.Rd | 13 +++++++++++-- 11 files changed, 60 insertions(+), 36 deletions(-)
Title: Discrete Nonlinear Filtering for Stochastic Volatility Models
Description: Generates simulated paths from various financial stochastic volatility models
with jumps and applies the discrete nonlinear filter (DNF) of Kitagawa (1987) <doi:10.1080/01621459.1987.10478534> to
compute likelihood evaluations, filtering distribution estimates, and maximum likelihood parameter estimates.
The algorithm is implemented following the work of Bégin and Boudreault (2021) <doi:10.1080/10618600.2020.1840995>.
Author: Louis Arsenault-Mahjoubi [aut, cre],
Jean-Francois Begin [aut],
Mathieu Boudreault [aut]
Maintainer: Louis Arsenault-Mahjoubi <larsenau@sfu.ca>
Diff between SVDNF versions 0.1.7 dated 2023-07-20 and 0.1.8 dated 2023-08-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/DNFOptim.R | 20 +++++++++++--------- 3 files changed, 16 insertions(+), 14 deletions(-)
More information about ranktreeEnsemble at CRAN
Permanent link
Title: Generalized Ridge Trace Plots for Ridge Regression
Description: The genridge package introduces generalizations of the standard univariate
ridge trace plot used in ridge regression and related methods. These graphical methods
show both bias (actually, shrinkage) and precision, by plotting the covariance ellipsoids of the estimated
coefficients, rather than just the estimates themselves. 2D and 3D plotting methods are provided,
both in the space of the predictor variables and in the transformed space of the PCA/SVD of the
predictors.
Author: Michael Friendly [aut, cre]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between genridge versions 0.6.7 dated 2020-01-29 and 0.7.0 dated 2023-08-08
genridge-0.6.7/genridge/NEWS |only genridge-0.6.7/genridge/man/genridge-internal.Rd |only genridge-0.6.7/genridge/man/pca.ridge.Rd |only genridge-0.6.7/genridge/man/plot3d.ridge.Rd |only genridge-0.7.0/genridge/DESCRIPTION | 34 ++- genridge-0.7.0/genridge/MD5 | 75 ++++---- genridge-0.7.0/genridge/NAMESPACE | 92 +++++---- genridge-0.7.0/genridge/NEWS.md |only genridge-0.7.0/genridge/R/biplot.pcaridge.R | 112 +++++++++++- genridge-0.7.0/genridge/R/contourf.R | 66 +++++++ genridge-0.7.0/genridge/R/data.R |only genridge-0.7.0/genridge/R/genridge-package.R |only genridge-0.7.0/genridge/R/pairs.ridge.R | 61 ++++++ genridge-0.7.0/genridge/R/pca.ridge.R | 57 ++++++ genridge-0.7.0/genridge/R/plot.ridge.R | 112 +++++++++++- genridge-0.7.0/genridge/R/plot3d.ridge.R | 116 +++++++++++- genridge-0.7.0/genridge/R/precision.R | 104 ++++++++++- genridge-0.7.0/genridge/R/ridge.R | 155 ++++++++++++++++ genridge-0.7.0/genridge/R/traceplot.R | 57 ++++++ genridge-0.7.0/genridge/R/trans.colors.R | 36 +++ genridge-0.7.0/genridge/R/vif.ridge.R | 72 +++++++ genridge-0.7.0/genridge/build |only genridge-0.7.0/genridge/inst |only genridge-0.7.0/genridge/man/Acetylene.Rd | 64 +++--- genridge-0.7.0/genridge/man/Detroit.Rd | 117 ++++++------ genridge-0.7.0/genridge/man/Manpower.Rd | 75 +++----- genridge-0.7.0/genridge/man/biplot.pcaridge.Rd | 196 +++++++++------------ genridge-0.7.0/genridge/man/contourf.Rd | 162 +++++++---------- genridge-0.7.0/genridge/man/figures |only genridge-0.7.0/genridge/man/genridge-package.Rd | 95 ++++------ genridge-0.7.0/genridge/man/pairs.ridge.Rd | 157 ++++++++-------- genridge-0.7.0/genridge/man/pca.Rd |only genridge-0.7.0/genridge/man/plot.ridge.Rd | 213 +++++++++++------------ genridge-0.7.0/genridge/man/plot3d.Rd |only genridge-0.7.0/genridge/man/precision.Rd | 112 ++++-------- genridge-0.7.0/genridge/man/prostate.Rd | 92 +++++---- genridge-0.7.0/genridge/man/ridge.Rd | 178 +++++++------------ genridge-0.7.0/genridge/man/traceplot.Rd | 137 ++++++-------- genridge-0.7.0/genridge/man/trans.colors.Rd | 62 ++---- genridge-0.7.0/genridge/man/vif.ridge.Rd | 69 +++---- 40 files changed, 1823 insertions(+), 1055 deletions(-)
Title: Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) <doi:10.12688/f1000research.7082.3>.
Author: Diogo Melo [aut, cre] ,
Ana Paula Assis [aut],
Edgar Zanella [ctb],
Fabio Andrade Machado [aut] ,
Guilherme Garcia [aut],
Alex Hubbe [rev] ,
Gabriel Marroig [ths]
Maintainer: Diogo Melo <diogro@gmail.com>
Diff between evolqg versions 0.3-2 dated 2023-03-22 and 0.3-3 dated 2023-08-08
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/MatrixStatistics.R | 6 ++++-- 3 files changed, 12 insertions(+), 10 deletions(-)
Title: Methods for Temporal Disaggregation and Interpolation of Time
Series
Description: Temporal disaggregation methods are used to disaggregate and
interpolate a low frequency time series to a higher frequency series, where
either the sum, the mean, the first or the last value of the resulting
high frequency series is consistent with the low frequency series. Temporal
disaggregation can be performed with or without one or more high frequency
indicator series. Contains the methods of Chow-Lin, Santos-Silva-Cardoso,
Fernandez, Litterman, Denton and Denton-Cholette, summarized in Sax and
Steiner (2013) <doi:10.32614/RJ-2013-028>. Supports most R time series
classes.
Author: Christoph Sax [aut, cre] ,
Peter Steiner [aut],
Tommaso Di Fonzo [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between tempdisagg versions 1.1 dated 2023-03-09 and 1.1.1 dated 2023-08-08
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS.md | 7 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/hf-disagg.html | 144 +++++++++++++++++++++---------------------- inst/doc/intro.html | 134 ++++++++++++++++++++-------------------- tests/test-all.R | 7 +- tests/testthat/test_output.R | 3 9 files changed, 164 insertions(+), 155 deletions(-)
Title: Fast Logistic Regression Wrapper
Description: Provides very fast logistic regression with coefficient inferences plus other useful methods such as a forward stepwise model generator (see the benchmarks by visiting the github page at the URL below). The inputs are flexible enough to accomodate GPU computations. The coefficient estimation employs the fastLR() method in the 'RcppNumerical' package by Yixuan Qiu et al. This package allows their work to be more useful to a wider community that consumes inference.
Author: Adam Kapelner [aut, cre] ,
Beau Walker [rev, dtc] ,
Gabriel Mayer [fnd, dtc]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between fastLogisticRegressionWrap versions 1.1 dated 2023-07-13 and 1.2.0 dated 2023-08-08
CHANGELOG | 11 ++ DESCRIPTION | 14 +-- MD5 | 21 ++--- NAMESPACE | 1 R/RcppExports.R | 4 R/code.R | 131 +++++++++++++++++++++++++++----- R/zzz.R | 37 --------- man/asymmetric_cost_explorer.Rd |only man/confusion_results.Rd | 4 man/summary.fast_logistic_regression.Rd | 4 src/RcppExports.cpp | 13 +++ src/routines.cpp | 19 ++++ 12 files changed, 184 insertions(+), 75 deletions(-)
More information about fastLogisticRegressionWrap at CRAN
Permanent link
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions for some common tasks,
such as data partition, variable selection, woe binning, scorecard scaling,
performance evaluation and report generation. These functions can also used
in the development of machine learning models.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.4.2 dated 2023-04-23 and 0.4.3 dated 2023-08-08
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NAMESPACE | 1 NEWS.md | 4 ++ R/scorecard.R | 7 ++++ R/split_df.R | 35 ++++++++++++++++++-- R/utils.R | 2 - R/woebin.R | 3 + build/vignette.rds |binary inst/doc/demo.html | 92 ++++++++++++++++++++++++++--------------------------- man/split_df.Rd | 5 ++ 11 files changed, 111 insertions(+), 66 deletions(-)
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] ,
Richard M. Heiberger [ctb] , *Bin, *Dec),
John C. Nash [ctb] , origin of unirootR),
Hans W. Borchers [ctb] ; origin of
hjkMpfr)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.9-2 dated 2023-04-21 and 0.9-3 dated 2023-08-08
DESCRIPTION | 10 ++++---- MD5 | 22 +++++++++---------- R/Summary.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 15 +++++++++++++ inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.pdf |binary man/Rmpfr-package.Rd | 6 ++--- src/Summary.c | 39 ++++++++++++++++++++-------------- tests/arith-ex.R | 27 +++++++++++++++++++++++ 12 files changed, 85 insertions(+), 35 deletions(-)
Title: Optimal Design and Statistical Power for Experimental Studies
Investigating Main, Mediation, and Moderation Effects
Description: Calculate the optimal sample size allocation that
produces the highest statistical power for experimental
studies under a budget constraint, and
perform power analyses with and without accommodating
cost structures of sampling. The designs cover single-level
and multilevel experiments detecting main, mediation,
and moderation effects (and some combinations).
The references for the proposed methods include:
(1) Shen, Z., & Kelcey, B. (2020).
Optimal sample allocation under unequal costs in
cluster-randomized trials.
Journal of Educational and Behavioral Statistics, 45(4): 446-474.
<doi:10.3102/1076998620912418>.
(2) Shen, Z., & Kelcey, B. (2022b). Optimal sample allocation for
three-level multisite cluster-randomized trials.
Journal of Research on Educational Effectiveness, 15 (1), 130-150.
<doi:10.1080/19345747.2021.1953200>.
(3) Shen, Z., & Kelcey, B. (2022a). Optimal sample allocation in
multisite randomized trials. The Journal of Experimental Education.
<d [...truncated...]
Author: Zuchao Shen [aut, cre] ,
Benjamin Kelcey [aut]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between odr versions 1.4.2 dated 2023-04-24 and 1.4.4 dated 2023-08-08
DESCRIPTION | 8 MD5 | 38 +-- R/od.1.111.R | 78 +++--- R/od.2.221.R | 640 +++++++++++++++++++---------------------------------- R/od.2m.R | 18 - R/power.1.111.R | 45 +-- R/power.2.221.R | 230 +++++++------------ R/re.R | 8 R/rpe.R | 10 build/vignette.rds |binary inst/doc/odr.R | 9 inst/doc/odr.Rmd | 9 inst/doc/odr.html | 293 ++++++++++++------------ man/od.1.111.Rd | 10 man/od.2.221.Rd | 125 ++++------ man/power.1.111.Rd | 22 - man/power.2.221.Rd | 70 +++-- man/re.Rd | 8 man/rpe.Rd | 10 vignettes/odr.Rmd | 9 20 files changed, 708 insertions(+), 932 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.4.1 dated 2023-04-14 and 1.4.2 dated 2023-08-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/jsBasicGadget.R | 4 ++-- R/jsPropensityGadget.R | 8 ++++---- R/jsRepeatedGadget.R | 4 ++-- R/tb1.R | 33 ++++++++++++++++++++++----------- README.md | 2 +- build/vignette.rds |binary inst/doc/jsmodule.html | 4 ++-- 11 files changed, 52 insertions(+), 36 deletions(-)
Title: Statistical Tests and Utilities for Genetic Association
Description: A collection of statistical tests for genetic association studies and summary data based Mendelian randomization.
Author: Dr. Kai Wang
Maintainer: Kai Wang <kai-wang@uiowa.edu>
Diff between iGasso versions 1.4 dated 2016-06-04 and 1.6 dated 2023-08-08
DESCRIPTION | 14 ++++--- MD5 | 31 +++++++++------ NAMESPACE | 20 ++++++++-- R/KAT.coin.R | 45 +++++++++++++++++++++++ R/MFree.test.R | 25 ++++++++++++ R/SKATplus.R | 38 +++++++++++++++++++ R/SMR_interval.R |only R/VSTF.test.R | 34 +++++++++++++++++ R/genome.plot.R | 30 +++++++++++++++ R/globals.R |only R/h2_snp.R |only R/tarq.R |only man/KAT.coin.Rd | 90 ++++++++++++++++++++-------------------------- man/MFree.test.Rd | 66 +++++++++++---------------------- man/SKATplus.Rd | 101 +++++++++++++++++++++++----------------------------- man/SMR_interval.Rd |only man/VSTF.test.Rd | 68 ++++++++++++----------------------- man/genome.plot.Rd | 101 ++++++++++++++++++++-------------------------------- man/h2_snp.Rd |only man/tarq.Rd |only 20 files changed, 387 insertions(+), 276 deletions(-)
Title: Individual and Group Farm Sustainability Assessments using the
IDEA4 Method
Description: Collection of tools to automate the processing of data collected though the IDEA4 method (see Zahm et al. (2018) <doi:10.1051/cagri/2019004> ). Starting from the original data collecting files this packages provides functions to compute IDEA indicators, draw modern and aesthetic plots, and produce a wide range of reporting materials.
Author: David Carayon [aut, cre, cph]
Maintainer: David Carayon <david.carayon@inrae.fr>
Diff between IDEATools versions 3.4.2 dated 2023-04-24 and 3.5.0 dated 2023-08-08
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/excel_reports.R | 14 +++++++++----- R/sysdata.rda |binary inst/doc/colored_trees.html | 2 +- inst/doc/decision_rules.html | 2 +- inst/doc/utils.html | 2 +- inst/report/group/pdf_group_report.Rmd | 4 ++-- inst/report/group/pdf_group_report_ref.Rmd | 6 +++--- man/figures/logo.png |binary 11 files changed, 34 insertions(+), 26 deletions(-)
Title: Simulation Tool for Causal Inference Using Longitudinal Data
Description: Implements a simulation study to assess the strengths and
weaknesses of causal inference methods for estimating policy effects
using panel data. See Griffin et al. (2021)
<doi:10.1007/s10742-022-00284-w> and Griffin et al. (2022)
<doi:10.1186/s12874-021-01471-y> for a description of our methods.
