Title: Access the 'Public Transport Victoria' Timetable API
Description: Access the 'Public Transport Victoria' Timetable API
<https://www.ptv.vic.gov.au/footer/data-and-reporting/datasets/ptv-timetable-api/>,
with results returned as familiar R data structures. Retrieve information on
stops, routes, disruptions, departures, and more.
Author: David Neuzerling [aut, cre, cph]
Maintainer: David Neuzerling <david@neuzerling.com>
Diff between ptvapi versions 2.0.3 dated 2022-08-15 and 2.0.5 dated 2024-02-17
ptvapi-2.0.3/ptvapi/man/ptvapi.Rd |only ptvapi-2.0.5/ptvapi/DESCRIPTION | 8 +++--- ptvapi-2.0.5/ptvapi/MD5 | 24 +++++++++--------- ptvapi-2.0.5/ptvapi/NEWS.md | 8 ++++++ ptvapi-2.0.5/ptvapi/R/geopath.R | 2 - ptvapi-2.0.5/ptvapi/R/helper-functions.R | 2 - ptvapi-2.0.5/ptvapi/R/ptvapi.R | 5 --- ptvapi-2.0.5/ptvapi/R/runs.R | 2 - ptvapi-2.0.5/ptvapi/man/assert_correct_attributes.Rd | 2 - ptvapi-2.0.5/ptvapi/man/geopath_to_tibble.Rd | 2 - ptvapi-2.0.5/ptvapi/man/ptvapi-package.Rd |only ptvapi-2.0.5/ptvapi/man/run_to_tibble.Rd | 2 - ptvapi-2.0.5/ptvapi/tests/testthat/test-disruptions.R | 6 ++-- ptvapi-2.0.5/ptvapi/tests/testthat/test-outlets.R | 6 +++- 14 files changed, 38 insertions(+), 31 deletions(-)
Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.33.2 or later.
A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.1.1 dated 2024-01-08 and 1.3.0 dated 2024-02-17
DESCRIPTION | 10 - MD5 | 43 +++-- NAMESPACE | 4 NEWS.md | 42 +++++ R/ReadConQuestLibrary.R | 26 +-- R/ReadConQuestState.R | 157 ++++++++++++++++++--- R/ReadConQuestState_createDF.R | 57 ++++--- R/conquestr.R | 34 ++++ R/generateHelpers.R | 71 +++++++++ R/pvHelpers.R | 6 inst/doc/data-cleaning-functions-in-conquestr.html | 146 ++++++------------- inst/doc/generateResponses.html | 46 +++--- inst/doc/intro-to-conquestr.html | 6 inst/doc/itanal-in-conquestr.html | 146 ++++++------------- inst/doc/plotting.html | 6 inst/doc/responseProbs.html | 4 inst/doc/test_item_review_sheet_markdown.html | 4 man/ConQuestSys.Rd | 7 man/DecompressSys.Rd |only man/ReadSys.Rd | 10 - man/ReadSysMini.Rd |only man/genItems.Rd | 2 man/pvMeanVar.Rd | 4 man/writeImportXsi.Rd |only 24 files changed, 515 insertions(+), 316 deletions(-)
More information about ThermalSampleR at CRAN
Permanent link
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support Summary and Analysis of
Extension Program Evaluation in R, and An R
Companion for the Handbook of Biological Statistics.
Vignettes are available at <https://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 2.4.34 dated 2023-09-17 and 2.4.35 dated 2024-02-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/cramerV.r | 2 +- R/transformTukey.r | 10 ++++++++++ inst/CITATION | 8 ++++---- man/transformTukey.Rd | 2 ++ 7 files changed, 35 insertions(+), 15 deletions(-)
Title: Genetic Linkage Maps in Autopolyploids
Description: Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologous chromosomes. For situations where pairwise
analysis has limited power, the algorithm relies on the multilocus
likelihood obtained through a hidden Markov model (HMM).
For more detail, please see Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.
Author: Marcelo Mollinari [aut, cre] ,
Gabriel Gesteira [aut] ,
Cristiane Taniguti [aut] ,
Jeekin Lau [aut] ,
Oscar Riera-Lizarazu [ctb] ,
Guilhereme Pereira [ctb] ,
Augusto Garcia [ctb] ,
Zhao-Bang Zeng [ctb] ,
Katharine Preedy [ctb, cph] ,
Robert Gentleman [...truncated...]
Maintainer: Marcelo Mollinari <mmollin@ncsu.edu>
Diff between mappoly versions 0.3.3 dated 2023-01-05 and 0.4.0 dated 2024-02-17
mappoly-0.3.3/mappoly/R/calc_genoprob_one_parent.R |only mappoly-0.3.3/mappoly/R/one_paprent_single_map_hmm.R |only mappoly-0.3.3/mappoly/R/poly_cross_simulate.R |only mappoly-0.3.3/mappoly/man/calc_genoprob_one_parent.Rd |only mappoly-0.3.3/mappoly/man/est_rf_hmm_single.Rd |only mappoly-0.3.3/mappoly/man/est_rf_hmm_single_one_parent.Rd |only mappoly-0.3.3/mappoly/man/get_counts_one_parent.Rd |only mappoly-0.3.3/mappoly/man/get_states_and_emission_one_parent.Rd |only mappoly-0.3.3/mappoly/man/imf_h.Rd |only mappoly-0.3.3/mappoly/man/imf_k.Rd |only mappoly-0.3.3/mappoly/man/imf_m.Rd |only mappoly-0.3.3/mappoly/man/mf_h.Rd |only mappoly-0.3.3/mappoly/man/mf_k.Rd |only mappoly-0.3.3/mappoly/man/mf_m.Rd |only mappoly-0.3.3/mappoly/man/mp_pallet1.Rd |only mappoly-0.3.3/mappoly/man/mp_pallet2.Rd |only mappoly-0.3.3/mappoly/man/mp_pallet3.Rd |only mappoly-0.3.3/mappoly/man/poly_cross_simulate.Rd |only mappoly-0.3.3/mappoly/src/hmm_one_parent.cpp |only mappoly-0.3.3/mappoly/tests |only mappoly-0.4.0/mappoly/DESCRIPTION | 30 mappoly-0.4.0/mappoly/MD5 | 261 +-- mappoly-0.4.0/mappoly/NAMESPACE | 46 mappoly-0.4.0/mappoly/NEWS.md | 8 mappoly-0.4.0/mappoly/R/RcppExports.R | 8 mappoly-0.4.0/mappoly/R/add_drop.R |only mappoly-0.4.0/mappoly/R/build_map_by_steps.R |only mappoly-0.4.0/mappoly/R/calc_genoprob.R | 3 mappoly-0.4.0/mappoly/R/calc_genoprob_single_parent.R |only mappoly-0.4.0/mappoly/R/cross_simulate.R |only mappoly-0.4.0/mappoly/R/est_map_hmm.R | 193 +- mappoly-0.4.0/mappoly/R/filters.R | 504 ++++- mappoly-0.4.0/mappoly/R/get_counts.R | 14 mappoly-0.4.0/mappoly/R/get_counts_from_web.R | 3 mappoly-0.4.0/mappoly/R/get_submap.R | 2 mappoly-0.4.0/mappoly/R/group.R | 2 mappoly-0.4.0/mappoly/R/haplotype_map_utils.R | 8 mappoly-0.4.0/mappoly/R/homolog_probs.R | 19 mappoly-0.4.0/mappoly/R/make_seq.R | 205 +- mappoly-0.4.0/mappoly/R/pairwise_rf.R | 65 mappoly-0.4.0/mappoly/R/plot_map_list.R | 2 mappoly-0.4.0/mappoly/R/plot_progeny_dosage_change.R |only mappoly-0.4.0/mappoly/R/prior_dist_hmm.R | 1 mappoly-0.4.0/mappoly/R/read_mappoly_csv.R | 3 mappoly-0.4.0/mappoly/R/reest_map_error.R | 2 mappoly-0.4.0/mappoly/R/reestimate_map.R | 38 mappoly-0.4.0/mappoly/R/rf_list_to_matrix.R | 2 mappoly-0.4.0/mappoly/R/sim_homologous.R | 123 - mappoly-0.4.0/mappoly/R/simulation_utils.R | 40 mappoly-0.4.0/mappoly/R/single_map_hmm.R | 31 mappoly-0.4.0/mappoly/R/single_paprent_single_phase_hmm.R |only mappoly-0.4.0/mappoly/R/split_and_rephase.R | 24 mappoly-0.4.0/mappoly/R/utils.R | 868 ++-------- mappoly-0.4.0/mappoly/README.md | 10 mappoly-0.4.0/mappoly/build/partial.rdb |binary mappoly-0.4.0/mappoly/build/vignette.rds |binary mappoly-0.4.0/mappoly/inst/CITATION | 68 mappoly-0.4.0/mappoly/inst/doc/mappoly_startguide.R | 28 mappoly-0.4.0/mappoly/inst/doc/mappoly_startguide.html | 144 - mappoly-0.4.0/mappoly/man/add_marker.Rd | 7 mappoly-0.4.0/mappoly/man/add_md_markers.Rd |only mappoly-0.4.0/mappoly/man/add_mrk_at_tail_ph_list.Rd | 3 mappoly-0.4.0/mappoly/man/aggregate_matrix.Rd | 3 mappoly-0.4.0/mappoly/man/calc_genoprob_haplo.Rd | 3 mappoly-0.4.0/mappoly/man/calc_genoprob_single_parent.Rd |only mappoly-0.4.0/mappoly/man/cat_phase.Rd | 3 mappoly-0.4.0/mappoly/man/check_data_dist_sanity.Rd | 3 mappoly-0.4.0/mappoly/man/check_data_dose_sanity.Rd | 3 mappoly-0.4.0/mappoly/man/check_if_rf_is_possible.Rd | 3 