Author: Beth Ann Griffin [aut, cph] ,
Pedro Nascimento de Lima [cre, aut]
,
Max Griswold [aut] ,
Adam Scherling [aut],
Joseph Pane [aut],
Geoffrey Grimm [aut]
Maintainer: Pedro Nascimento de Lima <plima@rand.org>
Diff between optic versions 1.0.0 dated 2023-05-26 and 1.0.1 dated 2023-08-08
DESCRIPTION | 6 - MD5 | 16 +-- NEWS.md | 5 + README.md | 185 +++++++++++++++++++++++++++++----------- inst/doc/intro_optic.R | 2 inst/doc/intro_optic.Rmd | 18 +-- inst/doc/intro_optic.html | 43 +++++---- vignettes/intro_optic.Rmd | 18 +-- vignettes/optic_refs.json | 211 ++++++++++++++++++++++++++++++++++++++++++++-- 9 files changed, 396 insertions(+), 108 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.5.2 dated 2023-06-14 and 0.6.0 dated 2023-08-08
naijR-0.5.2/naijR/R/class-regions.R |only naijR-0.5.2/naijR/R/isregion.R |only naijR-0.5.2/naijR/R/lgas_nigeria.R |only naijR-0.5.2/naijR/R/map-helpers.R |only naijR-0.5.2/naijR/R/map_nigeria.R |only naijR-0.5.2/naijR/R/methods-fix_region.R |only naijR-0.5.2/naijR/R/mobile.R |only naijR-0.5.2/naijR/man/coercion.Rd |only naijR-0.5.2/naijR/tests/testthat/test-class-regions.R |only naijR-0.5.2/naijR/tests/testthat/test-isregion.R |only naijR-0.5.2/naijR/tests/testthat/test-map_nigeria.R |only naijR-0.5.2/naijR/tests/testthat/test-methods-fix_region.R |only naijR-0.5.2/naijR/tests/testthat/test-mobile.R |only naijR-0.5.2/naijR/vignettes/img |only naijR-0.6.0/naijR/DESCRIPTION | 18 naijR-0.6.0/naijR/MD5 | 92 ++-- naijR-0.6.0/naijR/NAMESPACE | 12 naijR-0.6.0/naijR/NEWS.md | 15 naijR-0.6.0/naijR/R/asreg.R |only naijR-0.6.0/naijR/R/fct.R | 2 naijR-0.6.0/naijR/R/fixmob.R |only naijR-0.6.0/naijR/R/fixreg.R |only naijR-0.6.0/naijR/R/helpers.R | 96 ++++ naijR-0.6.0/naijR/R/isreg.R |only naijR-0.6.0/naijR/R/map.R |only naijR-0.6.0/naijR/R/regdata.R |only naijR-0.6.0/naijR/R/regions.R |only naijR-0.6.0/naijR/R/sysdata.rda |binary naijR-0.6.0/naijR/build/vignette.rds |binary naijR-0.6.0/naijR/data/lgas_nigeria.rda |binary naijR-0.6.0/naijR/data/states_nigeria.rda |only naijR-0.6.0/naijR/inst/doc/interactive.R | 51 +- naijR-0.6.0/naijR/inst/doc/interactive.Rmd | 126 ++---- naijR-0.6.0/naijR/inst/doc/interactive.html | 265 +++++++------ naijR-0.6.0/naijR/inst/doc/nigeria-maps.Rmd | 4 naijR-0.6.0/naijR/inst/doc/nigeria-maps.html | 134 +++--- naijR-0.6.0/naijR/man/coerce.Rd |only naijR-0.6.0/naijR/man/disambiguate_lga.Rd |only naijR-0.6.0/naijR/man/fix_mobile.Rd | 2 naijR-0.6.0/naijR/man/fix_region.Rd | 6 naijR-0.6.0/naijR/man/fix_region_manual.Rd | 2 naijR-0.6.0/naijR/man/is_lga.Rd | 2 naijR-0.6.0/naijR/man/is_state.Rd | 2 naijR-0.6.0/naijR/man/lgas.Rd | 2 naijR-0.6.0/naijR/man/lgas_nigeria.Rd | 3 naijR-0.6.0/naijR/man/map_ng.Rd | 13 naijR-0.6.0/naijR/man/states.Rd | 2 naijR-0.6.0/naijR/man/states_nigeria.Rd |only naijR-0.6.0/naijR/tests/testthat/data/mispelt-lga.rds |binary naijR-0.6.0/naijR/tests/testthat/test-asreg.R |only naijR-0.6.0/naijR/tests/testthat/test-fixmob.R |only naijR-0.6.0/naijR/tests/testthat/test-fixreg.R |only naijR-0.6.0/naijR/tests/testthat/test-isreg.R |only naijR-0.6.0/naijR/tests/testthat/test-map.R |only naijR-0.6.0/naijR/tests/testthat/test-regions.R |only naijR-0.6.0/naijR/vignettes/interactive.Rmd | 126 ++---- naijR-0.6.0/naijR/vignettes/nigeria-maps.Rmd | 4 57 files changed, 519 insertions(+), 460 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm() and glm(). A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre],
Solve Saeboe¸ [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.2.6 dated 2022-02-24 and 1.3.0 dated 2023-08-08
DESCRIPTION | 15 MD5 | 68 NAMESPACE | 180 +- NEWS | 92 - R/borrowed.R | 30 R/glm.R | 308 ++-- R/globals.R | 14 R/lm.R | 1182 ++++++++-------- R/mixlm.R | 220 +-- R/statistics.R | 3350 +++++++++++++++++++++++----------------------- R/utilities.R | 244 +-- README.md |only man/Anova.Rd | 76 - man/AnovaMix.Rd | 101 - man/CIgrandMean.Rd | 104 - man/PRESS.Rd | 104 - man/anova.lmm.Rd | 72 man/anova_reg.Rd | 50 man/best.subsets.Rd | 92 - man/confusion.Rd | 60 man/contr.weighted.Rd |only man/effect.labels.Rd | 56 man/forward.Rd | 156 +- man/fparse.Rd | 58 man/glm.Rd | 694 ++++----- man/is.balanced.Rd | 58 man/lm.Rd | 544 +++---- man/plotprops.Rd | 96 - man/print.AnovaMix.Rd | 70 man/print.summary.lmm.Rd | 172 +- man/prop.test.ordinary.Rd | 260 +-- man/rparse.Rd | 58 man/simple.glht.Rd | 188 +- man/spearson.Rd | 70 man/t_test.Rd | 238 +-- man/tally.Rd | 56 36 files changed, 4602 insertions(+), 4534 deletions(-)
Title: Missingness Aware Gaussian Mixture Models
Description: Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data. This package complements existing implementations by allowing for both missing elements in the input vectors and full (as opposed to strictly diagonal) covariance matrices. Estimation is performed using an expectation conditional maximization algorithm that accounts for missingness of both the cluster assignments and the vector components. The output includes the marginal cluster membership probabilities; the mean and covariance of each cluster; the posterior probabilities of cluster membership; and a completed version of the input data, with missing values imputed to their posterior expectations. For additional details, please see McCaw ZR, Julienne H, Aschard H. "Fitting Gaussian mixture models on incomplete data." <doi:10.1186/s12859-022-04740-9>.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>
Diff between MGMM versions 1.0.0 dated 2021-12-21 and 1.0.1 dated 2023-08-08
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++-------- R/04_Partition_Data.R | 2 +- R/05_Single_MVN.R | 2 +- R/06_Mix_MVN.R | 2 +- build/vignette.rds |binary inst/doc/MGMM.pdf |binary src/Makevars | 1 - src/Makevars.win | 1 - tests/testthat/test-onedim.R |only 10 files changed, 18 insertions(+), 19 deletions(-)
Title: Simple Presentation of Estimated Exponential Semi-Variograms
Description: User friendly interface based on the R package 'gstat' to fit
exponential parametric models to empirical semi-variograms in order to
model the spatial correlation structure of health data. Geo-located
health outcomes of survey participants may be used to model spatial
effects on health in an ego-centred approach. The package contains a
range of functions to help explore the spatial structure of the data
as well as visualize the fit of exponential models for various
metaparameter combinations with respect to the number of lag intervals
and maximal distance. Furthermore, the outcome of interest can be
adjusted for covariates by fitting a linear regression in a
preliminary step before the semi-variogram fitting process.
Author: Julia Dyck [aut, cre],
Odile Sauzet [aut],
Jan-Ole Koslik [aut]
Maintainer: Julia Dyck <j.dyck@uni-bielefeld.de>
Diff between EgoCor versions 1.0.0 dated 2022-08-11 and 1.1.0 dated 2023-08-08
EgoCor-1.0.0/EgoCor/R/bootstrap_uncertainty_check_filter_fct.R |only EgoCor-1.0.0/EgoCor/R/one_resample_analysis_check_fct.R |only EgoCor-1.0.0/EgoCor/README.md |only EgoCor-1.1.0/EgoCor/DESCRIPTION | 10 EgoCor-1.1.0/EgoCor/MD5 | 34 - EgoCor-1.1.0/EgoCor/R/coords.plot.function.R | 18 EgoCor-1.1.0/EgoCor/R/nscore_fct.R | 13 EgoCor-1.1.0/EgoCor/R/one_resample_analysis_check.R |only EgoCor-1.1.0/EgoCor/R/par.uncertainty.function.R | 157 ++++- EgoCor-1.1.0/EgoCor/R/sv.sep.R | 27 EgoCor-1.1.0/EgoCor/R/vario.mod.function.gstat.R | 36 - EgoCor-1.1.0/EgoCor/build/partial.rdb |binary EgoCor-1.1.0/EgoCor/build/vignette.rds |binary EgoCor-1.1.0/EgoCor/inst/doc/Intro_to_EgoCor.R | 2 EgoCor-1.1.0/EgoCor/inst/doc/Intro_to_EgoCor.Rmd | 4 EgoCor-1.1.0/EgoCor/inst/doc/Intro_to_EgoCor.html | 288 +++++----- EgoCor-1.1.0/EgoCor/man/coords.plot.Rd | 6 EgoCor-1.1.0/EgoCor/man/par.uncertainty.Rd | 8 EgoCor-1.1.0/EgoCor/man/vario.mod.Rd | 6 EgoCor-1.1.0/EgoCor/vignettes/Intro_to_EgoCor.Rmd | 4 20 files changed, 385 insertions(+), 228 deletions(-)
Title: 'data.table' Time-Series
Description: High-frequency time-series support via 'nanotime' and 'data.table'.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between dtts versions 0.1.0 dated 2022-03-09 and 0.1.1 dated 2023-08-08
dtts-0.1.0/dtts/man/align.idx.Rd |only dtts-0.1.0/dtts/man/grid.align.Rd |only dtts-0.1.0/dtts/src/Makevars |only dtts-0.1.1/dtts/ChangeLog | 49 +++ dtts-0.1.1/dtts/DESCRIPTION | 10 dtts-0.1.1/dtts/MD5 | 31 +- dtts-0.1.1/dtts/NAMESPACE | 7 dtts-0.1.1/dtts/R/RcppExports.R | 12 dtts-0.1.1/dtts/R/dtts.R | 128 +++++++-- dtts-0.1.1/dtts/README.md | 89 +++++- dtts-0.1.1/dtts/inst/NEWS.Rd | 13 dtts-0.1.1/dtts/inst/images/ops.svg |only dtts-0.1.1/dtts/inst/tinytest/test_dtts.R | 281 ++++++++++++++++----- dtts-0.1.1/dtts/man/align.Rd | 2 dtts-0.1.1/dtts/man/align_idx.Rd |only dtts-0.1.1/dtts/man/frequency-data.table-method.Rd | 2 dtts-0.1.1/dtts/man/grid_align.Rd |only dtts-0.1.1/dtts/man/ops.Rd |only dtts-0.1.1/dtts/src/RcppExports.cpp | 14 + dtts-0.1.1/dtts/src/align.cpp | 277 +++++++++++++------- 20 files changed, 693 insertions(+), 222 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, truncation,
rank transformation, and smoothing. An export function helps to generate
html and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2023)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-potsdam.de>
Diff between scan versions 0.59.0 dated 2023-06-03 and 0.60.0 dated 2023-08-08
DESCRIPTION | 13 - MD5 | 195 +++++++++++---------- NAMESPACE | 3 NEWS.md | 23 ++ R/coefficents.sc_plm.R | 4 R/convert.R | 9 R/corrected_tau.R | 43 +++- R/design.R | 2 R/export.R | 66 ++++++- R/export.sc_desc.R | 62 +++--- R/export.sc_hplm.R | 47 ++--- R/export.sc_nap.R | 20 -- R/export.sc_overlap.R | 70 +++---- R/export.sc_pem.R | 18 - R/export.sc_plm.R | 22 -- R/export.sc_power.R | 19 -- R/export.sc_smd.R | 41 ++-- R/export.sc_tauu.R | 24 +- R/export.sc_trend.R | 17 - R/export.scdf.R | 19 +- R/hplm.R | 1 R/ird.R |only R/mplm.R | 1 R/overlap.R | 7 R/pand.R | 383 ++++++++++++++++++++++++++++-------------- R/pet.R | 27 +- R/power_test.R | 1 R/print.sc_bctau.R | 7 R/print.sc_hplm.R | 4 R/print.sc_mplm.R | 9 R/print.sc_overlap.R | 2 R/print.sc_pand.R | 89 ++++----- R/print.sc_rand.R | 2 R/print.sc_tauu.R | 8 R/print.scdf.R | 8 R/private_options_mc.R | 61 ++++++ R/private_recombine_phases.R | 21 ++ R/private_regression.R | 53 ----- R/private_utilities.R | 10 + R/random_scdf.R | 2 R/read_scdf.R | 5 R/scan-Data.R | 2 R/scdf.R | 26 +- R/shinyscan.R | 1 R/summary.scdf.R | 2 R/tau_u.R | 1 R/warnings-messages.R |only data/Beretvas2008.rda |binary data/Borckardt2014.rda |binary data/Grosche2011.rda |binary data/Grosche2014.rda |binary data/GruenkeWilbert2014.rda |binary data/Huber2014.rda |binary data/Huitema2000.rda |binary data/Leidig2018.rda |binary data/Leidig2018_l2.rda |binary data/Lenz2013.rda |binary data/Parker2007.rda |only data/Parker2009.rda |only data/Parker2011.rda |binary data/Parker2011b.rda |only data/SSDforR2017.rda |binary data/Tarlow2017.rda |only data/Waddell2011.rda |binary data/byHeart2011.rda |binary data/exampleA1B1A2B2.rda |binary data/exampleA1B1A2B2_zvt.rda |binary data/exampleAB.rda |binary data/exampleABAB.rda |binary data/exampleABC.rda |binary data/exampleABC_150.rda |binary data/exampleABC_outlier.rda |binary data/exampleAB_50.l2.rda |binary data/exampleAB_50.rda |binary data/exampleAB_add.rda |binary data/exampleAB_decreasing.rda |binary data/exampleAB_mpd.rda |binary data/exampleAB_score.rda |binary data/exampleAB_simple.rda |binary data/example_A24.rda |binary inst/CITATION | 2 inst/shiny/resources.R | 61 ++++++ inst/shiny/server.R | 251 +++++++++++++++++++++------ inst/shiny/ui.R | 139 ++++++++++----- man/coef.sc_plm.Rd | 3 man/corrected_tau.Rd | 6 man/design.Rd | 2 man/example_data.Rd | 4 man/export.Rd | 48 +---- man/hplm.Rd | 55 +++++- man/ird.Rd |only man/mplm.Rd | 17 + man/overlap.Rd | 4 man/pand.Rd | 146 +++++++++++----- man/pet.Rd | 10 - man/print.sc.Rd | 36 --- man/random_scdf.Rd | 2 man/read_scdf.Rd | 3 man/scdf.Rd | 6 man/tau_u.Rd | 65 +++++++ tests/testthat/test-mplm.R |only tests/testthat/test-overlap.R | 6 tests/testthat/test-pand.R |only 103 files changed, 1521 insertions(+), 795 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, to plot the curves and their underlying data, to calibrate radiocarbon dates and to transform between different radiocarbon 'domains'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 0.6.2 dated 2023-07-16 and 0.6.3 dated 2023-08-08
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Title: Non-Normal Repeated Measurements Models
Description: Various functions to fit models for non-normal repeated
measurements, such as Binary Random Effects Models with Two Levels of Nesting,
Bivariate Beta-binomial Regression Models, Marginal Bivariate Binomial Regression Models,
Cormack capture-recapture models, Continuous-time Hidden Markov Chain Models,
Discrete-time Hidden Markov Chain Models,
Changepoint Location Models using a Continuous-time Two-state Hidden Markov Chain,
generalized nonlinear autoregression models, multivariate Gaussian copula models,
generalized non-linear mixed models with one random effect,
generalized non-linear mixed models using h-likelihood for one random effect,
Repeated Measurements Models for Counts with Frailty or Serial Dependence,
Repeated Measurements Models for Continuous Variables with Frailty or Serial Dependence,
Ordinal Random Effects Models with Dropouts, marginal homogeneity models for square
contingency tables, correlated negative binomial models with Kalman update.