mappoly-0.4.0/mappoly/man/check_ls_phase.Rd | 3 mappoly-0.4.0/mappoly/man/concatenate_ph_list.Rd | 3 mappoly-0.4.0/mappoly/man/create_map.Rd | 3 mappoly-0.4.0/mappoly/man/cross_simulate.Rd |only mappoly-0.4.0/mappoly/man/detect_info_par.Rd |only mappoly-0.4.0/mappoly/man/draw_cross.Rd | 5 mappoly-0.4.0/mappoly/man/drop_marker.Rd | 2 mappoly-0.4.0/mappoly/man/edit_order.Rd |only mappoly-0.4.0/mappoly/man/est_haplo_hmm.Rd | 3 mappoly-0.4.0/mappoly/man/est_map_haplo_given_genoprob.Rd | 3 mappoly-0.4.0/mappoly/man/est_pairwise_rf.Rd | 28 mappoly-0.4.0/mappoly/man/est_rf_hmm_single_phase.Rd |only mappoly-0.4.0/mappoly/man/est_rf_hmm_single_phase_single_parent.Rd |only mappoly-0.4.0/mappoly/man/filter_aneuploid.Rd |only mappoly-0.4.0/mappoly/man/filter_individuals.Rd | 14 mappoly-0.4.0/mappoly/man/filter_map_at_hmm_thres.Rd | 14 mappoly-0.4.0/mappoly/man/filter_missing.Rd | 23 mappoly-0.4.0/mappoly/man/filter_non_conforming_classes.Rd | 3 mappoly-0.4.0/mappoly/man/filter_segregation.Rd | 14 mappoly-0.4.0/mappoly/man/format_rf.Rd | 3 mappoly-0.4.0/mappoly/man/framework_map.Rd |only mappoly-0.4.0/mappoly/man/genetic-mapping-functions.Rd |only mappoly-0.4.0/mappoly/man/genotyping_global_error.Rd | 3 mappoly-0.4.0/mappoly/man/get_cache_two_pts_from_web.Rd | 3 mappoly-0.4.0/mappoly/man/get_counts.Rd | 3 mappoly-0.4.0/mappoly/man/get_counts_all_phases.Rd | 3 mappoly-0.4.0/mappoly/man/get_counts_single_parent.Rd |only mappoly-0.4.0/mappoly/man/get_counts_two_parents.Rd | 3 mappoly-0.4.0/mappoly/man/get_dosage_type.Rd | 18 mappoly-0.4.0/mappoly/man/get_full_info_tail.Rd | 3 mappoly-0.4.0/mappoly/man/get_ols_map.Rd | 5 mappoly-0.4.0/mappoly/man/get_ph_list_subset.Rd | 3 mappoly-0.4.0/mappoly/man/get_rf_from_mat.Rd | 3 mappoly-0.4.0/mappoly/man/get_states_and_emission_single_parent.Rd |only mappoly-0.4.0/mappoly/man/get_w_m.Rd | 3 mappoly-0.4.0/mappoly/man/gg_color_hue.Rd | 3 mappoly-0.4.0/mappoly/man/is.prob.data.Rd | 13 mappoly-0.4.0/mappoly/man/make_seq_mappoly.Rd | 109 - mappoly-0.4.0/mappoly/man/mappoly-color-palettes.Rd |only mappoly-0.4.0/mappoly/man/merge_parental_maps.Rd |only mappoly-0.4.0/mappoly/man/mrk_chisq_test.Rd | 3 mappoly-0.4.0/mappoly/man/msg.Rd | 3 mappoly-0.4.0/mappoly/man/paralell_pairwise_discrete.Rd | 23 mappoly-0.4.0/mappoly/man/paralell_pairwise_discrete_rcpp.Rd | 6 mappoly-0.4.0/mappoly/man/paralell_pairwise_probability.Rd | 23 mappoly-0.4.0/mappoly/man/perm_pars.Rd | 3 mappoly-0.4.0/mappoly/man/perm_tot.Rd | 3 mappoly-0.4.0/mappoly/man/plot_compare_haplotypes.Rd | 29 mappoly-0.4.0/mappoly/man/plot_mappoly.map2.Rd |only mappoly-0.4.0/mappoly/man/plot_one_map.Rd | 3 mappoly-0.4.0/mappoly/man/plot_progeny_dosage_change.Rd |only mappoly-0.4.0/mappoly/man/poly_hmm_est.Rd | 3 mappoly-0.4.0/mappoly/man/prepare_map.Rd | 3 mappoly-0.4.0/mappoly/man/print_ph.Rd | 3 mappoly-0.4.0/mappoly/man/rf_snp_filter.Rd | 16 mappoly-0.4.0/mappoly/man/sample_data.Rd | 4 mappoly-0.4.0/mappoly/man/select_rf.Rd | 3 mappoly-0.4.0/mappoly/man/sim_cross_one_informative_parent.Rd | 3 mappoly-0.4.0/mappoly/man/sim_cross_two_informative_parents.Rd | 3 mappoly-0.4.0/mappoly/man/sim_homologous.Rd | 25 mappoly-0.4.0/mappoly/man/split_and_rephase.Rd | 15 mappoly-0.4.0/mappoly/man/split_mappoly.Rd | 3 mappoly-0.4.0/mappoly/man/table_to_mappoly.Rd | 3 mappoly-0.4.0/mappoly/man/update_framework_map.Rd |only mappoly-0.4.0/mappoly/man/update_missing.Rd | 21 mappoly-0.4.0/mappoly/man/update_ph_list_at_hmm_thres.Rd | 3 mappoly-0.4.0/mappoly/man/v_2_m.Rd | 3 mappoly-0.4.0/mappoly/src/Makevars |only mappoly-0.4.0/mappoly/src/Makevars.win | 2 mappoly-0.4.0/mappoly/src/RcppExports.cpp | 64 mappoly-0.4.0/mappoly/src/genotypic_counts.cpp | 2 mappoly-0.4.0/mappoly/src/genotypic_counts.h | 2 mappoly-0.4.0/mappoly/src/hmm_elements.cpp | 4 mappoly-0.4.0/mappoly/src/hmm_elements.h | 4 mappoly-0.4.0/mappoly/src/hmm_single_parent.cpp |only mappoly-0.4.0/mappoly/src/pairwise_estimation_rcppparallel.cpp | 6 mappoly-0.4.0/mappoly/src/read_mappoly_vcf.cpp | 4 146 files changed, 1584 insertions(+), 1790 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Maelle Salmon [ctb],
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.0.1.1 dated 2024-01-30 and 2.0.2 dated 2024-02-17
igraph-2.0.1.1/igraph/R/scg.R |only igraph-2.0.1.1/igraph/man/scg-method.Rd |only igraph-2.0.2/igraph/DESCRIPTION | 12 igraph-2.0.2/igraph/MD5 | 325 +++-- igraph-2.0.2/igraph/NAMESPACE | 2 igraph-2.0.2/igraph/NEWS.md | 68 + igraph-2.0.2/igraph/R/aaa-auto.R | 72 - igraph-2.0.2/igraph/R/assortativity.R | 15 igraph-2.0.2/igraph/R/coloring.R | 24 igraph-2.0.2/igraph/R/components.R | 72 + igraph-2.0.2/igraph/R/lazyeval.R | 9 igraph-2.0.2/igraph/R/make.R | 78 + igraph-2.0.2/igraph/R/operators.R | 41 igraph-2.0.2/igraph/R/plot.R | 2 igraph-2.0.2/igraph/R/stochastic_matrix.R |only igraph-2.0.2/igraph/R/structural.properties.R | 53 igraph-2.0.2/igraph/R/topology.R | 16 igraph-2.0.2/igraph/configure | 29 igraph-2.0.2/igraph/inst/doc/igraph.R | 98 + igraph-2.0.2/igraph/inst/doc/igraph.Rmd | 187 +-- igraph-2.0.2/igraph/inst/doc/igraph.html | 542 +++++----- igraph-2.0.2/igraph/inst/doc/igraph_ES.R | 100 + igraph-2.0.2/igraph/inst/doc/igraph_ES.html | 520 +++++---- igraph-2.0.2/igraph/inst/doc/igraph_ES.rmd | 158 +- igraph-2.0.2/igraph/man/articulation_points.Rd | 8 igraph-2.0.2/igraph/man/assortativity.Rd | 15 igraph-2.0.2/igraph/man/bfs.Rd | 1 igraph-2.0.2/igraph/man/biconnected_components.Rd | 3 igraph-2.0.2/igraph/man/components.Rd | 4 igraph-2.0.2/igraph/man/constraint.Rd | 1 igraph-2.0.2/igraph/man/coreness.Rd | 1 igraph-2.0.2/igraph/man/decompose.Rd | 3 igraph-2.0.2/igraph/man/degree.Rd | 1 igraph-2.0.2/igraph/man/dfs.Rd | 1 igraph-2.0.2/igraph/man/distances.Rd | 33 igraph-2.0.2/igraph/man/edge_density.Rd | 1 igraph-2.0.2/igraph/man/ego.Rd | 1 igraph-2.0.2/igraph/man/feedback_arc_set.Rd | 1 igraph-2.0.2/igraph/man/get.stochastic.Rd | 2 igraph-2.0.2/igraph/man/girth.Rd | 1 igraph-2.0.2/igraph/man/greedy_vertex_coloring.Rd | 24 igraph-2.0.2/igraph/man/is_acyclic.Rd | 1 igraph-2.0.2/igraph/man/is_biconnected.Rd |only igraph-2.0.2/igraph/man/is_dag.Rd | 1 igraph-2.0.2/igraph/man/k_shortest_paths.Rd | 1 igraph-2.0.2/igraph/man/knn.Rd | 1 igraph-2.0.2/igraph/man/laplacian_matrix.Rd | 28 igraph-2.0.2/igraph/man/matching.Rd | 1 igraph-2.0.2/igraph/man/realize_bipartite_degseq.Rd |only igraph-2.0.2/igraph/man/realize_degseq.Rd | 2 igraph-2.0.2/igraph/man/reciprocity.Rd | 1 igraph-2.0.2/igraph/man/stochastic_matrix.Rd | 6 igraph-2.0.2/igraph/man/subcomponent.Rd | 1 igraph-2.0.2/igraph/man/subgraph.Rd | 1 igraph-2.0.2/igraph/man/topo_sort.Rd | 1 igraph-2.0.2/igraph/man/transitivity.Rd | 1 igraph-2.0.2/igraph/man/unfold_tree.Rd | 1 igraph-2.0.2/igraph/man/which_multiple.Rd | 1 igraph-2.0.2/igraph/man/which_mutual.Rd | 1 igraph-2.0.2/igraph/src/Makevars.in | 12 igraph-2.0.2/igraph/src/Makevars.ucrt | 11 igraph-2.0.2/igraph/src/Makevars.win | 11 igraph-2.0.2/igraph/src/cpp11.cpp | 6 igraph-2.0.2/igraph/src/rinterface.c | 276 +---- igraph-2.0.2/igraph/src/rinterface_extra.c | 26 igraph-2.0.2/igraph/src/simpleraytracer.cpp | 5 igraph-2.0.2/igraph/src/vendor/cigraph/CHANGELOG.md | 29 igraph-2.0.2/igraph/src/vendor/cigraph/CONTRIBUTORS.md | 1 igraph-2.0.2/igraph/src/vendor/cigraph/CONTRIBUTORS.txt | 1 igraph-2.0.2/igraph/src/vendor/cigraph/include/igraph_components.h | 1 igraph-2.0.2/igraph/src/vendor/cigraph/include/igraph_constructors.h | 1 igraph-2.0.2/igraph/src/vendor/cigraph/include/igraph_interface.h | 2 igraph-2.0.2/igraph/src/vendor/cigraph/include/igraph_types.h | 1 igraph-2.0.2/igraph/src/vendor/cigraph/interfaces/functions.yaml | 18 igraph-2.0.2/igraph/src/vendor/cigraph/src/CMakeLists.txt | 2 igraph-2.0.2/igraph/src/vendor/cigraph/src/centrality/hub_authority.c | 13 igraph-2.0.2/igraph/src/vendor/cigraph/src/centrality/truss.cpp | 2 igraph-2.0.2/igraph/src/vendor/cigraph/src/connectivity/components.c | 203 +++ igraph-2.0.2/igraph/src/vendor/cigraph/src/constructors/atlas.c | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/constructors/prufer.c | 7 igraph-2.0.2/igraph/src/vendor/cigraph/src/core/grid.c | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/games/sbm.c | 12 igraph-2.0.2/igraph/src/vendor/cigraph/src/graph/basic_query.c | 2 igraph-2.0.2/igraph/src/vendor/cigraph/src/graph/caching.c | 2 igraph-2.0.2/igraph/src/vendor/cigraph/src/graph/type_indexededgelist.c | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/graph/visitors.c | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/hrg/hrg_types.cc | 9 igraph-2.0.2/igraph/src/vendor/cigraph/src/io/graphml.c | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/io/pajek-lexer.l | 4 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/DensityGrid.cpp | 8 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/DensityGrid.h | 3 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/DensityGrid_3d.cpp | 8 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/DensityGrid_3d.h | 3 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/drl_graph.cpp | 35 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/drl_graph_3d.cpp | 33 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/drl_layout.cpp | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/drl_layout_3d.cpp | 11 igraph-2.0.2/igraph/src/vendor/cigraph/src/layout/drl/drl_parse.h | 4 igraph-2.0.2/igraph/src/vendor/cigraph/src/misc/bipartite.c | 26 igraph-2.0.2/igraph/src/vendor/cigraph/src/misc/cocitation.c | 12 igraph-2.0.2/igraph/src/vendor/cigraph/src/misc/degree_sequence.cpp | 351 ++++++ igraph-2.0.2/igraph/src/vendor/cigraph/src/paths/all_shortest_paths.c | 4 igraph-2.0.2/igraph/src/vendor/cigraph/src/paths/bellman_ford.c | 18 igraph-2.0.2/igraph/src/vendor/cigraph/src/paths/dijkstra.c | 16 igraph-2.0.2/igraph/src/vendor/cigraph/src/paths/sparsifier.c | 41 igraph-2.0.2/igraph/src/vendor/cigraph/src/paths/unweighted.c | 32 igraph-2.0.2/igraph/src/vendor/cigraph/src/properties/dag.c | 19 igraph-2.0.2/igraph/src/vendor/cigraph/src/properties/trees.c | 124 +- igraph-2.0.2/igraph/src/vendor/config.h | 9 igraph-2.0.2/igraph/src/vendor/igraph_config.h | 2 igraph-2.0.2/igraph/tests/testthat/_snaps/operators.md |only igraph-2.0.2/igraph/tests/testthat/test-adjacency.spectral.embedding.R | 12 igraph-2.0.2/igraph/tests/testthat/test-authority.score.R | 2 igraph-2.0.2/igraph/tests/testthat/test-ba.game.R | 12 igraph-2.0.2/igraph/tests/testthat/test-biconnected.components.R | 55 + igraph-2.0.2/igraph/tests/testthat/test-bipartite.projection.R | 4 igraph-2.0.2/igraph/tests/testthat/test-bipartite.random.game.R | 2 igraph-2.0.2/igraph/tests/testthat/test-cliques.R | 2 igraph-2.0.2/igraph/tests/testthat/test-clusters.R | 2 igraph-2.0.2/igraph/tests/testthat/test-communities.R | 4 igraph-2.0.2/igraph/tests/testthat/test-constraint.R | 2 igraph-2.0.2/igraph/tests/testthat/test-constructor-modifiers.R | 4 igraph-2.0.2/igraph/tests/testthat/test-contract.vertices.R | 2 igraph-2.0.2/igraph/tests/testthat/test-convex_hull.R | 2 igraph-2.0.2/igraph/tests/testthat/test-correlated.R | 12 igraph-2.0.2/igraph/tests/testthat/test-dimSelect.R | 2 igraph-2.0.2/igraph/tests/testthat/test-distances.R |only igraph-2.0.2/igraph/tests/testthat/test-dot.product.game.R | 2 igraph-2.0.2/igraph/tests/testthat/test-fastgreedy.community.R | 2 igraph-2.0.2/igraph/tests/testthat/test-forestfire.R | 2 igraph-2.0.2/igraph/tests/testthat/test-graph.dfs.R | 3 igraph-2.0.2/igraph/tests/testthat/test-graph.edgelist.R | 2 igraph-2.0.2/igraph/tests/testthat/test-graph.eigen.R | 2 igraph-2.0.2/igraph/tests/testthat/test-graph.knn.R | 2 igraph-2.0.2/igraph/tests/testthat/test-graph.subisomorphic.lad.R | 4 igraph-2.0.2/igraph/tests/testthat/test-graph.subisomorphic.vf2.R | 2 igraph-2.0.2/igraph/tests/testthat/test-graphlets.R | 2 igraph-2.0.2/igraph/tests/testthat/test-hrg.R | 4 igraph-2.0.2/igraph/tests/testthat/test-hsbm.R | 18 igraph-2.0.2/igraph/tests/testthat/test-is.bipartite.R | 2 igraph-2.0.2/igraph/tests/testthat/test-label.propagation.community.R | 2 igraph-2.0.2/igraph/tests/testthat/test-laplacian.spectral.embedding.R | 16 igraph-2.0.2/igraph/tests/testthat/test-layout.fr.R | 4 igraph-2.0.2/igraph/tests/testthat/test-layout.kk.R | 2 igraph-2.0.2/igraph/tests/testthat/test-layout.mds.R | 2 igraph-2.0.2/igraph/tests/testthat/test-layout.merge.R | 2 igraph-2.0.2/igraph/tests/testthat/test-leading.eigenvector.community.R | 2 igraph-2.0.2/igraph/tests/testthat/test-leiden.R | 4 igraph-2.0.2/igraph/tests/testthat/test-maximal_cliques.R | 6 igraph-2.0.2/igraph/tests/testthat/test-motifs.R | 4 igraph-2.0.2/igraph/tests/testthat/test-multilevel.community.R | 2 igraph-2.0.2/igraph/tests/testthat/test-operators.R | 41 igraph-2.0.2/igraph/tests/testthat/test-operators4.R | 4 igraph-2.0.2/igraph/tests/testthat/test-optimal.community.R | 2 igraph-2.0.2/igraph/tests/testthat/test-print.R | 4 igraph-2.0.2/igraph/tests/testthat/test-random_walk.R | 12 igraph-2.0.2/igraph/tests/testthat/test-sample.R | 2 igraph-2.0.2/igraph/tests/testthat/test-scan.R | 6 igraph-2.0.2/igraph/tests/testthat/test-sgm.R | 4 igraph-2.0.2/igraph/tests/testthat/test-sir.R | 2 igraph-2.0.2/igraph/tests/testthat/test-sphere.R | 4 igraph-2.0.2/igraph/tests/testthat/test-topology.R | 34 igraph-2.0.2/igraph/tests/testthat/test-transitivity.R | 4 igraph-2.0.2/igraph/tests/testthat/test-vs-es-printing.R | 8 igraph-2.0.2/igraph/tests/testthat/test-walktrap.community.R | 2 igraph-2.0.2/igraph/vignettes/igraph.Rmd | 187 +-- igraph-2.0.2/igraph/vignettes/igraph_ES.rmd | 158 +- 167 files changed, 2847 insertions(+), 1894 deletions(-)
Title: Print Debugging Made Sweeter
Description: Provides user-friendly and configurable print debugging via a
single function, ic(). Wrap an expression in ic() to print the
expression, its value and (where available) its source location.
Debugging output can be toggled globally without modifying code.