References include Lindsey's [...truncated...]
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] ,
T.R. Ten Have [ctb, cph] .),
Richard Cook [ctb, cph] ,
Iain MacDonald [ctb, cph] ,
Walter Zucchini [ctb, cph] ,
Burton Garbow [ctb, cph] ,
Euginia Zharichenko [ctb, cph]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between repeated versions 1.1.6 dated 2022-10-27 and 1.1.7 dated 2023-08-08
DESCRIPTION | 10 - MD5 | 40 ++-- NAMESPACE | 5 NEWS.md | 11 + R/binnest.r | 9 R/bivbetab.r | 5 R/bivbinom.r | 5 R/gar.r | 41 ++-- R/glmm.r | 12 - R/gnlmm.r | 6 R/gnlmm3.r | 6 R/hidden.r | 7 R/kalcount.r | 70 +++---- man/binnest.Rd | 4 man/gar.Rd | 41 ++-- man/gnlmm.Rd | 6 man/gnlmm3.Rd | 6 man/hidden.Rd | 7 man/kalcount.Rd | 50 ++--- src/binnest.f | 235 +++++++++++------------ src/logitord.f | 555 +++++++++++++++++++++++++++++--------------------------- 21 files changed, 587 insertions(+), 544 deletions(-)
Title: A Compilation of Some Frequently Used R Functions
Description: The NOT functions and a simple compilation of various functions for easy usage. Shorthand code to save memory usage.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 0.1 dated 2023-07-18 and 0.2 dated 2023-08-08
quickcode-0.1/quickcode/inst/doc/simple_samples.R |only quickcode-0.1/quickcode/inst/doc/simple_samples.Rmd |only quickcode-0.1/quickcode/inst/doc/simple_samples.html |only quickcode-0.1/quickcode/vignettes/simple_samples.Rmd |only quickcode-0.2/quickcode/DESCRIPTION | 6 quickcode-0.2/quickcode/MD5 | 48 - quickcode-0.2/quickcode/NAMESPACE | 8 quickcode-0.2/quickcode/NEWS.md | 7 quickcode-0.2/quickcode/R/functions.R | 394 +++++++++- quickcode-0.2/quickcode/R/quickcode-package.R | 2 quickcode-0.2/quickcode/README.md | 44 - quickcode-0.2/quickcode/build/vignette.rds |binary quickcode-0.2/quickcode/inst/doc/quickcode_r_introduction.R |only quickcode-0.2/quickcode/inst/doc/quickcode_r_introduction.Rmd |only quickcode-0.2/quickcode/inst/doc/quickcode_r_introduction.html |only quickcode-0.2/quickcode/inst/rstudio/addins.dcf | 7 quickcode-0.2/quickcode/man/add_key.Rd |only quickcode-0.2/quickcode/man/ai.duplicate.Rd |only quickcode-0.2/quickcode/man/clean.Rd | 4 quickcode-0.2/quickcode/man/data_shuffle.Rd | 23 quickcode-0.2/quickcode/man/duplicate.Rd |only quickcode-0.2/quickcode/man/grapes-nin-grapes.Rd | 2 quickcode-0.2/quickcode/man/inc.Rd |only quickcode-0.2/quickcode/man/init.Rd |only quickcode-0.2/quickcode/man/list_push.Rd |only quickcode-0.2/quickcode/man/not.logical.Rd |only quickcode-0.2/quickcode/man/not.null.Rd | 2 quickcode-0.2/quickcode/man/number.Rd |only quickcode-0.2/quickcode/man/refresh.Rd | 4 quickcode-0.2/quickcode/man/sample_by_column.Rd | 4 quickcode-0.2/quickcode/man/vector_push.Rd | 4 quickcode-0.2/quickcode/man/vector_shuffle.Rd | 24 quickcode-0.2/quickcode/vignettes/quickcode_r_introduction.Rmd |only 33 files changed, 520 insertions(+), 63 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://docs.openalex.org>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 1.1.0 dated 2023-05-04 and 1.2.0 dated 2023-08-08
DESCRIPTION | 6 MD5 | 46 ++-- NAMESPACE | 8 NEWS.md | 16 + R/oa2bibliometrix.R | 49 ++-- R/oa2df.R | 348 ++++++++++++++++++++++++++++++---- R/oa_fetch.R | 37 ++- R/oa_ngrams.R | 2 R/oa_snowball.R | 4 R/openalexR-internal.R |only R/utils.R | 49 +++- README.md | 112 ++++++---- man/authors2df.Rd | 6 man/concepts2df.Rd | 6 man/funders2df.Rd |only man/institutions2df.Rd | 6 man/oa2bibliometrix.Rd | 1 man/oa2df.Rd | 5 man/oa_request.Rd | 4 man/oa_snowball.Rd | 2 man/publishers2df.Rd |only man/sources2df.Rd |only man/venues2df.Rd | 6 man/works2df.Rd | 9 tests/testthat/test-oa2bibliometrix.R | 7 tests/testthat/test-oa_fetch.R | 80 ++++++- 26 files changed, 620 insertions(+), 189 deletions(-)
Title: Dose-Response MBNMA Models
Description: Fits Bayesian dose-response model-based network meta-analysis (MBNMA)
that incorporate multiple doses within an agent by modelling different dose-response functions, as
described by Mawdsley et al. (2016) <doi:10.1002/psp4.12091>.
By modelling dose-response relationships this can connect networks of evidence that might
otherwise be disconnected, and can improve precision on treatment estimates. Several common
dose-response functions are provided; others may be added by the user. Various characteristics
and assumptions can be flexibly added to the models, such as shared class effects. The consistency
of direct and indirect evidence in the network can be assessed using unrelated mean effects models
and/or by node-splitting at the treatment level.
Author: Hugo Pedder [aut, cre] ,
Adil Karim [ctb]
Maintainer: Hugo Pedder <hugopedder@gmail.com>
Diff between MBNMAdose versions 0.4.1 dated 2022-02-24 and 0.4.2 dated 2023-08-08
MBNMAdose-0.4.1/MBNMAdose/inst/doc/mbnmadose.R |only MBNMAdose-0.4.1/MBNMAdose/inst/doc/mbnmadose.Rmd |only MBNMAdose-0.4.1/MBNMAdose/inst/doc/mbnmadose.html |only MBNMAdose-0.4.1/MBNMAdose/man/mbnma.emax.Rd |only MBNMAdose-0.4.1/MBNMAdose/man/mbnma.emax.hill.Rd |only MBNMAdose-0.4.1/MBNMAdose/man/mbnma.exponential.Rd |only MBNMAdose-0.4.1/MBNMAdose/man/mbnma.linear.Rd |only MBNMAdose-0.4.1/MBNMAdose/vignettes/mbnmadose.Rmd |only MBNMAdose-0.4.2/MBNMAdose/DESCRIPTION | 23 MBNMAdose-0.4.2/MBNMAdose/MD5 | 153 + MBNMAdose-0.4.2/MBNMAdose/NAMESPACE | 8 MBNMAdose-0.4.2/MBNMAdose/NEWS.md | 19 MBNMAdose-0.4.2/MBNMAdose/R/datasets.R | 21 MBNMAdose-0.4.2/MBNMAdose/R/dose.functions.R | 246 ++- MBNMAdose-0.4.2/MBNMAdose/R/globals.R | 2 MBNMAdose-0.4.2/MBNMAdose/R/inconsistency.functions.R | 564 +++++-- MBNMAdose-0.4.2/MBNMAdose/R/mbnma-class.R | 127 + MBNMAdose-0.4.2/MBNMAdose/R/mbnma.predict-class.R | 100 - MBNMAdose-0.4.2/MBNMAdose/R/mbnma.rank-class.R | 45 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MBNMAdose-0.4.2/MBNMAdose/tests/testthat/test_prepare.functions.R | 12 MBNMAdose-0.4.2/MBNMAdose/tests/testthat/test_rank.functions.R | 8 MBNMAdose-0.4.2/MBNMAdose/tests/testthat/test_run.functions.R | 43 MBNMAdose-0.4.2/MBNMAdose/vignettes/REFERENCES.bib | 52 MBNMAdose-0.4.2/MBNMAdose/vignettes/consistencychecking-3.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/dataexploration-1.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/mbnmadose-overview.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/metaregression-6.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/nma_in_mbnmadose.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/outputs-4.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/predictions-5.Rmd |only MBNMAdose-0.4.2/MBNMAdose/vignettes/runmbnmadose-2.Rmd |only 101 files changed, 2777 insertions(+), 1413 deletions(-)
Title: Generalized Price and Quantity Indexes
Description: A small package for calculating lots of different price indexes, and by extension quantity indexes. Provides tools to build and work with any type of bilateral generalized-mean index (of which most price indexes are), along with a few important indexes that don't belong to the generalized-mean family (e.g., superlative quadratic-mean indexes, GEKS). Implements and extends many of the methods in Balk (2008, ISBN:978-1-107-40496-0), von der Lippe (2001, ISBN:3-8246-0638-0), and the CPI manual (2020, ISBN:978-1-51354-298-0) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>
Diff between gpindex versions 0.4.3 dated 2022-04-30 and 0.5.0 dated 2023-08-08
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Title: Classes for 'GeoJSON'
Description: Classes for 'GeoJSON' to make working with 'GeoJSON' easier.
Includes S3 classes for 'GeoJSON' classes with brief summary output,
and a few methods such as extracting and adding bounding boxes,
properties, and coordinate reference systems; working with
newline delimited 'GeoJSON'; and serializing to/from 'Geobuf' binary 'GeoJSON'
format.
Author: Scott Chamberlain [aut] ,
Jeroen Ooms [aut],
Michael Sumner [cre]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between geojson versions 0.3.4 dated 2020-06-23 and 0.3.5 dated 2023-08-08
geojson-0.3.4/geojson/tests/testthat/helper-geojson.R |only geojson-0.3.5/geojson/DESCRIPTION | 28 geojson-0.3.5/geojson/MD5 | 87 - geojson-0.3.5/geojson/NEWS.md | 10 geojson-0.3.5/geojson/R/bbox.R | 8 geojson-0.3.5/geojson/R/crs.R | 6 geojson-0.3.5/geojson/R/geojson-package.R | 4 geojson-0.3.5/geojson/R/linting.R | 73 - geojson-0.3.5/geojson/R/ndgeojson.R | 58 geojson-0.3.5/geojson/R/onLoad.R | 1 geojson-0.3.5/geojson/R/properties.R | 2 geojson-0.3.5/geojson/R/zzz.R | 12 geojson-0.3.5/geojson/README.md | 175 +- geojson-0.3.5/geojson/build/vignette.rds |binary geojson-0.3.5/geojson/inst/doc/geojson-operations.html | 618 +++++----- geojson-0.3.5/geojson/inst/doc/geojson.html | 325 ++--- geojson-0.3.5/geojson/man/bbox.Rd | 2 geojson-0.3.5/geojson/man/crs.Rd | 6 geojson-0.3.5/geojson/man/geojson-package.Rd | 4 geojson-0.3.5/geojson/man/linting_opts.Rd | 16 geojson-0.3.5/geojson/man/ndgeo.Rd | 10 geojson-0.3.5/geojson/man/properties.Rd | 2 geojson-0.3.5/geojson/tests/testthat/test-as.geojson.R | 2 geojson-0.3.5/geojson/tests/testthat/test-bbox.R | 2 geojson-0.3.5/geojson/tests/testthat/test-crs.R | 2 geojson-0.3.5/geojson/tests/testthat/test-feature.R | 30 geojson-0.3.5/geojson/tests/testthat/test-featurecollection.R | 15 geojson-0.3.5/geojson/tests/testthat/test-geo_bbox.R | 2 geojson-0.3.5/geojson/tests/testthat/test-geo_pretty.R | 2 geojson-0.3.5/geojson/tests/testthat/test-geo_type.R | 2 geojson-0.3.5/geojson/tests/testthat/test-geo_write.R | 2 geojson-0.3.5/geojson/tests/testthat/test-geobuf.R | 2 geojson-0.3.5/geojson/tests/testthat/test-geometrycollection.R | 15 geojson-0.3.5/geojson/tests/testthat/test-is.methods.R | 10 geojson-0.3.5/geojson/tests/testthat/test-linestring.R | 16 geojson-0.3.5/geojson/tests/testthat/test-multilinestring.R | 13 geojson-0.3.5/geojson/tests/testthat/test-multipoint.R | 16 geojson-0.3.5/geojson/tests/testthat/test-multipolygon.R | 16 geojson-0.3.5/geojson/tests/testthat/test-ndgeo.R | 4 geojson-0.3.5/geojson/tests/testthat/test-point.R | 20 geojson-0.3.5/geojson/tests/testthat/test-polygon.R | 22 geojson-0.3.5/geojson/tests/testthat/test-properties.R | 2 geojson-0.3.5/geojson/tests/testthat/test-stream_in_geojson.R | 4 geojson-0.3.5/geojson/tests/testthat/test-tibbles.R | 2 geojson-0.3.5/geojson/tests/testthat/test-to_geojson.R | 2 45 files changed, 751 insertions(+), 899 deletions(-)
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre] ,
Jasper Cooper [aut] ,
Alexander Coppock [aut] ,
Macartan Humphreys [aut] ,
Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between DeclareDesign versions 1.0.2 dated 2023-01-10 and 1.0.4 dated 2023-08-08
DESCRIPTION | 6 - MD5 | 96 +++++++++---------- NEWS.md | 5 + R/compare_diagnoses.R | 17 +-- R/construct_design.R | 9 - R/declare_assignment.R | 15 +++ R/declare_diagnosands.R | 73 ++++++++------ R/declare_estimator.R | 7 - R/declare_inquiry.R | 5 + R/declare_measurement.R | 10 +- R/declare_model.R | 85 +++++++++-------- R/declare_reveal.R | 6 + R/declare_sampling.R | 11 +- R/design_helper_functions.R | 75 +++++++++------ R/design_print_summary.R | 26 +---- R/diagnose_design.R | 202 ++++++++++++++++++++++++++++++----------- R/diagnosis_helper_functions.R | 105 ++++++++++++++------- R/draw_functions.R | 22 ++-- R/expand_design.R | 22 ++-- R/modify_design.R | 64 ++++++++++-- R/modify_edit.R | 18 --- R/redesign.R | 89 ++++++++++-------- R/set_citation.R | 10 +- R/set_diagnosands.R | 88 ++++++++++++++--- R/simulate_design.R | 65 +++++++------ inst/CITATION | 34 +++++- man/compare_diagnoses.Rd | 17 +-- man/declare_assignment.Rd | 15 +++ man/declare_design.Rd | 7 - man/declare_diagnosands.Rd | 65 +++++++------ man/declare_estimator.Rd | 7 - man/declare_inquiry.Rd | 5 + man/declare_measurement.Rd | 10 +- man/declare_model.Rd | 85 +++++++++-------- man/declare_reveal.Rd | 6 + man/declare_sampling.Rd | 11 +- man/diagnose_design.Rd | 177 +++++++++++++++++++++++++++-------- man/diagnosis_helpers.Rd | 47 +++++---- man/draw_functions.Rd | 19 ++- man/edit.Rd | 17 --- man/expand_design.Rd | 22 ++-- man/modify_design.Rd | 61 ++++++++++-- man/post_design.Rd | 73 +++++++------- man/redesign.Rd | 38 +++++-- man/reshape_diagnosis.Rd | 44 +++++++- man/run_design.Rd | 16 ++- man/set_citation.Rd | 8 + man/set_diagnosands.Rd | 80 ++++++++++++++-- man/simulate_design.Rd | 48 ++++----- 49 files changed, 1351 insertions(+), 692 deletions(-)
Title: Evaluation of Algorithm Collections Using Item Response Theory
Description: An evaluation framework for algorithm portfolios using Item Response
Theory (IRT). We use continuous and polytomous IRT models to evaluate algorithms and introduce
algorithm characteristics such as stability, effectiveness and anomalousness
(Kandanaarachchi, Smith-Miles 2020) <doi:10.13140/RG.2.2.11363.09760>.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between airt versions 0.2.1 dated 2021-12-17 and 0.2.2 dated 2023-08-08
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Title: Hybrid FA-CFA for Controlling Acquiescence in Restricted
Factorial Solutions
Description: Performs hybrid multi-stage factor analytic procedure for controlling acquiescence in restricted solutions (Ferrando & Lorenzo-Seva, 2000 <https://www.uv.es/revispsi/articulos3.00/ferran7.pdf>).