Author: Lewin Appleton-Fox [aut, cre],
Dominik Rafacz [aut] ,
Ben Stiles [ctb]
Maintainer: Lewin Appleton-Fox <lewin.a.f@gmail.com>
Diff between icecream versions 0.2.1 dated 2023-09-27 and 0.2.2 dated 2024-02-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/print.R | 19 ++++++++++--------- README.md | 31 ++++++++++++++++--------------- tests/testthat/test-icecream.R | 9 +++++++++ 6 files changed, 47 insertions(+), 32 deletions(-)
More information about teal.transform at CRAN
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Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ),
David Fletcher [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.6.4 dated 2023-10-17 and 4.6.5 dated 2024-02-17
secr-4.6.4/secr/R/model.average.R |only secr-4.6.5/secr/DESCRIPTION | 8 - secr-4.6.5/secr/MD5 | 107 ++++++++--------- secr-4.6.5/secr/NAMESPACE | 8 - secr-4.6.5/secr/NEWS | 27 ++++ secr-4.6.5/secr/R/AIC.R | 18 ++ secr-4.6.5/secr/R/ClosedN.R | 6 secr-4.6.5/secr/R/binCovariate.R |only secr-4.6.5/secr/R/defunct.R |only secr-4.6.5/secr/R/fastsecrloglik.R | 39 ++++-- secr-4.6.5/secr/R/fxi.R | 9 - secr-4.6.5/secr/R/generalsecrloglik.R | 65 ++++++---- secr-4.6.5/secr/R/loglikhelperfn.R | 10 - secr-4.6.5/secr/R/make.capthist.R | 5 secr-4.6.5/secr/R/make.mask.R | 10 - secr-4.6.5/secr/R/makeStart.R | 18 ++ secr-4.6.5/secr/R/mask.check.R | 4 secr-4.6.5/secr/R/methods.R | 20 ++- secr-4.6.5/secr/R/modelAverage.R | 4 secr-4.6.5/secr/R/plot.capthist.r | 14 +- secr-4.6.5/secr/R/plot.mask.r | 2 secr-4.6.5/secr/R/preparedata.R | 12 + secr-4.6.5/secr/R/score.test.R | 7 - secr-4.6.5/secr/R/secr.fit.R | 44 ++++--- secr-4.6.5/secr/R/sim.capthist.R | 61 ++++++--- secr-4.6.5/secr/R/sim.popn.R | 174 +++++++++++++++++----------- secr-4.6.5/secr/R/sim.secr.R | 2 secr-4.6.5/secr/R/split.capthist.R | 61 --------- secr-4.6.5/secr/R/split.traps.R | 4 secr-4.6.5/secr/R/suggest.buffer.R | 6 secr-4.6.5/secr/R/summary.traps.R | 2 secr-4.6.5/secr/R/utility.R | 22 +-- secr-4.6.5/secr/R/verify.R | 9 - secr-4.6.5/secr/R/writeGPS.R | 4 secr-4.6.5/secr/build/partial.rdb |binary secr-4.6.5/secr/build/vignette.rds |binary secr-4.6.5/secr/inst/doc/secr-datainput.R | 8 - secr-4.6.5/secr/inst/doc/secr-datainput.pdf |binary secr-4.6.5/secr/inst/doc/secr-overview.R | 10 - secr-4.6.5/secr/inst/doc/secr-overview.pdf |binary secr-4.6.5/secr/man/AIC.secr.Rd | 5 secr-4.6.5/secr/man/FAQ.Rd | 21 +-- secr-4.6.5/secr/man/Parallel.Rd | 1 secr-4.6.5/secr/man/binCovariate.Rd |only secr-4.6.5/secr/man/chat.Rd | 8 - secr-4.6.5/secr/man/details.Rd | 4 secr-4.6.5/secr/man/homerange.Rd | 4 secr-4.6.5/secr/man/secr-defunct.Rd | 3 secr-4.6.5/secr/man/secr-package.Rd | 4 secr-4.6.5/secr/man/secr.design.MS.Rd | 7 - secr-4.6.5/secr/man/secr.fit.Rd | 2 secr-4.6.5/secr/man/secrRNG.Rd | 7 - secr-4.6.5/secr/man/sim.popn.Rd | 8 - secr-4.6.5/secr/src/detectfn.cpp | 96 +++++++-------- secr-4.6.5/secr/src/prwisimple.cpp | 9 - secr-4.6.5/secr/src/secr.h | 4 secr-4.6.5/secr/tests/testthat/test-start.R |only 57 files changed, 563 insertions(+), 420 deletions(-)
More information about ReliabilityTheory at CRAN
Permanent link
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pmcardoso@fc.ul.pt>
Diff between BAT versions 2.9.5 dated 2023-12-04 and 2.9.6 dated 2024-02-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/BAT.R | 28 +++++++++++++--------------- man/optim.alpha.Rd | 3 +-- man/optim.beta.Rd | 3 +-- 5 files changed, 23 insertions(+), 27 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between ACNE versions 0.9.0 dated 2023-06-25 and 0.9.1 dated 2024-02-17
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 11 ++++++++++- R/fitSnpNmfArray.R | 5 +---- inst/CITATION |only man/fitSnpNmfArray.Rd | 5 +---- 6 files changed, 20 insertions(+), 16 deletions(-)
More information about mult.latent.reg at CRAN
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Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix
estimation, particularly useful in high-dimensional settings. This
method relies upon the theory of high-dimensional loss-based covariance
matrix estimator selection developed by Boileau et al. (2022)
<doi:10.1080/10618600.2022.2110883> to identify the optimal estimator
from among a prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph]
,
Nima Hejazi [aut] ,
Brian Collica [aut] ,
Jamarcus Liu [ctb],
Mark van der Laan [ctb, ths] ,
Sandrine Dudoit [ctb, ths]
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between cvCovEst versions 1.2.1 dated 2023-06-23 and 1.2.2 dated 2024-02-17
DESCRIPTION | 8 - MD5 | 26 ++-- NEWS.md | 6 + R/estimators.R | 14 +- R/plot_functions.R | 2 R/summary_functions.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/using_cvCovEst.html | 243 +++++++++++++++++++++---------------------- man/bandingEst.Rd | 4 man/cvRiskPlot.Rd | 6 - man/matrixMetrics.Rd | 4 man/sampleCovEst.Rd | 4 man/taperingEst.Rd | 6 - 14 files changed, 166 insertions(+), 161 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.cn versions 1.7.0 dated 2022-07-20 and 1.7.1 dated 2024-02-17
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 7 + R/MultiSourceCopyNumberNormalization.R | 1 inst/CITATION | 108 ++++++++++++++--------- man/MultiSourceCopyNumberNormalization.Rd | 6 - man/aroma.cn-package.Rd | 32 +++--- man/fitOne.MultiSourceCopyNumberNormalization.Rd | 1 8 files changed, 106 insertions(+), 69 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut],
Frank E Harrell Jr [ctb] )
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.66.0 dated 2021-10-23 and 0.67.0 dated 2024-02-17
PSCBS-0.66.0/PSCBS/NEWS |only PSCBS-0.66.0/PSCBS/R/006.fixVarArgs.R |only PSCBS-0.66.0/PSCBS/man/append.AbstractCBS.Rd |only PSCBS-0.66.0/PSCBS/man/load.AbstractCBS.Rd |only PSCBS-0.66.0/PSCBS/man/plotTracks.PairedPSCBS.Rd |only PSCBS-0.66.0/PSCBS/man/save.AbstractCBS.Rd |only PSCBS-0.66.0/PSCBS/tests/weightedQuantile.R |only PSCBS-0.67.0/PSCBS/DESCRIPTION | 15 - PSCBS-0.67.0/PSCBS/MD5 | 55 ++---- PSCBS-0.67.0/PSCBS/NAMESPACE | 14 - PSCBS-0.67.0/PSCBS/NEWS.md |only PSCBS-0.67.0/PSCBS/R/AbstractCBS.HCLUST.R | 4 PSCBS-0.67.0/PSCBS/R/AbstractCBS.R | 103 ------------ PSCBS-0.67.0/PSCBS/R/AbstractCBS.RESTRUCT.R | 45 ----- PSCBS-0.67.0/PSCBS/R/PairedPSCBS.PLOT.R | 4 PSCBS-0.67.0/PSCBS/R/PairedPSCBS.estimateDeltaLOH.R | 1 PSCBS-0.67.0/PSCBS/build/vignette.rds |binary PSCBS-0.67.0/PSCBS/inst/CITATION | 47 ++--- PSCBS-0.67.0/PSCBS/inst/doc/CBS.pdf |binary PSCBS-0.67.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary PSCBS-0.67.0/PSCBS/man/AbstractCBS.Rd | 29 +-- PSCBS-0.67.0/PSCBS/man/CBS.Rd | 16 - PSCBS-0.67.0/PSCBS/man/Non-documented_objects.Rd | 2 PSCBS-0.67.0/PSCBS/man/NonPairedPSCBS.Rd | 6 PSCBS-0.67.0/PSCBS/man/PSCBS.Rd | 8 PSCBS-0.67.0/PSCBS/man/PairedPSCBS.Rd | 24 +- PSCBS-0.67.0/PSCBS/man/Restructuring_AbstractCBS_objects.Rd | 3 PSCBS-0.67.0/PSCBS/man/estimateDeltaLOH.PairedPSCBS.Rd | 1 PSCBS-0.67.0/PSCBS/man/getLocusData.AbstractCBS.Rd | 2 PSCBS-0.67.0/PSCBS/man/getSegments.AbstractCBS.Rd | 3 PSCBS-0.67.0/PSCBS/man/mergeTwoSegments.AbstractCBS.Rd | 4 PSCBS-0.67.0/PSCBS/man/plotTracks1.PairedPSCBS.Rd |only PSCBS-0.67.0/PSCBS/man/updateMeansTogether.AbstractCBS.Rd | 4 33 files changed, 99 insertions(+), 291 deletions(-)
Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.rsp versions 0.45.0 dated 2022-06-27 and 0.46.0 dated 2024-02-17
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Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models, and
it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel,
RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr'
dynamic documents. Details can be found in Arel-Bundock (2022)
<doi:10.18637/jss.v103.i01>.
Author: Vincent Arel-Bundock [aut, cre]
,
Joachim Gassen [ctb] ,
Nathan Eastwood [ctb],
Nick Huntington-Klein [ctb] ,
Moritz Schwarz [ctb] ,
Benjamin Elbers [ctb] ,
Grant McDermott [ctb] ,
Lukas Wallrich [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 1.4.3 dated 2023-10-15 and 1.4.5 dated 2024-02-17
modelsummary-1.4.3/modelsummary/inst/tinytest/_tinysnapshot/test-escape_label_title.txt |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-1.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-2.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-3.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-4.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-5.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-6.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-7.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-8.png |only modelsummary-1.4.3/modelsummary/man/figures/unnamed-chunk-1-9.png |only modelsummary-1.4.5/modelsummary/DESCRIPTION | 63 +- modelsummary-1.4.5/modelsummary/MD5 | 125 ++-- modelsummary-1.4.5/modelsummary/NAMESPACE | 18 modelsummary-1.4.5/modelsummary/NEWS.md | 92 ++- modelsummary-1.4.5/modelsummary/R/config_modelsummary.R | 3 modelsummary-1.4.5/modelsummary/R/datasummary_functions.R | 2 modelsummary-1.4.5/modelsummary/R/datasummary_skim.R | 27 - modelsummary-1.4.5/modelsummary/R/factory.R | 4 modelsummary-1.4.5/modelsummary/R/factory_markdown.R | 10 modelsummary-1.4.5/modelsummary/R/factory_tinytable.R |only modelsummary-1.4.5/modelsummary/R/get_estimates.R | 3 modelsummary-1.4.5/modelsummary/R/get_gof.R | 8 modelsummary-1.4.5/modelsummary/R/modelsummary.R | 14 modelsummary-1.4.5/modelsummary/R/modelsummary_rbind.R | 4 modelsummary-1.4.5/modelsummary/R/poorman.R | 3 modelsummary-1.4.5/modelsummary/R/sanitize_output.R | 13 modelsummary-1.4.5/modelsummary/R/sanity_checks.R | 14 modelsummary-1.4.5/modelsummary/R/zzz.R | 36 - modelsummary-1.4.5/modelsummary/README.md | 270 ++++------ modelsummary-1.4.5/modelsummary/build/partial.rdb |binary modelsummary-1.4.5/modelsummary/inst/tinytest/_tinysnapshot/escape-hat_I_formula.txt |only modelsummary-1.4.5/modelsummary/inst/tinytest/_tinysnapshot/escape-hat_fixest.txt |only modelsummary-1.4.5/modelsummary/inst/tinytest/_tinysnapshot/escape_label_title.txt |only modelsummary-1.4.5/modelsummary/inst/tinytest/_tinysnapshot/rbind-add_rows_rbind.txt | 38 - modelsummary-1.4.5/modelsummary/inst/tinytest/helpers.R | 1 modelsummary-1.4.5/modelsummary/inst/tinytest/test-datasummary_balance.R | 2 modelsummary-1.4.5/modelsummary/inst/tinytest/test-escape.R | 22 modelsummary-1.4.5/modelsummary/inst/tinytest/test-output.R | 3 modelsummary-1.4.5/modelsummary/inst/tinytest/test-pkg-marginaleffects.R | 13 modelsummary-1.4.5/modelsummary/inst/tinytest/test-rbind.R | 3 modelsummary-1.4.5/modelsummary/inst/tinytest/test-shape.R | 4 modelsummary-1.4.5/modelsummary/inst/tinytest/test-supported.R | 35 - modelsummary-1.4.5/modelsummary/man/All.Rd | 25 modelsummary-1.4.5/modelsummary/man/AllObs.Rd | 15 modelsummary-1.4.5/modelsummary/man/Arguments.Rd | 15 modelsummary-1.4.5/modelsummary/man/DropEmpty.Rd | 15 modelsummary-1.4.5/modelsummary/man/Factor.Rd | 22 modelsummary-1.4.5/modelsummary/man/Format.Rd | 15 modelsummary-1.4.5/modelsummary/man/Heading.Rd | 15 modelsummary-1.4.5/modelsummary/man/Histogram.Rd | 2 modelsummary-1.4.5/modelsummary/man/Multicolumn.Rd | 25 modelsummary-1.4.5/modelsummary/man/Paste.Rd | 24 modelsummary-1.4.5/modelsummary/man/Percent.Rd | 15 modelsummary-1.4.5/modelsummary/man/PlusMinus.Rd | 15 modelsummary-1.4.5/modelsummary/man/RowFactor.Rd | 26 modelsummary-1.4.5/modelsummary/man/RowNum.Rd | 15 modelsummary-1.4.5/modelsummary/man/colLabels.Rd | 15 modelsummary-1.4.5/modelsummary/man/datasummary.Rd | 2 modelsummary-1.4.5/modelsummary/man/datasummary_balance.Rd | 2 modelsummary-1.4.5/modelsummary/man/datasummary_correlation.Rd | 2 modelsummary-1.4.5/modelsummary/man/datasummary_crosstab.Rd | 2 modelsummary-1.4.5/modelsummary/man/datasummary_df.Rd | 2 modelsummary-1.4.5/modelsummary/man/datasummary_skim.Rd | 3 modelsummary-1.4.5/modelsummary/man/dsummary.Rd | 2 modelsummary-1.4.5/modelsummary/man/figures/modelsummary_gallery.gif |only modelsummary-1.4.5/modelsummary/man/get_estimates.Rd | 3 modelsummary-1.4.5/modelsummary/man/get_gof.Rd | 9 modelsummary-1.4.5/modelsummary/man/labelSubset.Rd | 15 modelsummary-1.4.5/modelsummary/man/modelsummary.Rd | 6 modelsummary-1.4.5/modelsummary/man/msummary.Rd | 6 modelsummary-1.4.5/modelsummary/man/rowLabels.Rd | 15 71 files changed, 614 insertions(+), 544 deletions(-)
Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis provided, as described in for CATA data analysis by Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis. The quality of cluster analysis solutions can be evaluated using various measures. The methods related to b-cluster analysis are described in a manuscript by Castura, Meyners, Varela & Næs (2022) <doi:10.1016/j.foodqual.2022.104564>. Methods are adapted to product-related hedonic responses by Castura, Meyners, Pohjanheimo, Varela & Næs (2023) <doi:10.1111/joss.12860>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>
Diff between cata versions 0.0.10.12 dated 2023-08-15 and 0.1.0.2 dated 2024-02-17
DESCRIPTION | 12 - MD5 | 46 ++--- R/cata-internal.R | 4 R/cata.R | 363 +++++++++++++++++++++++++++++------------- R/evalClusterQuality.R | 18 +- R/pLift.R | 6 build/partial.rdb |binary man/ARI.Rd | 4 man/barray.Rd | 4 man/bcluster.Rd | 18 +- man/bcluster.h.Rd | 10 - man/bcluster.n.Rd | 8 man/cochranQ.Rd | 4 man/code.topk.Rd | 2 man/evaluateClusterQuality.Rd | 4 man/getb.Rd | 12 + man/homogeneity.Rd | 2 man/inspect.Rd | 4 man/mcnemarQ.Rd | 4 man/pLift.Rd | 6 man/selectionPlot.Rd | 8 man/toMatrix.Rd | 4 man/toWideMatrix.Rd | 4 man/topc.Rd | 2 24 files changed, 349 insertions(+), 200 deletions(-)
Title: Smoothing Methods for Nonparametric Regression and Density
Estimation
Description: This is software linked to the book
'Applied Smoothing Techniques for Data Analysis -
The Kernel Approach with S-Plus Illustrations' Oxford University Press.
Author: Adrian Bowman and Adelchi Azzalini.
Ported to R by B. D. Ripley <ripley@stats.ox.ac.uk> up to version 2.0,
version 2.1 by Adrian Bowman and Adelchi Azzalini,
version 2.2 by Adrian Bowman.
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between sm versions 2.2-5.7.1 dated 2022-07-04 and 2.2-6.0 dated 2024-02-17
sm-2.2-5.7.1/sm/R/sm.r |only sm-2.2-5.7.1/sm/data/geyser.tab.gz |only sm-2.2-6.0/sm/ChangeLog | 2 sm-2.2-6.0/sm/DESCRIPTION | 10 ++-- sm-2.2-6.0/sm/MD5 | 40 ++++++++--------- sm-2.2-6.0/sm/NAMESPACE | 16 ++++++- sm-2.2-6.0/sm/NEWS.md | 5 -- sm-2.2-6.0/sm/R/ancova.r | 2 sm-2.2-6.0/sm/R/density.r | 2 sm-2.2-6.0/sm/R/regression.r | 5 +- sm-2.2-6.0/sm/R/rpanel.r | 74 ++++++++++++++++----------------- sm-2.2-6.0/sm/R/sm.R |only sm-2.2-6.0/sm/R/variogram.r | 54 +++++++++++++++++++++++- sm-2.2-6.0/sm/R/zzz.R | 18 +++++--- sm-2.2-6.0/sm/data/geyser.tab |only sm-2.2-6.0/sm/inst/CITATION | 10 ++-- sm-2.2-6.0/sm/man/sm-internal.Rd | 1 sm-2.2-6.0/sm/man/sm.Rd | 4 - sm-2.2-6.0/sm/man/sm.rm.Rd | 7 ++- sm-2.2-6.0/sm/man/sm.sigma.Rd | 2 sm-2.2-6.0/sm/man/sm.sigma2.compare.Rd | 2 sm-2.2-6.0/sm/man/sm.variogram.Rd | 19 ++------ sm-2.2-6.0/sm/man/worm.Rd | 21 ++++----- 23 files changed, 183 insertions(+), 111 deletions(-)
Title: Client Interface for 'openEO' Servers
Description: Access data and processing functionalities of 'openEO' compliant back-ends in R.
Author: Florian Lahn [aut, cre],
Peter James Zellner [ctb],
Matthias Mohr [ctb]
Maintainer: Florian Lahn <florian.lahn@eftas.com>
Diff between openeo versions 1.3.0 dated 2022-11-17 and 1.3.1 dated 2024-02-17
DESCRIPTION | 9 MD5 | 78 - NAMESPACE | 7 NEWS.md | 20 R/argument_types.R | 55 R/authentication.R | 73 - R/client.R | 129 +- R/collections.R | 2 R/debugging.R | 22 R/jobs.R | 30 R/print-functions.R | 26 R/sample_data.R | 30 R/server_metadata.R | 536 ++++---- R/user.R | 824 ++++++------- R/utilities.R | 5 README.md | 8 build/vignette.rds |binary inst/doc/openeo-01-getting_started.R | 100 - inst/doc/openeo-01-getting_started.Rmd | 4 inst/doc/openeo-01-getting_started.html | 254 ++-- inst/doc/openeo-02-sample_data.R | 42 inst/doc/openeo-02-sample_data.html | 166 +- inst/doc/openeo-03-package-software-architecture.Rmd | 148 +- inst/doc/openeo-03-package-software-architecture.html | 1 inst/doc/openeo-04-process_graph_concepts.R | 8 inst/doc/openeo-04-process_graph_concepts.html | 165 +- inst/doc/openeo-05-process_graph_building_application.R | 38 inst/doc/openeo-05-process_graph_building_application.html | 206 +-- inst/doc/openeo-06-developer_implementation_details.R | 4 inst/doc/openeo-06-developer_implementation_details.Rmd | 8 inst/doc/openeo-06-developer_implementation_details.html | 48 man/GeoJson.Rd | 2 man/unary_ops.Rd | 4 tests/testthat/test-OIDC-provider-selection.R |only tests/testthat/test-argument-collection-id.R |only tests/testthat/test-argument-outputformat.R |only tests/testthat/test-argument-string.R |only tests/testthat/test-client.R | 3 tests/testthat/test-compute_result_components.R |only tests/testthat/test-oidc-default-client-select.R |only vignettes/openeo-01-getting_started.Rmd | 4 vignettes/openeo-03-package-software-architecture.Rmd | 148 +- vignettes/openeo-06-developer_implementation_details.Rmd | 8 43 files changed, 1715 insertions(+), 1500 deletions(-)
Title: Efficient Learning of Word Representations and Sentence
Classification
Description: An interface to the 'fastText' <https://github.com/facebookresearch/fastText> library for efficient learning of word representations and sentence classification. The 'fastText' algorithm is explained in detail in (i) "Enriching Word Vectors with subword Information", Piotr Bojanowski, Edouard Grave, Armand Joulin, Tomas Mikolov, 2017, <doi:10.1162/tacl_a_00051>; (ii) "Bag of Tricks for Efficient Text Classification", Armand Joulin, Edouard Grave, Piotr Bojanowski, Tomas Mikolov, 2017, <doi:10.18653/v1/e17-2068>; (iii) "FastText.zip: Compressing text classification models", Armand Joulin, Edouard Grave, Piotr Bojanowski, Matthijs Douze, Herve Jegou, Tomas Mikolov, 2016, <arXiv:1612.03651>.