Author: David Navarro-Gonzalez [aut, cre],
Pere J. Ferrando [aut],
Fabia Morales-Vives [aut],
Ana Hernandez-Dorado [aut]
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>
Diff between siren versions 1.0.1 dated 2022-03-09 and 1.0.3 dated 2023-08-08
DESCRIPTION | 8 ++--- MD5 | 14 ++++---- NAMESPACE | 1 R/acquihybrid.R | 79 +++++++++++++++++++++++++++++++++++++++++++++----- build/partial.rdb |binary man/acquihybrid.Rd | 12 +++---- man/psymas.Rd | 2 - man/siren-internal.Rd | 3 - 8 files changed, 91 insertions(+), 28 deletions(-)
Title: Detect Copy Number Variants from SNPs Data
Description: Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).
Author: Piyal Karunarathne [aut, cre] ,
Qiujie Zhou [aut] ,
Klaus Schliep [aut] ,
Pascal Milesi [aut]
Maintainer: Piyal Karunarathne <piyalkarumail@yahoo.com>
Diff between rCNV versions 1.1.0 dated 2022-10-26 and 1.2.0 dated 2023-08-08
DESCRIPTION | 11 +-- MD5 | 28 ++++---- NEWS.md | 7 ++ R/TMM_normalz.R | 9 +- R/bias.det.R | 118 +++++++++++++++++++++++++++++++++- R/detect.R | 84 +++++++++++++++++++++++- R/raw_process.R | 75 +++++++++++---------- R/sim.als.R | 7 +- R/statistics.R | 181 ++++++++++++++++++++++++++++++++++++++++------------- README.md | 4 - inst/CITATION | 25 ++----- man/allele.info.Rd | 2 man/cnv.Rd | 7 ++ man/cpm.normal.Rd | 2 man/relatedness.Rd | 2 15 files changed, 430 insertions(+), 132 deletions(-)
Title: Event Prediction for Time-to-Event Endpoints
Description: Implements the hybrid framework for event prediction described in Fang & Zheng (2011, <doi:10.1016/j.cct.2011.05.013>). To estimate the survival function the event prediction is based on, a piecewise exponential hazard function is fit to the time-to-event data to infer the potential change points. Prior to the last identified change point, the survival function is estimated using Kaplan-Meier, and the tail after the change point is fit using piecewise exponential.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>
Diff between eventTrack versions 1.0.2 dated 2022-08-25 and 1.0.3 dated 2023-08-08
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eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-3_eef35482668dfea612c5c0cac8b4cd37.rdx |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-4_0c47ebdd22823cf75cc23590299148f0.RData |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-4_0c47ebdd22823cf75cc23590299148f0.rdb |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-4_0c47ebdd22823cf75cc23590299148f0.rdx |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-5_e43144d65d50855919fcd1a5c73d6e21.RData |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-5_e43144d65d50855919fcd1a5c73d6e21.rdb |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-5_e43144d65d50855919fcd1a5c73d6e21.rdx |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-6_bca4a446631d260a19acbb8e66c7ff21.RData |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-6_bca4a446631d260a19acbb8e66c7ff21.rdb |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-6_bca4a446631d260a19acbb8e66c7ff21.rdx |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-7_b283876d9ce3582ff85b495996dbc356.RData |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-7_b283876d9ce3582ff85b495996dbc356.rdb |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-7_b283876d9ce3582ff85b495996dbc356.rdx |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-8_78689dd487c4c9a048058f825f816a38.RData |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-8_78689dd487c4c9a048058f825f816a38.rdb |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-8_78689dd487c4c9a048058f825f816a38.rdx |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-9_4cf5687c3d7504d01b242bb2c19c0f12.RData |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-9_4cf5687c3d7504d01b242bb2c19c0f12.rdb |only eventTrack-1.0.3/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-9_4cf5687c3d7504d01b242bb2c19c0f12.rdx |only 113 files changed, 885 insertions(+), 600 deletions(-)
Title: Goodness-of-Fit Test for Weibull Distribution (Weibullness)
Description: Performs a goodness-of-fit test for Weibull distribution (weibullness test) and provides the parameter estimates of the two- and three-parameter Weibull distributions. Note that the threshold parameter is estimated based on the correlation from the Weibull plot. For more details, see <doi:10.23055/ijietap.2017.24.4.2848>, <doi:10.1155/2018/6056975>, and <doi:10.3390/math11143156>. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2022R1A2C1091319, RS-2023-00242528).
Author: Chanseok Park [aut, cre]
Maintainer: Chanseok Park <statpnu@gmail.com>
Diff between weibullness versions 1.22.12 dated 2022-12-02 and 1.23.8 dated 2023-08-08
DESCRIPTION | 12 +-- MD5 | 37 ++++++---- NAMESPACE | 11 ++- R/weibull.estimate.R | 144 +++++++++++++++++++++++++++++++++++++++++- R/weibullness.R | 2 R/wp.plot.R |only build/partial.rdb |binary data/Wdata.rda |only inst/CITATION | 49 +++++++++++--- inst/NEWS.Rd | 7 ++ man/Wdata.Rd |only man/Weibull.Plot.Quantiles.Rd | 2 man/print.weibull.estimate.Rd | 2 man/weibull.ic.Rd |only man/weibull.mle.Rd | 6 + man/weibull.rm.Rd | 2 man/weibull.threshold.Rd | 2 man/weibull.wp.Rd | 12 +-- man/wp.plot.Rd |only man/wp.test.Rd | 2 man/wp.test.critical.Rd | 2 man/wp.test.pvalue.Rd | 2 22 files changed, 241 insertions(+), 53 deletions(-)
Title: Comfortable Search for R Packages on CRAN, Either Directly from
the R Console or with an R Studio Add-in
Description: Search for R packages on CRAN directly from the R console, based on the packages' titles, short and long descriptions, or other fields. Combine multiple keywords with logical operators ('and', 'or'), view detailed information on any package and keep track of the latest package contributions to CRAN. If you don't want to search from the R console, use the comfortable R Studio add-in.
Author: Joachim Zuckarelli [aut, cre]
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between packagefinder versions 0.3.4 dated 2023-01-06 and 0.3.5 dated 2023-08-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 +++++++ R/packagefinder.r | 39 ++++++++++++++++++++++----------------- 4 files changed, 35 insertions(+), 23 deletions(-)
Title: Retrieve Weather Data from the Open-Meteo API
Description: A client for the Open-Meteo API that retrieves Open-Meteo
weather data in a tidy format. No API key is required. The API specification
is located at <https://open-meteo.com/en/docs>.
Author: Tom Pisel [aut, cre, cph]
Maintainer: Tom Pisel <mail@tompisel.com>
Diff between openmeteo versions 0.1.1 dated 2023-03-10 and 0.2.1 dated 2023-08-08
openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-360311.R |only openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-8562a2.json |only openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-a45db0.json |only openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-afa268.json |only openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-bdf28e.R |only openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-ea80bc.json |only openmeteo-0.1.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-fe9da1.json |only openmeteo-0.1.1/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-5aea07.json |only openmeteo-0.1.1/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-6aebf2.json |only openmeteo-0.1.1/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-ac266c.json |only openmeteo-0.1.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-65c285.json |only openmeteo-0.2.1/openmeteo/DESCRIPTION | 8 openmeteo-0.2.1/openmeteo/MD5 | 94 +++++----- openmeteo-0.2.1/openmeteo/NAMESPACE | 4 openmeteo-0.2.1/openmeteo/NEWS.md | 8 openmeteo-0.2.1/openmeteo/R/air_quality.R |only openmeteo-0.2.1/openmeteo/R/climate_forecast.R |only openmeteo-0.2.1/openmeteo/R/geocode.R | 4 openmeteo-0.2.1/openmeteo/R/marine_forecast.R |only openmeteo-0.2.1/openmeteo/R/openmeteo.R | 13 - openmeteo-0.2.1/openmeteo/R/river_discharge.R |only openmeteo-0.2.1/openmeteo/R/utils.R | 14 - openmeteo-0.2.1/openmeteo/R/weather_forecast.R | 2 openmeteo-0.2.1/openmeteo/R/weather_history.R | 3 openmeteo-0.2.1/openmeteo/R/weather_now.R | 1 openmeteo-0.2.1/openmeteo/README.md | 29 +-- openmeteo-0.2.1/openmeteo/man/air_quality.Rd |only openmeteo-0.2.1/openmeteo/man/climate_forecast.Rd |only openmeteo-0.2.1/openmeteo/man/geocode.Rd | 4 openmeteo-0.2.1/openmeteo/man/marine_forecast.Rd |only openmeteo-0.2.1/openmeteo/man/openmeteo.Rd | 16 + openmeteo-0.2.1/openmeteo/man/river_discharge.Rd |only openmeteo-0.2.1/openmeteo/man/weather_forecast.Rd | 2 openmeteo-0.2.1/openmeteo/man/weather_history.Rd | 3 openmeteo-0.2.1/openmeteo/tests/testthat/air-quality-api.open-meteo.com |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-073b9d.json |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-5c7be9.R |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-7d2d21.R |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-870826.json |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-b38ace.json |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-d1305e.json |only openmeteo-0.2.1/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-dfbcef.json |only openmeteo-0.2.1/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-43cae1.json |only openmeteo-0.2.1/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-466132.json |only openmeteo-0.2.1/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-f5378f.json |only openmeteo-0.2.1/openmeteo/tests/testthat/climate-api.open-meteo.com |only openmeteo-0.2.1/openmeteo/tests/testthat/flood-api.open-meteo.com |only openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-03439e.json |only openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-053f48.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-2728d6.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-307695.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-3581ca.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-3655a5.json |only openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-415fcc.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-4200be.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-62759c.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-83a9f2.json |only openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-93c3e8.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-d132b4.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-ecd5a0.json | 2 openmeteo-0.2.1/openmeteo/tests/testthat/marine-api.open-meteo.com |only openmeteo-0.2.1/openmeteo/tests/testthat/test-air_quality.R |only openmeteo-0.2.1/openmeteo/tests/testthat/test-climate_forecast.R |only openmeteo-0.2.1/openmeteo/tests/testthat/test-marine_forecast.R |only openmeteo-0.2.1/openmeteo/tests/testthat/test-river_discharge.R |only openmeteo-0.2.1/openmeteo/tests/testthat/test-utils.R | 9 openmeteo-0.2.1/openmeteo/tests/testthat/test-weather_forecast.R | 7 openmeteo-0.2.1/openmeteo/tests/testthat/test-weather_history.R | 1 68 files changed, 145 insertions(+), 97 deletions(-)
Title: Statistics for Matrix Distributions
Description: Tools for phase-type distributions including the following variants:
continuous, discrete, multivariate, in-homogeneous, right-censored, and regression.
Methods for functional evaluation, simulation and estimation using the
expectation-maximization (EM) algorithm are provided for all models.
The methods of this package are based on the following references.
Asmussen, S., Nerman, O., & Olsson, M. (1996). Fitting phase-type distributions via the EM algorithm,
Olsson, M. (1996). Estimation of phase-type distributions from censored data,
Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60>,
Albrecher, H., Bladt, M., & Yslas, J. (2022) <doi:10.1111/sjos.12505>,
Albrecher, H., Bladt, M., Bladt, M., & Yslas, J. (2022) <doi:10.1016/j.insmatheco.2022.08.001>,
Bladt, M., & Yslas, J. (2022) <doi:10.1080/03461238.2022.2097019>,
Bladt, M. (2022) <doi:10.1017/asb.2021.40>,
Bladt, M. (2023) <doi:10.1080/10920277.2023.2167833>,
Albrecher, [...truncated...]