Author: Lampros Mouselimis [aut, cre] ,
Facebook Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fastText versions 1.0.3 dated 2022-10-08 and 1.0.4 dated 2024-02-17
DESCRIPTION | 10 MD5 | 36 NEWS.md | 7 README.md | 71 + build/vignette.rds |binary inst/doc/language_identification.R | 98 +- inst/doc/language_identification.Rmd | 2 inst/doc/language_identification.html | 1334 +++++++++++++++++++++------------- inst/doc/the_fastText_R_package.html | 1249 +++++++++++++++++++------------ inst/include/utils.h | 1 man/figures |only src/Makevars | 1 src/Makevars.win | 1 src/args.cc | 1 src/dictionary.cc | 1 src/fasttext.cc | 1 src/init.c | 24 src/main.cc | 1 vignettes/language_identification.Rmd | 2 19 files changed, 1763 insertions(+), 1077 deletions(-)
Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre],
Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotRgui versions 6.0 dated 2023-12-21 and 6.1 dated 2024-02-17
DESCRIPTION | 12 +-- MD5 | 38 ++++----- R/IsoplotR.R | 2 R/server.R | 18 ++++ build/docker.md | 78 +++++++++++++++++-- build/docker.sh | 2 build/git.md | 10 +- inst/www/help/U-Pb.html | 122 ++++++++++++++++++++++--------- inst/www/home/news.html | 8 +- inst/www/js/IsoplotR.js | 86 ++++++++++++++------- inst/www/js/examples.js | 118 +++++++++++++++++++++++------ inst/www/locales/en/contextual_help.json | 4 - inst/www/locales/en/dictionary_id.json | 16 +++- inst/www/locales/en/home_id.json | 2 inst/www/options/CAD.html | 4 - inst/www/options/KDE.html | 4 - inst/www/options/U-Pb.html | 4 + inst/www/options/average.html | 4 - inst/www/options/radial.html | 6 + inst/www/version.txt | 2 20 files changed, 396 insertions(+), 144 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R.
It further includes fast functions for common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data.
It is well integrated with base R classes, 'dplyr'/' [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.0.9 dated 2024-01-11 and 2.0.10 dated 2024-02-17
DESCRIPTION | 8 ++-- MD5 | 50 ++++++++++++++--------------- NEWS.md | 13 +++++++ R/fhdbetween_fhdwithin.R | 7 ++-- R/fmean.R | 4 +- R/fmode.R | 4 +- R/fnth_fmedian.R | 8 ++-- R/fprod.R | 4 +- R/fsum.R | 5 +- R/fvar_fsd.R | 8 ++-- R/global_macros.R | 4 +- inst/doc/collapse_documentation.html | 4 +- inst/doc/collapse_for_tidyverse_users.html | 4 +- man/collapse-documentation.Rd | 4 +- man/efficient-programming.Rd | 4 +- man/extract_list.Rd | 2 - man/fast-statistical-functions.Rd | 4 +- man/fmean.Rd | 4 +- man/fmode.Rd | 4 +- man/fnth_fmedian.Rd | 6 ++- man/fprod.Rd | 5 ++ man/fsum.Rd | 6 ++- man/fvar_fsd.Rd | 6 ++- src/Makevars.win | 6 +-- src/match.c | 23 ++++++++----- tests/testthat/test-join.R | 14 ++++++++ 26 files changed, 132 insertions(+), 79 deletions(-)
Title: Wilcoxon Rank Tests for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test)
for clustered data documented in
Jiang et. al (2020) <doi:10.18637/jss.v096.i06>.
Author: Wenjie Wang [cre, ctb] ,
Yujing Jiang [aut],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between clusrank versions 1.0-3 dated 2022-08-12 and 1.0-4 dated 2024-02-17
DESCRIPTION | 13 +-- MD5 | 38 +++++---- NEWS.md | 17 ++++ R/amd.R | 114 ++++++++++++++--------------- R/clusWilcox.R | 122 +++++++++++++------------------ R/clusranksum.R | 165 ++++++++++++++++++------------------------- R/clussignrank.R | 70 +++++++----------- R/crd.R | 46 ++++++----- R/crdstr.R | 46 ++++++----- R/crsd.R | 48 ++++++------ R/crsdunb.R | 46 ++++++----- R/helpers.R |only R/pairwise.clusWilcox.test.R | 4 - R/print.R | 10 +- R/recodeFun.R | 8 +- R/special.R | 76 +++++++++---------- inst/examples |only man/amd.Rd | 12 +-- man/clusWilcox.test.Rd | 5 - src/Fprop.cpp | 5 + src/exact.cpp | 5 + 21 files changed, 413 insertions(+), 437 deletions(-)
Title: Data Science for Wind Energy
Description: Data science methods used in wind energy applications.
Current functionalities include creating a multi-dimensional power curve model,
performing power curve function comparison, covariate matching, and energy decomposition.
Relevant works for the developed functions are:
funGP() - Prakash et al. (2022) <doi:10.1080/00401706.2021.1905073>,
AMK() - Lee et al. (2015) <doi:10.1080/01621459.2014.977385>,
tempGP() - Prakash et al. (2022) <doi:10.1080/00401706.2022.2069158>,
ComparePCurve() - Ding et al. (2021) <doi:10.1016/j.renene.2021.02.136>,
deltaEnergy() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
syncSize() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
imptPower() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
All other functions - Ding (2019, ISBN:9780429956508).
Author: Nitesh Kumar [aut],
Abhinav Prakash [aut],
Yu Ding [aut, cre],
Effi Latiffianti [ctb, cph],
Ahmadreza Chokhachian [ctb, cph]
Maintainer: Yu Ding <yuding2007@gmail.com>
Diff between DSWE versions 1.8.1 dated 2024-02-09 and 1.8.2 dated 2024-02-17
DESCRIPTION | 10 ++++---- MD5 | 18 ++++++++------ NAMESPACE | 10 -------- R/RcppExports.R | 16 ++++++++++++ R/VecchiaSubroutines.R | 30 ++++++++++++------------ R/Vecchia_R_attachments.R |only R/tempGP.R | 1 build/partial.rdb |binary man/tempGP.Rd | 2 + src/RcppExports.cpp | 55 ++++++++++++++++++++++++++++++++++++++++++++ src/Vecchia_attachments.cpp |only 11 files changed, 105 insertions(+), 37 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.2.0 dated 2024-01-08 and 0.2.1 dated 2024-02-17
DESCRIPTION | 14 +++--- MD5 | 40 +++++++++--------- NAMESPACE | 2 NEWS.md | 9 ++++ R/gg_genetracks.R | 22 ++++----- R/gg_scatter.R | 43 ++++++++++++++++++- R/link_LD.R | 11 ++++ R/link_recomb.R | 22 ++++++++- R/locus.R | 6 ++ R/locus_ggplot.R | 104 +++++++++++++++++++++-------------------------- R/scatter_plot.R | 19 ++++---- inst/doc/locuszoomr.R | 17 ++++++- inst/doc/locuszoomr.Rmd | 20 +++++++-- inst/doc/locuszoomr.html | 32 +++++++++----- man/gg_genetracks.Rd | 8 +-- man/gg_scatter.Rd | 11 ++++ man/link_LD.Rd | 3 + man/link_recomb.Rd | 8 +++ man/locus_ggplot.Rd | 77 ++++++++++++++++++---------------- man/scatter_plot.Rd | 9 +--- vignettes/locuszoomr.Rmd | 20 +++++++-- 21 files changed, 318 insertions(+), 179 deletions(-)
Title: Testing Differences Between Families of Trees
Description: Perform test to detect differences in structure between families of
trees. The method is based on cophenetic distances and aggregated
Student's tests.
Author: Nathalie Vialaneix [aut, cre] ,
Gwendaelle Cardenas [aut],
Marie Chavent [aut],
Sylvain Foissac [aut],
Pierre Neuvial [aut] ,
Nathanael Randriamihamison [aut]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between treediff versions 0.2 dated 2023-05-27 and 0.2.1 dated 2024-02-17
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NEWS.md | 7 +++++++ R/HiC2Tree.R | 36 ++++++++++++++++++++---------------- R/treediff.R | 28 +++++++++++++--------------- inst/CITATION |only man/HiC2Tree.Rd | 36 ++++++++++++++++++++---------------- man/treediff.Rd | 28 +++++++++++++--------------- 8 files changed, 86 insertions(+), 74 deletions(-)
Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette.
'tinycodet' primarily focuses on 4 aspects.
1) Safer decimal (in)equality testing, safer atomic conversions, and other functions for safer coding.
2) A new package import system,
that attempts to combine the benefits of using a package without attaching it,
with the benefits of attaching a package.
3) Extending the string manipulation capabilities of the 'stringi' R package.
4) Reducing repetitive code.
Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between tinycodet versions 0.4.0 dated 2024-01-11 and 0.4.1 dated 2024-02-17
tinycodet-0.4.0/tinycodet/inst/tinytest/regular/test-decimal_truth.R |only tinycodet-0.4.0/tinycodet/src/rcpp_anybad.cpp |only tinycodet-0.4.1/tinycodet/DESCRIPTION | 6 tinycodet-0.4.1/tinycodet/MD5 | 83 +- tinycodet-0.4.1/tinycodet/NAMESPACE | 161 ++-- tinycodet-0.4.1/tinycodet/NEWS.md | 9 tinycodet-0.4.1/tinycodet/R/RcppExports.R | 10 tinycodet-0.4.1/tinycodet/R/atomic_conversions.R | 13 tinycodet-0.4.1/tinycodet/R/decimal_truth.R | 82 +- tinycodet-0.4.1/tinycodet/R/matrix_ops.R | 11 tinycodet-0.4.1/tinycodet/R/str_arithmetic.R | 11 tinycodet-0.4.1/tinycodet/R/str_search.R | 340 ++++++-- tinycodet-0.4.1/tinycodet/R/str_subset_ops.R | 52 + tinycodet-0.4.1/tinycodet/R/strcut.R | 104 +- tinycodet-0.4.1/tinycodet/R/stri_locate_ith.R | 11 tinycodet-0.4.1/tinycodet/R/tinycodetWrappers.R |only tinycodet-0.4.1/tinycodet/R/tinycodet_help.R | 1 tinycodet-0.4.1/tinycodet/R/tinycodet_strings.R | 27 tinycodet-0.4.1/tinycodet/R/transform_if.R | 2 tinycodet-0.4.1/tinycodet/R/x.import.R | 2 tinycodet-0.4.1/tinycodet/inst/tinytest/count/count_number_of_tests.R | 2 tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-atomic_conversions.R | 46 - tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-decimal-between.R |only tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-decimal-eq.R |only tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-decimal-is_wholenumber.R |only tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-import_general.R | 19 tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-str_arithmetic.R | 7 tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-str_search.R | 2 tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-str_search_at.R | 1 tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-str_subset_ops.R | 28 tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-strcut.R | 95 ++ tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-strfind.R | 399 +++++++++- tinycodet-0.4.1/tinycodet/inst/tinytest/regular/test-stri_locate_ith.R | 1 tinycodet-0.4.1/tinycodet/man/aaa3_tinycodet_strings.Rd | 30 tinycodet-0.4.1/tinycodet/man/atomic_conversions.Rd | 10 tinycodet-0.4.1/tinycodet/man/decimal_truth.Rd | 21 tinycodet-0.4.1/tinycodet/man/matrix_ops.Rd | 8 tinycodet-0.4.1/tinycodet/man/str_arithmetic.Rd | 9 tinycodet-0.4.1/tinycodet/man/str_search.Rd | 178 +++- tinycodet-0.4.1/tinycodet/man/strcut.Rd | 31 tinycodet-0.4.1/tinycodet/man/stri_locate_ith.Rd | 10 tinycodet-0.4.1/tinycodet/man/transform_if.Rd | 2 tinycodet-0.4.1/tinycodet/man/x.import.Rd | 2 tinycodet-0.4.1/tinycodet/src/C_any_neg.c |only tinycodet-0.4.1/tinycodet/src/C_any_nonpos.c |only tinycodet-0.4.1/tinycodet/src/RcppExports.cpp | 30 tinycodet-0.4.1/tinycodet/src/rcpp_anybad_loc.cpp |only 47 files changed, 1350 insertions(+), 506 deletions(-)
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Author: Jan-Philipp Quast [aut, cre] ,
Dina Schuster [aut] ,
ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between protti versions 0.6.0 dated 2023-01-20 and 0.7.0 dated 2024-02-17
DESCRIPTION | 6 MD5 | 212 ++--- NAMESPACE | 2 NEWS.md | 25 R/assign_missingness.R | 54 - R/assign_peptide_type.R | 8 R/barcode_plot.R | 17 R/calculate_aa_scores.R | 2 R/calculate_diff_abundance.R | 77 - R/calculate_go_enrichment.R | 143 +-- R/calculate_kegg_enrichment.R | 15 R/calculate_protein_abundance.R | 28 R/calculate_sequence_coverage.R | 4 R/calculate_treatment_enrichment.R | 165 +++ R/correct_lip_for_abundance.R |only R/create_queue.R | 22 R/create_structure_contact_map.R | 96 +- R/create_synthetic_data.R | 76 - R/extract_metal_binders.R | 257 +++--- R/fetch_alphafold_aligned_error.R | 16 R/fetch_alphafold_prediction.R | 93 +- R/fetch_chebi.R | 127 +-- R/fetch_eco.R | 48 - R/fetch_kegg.R | 7 R/fetch_metal_pdb.R | 58 - R/fetch_mobidb.R | 8 R/fetch_pdb.R | 421 +++++---- R/fetch_pdb_structure.R | 66 - R/fetch_quickgo.R | 40 R/filter_cv.R | 2 R/find_peptide.R | 5 R/find_peptide_in_structure.R | 96 +- R/fit_drc_4p.R | 40 R/impute.R | 2 R/map_peptides_on_structure.R | 58 - R/peptide_profile_plot.R | 27 R/predict_alphafold_domain.R | 18 R/qc_charge_states.R | 23 R/qc_contaminants.R | 10 R/qc_cvs.R | 32 R/qc_data_completeness.R | 15 R/qc_ids.R | 12 R/qc_intensity_distribution.R | 2 R/qc_median_intensities.R | 12 R/qc_missed_cleavages.R | 26 R/qc_pca.R | 41 R/qc_peptide_type.R | 28 R/qc_proteome_coverage.R | 14 R/qc_ranked_intensities.R | 2 R/qc_sample_correlation.R | 3 R/randomise_queue.R | 1 R/try_query.R | 4 R/volcano_plot.R | 55 - R/woods_plot.R | 40 build/vignette.rds |binary inst/CITATION | 2 inst/doc/data_analysis_dose_response_workflow.R | 153 ++- inst/doc/data_analysis_dose_response_workflow.Rmd | 187 ++-- inst/doc/data_analysis_dose_response_workflow.html | 265 +++--- inst/doc/data_analysis_single_dose_treatment_workflow.R | 126 +- inst/doc/data_analysis_single_dose_treatment_workflow.Rmd | 148 +-- inst/doc/data_analysis_single_dose_treatment_workflow.html | 427 +++++----- inst/doc/input_preparation_workflow.R | 9 inst/doc/input_preparation_workflow.Rmd | 39 inst/doc/input_preparation_workflow.html | 464 +++++------ inst/doc/protein_structure_workflow.R | 288 +++--- inst/doc/protein_structure_workflow.Rmd | 324 ++++--- inst/doc/protein_structure_workflow.html | 424 +++++----- inst/doc/quality_control_workflow.R | 227 +++-- inst/doc/quality_control_workflow.Rmd | 229 +++-- inst/doc/quality_control_workflow.html | 301 +++---- man/assign_missingness.Rd | 17 man/calculate_diff_abundance.Rd | 17 man/calculate_go_enrichment.Rd | 74 - man/calculate_kegg_enrichment.Rd | 15 man/calculate_protein_abundance.Rd | 4 man/calculate_treatment_enrichment.Rd | 6 man/correct_lip_for_abundance.Rd |only man/diff_abundance.Rd | 16 man/extract_metal_binders.Rd | 57 - man/fetch_alphafold_aligned_error.Rd | 12 man/fetch_alphafold_prediction.Rd | 42 man/fetch_metal_pdb.Rd | 30 man/fetch_pdb.Rd | 34 man/fetch_pdb_structure.Rd | 60 - man/find_peptide_in_structure.Rd | 42 man/fit_drc_4p.Rd | 6 man/peptide_profile_plot.Rd | 6 man/predict_alphafold_domain.Rd | 6 man/qc_charge_states.Rd | 2 man/qc_contaminants.Rd | 2 man/qc_cvs.Rd | 6 man/qc_data_completeness.Rd | 2 man/qc_ids.Rd | 2 man/qc_median_intensities.Rd | 2 man/qc_missed_cleavages.Rd | 2 man/qc_pca.Rd | 2 man/qc_peptide_type.Rd | 2 man/try_query.Rd | 4 man/volcano_plot.Rd | 7 tests/testthat/test-fetch_extract_and_enrichment_functions.R | 6 tests/testthat/test-structure_functions.R | 10 tests/testthat/test-workflow.R | 74 + vignettes/data_analysis_dose_response_workflow.Rmd | 187 ++-- vignettes/data_analysis_single_dose_treatment_workflow.Rmd | 148 +-- vignettes/input_preparation_workflow.Rmd | 39 vignettes/protein_structure_workflow.Rmd | 324 ++++--- vignettes/quality_control_workflow.Rmd | 229 +++-- 108 files changed, 4266 insertions(+), 3502 deletions(-)
Title: Cluster-Based Permutation Analysis for Densely Sampled Time Data
Description: An implementation of fast cluster-based permutation analysis
(CPA) for densely-sampled time data developed in Maris & Oostenveld,
2007 <doi:10.1016/j.jneumeth.2007.03.024>. Supports (generalized,
mixed-effects) regression models for the calculation of timewise
statistics. Provides both a wholesale and a piecemeal interface to the
CPA procedure with an emphasis on interpretability and diagnostics.
Integrates 'Julia' libraries 'MixedModels.jl' and 'GLM.jl' for
performance improvements, with additional functionalities for
interfacing with 'Julia' from 'R' powered by the 'JuliaConnectoR'
package.
Author: June Choe [aut, cre, cph]
Maintainer: June Choe <jchoe001@gmail.com>
Diff between jlmerclusterperm versions 1.1.1 dated 2024-02-08 and 1.1.2 dated 2024-02-17
DESCRIPTION | 6 MD5 | 62 ++-- NEWS.md | 188 +++++++------- R/aaa.R | 33 +- R/calculate_pvalue.R | 2 R/clusterpermute.R | 170 ++++++------- R/compute_timewise_statistics.R | 234 +++++++++--------- R/extract_clusters.R | 330 ++++++++++++------------- R/interop-utils.R | 2 R/jlmer.R | 4 R/julia_rng.R | 160 ++++++------ R/permute.R | 176 ++++++------- R/permute_timewise_statistics.R | 2 R/threshold_search.R | 126 ++++----- R/tidy.R | 480 ++++++++++++++++++------------------- inst/julia/Project.toml | 5 man/calculate_clusters_pvalues.Rd | 2 man/cluster_permutation_tidiers.Rd | 2 man/clusterpermute.Rd | 2 man/compute_timewise_statistics.Rd | 2 man/extract_empirical_clusters.Rd | 2 man/extract_null_cluster_dists.Rd | 2 man/jlmer.Rd | 2 man/jlmerclusterperm_setup.Rd | 8 man/julia_model_tidiers.Rd | 2 man/julia_progress.Rd | 2 man/julia_rng.Rd | 2 man/permute_by_predictor.Rd | 2 man/permute_timewise_statistics.Rd | 2 man/to_jlmer.Rd | 2 man/walk_threshold_steps.Rd | 2 tests/testthat/test-aaa-b-setup.R | 14 - 32 files changed, 1020 insertions(+), 1010 deletions(-)
More information about jlmerclusterperm at CRAN
Permanent link
Title: Joint Estimation and Identification of Latent Groups in Panel
Data Models
Description: In panel data analysis, unobservable group structures are a common challenge. Disregarding group-level heterogeneity by assuming an entirely homogeneous panel can introduce bias. Conversely, estimating individual coefficients for each cross-sectional unit is inefficient and may lead to high uncertainty.
This package addresses this issue by implementing the pairwise adaptive group fused Lasso (PAGFL) by Mehrabani (2023) <doi:10.1016/j.jeconom.2022.12.002>.
PAGFL is an efficient methodology to identify latent group structures and estimate group-specific coefficients simultaneously.