Author: Martin Bladt [aut, cre],
Jorge Yslas [aut],
Alaric Mueller [ctb]
Maintainer: Martin Bladt <martinbladt@gmail.com>
Diff between matrixdist versions 1.1.8 dated 2023-04-07 and 1.1.9 dated 2023-08-08
matrixdist-1.1.8/matrixdist/man/logLikelihoodMgompertz_RK.Rd |only matrixdist-1.1.8/matrixdist/man/logLikelihoodMloglogistic_RK.Rd |only matrixdist-1.1.8/matrixdist/man/logLikelihoodMlognormal_RK.Rd |only matrixdist-1.1.8/matrixdist/man/logLikelihoodMpareto_RK.Rd |only matrixdist-1.1.8/matrixdist/man/logLikelihoodMweibull_RK.Rd |only matrixdist-1.1.8/matrixdist/man/matrix_vanloan.Rd |only matrixdist-1.1.8/matrixdist/man/mgompertzcdf.Rd |only matrixdist-1.1.8/matrixdist/man/mgompertzden.Rd |only matrixdist-1.1.8/matrixdist/man/mloglogisticcdf.Rd |only matrixdist-1.1.8/matrixdist/man/mloglogisticden.Rd |only matrixdist-1.1.8/matrixdist/man/mlognormalcdf.Rd |only matrixdist-1.1.8/matrixdist/man/mlognormalden.Rd |only matrixdist-1.1.8/matrixdist/man/mparetocdf.Rd |only matrixdist-1.1.8/matrixdist/man/mparetoden.Rd |only matrixdist-1.1.8/matrixdist/man/mweibullcdf.Rd |only matrixdist-1.1.8/matrixdist/man/mweibullden.Rd |only matrixdist-1.1.9/matrixdist/DESCRIPTION | 8 - matrixdist-1.1.9/matrixdist/MD5 | 64 +++++----- matrixdist-1.1.9/matrixdist/NEWS.md | 10 + matrixdist-1.1.9/matrixdist/R/1.ph.R | 14 +- matrixdist-1.1.9/matrixdist/R/2b.iph_regression.R | 6 matrixdist-1.1.9/matrixdist/R/3b.miph.MoE.R | 12 - matrixdist-1.1.9/matrixdist/R/5.phMoE.R | 13 +- matrixdist-1.1.9/matrixdist/R/7.dph.R | 7 + matrixdist-1.1.9/matrixdist/R/8.bivdph.R | 7 + matrixdist-1.1.9/matrixdist/R/9.mdph.R | 9 + matrixdist-1.1.9/matrixdist/man/MoE-bivdph-method.Rd | 8 + matrixdist-1.1.9/matrixdist/man/MoE-dph-method.Rd | 8 + matrixdist-1.1.9/matrixdist/man/MoE-mdph-method.Rd | 8 + matrixdist-1.1.9/matrixdist/man/MoE-mph-method.Rd | 12 - matrixdist-1.1.9/matrixdist/man/MoE-ph-method.Rd | 8 + matrixdist-1.1.9/matrixdist/man/logLikelihoodMGompertz_RK.Rd |only matrixdist-1.1.9/matrixdist/man/logLikelihoodMLogLogistic_RK.Rd |only matrixdist-1.1.9/matrixdist/man/logLikelihoodMLogNormal_RK.Rd |only matrixdist-1.1.9/matrixdist/man/logLikelihoodMPareto_RK.Rd |only matrixdist-1.1.9/matrixdist/man/logLikelihoodMWeibull_RK.Rd |only matrixdist-1.1.9/matrixdist/man/mGompertzcdf.Rd |only matrixdist-1.1.9/matrixdist/man/mGompertzden.Rd |only matrixdist-1.1.9/matrixdist/man/mLogLogisticcdf.Rd |only matrixdist-1.1.9/matrixdist/man/mLogLogisticden.Rd |only matrixdist-1.1.9/matrixdist/man/mLogNormalcdf.Rd |only matrixdist-1.1.9/matrixdist/man/mLogNormalden.Rd |only matrixdist-1.1.9/matrixdist/man/mParetocdf.Rd |only matrixdist-1.1.9/matrixdist/man/mParetoden.Rd |only matrixdist-1.1.9/matrixdist/man/mWeibullcdf.Rd |only matrixdist-1.1.9/matrixdist/man/mWeibullden.Rd |only matrixdist-1.1.9/matrixdist/man/matrix_VanLoan.Rd |only matrixdist-1.1.9/matrixdist/man/mdph.Rd | 3 matrixdist-1.1.9/matrixdist/man/reg-ph-method.Rd | 7 + 49 files changed, 148 insertions(+), 56 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for
the sample selection bias from observed outcomes in matching
markets. This includes one-sided matching of agents into groups
(Klein, 2015) <https://www.econ.cam.ac.uk/research-files/repec/cam/pdf/cwpe1521.pdf>
as well as two-sided matching of students to schools
(Aue et al., 2020) <https://ftp.zew.de/pub/zew-docs/dp/dp20032.pdf>.
The package also contains algorithms to find stable matchings
in the three most common matching problems: the stable roommates
problem (Irving, 1985) <doi:10.1016/0196-6774(85)90033-1>,
the college admissions problem (Gale and Shapley, 1962) <doi:10.2307/2312726>,
and the house allocation problem (Shapley and Scarf, 1974) <doi:10.1016/0304-4068(74)90033-0>.
Author: Thilo Klein [aut, cre, cph],
Robert Aue [ctb],
Fahiem Bacchus [cph],
Sven Giegerich [ctb],
Matthias Hericks [ctb],
Alexander Sauer [ctb],
Niklas Sorensson [cph]
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 1.0-3 dated 2023-07-21 and 1.0-4 dated 2023-08-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 2 +- inst/doc/matching.pdf |binary inst/include/IntTypes.h | 2 +- man/matchingMarkets-package.Rd | 2 +- src/kprmatcher.cc | 2 +- 7 files changed, 14 insertions(+), 14 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Reproducibility for Interval-Censored Data
Description: Calculates intraclass correlation coefficient (ICC) for assessing reproducibility of interval-censored data with two repeated measurements (Kovacic and Varnai (2014) <doi:10.1097/EDE.0000000000000139>). ICC is estimated by maximum likelihood from model with one fixed and one random effect (both intercepts). Help in model checking (normality of subjects' means and residuals) is provided.
Author: Jelena Kovacic
Maintainer: Jelena Kovacic <jkovacic@imi.hr>
Diff between iRepro versions 1.1 dated 2018-06-12 and 1.2 dated 2023-08-08
iRepro-1.1/iRepro/man/iRepro-internal.Rd |only iRepro-1.2/iRepro/DESCRIPTION | 8 - iRepro-1.2/iRepro/MD5 | 11 +- iRepro-1.2/iRepro/R/iRepro-internal.R | 127 ------------------------------- iRepro-1.2/iRepro/man/iRepro-package.Rd | 4 iRepro-1.2/iRepro/man/ntest.means.Rd | 2 iRepro-1.2/iRepro/man/ntest.res.Rd | 2 7 files changed, 13 insertions(+), 141 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Author: David Hodge [aut, cre, cph] ,
Nik Mitchell [ctb]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 3.0.0 dated 2023-06-30 and 4.0.0 dated 2023-08-08
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Title: Chinese Name Database 1930-2008
Description: A database of Chinese surnames and Chinese given names (1930-2008).
This database contains nationwide frequency statistics of
1,806 Chinese surnames and 2,614 Chinese characters used in given names,
covering about 1.2 billion Han Chinese population
(96.8% of the Han Chinese household-registered population
born from 1930 to 2008 and still alive in 2008).
This package also contains a function for computing multiple features of
Chinese surnames and Chinese given names for scientific research (e.g.,
name uniqueness, name gender, name valence, and name warmth/competence).
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between ChineseNames versions 1.1.1 dated 2021-11-29 and 2023.8 dated 2023-08-08
ChineseNames-1.1.1/ChineseNames/inst |only ChineseNames-2023.8/ChineseNames/DESCRIPTION | 39 - ChineseNames-2023.8/ChineseNames/MD5 | 26 - ChineseNames-2023.8/ChineseNames/NEWS.md | 14 ChineseNames-2023.8/ChineseNames/R/ChineseNames.R | 325 ++++++------- ChineseNames-2023.8/ChineseNames/README.md | 70 +- ChineseNames-2023.8/ChineseNames/build |only ChineseNames-2023.8/ChineseNames/man/ChineseNames.Rd | 10 ChineseNames-2023.8/ChineseNames/man/compute_name_index.Rd | 38 - ChineseNames-2023.8/ChineseNames/man/familyname.Rd | 2 ChineseNames-2023.8/ChineseNames/man/givenname.Rd | 2 ChineseNames-2023.8/ChineseNames/man/population.Rd | 2 ChineseNames-2023.8/ChineseNames/man/top1000name.prov.Rd | 2 ChineseNames-2023.8/ChineseNames/man/top100name.year.Rd | 2 ChineseNames-2023.8/ChineseNames/man/top50char.year.Rd | 2 15 files changed, 280 insertions(+), 254 deletions(-)
Title: Bayesian Consensus Clustering for Multiple Longitudinal Features
Description: It is very common nowadays for a study to collect multiple
features and appropriately integrating multiple longitudinal features
simultaneously for defining individual clusters becomes increasingly
crucial to understanding population heterogeneity and predicting
future outcomes. 'BCClong' implements a Bayesian consensus clustering
(BCC) model for multiple longitudinal features via a generalized
linear mixed model. Compared to existing packages, several key
features make the 'BCClong' package appealing: (a) it allows
simultaneous clustering of mixed-type (e.g., continuous, discrete and
categorical) longitudinal features, (b) it allows each longitudinal
feature to be collected from different sources with measurements taken
at distinct sets of time points (known as irregularly sampled
longitudinal data), (c) it relaxes the assumption that all features
have the same clustering structure by estimating the feature-specific
(local) clusterings and consensus (global) clustering.
Author: Zhiwen Tan [aut, cre],
Zihang Lu [ctb],
Chang Shen [ctb]
Maintainer: Zhiwen Tan <21zt9@queensu.ca>
Diff between BCClong versions 1.0.0 dated 2023-01-13 and 1.0.1 dated 2023-08-08
DESCRIPTION | 6 MD5 | 34 - R/RcppExports.R | 4 R/Trajplot.R | 8 R/bccLong.R | 95 ++-- build/vignette.rds |binary inst/CITATION | 23 - inst/doc/ContinuousData.Rmd | 4 inst/doc/ContinuousData.html | 895 ++++++++++++++++++++---------------------- inst/doc/MixedTypeData.html | 296 +++++++------ man/BCC.multi.Rd | 17 src/BCC.cpp | 88 +--- src/Makevars | 5 src/Makevars.win | 5 src/RcppExports.cpp | 9 tests/testthat.R | 24 - tests/testthat/test-bccLong.R | 6 vignettes/ContinuousData.Rmd | 4 18 files changed, 742 insertions(+), 781 deletions(-)
Title: Bayesian Mode Inference
Description: A Bayesian approach for mode inference which works in two steps. First, a mixture distribution is
fitted on the data using a sparse finite mixture (SFM) Markov chain Monte Carlo
(MCMC) algorithm following Malsiner-Walli, Frühwirth-Schnatter and Grün (2016)
<doi:10.1007/s11222-014-9500-2>). The number of mixture components does not have
to be known; the size of the mixture is estimated endogenously through the SFM
approach. Second, the modes of the estimated mixture at each MCMC draw are retrieved
using algorithms specifically tailored for mode detection. These estimates are then
used to construct posterior probabilities for the number of modes, their locations
and uncertainties, providing a powerful tool for mode inference.
Author: Nalan Bastuerk [aut],
Jamie Cross [aut],
Peter de Knijff [aut],
Lennart Hoogerheide [aut],
Paul Labonne [aut, cre],
Herman van Dijk [aut]
Maintainer: Paul Labonne <paul.labonne@bi.no>
Diff between BayesMultiMode versions 0.5.1 dated 2023-04-06 and 0.6.0 dated 2023-08-08
DESCRIPTION | 6 - MD5 | 64 ++++++++-------- NEWS.md | 8 +- R/MEM.R | 41 +++++++--- R/bayes_estimation.R | 119 ++++++++++++++++++++++++++---- R/bayes_mode.R | 96 ++++++++++++++++++------ R/bayes_trace.R | 8 +- R/discrete_MF.R | 32 ++++++-- R/fixed_point.R | 46 ++++++++--- R/gibbs_SFM_normal.R | 2 R/gibbs_SFM_poisson.R | 2 R/gibbs_SFM_sp.R | 3 R/new_BayesMixture.R | 58 ++++++++++---- R/plot_methods.R | 28 ++++--- R/summary_methods.R | 8 +- README.md | 119 +++++++++++++++--------------- build/partial.rdb |binary inst/REFERENCES.bib | 13 +++ man/MEM.Rd | 39 +++++++-- man/bayes_estimation.Rd | 116 +++++++++++++++++++++++++---- man/bayes_mode.Rd | 85 +++++++++++++++++---- man/bayes_trace.Rd | 8 +- man/discrete_MF.Rd | 30 +++++-- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-5-1.png |binary man/fixed_point.Rd | 40 ++++++++-- man/gibbs_SFM_normal.Rd | 2 man/new_BayesMixture.Rd | 55 ++++++++++--- man/plot.BayesMixture.Rd | 6 - man/plot.BayesMode.Rd | 6 - man/summary.BayesMode.Rd | 6 - tests/testthat/test-bayes_mode.R |only tests/testthat/test-new_BayesMixture.R | 32 +++++++- 34 files changed, 801 insertions(+), 277 deletions(-)
More information about BayesMultiMode at CRAN
Permanent link
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 0.7.1 dated 2023-07-14 and 0.7.2 dated 2023-08-08
DESCRIPTION | 6 +-- MD5 | 51 +++++++++++++------------- NAMESPACE | 1 NEWS.md | 18 +++++++-- R/interface.R | 8 ++++ R/tree-sequences.R | 29 +++++++++++++++ R/visualization.R | 28 +++++++++++--- inst/doc/vignette-00-installation.Rmd | 12 ++++-- inst/doc/vignette-00-installation.html | 31 +++++++++++++--- inst/doc/vignette-01-tutorial.html | 8 ++-- inst/doc/vignette-02-grid-model.html | 8 ++-- inst/doc/vignette-05-tree-sequences.html | 6 +-- inst/doc/vignette-07-backends.html | 2 - inst/doc/vignette-08-nonslendr-tskit.html | 4 +- inst/doc/vignette-09-paper.html | 8 ++-- man/plot_model.Rd | 14 ++++++- man/ts_names.Rd |only tests/testthat/f4_Linux.tsv.gz |binary tests/testthat/f4ratio_Linux.tsv.gz |binary tests/testthat/test-ibd.R | 2 - tests/testthat/test-interaction-changes.R | 4 +- tests/testthat/test-msprime-geneflow.R | 58 +++++++++++++++--------------- tests/testthat/test-msprime.R | 4 +- tests/testthat/test-population.R | 20 ++++++++++ tests/testthat/test-ts.R | 30 +++++++++++++++ tests/testthat/test-utililites.R | 6 +++ vignettes/vignette-00-installation.Rmd | 12 ++++-- 27 files changed, 270 insertions(+), 100 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 0.2.4 dated 2023-01-20 and 0.3.0 dated 2023-08-08
DESCRIPTION | 38 - MD5 | 234 ++++--- NAMESPACE | 3 NEWS.md | 50 + R/audit-cols-minimal.R | 4 R/audit.R | 175 +++-- R/baseline-consistency-tests.R |only R/before-inside-parens.R | 18 R/data-doc.R | 50 - R/debit-map-seq.R | 5 R/debit-map-total-n.R | 16 R/debit-map.R | 1 R/debit-plot.R | 59 - R/debit-table.R | 14 R/decimal-places.R | 11 R/disperse.R | 21 R/duplicate-count-colpair.R | 140 ++-- R/duplicate-count.R | 178 +++-- R/duplicate-detect.R | 325 +++++++--- R/function-factory-helpers.R | 10 R/function-map-seq.R | 371 +++++------ R/function-map-total-n.R | 727 ++++++++++++++--------- R/function-map.R | 170 ++--- R/grim-map-seq.R | 23 R/grim-map.R | 1 R/grim-plot.R | 2 R/grimmer-map-seq.R | 9 R/grimmer-map-total-n.R | 4 R/grimmer-map.R | 18 R/grimmer.R | 10 R/mapper-function-helpers.R | 52 - R/method-audit-seq.R | 4 R/method-audit-total-n.R | 4 R/method-debit-map.R | 4 R/method-detect.R | 46 - R/method-dup-count-colpair.R | 36 - R/method-dup-count.R | 27 R/method-grim-map.R | 4 R/method-grim-sequence.R | 4 R/method-grimmer-map.R | 4 R/method-tally.R |only R/reround.R | 2 R/restore-zeros.R | 63 + R/reverse-map-seq.R | 20 R/reverse-map-total-n.R | 11 R/round.R | 2 R/row-to-colnames.R | 4 R/scrutiny-package.R |only R/seq-decimal.R | 16 R/seq-disperse.R | 8 R/seq-length.R | 11 R/split-by-parens.R | 6 R/unround.R | 9 R/utils.R | 202 ++++-- R/write-doc-audit.R | 33 - README.md | 40 - build/partial.rdb |only build/vignette.rds |binary data/pigs1.rda |binary data/pigs2.rda |binary data/pigs3.rda |binary data/pigs4.rda |binary data/pigs5.rda |binary inst/doc/consistency-tests.Rmd | 8 inst/doc/consistency-tests.html | 708 +++++++++++----------- inst/doc/debit.html | 403 ++++++------ inst/doc/duplicates.R |only inst/doc/duplicates.Rmd |only inst/doc/duplicates.html |only inst/doc/grim.html | 582 +++++++++--------- inst/doc/grimmer.html | 410 ++++++------ inst/doc/infrastructure.html | 364 +++++------ inst/doc/related.Rmd | 2 inst/doc/related.html | 6 inst/doc/rounding.html | 348 +++++------ inst/doc/wrangling.Rmd | 2 inst/doc/wrangling.html | 385 ++++++------ man/audit-special.Rd |only man/audit.Rd | 59 - man/audit_list.Rd |only man/debit_map_seq.Rd | 17 man/debit_map_total_n.Rd | 26 man/duplicate_count.Rd | 64 +- man/duplicate_count_colpair.Rd | 50 - man/duplicate_detect.Rd | 74 +- man/duplicate_tally.Rd |only man/figures/README-unnamed-chunk-6-1.png |binary man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/function_map.Rd | 9 man/function_map_seq.Rd | 105 +-- man/function_map_total_n.Rd | 108 --- man/grim_map_seq.Rd | 15 man/grim_map_total_n.Rd | 10 man/grimmer.Rd | 2 man/grimmer_map.Rd | 6 man/grimmer_map_seq.Rd | 21 man/grimmer_map_total_n.Rd | 14 man/pigs1.Rd | 4 man/pigs2.Rd | 3 man/pigs3.Rd | 4 man/pigs4.Rd | 15 man/restore_zeros.Rd | 10 man/scrutiny-package.Rd |only man/write_doc_factory_map_conventions.Rd | 12 tests/testthat/test-audit.R | 33 - tests/testthat/test-baseline-consistency-tests.R |only tests/testthat/test-debit-map.R | 79 -- tests/testthat/test-duplicate-count-colpair.R | 106 +++ tests/testthat/test-duplicate-count.R | 279 +++++++- tests/testthat/test-duplicate-detect.R |only tests/testthat/test-grim-map-seq.R |only tests/testthat/test-grim-map-total-n.R | 61 + tests/testthat/test-grim-map.R | 8 tests/testthat/test-method-audit-seq.R |only tests/testthat/test-method-audit-total-n.R |only tests/testthat/test-method-detect.R | 99 ++- tests/testthat/test-method-dup-count-colpair.R |only tests/testthat/test-method-dup-count.R |only tests/testthat/test-method-tally.R |only tests/testthat/test-round.R |only tests/testthat/test-utils.R | 8 vignettes/consistency-tests.Rmd | 8 vignettes/duplicates.Rmd |only vignettes/related.Rmd | 2 vignettes/wrangling.Rmd | 2 133 files changed, 4284 insertions(+), 3546 deletions(-)
Title: Word Embedding Research Framework for Psychological Science
Description: An integrative toolbox of word embedding research that provides:
(1) a collection of 'pre-trained' static word vectors in the '.RData'
compressed format <https://psychbruce.github.io/WordVector_RData.pdf>;
(2) a series of functions to process, analyze, and visualize word vectors;
(3) a range of tests to examine conceptual associations, including
the Word Embedding Association Test <doi:10.1126/science.aal4230>
and the Relative Norm Distance <doi:10.1073/pnas.1720347115>,
with permutation test of significance;
(4) a set of training methods to locally train (static) word vectors
from text corpora, including 'Word2Vec' <arXiv:1301.3781>,
'GloVe' <doi:10.3115/v1/D14-1162>, and 'FastText' <arXiv:1607.04606>;
(5) a group of functions to download 'pre-trained' language models
(e.g., 'GPT', 'BERT') and extract contextualized (dynamic) word vectors
(based on the R package 'text').
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between PsychWordVec versions 0.3.2 dated 2023-03-04 and 2023.8 dated 2023-08-08
DESCRIPTION | 42 +++++++++++++++++++++--------------------- MD5 | 22 +++++++++++----------- NEWS.md | 11 +++++++++-- R/01-basic.R | 36 +++++++++++++++++++----------------- R/02-static.R | 4 ++-- R/03-dynamic.R | 15 +++++++++++---- README.md | 20 +++++++++++--------- man/orth_procrustes.Rd | 4 ++-- man/test_RND.Rd | 4 ++-- man/test_WEAT.Rd | 4 ++-- man/text_unmask.Rd | 7 ++++++- man/tokenize.Rd | 4 ++-- 12 files changed, 98 insertions(+), 75 deletions(-)
Title: Projection Based Clustering
Description: A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is based on Thrun and Ultsch, "Using Projection based Clustering to Find Distance and Density based Clusters in High-Dimensional Data" <DOI:10.1007/s00357-020-09373-2>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' softw [...truncated...]
Author: Michael Thrun [aut, cre, cph],
Quirin Stier [ctb, rev] ,
Brinkmann Luca [ctb],
Florian Lerch [aut],
Felix Pape [aut],
Tim Schreier [aut],
Luis Winckelmann [aut],
Kristian Nybo [cph],
Jarkko Venna [cph],
van der Maaten Laurens [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ProjectionBasedClustering versions 1.1.8 dated 2022-05-26 and 1.2.0 dated 2023-08-08
DESCRIPTION | 20 +- MD5 | 43 +++--- NAMESPACE | 29 +--- R/RcppExports.R | 4 R/UniformManifoldApproximationProjection.R | 16 ++ R/interactiveProjectionBasedClustering.R | 19 ++ R/tSNE.R | 134 ++++++++++++++++++- build/partial.rdb |binary inst/CITATION | 4 man/CCA.Rd | 9 - man/PlotProjectedPoints.Rd | 94 ++++++------- man/PolarSwarm.Rd | 2 man/ProjectionBasedClustering-package.Rd | 177 +++++++++++++------------- man/ProjectionBasedClustering.Rd | 2 man/UniformManifoldApproximationProjection.Rd | 10 - man/interactiveGeneralizedUmatrixIsland.Rd | 18 +- man/tSNE.Rd | 34 +++- src/Makevars | 5 src/Makevars.win | 14 +- src/RcppExports.cpp | 23 +++ src/splittree.cpp |only src/splittree.h |only src/tsne.cpp |only src/tsne.h |only src/vptree.h |only 25 files changed, 435 insertions(+), 222 deletions(-)
More information about ProjectionBasedClustering at CRAN
Permanent link
Title: Probabilistic Sex Estimate using Logistic Regression, Based on
VISual Traits of the Human Os Coxae
Description: An R-Shiny application implementing a method of sexing the human os coxae based on logistic regressions and Bruzek's nonmetric traits <doi:10.1002/ajpa.23855>.
Author: Frederic Santos [aut, cre] ,
Élodie Bernardeau [ctb]
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between PELVIS versions 2.0.3 dated 2021-05-07 and 2.0.4 dated 2023-08-08
DESCRIPTION | 8 ++++---- LICENSE | 4 ++-- MD5 | 12 ++++++------ NEWS.md | 8 +++++++- README.md | 25 ++++++++++++++++--------- build/partial.rdb |binary man/PELVIS-package.Rd | 2 -- 7 files changed, 35 insertions(+), 24 deletions(-)
Title: Efficient Algorithm for High-Dimensional Frailty Model
Description: The penalized and non-penalized Minorize-Maximization (MM) method for frailty models to fit the clustered data, multi-event data and recurrent data. Least absolute shrinkage and selection operator (LASSO), minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalized functions are implemented. All the methods are computationally efficient. These general methods are proposed based on the following papers,
Huang, Xu and Zhou (2022) <doi:10.3390/math10040538>,
Huang, Xu and Zhou (2023) <doi:10.1177/09622802221133554>.
Author: Xifen Huang [aut],
Yunpeng Zhou [aut, cre],
Jinfeng Xu [ctb]
Maintainer: Yunpeng Zhou <u3514104@connect.hku.hk>
Diff between frailtyMMpen versions 1.1.2 dated 2023-07-07 and 1.2.1 dated 2023-08-08
frailtyMMpen-1.1.2/frailtyMMpen/data/hdCLdata.RData |only frailtyMMpen-1.1.2/frailtyMMpen/data/simdataCL.RData |only frailtyMMpen-1.1.2/frailtyMMpen/data/simdataME.RData |only frailtyMMpen-1.1.2/frailtyMMpen/data/simdataRE.RData |only frailtyMMpen-1.2.1/frailtyMMpen/DESCRIPTION | 8 frailtyMMpen-1.2.1/frailtyMMpen/MD5 | 33 - frailtyMMpen-1.2.1/frailtyMMpen/NAMESPACE | 1 frailtyMMpen-1.2.1/frailtyMMpen/NEWS.md | 4 frailtyMMpen-1.2.1/frailtyMMpen/R/RcppExports.R | 4 frailtyMMpen-1.2.1/frailtyMMpen/R/fcollect.R | 3 frailtyMMpen-1.2.1/frailtyMMpen/R/frailtyMM.R | 17 frailtyMMpen-1.2.1/frailtyMMpen/R/frailtyMMcal.R | 8 frailtyMMpen-1.2.1/frailtyMMpen/R/frailtyMMpen.R | 71 ++- frailtyMMpen-1.2.1/frailtyMMpen/R/simdata.R | 6 frailtyMMpen-1.2.1/frailtyMMpen/R/zzz.R |only frailtyMMpen-1.2.1/frailtyMMpen/data/hdCLdata.rda |only frailtyMMpen-1.2.1/frailtyMMpen/data/simdataCL.rda |only frailtyMMpen-1.2.1/frailtyMMpen/data/simdataME.rda |only frailtyMMpen-1.2.1/frailtyMMpen/data/simdataRE.rda |only frailtyMMpen-1.2.1/frailtyMMpen/man/hdCLdata.Rd | 8 frailtyMMpen-1.2.1/frailtyMMpen/src/MMroutine.cpp | 386 ++++++++++++++++++- frailtyMMpen-1.2.1/frailtyMMpen/src/RcppExports.cpp | 26 + 22 files changed, 510 insertions(+), 65 deletions(-)
Title: An R Package for the Mean Measure of Divergence (MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Author: Frederic Santos [aut, cre]
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 3.1.0 dated 2020-07-20 and 4.0.2 dated 2023-08-08
DESCRIPTION | 13 LICENSE | 4 MD5 | 40 +- NAMESPACE | 15 NEWS.md | 37 +- R/binary_to_table.R | 48 +- R/mmd.R | 75 ++-- R/mmd_boot.R |only R/plot.anthropmmd_boot.R |only R/plot_mmd.R | 146 +++++--- R/server.R | 25 + R/small_utils.R | 14 README.md | 54 +-- build/vignette.rds |binary inst/doc/intro_AnthropMMD.R | 22 + inst/doc/intro_AnthropMMD.Rmd | 53 ++- inst/doc/intro_AnthropMMD.html | 711 ++++++++++++++++++++++++++--------------- man/AnthropMMD-package.Rd | 4 man/mmd.Rd | 8 man/mmd_boot.Rd |only man/plot.anthropmmd_boot.Rd |only vignettes/biblio.bib | 25 + vignettes/intro_AnthropMMD.Rmd | 53 ++- 23 files changed, 896 insertions(+), 451 deletions(-)
Title: Graph Neural Network-Based Framework for Single Cell Active
Pathways and Gene Modules Analysis
Description: It is a single cell active pathway analysis tool based on the graph neural network (F. Scarselli (2009) <doi:10.1109/TNN.2008.2005605>; Thomas N. Kipf (2017) <arXiv:1609.02907v4>) to construct the gene-cell association network, infer pathway activity scores from different single cell modalities data, integrate multiple modality data on the same cells into one pathway activity score matrix, identify cell phenotype activated gene modules and parse association networks of gene modules under multiple cell phenotype. In addition, abundant visualization programs are provided to display the results.
Author: Xudong Han [aut, cre, cph],
Xujiang Guo [fnd]
Maintainer: Xudong Han <hanxd1217@163.com>
Diff between scapGNN versions 0.1.3 dated 2022-12-02 and 0.1.4 dated 2023-08-08
DESCRIPTION | 12 - MD5 | 44 ++-- NAMESPACE | 2 R/ConNetGNN.R | 64 ++++--- R/InteNet.R | 25 ++ R/Preprocessing.R | 59 ++++-- R/cpGModule.R | 28 ++- R/plotCCNetwork.R | 102 +++++++---- R/plotGANetwork.R | 2 R/scPathway.R | 101 ++++++++--- build/vignette.rds |binary inst/doc/vignette.R | 1 inst/doc/vignette.Rmd | 8 inst/doc/vignette.html | 356 ++++++++++++++++++++-------------------- inst/python/AutoEncoder.py | 18 +- inst/python/GraphAutoEncoder.py | 244 +++++++++------------------ man/ConNetGNN.Rd | 12 - man/Preprocessing.Rd | 32 ++- man/cpGModule.Rd | 3 man/plotCCNetwork.Rd | 5 man/plotGANetwork.Rd | 2 man/scPathway.Rd | 12 + vignettes/vignette.Rmd | 8 23 files changed, 628 insertions(+), 512 deletions(-)
Title: Translate Text
Description: The goal of the this package is to provide easy methods to
translate pieces of text. Functions send requests to translation services online.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between polyglotr versions 1.2.0 dated 2023-07-17 and 1.2.1 dated 2023-08-08
DESCRIPTION | 6 - MD5 | 51 +++++------ NAMESPACE | 22 ++--- NEWS.md | 2 R/create_translation_table.R | 62 +++++++------- R/google_translate.R | 116 +++++++++++++------------- R/google_translate_file.R | 86 +++++++++---------- R/language_detect.R | 54 ++++++------ R/linguee_word_translation.R | 92 ++++++++++---------- R/mymemory_translate.R | 64 +++++++------- README.md | 120 ++++++++++++++------------- inst/doc/Movie_Reviews.Rmd | 136 +++++++++++++++---------------- inst/doc/Movie_Reviews.html | 4 inst/doc/polyglotr.Rmd | 114 ++++++++++++------------- man/create_translation_table.Rd | 50 +++++------ man/google_translate.Rd | 62 +++++++------- man/language_detect.Rd | 34 +++---- man/linguee_word_translation.Rd | 76 ++++++++--------- man/mymemory_translate.Rd | 52 +++++------ man/translate_file.Rd | 60 ++++++------- tests/testthat.R | 20 ++-- tests/testthat/helpers.R |only tests/testthat/test-google_translate.R | 52 +++++------ tests/testthat/test-language_detect.R | 14 +-- tests/testthat/test-mymemory_translate.R | 20 ++-- vignettes/Movie_Reviews.Rmd | 136 +++++++++++++++---------------- vignettes/polyglotr.Rmd | 114 ++++++++++++------------- 27 files changed, 814 insertions(+), 805 deletions(-)
Title: Network Meta-Analysis Based on Multivariate Meta-Analysis Models
Description: Network meta-analysis tools based on contrast-based approach using the multivariate meta-analysis and meta-regression models (Noma et al. (2023) <Forthcoming>). Standard analysis tools for network meta-analysis and meta-regression (e.g., synthesis analysis, ranking analysis, and creating league table) are available by simple commands. For inconsistency analyses, the local and global inconsistency tests based on the Higgins' design-by-treatment interaction model can be applied. Also, the side-splitting and the Jackson's random inconsistency model are available. Standard graphical tools for network meta-analysis (e.g., network plot, ranked forest plot, and transitivity analysis) can also be utilized. For the synthesis analyses, the Noma-Hamura's improved REML (restricted maximum likelihood)-based methods (Noma et al. (2023) <doi:10.1002/jrsm.1652> <doi:10.1002/jrsm.1651>) are adopted as the default methods.
Author: Hisashi Noma [aut, cre] ,
Kazushi Maruo [aut],
Shiro Tanaka [aut],
Toshi A. Furukawa [aut]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between NMA versions 1.2-1 dated 2023-07-17 and 1.3-1 dated 2023-08-08
DESCRIPTION | 10 +- MD5 | 26 +++-- NAMESPACE | 2 NEWS.md | 5 + R/global.ict.r | 2 R/local.ict.r | 56 ++++++++---- R/nmaQ.r |only R/nmafunnel.r | 4 R/pairwise.r | 16 +-- R/random.icm.r |only R/setup.r | 18 ++-- R/sidesplit.r | 237 ++++++++++++++++++++++++++++++++++------------------- man/NMA-package.Rd | 2 man/nma.Rd | 2 man/nmaQ.Rd |only man/random.icm.Rd |only 16 files changed, 244 insertions(+), 136 deletions(-)
Title: Resolution-Optimised SNPs Searcher
Description: This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) <doi:10.1186/1471-2105-8-278> "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants."
Author: Ludwig Kian Soon Hoon [aut, cre]
,
Peter Shaw [aut, ctb] ,
Phil Giffard [aut, ctb]
Maintainer: Ludwig Kian Soon Hoon <ldwgkshoon@gmail.com>
Diff between minSNPs versions 0.0.4 dated 2023-04-19 and 0.1.0 dated 2023-08-08
DESCRIPTION | 6 MD5 | 51 +++++-- NAMESPACE | 25 +++ NEWS.md | 7 + R/output.R | 38 +++-- R/process.R | 1 R/search.R | 166 ++++++++++++++++++++----- R/search_from_reads.R |only R/search_string_generation.R | 20 ++- R/utility.R | 106 ++++++++++++++- inst/doc/MinSNPs_Workflow.html | 2 man/cal_met_snp.Rd | 1 man/calculate_percent.Rd | 2 man/calculate_simpson.Rd | 2 man/calculate_variant_within_group.Rd |only man/check_multistate.Rd | 1 man/combine_fastq_search_result.Rd |only man/combine_search_string_result.Rd |only man/combine_search_string_result_from_files.Rd |only man/combine_search_string_result_from_list.Rd |only man/estimate_coverage.Rd |only man/find_optimised_snps.Rd | 8 + man/generate_snp_search_string.Rd | 5 man/get_all_process_methods.Rd |only man/get_snps_set.Rd |only man/infer_from_combined.Rd |only man/iterate_through.Rd |only man/output_parsed.Rd | 10 + man/process_kmer_result.Rd |only man/process_result_file.Rd |only man/process_snp_result.Rd |only man/read_sequences_from_fastq.Rd | 9 + man/remove_snp_conflict.Rd |only man/search_from_fastq_reads.Rd |only man/sequence_reads_match_count.Rd |only 35 files changed, 375 insertions(+), 85 deletions(-)
Title: Compare Microbial Networks of 'trans_network' Class of
'microeco' Package
Description: Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>.
This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.
Author: Chi Liu [aut, cre],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between meconetcomp versions 0.2.0 dated 2022-10-05 and 0.3.0 dated 2023-08-08
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ R/edge_comp.R | 1 - R/edge_node_distance.R | 9 +++++---- R/help.R |only R/node_comp.R | 2 +- R/subset_network.R | 49 ++++++++++++++++++++++++++++++++++++++++++------- inst/CITATION | 28 ++++++++++++---------------- man/meconetcomp.Rd |only 9 files changed, 73 insertions(+), 40 deletions(-)
Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation
and initialization of the hidden hybrid Markov/semi-Markov model,
introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>,
which also includes several tools for handling missing data,
nonparametric mixture of B-splines emissions (Langrock et al., 2015
<doi:10.1111/biom.12282>), fitting regime switching regression
(Kim et al., 2008 <doi:10.1016/j.jeconom.2007.10.002>) and auto-regressive
hidden hybrid Markov/semi-Markov model, spline-based nonparametric
estimation of additive state-switching models
(Langrock et al., 2018 <doi:10.1111/stan.12133>)
and many other useful tools
(read for more description: Amini et al., 2022 <doi:10.1007/s00180-022-01248-x> and its
arxiv version: <arXiv:2109.12489>).
Author: Morteza Amini [aut, cre, cph],
Afarin Bayat [aut],
Reza Salehian [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>
Diff between hhsmm versions 0.3.5 dated 2023-03-06 and 0.3.6 dated 2023-08-08
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ R/addpred.R | 8 +++++--- R/densComputeMiss.R | 2 ++ R/dnorm-additive-reg.R | 3 ++- R/initial-cluster.R | 1 + R/mstep-missing-mix-mvnorm.R | 4 ++-- R/symetric.R |only 8 files changed, 23 insertions(+), 16 deletions(-)
Title: Resampling Methods for Triangular and Trapezoidal Fuzzy Numbers
Description: The classical (i.e. Efron's, see Efron and Tibshirani (1994, ISBN:978-0412042317) "An Introduction to the Bootstrap") bootstrap is widely used for both the real (i.e. "crisp") and fuzzy data.
The main aim of the algorithms implemented in this package is to overcome a problem with repetition of a few distinct values and to create fuzzy numbers, which are "similar" (but not the same) to values from the initial sample.
To do this, different characteristics of triangular/trapezoidal numbers are kept (like the value, the ambiguity, etc., see Grzegorzewski et al. <doi:10.2991/eusflat-19.2019.68>, Grzegorzewski et al. (2020) <doi:10.2991/ijcis.d.201012.003>, Grzegorzewski et al. (2020) <doi:10.34768/amcs-2020-0022>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-030-95929-6_3>, Romaniuk and Hryniewicz (2019) <doi:10.1007/s00500-018-3251-5>).
Some additional procedures related to these resampling methods are also provided,
like calculation of the Bertoluz [...truncated...]
Author: Maciej Romaniuk [aut, cre],
Przemyslaw Grzegorzewski [aut],
Olgierd Hryniewicz [aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyResampling versions 0.6.0 dated 2022-12-15 and 0.6.1 dated 2023-08-08
DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- build/partial.rdb |binary inst |only 4 files changed, 9 insertions(+), 8 deletions(-)
More information about FuzzyResampling at CRAN
Permanent link
Title: Descriptive 3D Multidimensional Item Response Theory Modeling
Description: For identifying, estimating, and plotting descriptive multidimensional item response theory models, restricted to 3D and dichotomous or polytomous data that fit the two-parameter logistic model or the graded response model. The method is foremost explorative and centered around the plot function that exposes item characteristics and constructs, represented by vector arrows, located in a three-dimensional interactive space. The results can be useful for item-level analysis as well as test development.
Author: Erik Forsberg [aut, cre, cph]
Maintainer: Erik Forsberg <forsbergpsychometrics@gmail.com>
Diff between D3mirt versions 1.0.5 dated 2023-07-20 and 1.1.0 dated 2023-08-08
DESCRIPTION | 10 MD5 | 49 - NEWS.md | 4 R/D3mirt.R | 38 - R/data.R | 2 R/modid.R | 79 -- R/plotD3mirt.R | 49 - R/printD3mirt.R | 8 R/printmodid.R | 8 R/summaryD3mirt.R | 6 R/summarymodid.R | 8 README.md | 250 +++++---- inst/doc/IntrotoD3mirt.R | 45 - inst/doc/IntrotoD3mirt.Rmd | 506 ++++++------------ inst/doc/IntrotoD3mirt.html | 1193 +++++++++++++++++++++----------------------- man/D3mirt.Rd | 40 - man/anes0809offwaves.Rd | 2 man/modid.Rd | 80 -- man/plot.D3mirt.Rd | 57 -- man/print.D3mirt.Rd | 8 man/print.modid.Rd | 8 man/summary.D3mirt.Rd | 6 man/summary.modid.Rd | 8 vignettes/IntrotoD3mirt.Rmd | 506 ++++++------------ vignettes/efa.Rdata |only vignettes/fscores.Rdata |only vignettes/mod1.Rdata |only 27 files changed, 1301 insertions(+), 1669 deletions(-)
Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected
Areas (WDPA) and the World Database on Other Effective Area-Based
Conservation Measures (WDOECM). Data is obtained from Protected Planet
<https://www.protectedplanet.net/en>. To augment data cleaning procedures,
users can install the 'prepr' R package (available at
<https://github.com/dickoa/prepr>). For more information on this package,
see Hanson (2022) <doi:10.21105/joss.04594>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between wdpar versions 1.3.4 dated 2023-02-24 and 1.3.5 dated 2023-08-08
DESCRIPTION | 12 ++-- MD5 | 24 ++++---- NAMESPACE | 1 NEWS.md | 9 ++- R/internal.R | 6 -- R/package.R | 4 + R/st_erase_overlaps.R | 62 ++++++++++++++------- R/wdpa_url.R | 2 README.md | 32 +++++----- build/vignette.rds |binary inst/doc/wdpar.html | 105 +++++++++++++++++------------------- man/figures/README-readme-map-1.png |binary tests/testthat/test_wdpa_clean.R | 16 +++++ 13 files changed, 157 insertions(+), 116 deletions(-)
Title: Time-Weighted Dynamic Time Warping
Description: Implements Time-Weighted Dynamic Time Warping (TWDTW),
a measure for quantifying time series similarity. The TWDTW algorithm,
described in Maus et al. (2016) <doi:10.1109/JSTARS.2016.2517118> and
Maus et al. (2019) <doi:10.18637/jss.v088.i05>, is applicable to multi-dimensional
time series of various resolutions. It is particularly suitable for comparing
time series with seasonality for environmental and ecological data analysis,
covering domains such as remote sensing imagery, climate data, hydrology,
and animal movement. The 'twdtw' package offers a user-friendly 'R' interface,
efficient 'Fortran' routines for TWDTW calculations, flexible time weighting
definitions, as well as utilities for time series preprocessing and visualization.
Author: Victor Maus [aut, cre]
Maintainer: Victor Maus <vwmaus1@gmail.com>
Diff between twdtw versions 1.0-0 dated 2023-07-13 and 1.0-1 dated 2023-08-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ README.md | 21 ++++++++++++++------- src/twdtwf90.f90 | 10 +++++----- tests/testthat/test-twdtw_calls.R | 9 ++++++++- 6 files changed, 40 insertions(+), 22 deletions(-)
Title: Estimating Hidden Population Size using Respondent Driven
Sampling Data
Description: Estimate the size of a networked population based on
respondent-driven sampling data. The package is part of the "RDS Analyst"
suite of packages for the analysis of respondent-driven sampling data.
See Handcock, Gile and Mar (2014) <doi:10.1214/14-EJS923> and
Handcock, Gile and Mar (2015) <doi:10.1111/biom.12255>.
Author: Mark S. Handcock [aut, cre, cph]
,
Krista J. Gile [aut, cph],
Brian Kim [ctb],
Katherine R. McLaughlin [ctb]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between sspse versions 1.0.3 dated 2022-09-04 and 1.1.0 dated 2023-08-08
DESCRIPTION | 15 +- MD5 | 40 ++++--- NAMESPACE | 2 R/plot.sspse.R | 22 +--- R/poscmp.R | 49 +++++---- R/poscmpwp.R | 48 ++++----- R/pospreddeg.R |only R/posteriorsize.R | 80 ++++++++------- inst/CITATION | 67 +++++++++---- man/figures/reingold.tilford.png |only man/plot.pospreddeg.Rd |only man/plot.sspse.Rd | 11 -- man/pospreddeg.Rd |only man/posteriorsize.Rd | 72 ++++++++------ src/posteriorcmpvis.c | 164 ++++++++++++++++---------------- src/posteriorcmpvis.h | 45 ++++---- src/posteriorcmpvis2.c | 198 +++++++++++++++++---------------------- src/posteriorcmpvis2.h | 18 +-- src/posteriorcmpwpvis.c | 149 +++++++++++++++++------------ src/posteriorcmpwpvis.h | 48 ++++----- src/posteriorcmpwpvis2.c | 180 +++++++++++++++++------------------ src/posteriorcmpwpvis2.h | 67 ++++++------- src/posteriorcmpwpvis_binomial.c |only src/posteriorcmpwpvis_binomial.h |only 24 files changed, 669 insertions(+), 606 deletions(-)
Title: Shape Selection for Landsat Time Series of Forest Dynamics
Description: Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <https://landsat.gsfc.nasa.gov/>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal [...truncated...]
Author: Xiyue Liao [aut, cre] ,
Mary Meyer [aut],
Elizabeth Freeman [aut],
Gretchen Moisen [aut]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between ShapeSelectForest versions 1.5 dated 2022-08-15 and 1.6 dated 2023-08-08
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- inst/CITATION | 13 +++++++++++-- 3 files changed, 19 insertions(+), 10 deletions(-)
More information about ShapeSelectForest at CRAN
Permanent link
Title: Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Description: Downloads, imports, and tidies time series data from the
Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre] ,
Zoe Meers [aut],
Jaron Lee [aut],
David Diviny [aut],
Hugh Parsonage [ctb],
Kinto Behr [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readabs versions 0.4.13 dated 2023-01-29 and 0.4.14 dated 2023-08-08
DESCRIPTION | 18 - MD5 | 111 +++---- NAMESPACE | 4 NEWS.md | 6 R/check_latest_date.R | 1 R/download_abs.R | 2 R/download_data_cube.r | 3 R/fst-utils.R | 29 - R/get_abs_xml_metadata.R | 13 R/read_abs.R | 7 R/read_abs_local.R | 22 - R/read_api.R |only R/read_job_mobility.R | 10 R/read_payrolls.R | 2 R/scrape_abs_catalogues.r | 1 R/search_catalogues.R | 3 R/separate_series.R | 1 R/show_available_catalogues.r | 3 R/show_available_files.r | 4 R/sysdata.rda |binary R/zzz.R | 1 README.md | 394 ++++++++++++++++--------- build/vignette.rds |binary inst/doc/readabs_vignette.R | 38 -- inst/doc/readabs_vignette.Rmd | 38 -- inst/doc/readabs_vignette.html | 386 ++++++++++++------------ man/abs_api.Rd |only man/check_latest_date.Rd | 7 man/download_abs_data_cube.Rd | 17 - man/download_previous_payrolls.Rd | 8 man/extract_abs_sheets.Rd | 6 man/figures/README-all-in-one-example-1.png |binary man/read_abs.Rd | 46 +- man/read_abs_data.Rd | 6 man/read_abs_local.Rd | 34 +- man/read_abs_url.Rd | 12 man/read_awe.Rd | 40 +- man/read_job_mobility.Rd | 4 man/read_lfs_grossflows.Rd | 8 man/read_payrolls.Rd | 34 +- man/search_catalogues.Rd | 13 man/search_files.Rd | 2 man/show_available_catalogues.Rd | 4 man/show_available_files.Rd | 15 man/tidy_abs.Rd | 4 man/tidy_abs_list.Rd | 4 man/tidy_awe.Rd | 2 tests/testthat/test-abs_api.R |only tests/testthat/test-data-uptodate.R | 1 tests/testthat/test-download-data-cube.r | 1 tests/testthat/test-download_abs.R | 2 tests/testthat/test-fst.R | 2 tests/testthat/test-individual-readabs-steps.R | 1 tests/testthat/test-old-functions.R | 1 tests/testthat/test-read_abs_url.R | 13 tests/testthat/test-read_payrolls.R | 1 tests/testthat/test-readabs.R | 12 vignettes/readabs_vignette.Rmd | 38 -- 58 files changed, 773 insertions(+), 662 deletions(-)
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks
(walk, bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks engine
<https://github.com/conveyal/r5>. The package allows users to generate
detailed routing analysis or calculate travel time matrices using
seamless parallel computing on top of the R5 Java machine. While R5
is developed by Conveyal, the package r5r is independently developed
by a team at the Institute for Applied Economic Research (Ipea) with
contributions from collaborators. Apart from the documentation in this
package, users will find additional information on R5 documentation at
<https://docs.conveyal.com/>. Although we try to keep new releases of
r5r in synchrony with R5, the development of R5 follows Conveyal's
independent update process. Hence, users should confirm the R5 version
implied by the Conveyal user manual (see
<https://docs.conveyal.com/changelog>) corresponds with the R5 ver [...truncated...]
Author: Marcus Saraiva [aut] ,
Rafael H. M. Pereira [aut, cre]
,
Daniel Herszenhut [aut] ,
Carlos Kaue Vieira Braga [aut]
,
Matthew Wigginton Conway [aut]
,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 1.0.1 dated 2023-03-06 and 1.1.0 dated 2023-08-08
r5r-1.0.1/r5r/inst/doc/calculating_accessibility.R |only r5r-1.0.1/r5r/inst/doc/calculating_accessibility.Rmd |only r5r-1.0.1/r5r/inst/doc/calculating_accessibility.html |only r5r-1.0.1/r5r/inst/doc/calculating_isochrones.R |only r5r-1.0.1/r5r/inst/doc/calculating_isochrones.Rmd |only r5r-1.0.1/r5r/inst/doc/calculating_isochrones.html |only r5r-1.0.1/r5r/vignettes/calculating_accessibility.Rmd |only r5r-1.0.1/r5r/vignettes/calculating_isochrones.Rmd |only r5r-1.0.1/r5r/vignettes/pandoc16e8532d55d5.html |only r5r-1.1.0/r5r/DESCRIPTION | 15 r5r-1.1.0/r5r/MD5 | 99 - r5r-1.1.0/r5r/NAMESPACE | 1 r5r-1.1.0/r5r/NEWS.md | 19 r5r-1.1.0/r5r/R/accessibility.R | 558 +++++----- r5r-1.1.0/r5r/R/detailed_itineraries.R | 6 r5r-1.1.0/r5r/R/expanded_travel_time_matrix.R | 8 r5r-1.1.0/r5r/R/isochrone.R |only r5r-1.1.0/r5r/R/pareto_frontier.R | 420 +++---- r5r-1.1.0/r5r/R/r5r.R | 186 +-- r5r-1.1.0/r5r/R/setup_r5.R | 372 +++--- r5r-1.1.0/r5r/R/travel_time_matrix.R | 494 ++++---- r5r-1.1.0/r5r/build/partial.rdb |binary r5r-1.1.0/r5r/build/vignette.rds |binary r5r-1.1.0/r5r/inst/doc/accessibility.R |only r5r-1.1.0/r5r/inst/doc/accessibility.Rmd |only r5r-1.1.0/r5r/inst/doc/accessibility.html |only r5r-1.1.0/r5r/inst/doc/detailed_itineraries.Rmd | 4 r5r-1.1.0/r5r/inst/doc/detailed_itineraries.html | 8 r5r-1.1.0/r5r/inst/doc/faq.R |only r5r-1.1.0/r5r/inst/doc/faq.Rmd |only r5r-1.1.0/r5r/inst/doc/faq.html |only r5r-1.1.0/r5r/inst/doc/fare_structure.html | 4 r5r-1.1.0/r5r/inst/doc/isochrones.R |only r5r-1.1.0/r5r/inst/doc/isochrones.Rmd |only r5r-1.1.0/r5r/inst/doc/isochrones.html |only r5r-1.1.0/r5r/inst/doc/pareto_frontier.Rmd | 4 r5r-1.1.0/r5r/inst/doc/pareto_frontier.html | 10 r5r-1.1.0/r5r/inst/doc/r5r.Rmd | 5 r5r-1.1.0/r5r/inst/doc/r5r.html | 11 r5r-1.1.0/r5r/inst/doc/time_window.Rmd | 9 r5r-1.1.0/r5r/inst/doc/time_window.html | 7 r5r-1.1.0/r5r/inst/doc/travel_time_matrix.Rmd | 4 r5r-1.1.0/r5r/inst/doc/travel_time_matrix.html | 8 r5r-1.1.0/r5r/man/accessibility.Rd | 6 r5r-1.1.0/r5r/man/detailed_itineraries.Rd | 6 r5r-1.1.0/r5r/man/expanded_travel_time_matrix.Rd | 9 r5r-1.1.0/r5r/man/isochrone.Rd |only r5r-1.1.0/r5r/man/pareto_frontier.Rd | 6 r5r-1.1.0/r5r/man/roxygen/templates/time_window_related_args.R | 4 r5r-1.1.0/r5r/man/setup_r5.Rd | 2 r5r-1.1.0/r5r/man/travel_time_matrix.Rd | 6 r5r-1.1.0/r5r/tests/tests_rafa/isochrone.R | 338 +++--- r5r-1.1.0/r5r/tests/tests_rafa/test_iso.R |only r5r-1.1.0/r5r/tests/tests_rafa/test_rafa.R | 33 r5r-1.1.0/r5r/tests/testthat/test-isochrone.R |only r5r-1.1.0/r5r/vignettes/accessibility.Rmd |only r5r-1.1.0/r5r/vignettes/detailed_itineraries.Rmd | 4 r5r-1.1.0/r5r/vignettes/faq.Rmd |only r5r-1.1.0/r5r/vignettes/isochrones.Rmd |only r5r-1.1.0/r5r/vignettes/pareto_frontier.Rmd | 4 r5r-1.1.0/r5r/vignettes/r5r.Rmd | 5 r5r-1.1.0/r5r/vignettes/time_window.Rmd | 9 r5r-1.1.0/r5r/vignettes/travel_time_matrix.Rmd | 4 63 files changed, 1401 insertions(+), 1287 deletions(-)
Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, it consists of several functions to perform various tasks, including
simulating or analyzing data, computing the significance thresholds and visualizing the
QTL mapping results. The single-QTL or multiple-QTL method that allows a host of
statistical models to be fitted and compared is applied to analyze the data for the
estimation of QTL parameters. The models include the linear regression, permutation test,
normal mixture model and truncated normal mixture model. The Gaussian stochastic process
is implemented to compute the significance thresholds for QTL detection onto a genetic
linkage map in the experimental populations. Two types of data, the complete genotyping
or selective genotyping data, from various experimental populations, including backcross,
F2, recombinant inbred (RI) populations, advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotpot detection, the statistical methods
can be developed based on either using the [...truncated...]
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut],
Y.-T. Guo [aut],
H.-N. Ho [aut],
H.-I. Lee [aut],
P.-Y. Wu [aut],
M.-H. Yang [aut],
M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 1.2.0 dated 2023-06-05 and 1.3.0 dated 2023-08-08
DESCRIPTION | 22 +++++++++++++++---- MD5 | 34 +++++++++++++++--------------- R/EM.MIM.R | 30 ++++++++++++++++---------- R/EM.MIM2.R | 59 +++++++++++++++++++++++++++++++++++------------------ R/IM.search.R | 28 ++++++++++++++----------- R/IM.search2.R | 28 ++++++++++++++----------- R/MIM.points.R | 21 ++++++++---------- R/MIM.points2.R | 21 ++++++++---------- R/MIM.search.R | 33 +++++++++++++++++++---------- R/MIM.search2.R | 33 +++++++++++++++++++---------- man/EM.MIM.Rd | 9 ++++++-- man/EM.MIM2.Rd | 9 ++++++-- man/IM.search.Rd | 6 ++--- man/IM.search2.Rd | 6 ++--- man/MIM.points.Rd | 4 +-- man/MIM.points2.Rd | 4 +-- man/MIM.search.Rd | 8 +++++-- man/MIM.search2.Rd | 8 +++++-- 18 files changed, 221 insertions(+), 142 deletions(-)
Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the
L0-Pseudonorm
Description: Optimal Subset Cardinality Regression (OSCAR) models offer
regularized linear regression using the L0-pseudonorm, conventionally
known as the number of non-zero coefficients. The package estimates an
optimal subset of features using the L0-penalization via
cross-validation, bootstrapping and visual diagnostics. Effective
Fortran implementations are offered along the package for finding
optima for the DC-decomposition, which is used for transforming the
discrete L0-regularized optimization problem into a continuous
non-convex optimization task. These optimization modules include DBDC
('Double Bundle method for nonsmooth DC optimization' as described in
Joki et al. (2018) <doi:10.1137/16M1115733>) and LMBM ('Limited
Memory Bundle Method for large-scale nonsmooth optimization' as
in Haarala et al. (2004) <doi:10.1080/10556780410001689225>). The
OSCAR models are comprehensively exemplified in Halkola et al. (2023)
<doi:10.1371/journal.pcbi.1010333>). Multiple regression m [...truncated...]
Author: Teemu Daniel Laajala [aut, cre]
,
Kaisa Joki [aut],
Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between oscar versions 1.1.4 dated 2023-03-28 and 1.1.7 dated 2023-08-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/helpers.R | 18 ++++++++++++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/example.R | 6 +++--- inst/doc/example.Rmd | 8 ++++---- inst/doc/example.html | 32 ++++++++++++++++---------------- src/Makevars | 4 +--- src/dbdc.f90 | 6 ++++-- vignettes/example.Rmd | 8 ++++---- 11 files changed, 62 insertions(+), 48 deletions(-)
Title: Clinical Trials with Intercurrent Events Simulator
Description: Simulates clinical trials and summarizes causal effects and treatment policy estimands in the presence of intercurrent events in a transparent and intuitive manner.
Author: Ahmad Hakeem Abdul Wahab [aut, cre]
,
Yongming Qu [aut],
Hege Michiels [aut],
Junxiang Luo [aut],
Run Zhuang [aut],
Dominique McDaniel [aut],
Dong Xi [aut],
Elena Polverejan [aut],
Steven Gilbert [aut],
Stephen Ruberg [aut],
Arman Sabbagh [aut]
Maintainer: Ahmad Hakeem Abdul Wahab <hakeemwahab00@gmail.com>
Diff between cities versions 0.1.2 dated 2023-05-23 and 0.1.3 dated 2023-08-08
DESCRIPTION | 6 MD5 | 14 NAMESPACE | 44 - R/data_generator.R | 1154 ++++++++++++++++++++-------------------- inst/doc/CITIES_demo.R | 67 +- inst/doc/CITIES_demo.Rmd | 1323 +++++++++++++++++++++++----------------------- inst/doc/CITIES_demo.html | 1164 ++++++++++++++++++++-------------------- vignettes/CITIES_demo.Rmd | 1323 +++++++++++++++++++++++----------------------- 8 files changed, 2606 insertions(+), 2489 deletions(-)
Title: Consistency in the Analytic Hierarchy Process
Description: A Swiss Army knife of utility functions for AHP users which will
help you assess the consistency of a PCM as well as improve the
consistency ratio, compute the sensitivity of a PCM, create a logical,
not a random PCM, from the preferences you provide for the alternatives,
and a function that helps evaluate the actual consistency of a PCM based on
objective, fair bench marking. The toolkit additionally allows a user to
specify only the upper triangular comparison ratios of the PCM and performs
its assigned task.
Author: Amarnath Bose [aut, cre]
Maintainer: Amarnath Bose <amarnath.bose@gmail.com>
Diff between AHPtools versions 0.1.0 dated 2023-04-17 and 0.2.0 dated 2023-08-08
DESCRIPTION | 32 ++-- MD5 | 25 ++- NAMESPACE | 3 NEWS.md | 15 +- R/AHPtools.R | 282 +++++++++++++++++++++++++++++++++++++---- build/partial.rdb |only inst/WORDLIST | 12 + inst/doc/AHPtools.html | 2 man/CR.Rd | 17 +- man/createLogicalPCM.Rd |only man/createPCM.Rd |only man/improveCR.Rd | 12 + man/revisedConsistency.Rd |only man/sensitivity.Rd | 13 + tests/testthat.R |only tests/testthat/test-AHPtools.R | 52 ++++++- 16 files changed, 384 insertions(+), 81 deletions(-)