Author: Paul Haimerl [aut, cre] ,
Ali Mehrabani [ctb]
Maintainer: Paul Haimerl <paul.haimerl@maastrichtuniversity.nl>
Diff between PAGFL versions 1.0.0 dated 2024-02-16 and 1.0.1 dated 2024-02-17
DESCRIPTION | 6 MD5 | 10 - NEWS.md | 4 R/Sim.R | 5 README.md | 447 +++++++++++++++++++++++++++++++-------------------------- man/sim_DGP.Rd | 5 6 files changed, 256 insertions(+), 221 deletions(-)
Title: Univariate GARCH-MIDAS, Double-Asymmetric GARCH-MIDAS and
MEM-MIDAS
Description: Adds the MIxing-Data Sampling (MIDAS, Ghysels et al. (2007) <doi:10.1080/07474930600972467>) components to a variety of GARCH and MEM (Engle (2002) <doi:10.1002/jae.683>, Engle and Gallo (2006) <doi:10.1016/j.jeconom.2005.01.018>, and Amendola et al. (2024) <doi:10.1016/j.seps.2023.101764>) models, with the aim of predicting the volatility with additional low-frequency (that is, MIDAS) terms. The estimation takes place through simple functions, which provide in-sample and (if present) and out-of-sample evaluations. 'rumidas' also offers a summary tool, which synthesizes the main information of the estimated model. There is also the possibility of generating one-step-ahead and multi-step-ahead forecasts.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vcandila@unisa.it>
Diff between rumidas versions 0.1.1 dated 2021-02-01 and 0.1.2 dated 2024-02-17
DESCRIPTION | 20 MD5 | 126 +- NAMESPACE | 7 NEWS.md | 6 R/data.R | 10 R/functions.R | 61 - R/midas_functions.R | 2179 +++++++++++++++++++++++++++++++------ build/partial.rdb |binary inst/CITATION | 6 inst/REFERENCES.bib | 15 man/DAGM_2M_cond_vol.Rd |only man/DAGM_2M_cond_vol_no_skew.Rd |only man/DAGM_2M_loglik.Rd |only man/DAGM_2M_loglik_no_skew.Rd |only man/DAGM_2M_long_run.Rd |only man/DAGM_2M_long_run_no_skew.Rd |only man/DAGM_X_cond_vol.Rd | 14 man/DAGM_X_cond_vol_no_skew.Rd | 14 man/DAGM_X_loglik.Rd | 13 man/DAGM_X_loglik_no_skew.Rd | 13 man/DAGM_X_long_run_vol.Rd | 12 man/DAGM_X_long_run_vol_no_skew.Rd | 12 man/DAGM_cond_vol.Rd | 12 man/DAGM_cond_vol_no_skew.Rd | 2 man/DAGM_loglik.Rd | 11 man/DAGM_loglik_no_skew.Rd | 18 man/DAGM_long_run_vol.Rd | 10 man/DAGM_long_run_vol_no_skew.Rd | 4 man/GM_X_cond_vol.Rd | 12 man/GM_X_cond_vol_no_skew.Rd | 12 man/GM_X_loglik.Rd | 22 man/GM_X_loglik_no_skew.Rd | 22 man/GM_X_long_run_vol.Rd | 12 man/GM_X_long_run_vol_no_skew.Rd | 12 man/GM_cond_vol.Rd | 10 man/GM_cond_vol_no_skew.Rd | 10 man/GM_loglik.Rd | 18 man/GM_loglik_no_skew.Rd | 18 man/GM_long_run_vol.Rd | 10 man/GM_long_run_vol_no_skew.Rd | 10 man/MEM_MIDAS_X_loglik.Rd | 13 man/MEM_MIDAS_X_loglik_no_skew.Rd | 11 man/MEM_MIDAS_X_lr_pred.Rd | 1 man/MEM_MIDAS_X_lr_pred_no_skew.Rd | 1 man/MEM_MIDAS_X_pred.Rd | 1 man/MEM_MIDAS_X_pred_no_skew.Rd | 1 man/MEM_MIDAS_loglik.Rd | 13 man/MEM_MIDAS_loglik_no_skew.Rd | 11 man/MEM_MIDAS_lr_pred.Rd | 15 man/MEM_MIDAS_lr_pred_no_skew.Rd | 13 man/MEM_MIDAS_pred.Rd | 15 man/MEM_MIDAS_pred_no_skew.Rd | 11 man/MEM_X_loglik.Rd | 13 man/MEM_X_loglik_no_skew.Rd | 11 man/MEM_X_pred.Rd | 1 man/MEM_X_pred_no_skew.Rd | 1 man/MEM_loglik.Rd | 10 man/MEM_loglik_no_skew.Rd | 8 man/MEM_pred.Rd | 10 man/MEM_pred_no_skew.Rd | 8 man/multi_step_ahead_pred.Rd | 12 man/mv_into_mat.Rd | 34 man/rv5.Rd | 2 man/sp500.Rd | 4 man/summary.rumidas.Rd | 11 man/ugmfit.Rd | 69 - man/umemfit.Rd | 30 67 files changed, 2347 insertions(+), 716 deletions(-)
Title: Multiple Empirical Likelihood Tests
Description: Performs multiple empirical likelihood tests. It offers an
easy-to-use interface and flexibility in specifying hypotheses and
calibration methods, extending the framework to simultaneous
inferences. The core computational routines are implemented using the
'Eigen' 'C++' library and 'RcppEigen' interface, with 'OpenMP' for
parallel computation. Details of the testing procedures are provided
in Kim, MacEachern, and Peruggia (2023)
<doi:10.1080/10485252.2023.2206919>. A companion paper by Kim,
MacEachern, and Peruggia (2024) <doi:10.18637/jss.v108.i05> is
available for further information. This work was supported by the U.S.
National Science Foundation under Grants No. SES-1921523 and
DMS-2015552.
Author: Eunseop Kim [aut, cph, cre],
Steven MacEachern [ctb, ths],
Mario Peruggia [ctb, ths],
Pierre Chausse [rev],
Alex Stringer [rev]
Maintainer: Eunseop Kim <markean@pm.me>
Diff between melt versions 1.10.0 dated 2023-05-23 and 1.11.0 dated 2024-02-17
melt-1.10.0/melt/R/deprecated.R |only melt-1.10.0/melt/inst/doc/article.pdf |only melt-1.10.0/melt/inst/doc/article.pdf.asis |only melt-1.10.0/melt/man/el_pairwise.Rd |only melt-1.10.0/melt/src/deprecated.cpp |only melt-1.10.0/melt/src/deprecated.h |only melt-1.10.0/melt/vignettes/article.pdf.asis |only melt-1.11.0/melt/DESCRIPTION | 37 ++--- melt-1.11.0/melt/MD5 | 105 +++++++------- melt-1.11.0/melt/NAMESPACE | 4 melt-1.11.0/melt/NEWS.md | 10 + melt-1.11.0/melt/R/AllClasses.R | 25 ++- melt-1.11.0/melt/R/AllGenerics.R | 93 ++++++++----- melt-1.11.0/melt/R/RcppExports.R | 4 melt-1.11.0/melt/R/data-clothianidin.R | 6 melt-1.11.0/melt/R/data-thiamethoxam.R | 8 - melt-1.11.0/melt/R/el_eval.R | 7 melt-1.11.0/melt/R/el_glm.R | 14 + melt-1.11.0/melt/R/el_lm.R | 7 melt-1.11.0/melt/R/el_mean.R | 7 melt-1.11.0/melt/R/melt-package.R | 13 + melt-1.11.0/melt/README.md | 48 ++---- melt-1.11.0/melt/build/partial.rdb |binary melt-1.11.0/melt/build/vignette.rds |binary melt-1.11.0/melt/inst/CITATION |only melt-1.11.0/melt/inst/WORDLIST | 12 + melt-1.11.0/melt/inst/doc/model.R | 6 melt-1.11.0/melt/inst/doc/model.Rmd | 50 ++++--- melt-1.11.0/melt/inst/doc/model.html | 6 melt-1.11.0/melt/inst/doc/performance.R | 10 - melt-1.11.0/melt/inst/doc/performance.Rmd | 44 ++++-- melt-1.11.0/melt/inst/doc/performance.html | 141 +++++++++----------- melt-1.11.0/melt/inst/doc/usage.R |only melt-1.11.0/melt/inst/doc/usage.Rmd |only melt-1.11.0/melt/inst/doc/usage.html |only melt-1.11.0/melt/man/CEL-class.Rd | 8 - melt-1.11.0/melt/man/EL-class.Rd | 7 melt-1.11.0/melt/man/clothianidin.Rd | 5 melt-1.11.0/melt/man/confint.Rd | 4 melt-1.11.0/melt/man/confreg.Rd | 4 melt-1.11.0/melt/man/el_eval.Rd | 4 melt-1.11.0/melt/man/el_glm.Rd | 8 - melt-1.11.0/melt/man/el_lm.Rd | 4 melt-1.11.0/melt/man/el_mean.Rd | 4 melt-1.11.0/melt/man/eld.Rd | 12 - melt-1.11.0/melt/man/elmt.Rd | 9 - melt-1.11.0/melt/man/elt.Rd | 13 + melt-1.11.0/melt/man/figures/logo.png |binary melt-1.11.0/melt/man/logL.Rd | 5 melt-1.11.0/melt/man/logLR.Rd | 5 melt-1.11.0/melt/man/melt-package.Rd | 16 +- melt-1.11.0/melt/man/sigTests.Rd | 15 -- melt-1.11.0/melt/man/thiamethoxam.Rd | 7 melt-1.11.0/melt/man/weights.Rd | 5 melt-1.11.0/melt/src/RcppExports.cpp | 23 --- melt-1.11.0/melt/tests/testthat/test-skip_on_cran.R | 24 --- melt-1.11.0/melt/vignettes/model.Rmd | 50 ++++--- melt-1.11.0/melt/vignettes/performance.Rmd | 44 ++++-- melt-1.11.0/melt/vignettes/references.bib |only melt-1.11.0/melt/vignettes/usage.Rmd |only 60 files changed, 501 insertions(+), 432 deletions(-)
Title: Estimation Methods for Markets in Equilibrium and Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
Also provides post-estimation analysis tools, such as aggregation,
marginal effect, and shortage calculations. See Karapanagiotis (2024)
<doi:10.18637/jss.v108.i02> for an overview of the functionality
and examples. The estimation methods are based on full information
maximum likelihood techniques given in
Maddala and Nelson (1974) <doi:10.2307/1914215>. They are implemented
using the analytic derivative expressions calculated in
Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>. Standard
errors can be estimated by adjusting for heteroscedasticity or clustering.
The equilibrium estimation constitutes a case of a system of linear,
simultaneous equations. Instead, the disequilibrium models replace the
market-clearing condition with a non-linear,
short-side rule and allow for differ [...truncated...]
Author: Pantelis Karapanagiotis [aut, cre]
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between markets versions 1.1.4 dated 2023-01-05 and 1.1.5 dated 2024-02-17
markets-1.1.4/markets/inst/doc/markets.pdf |only markets-1.1.4/markets/vignettes/.install_extras |only markets-1.1.4/markets/vignettes/markets.pdf |only markets-1.1.5/markets/DESCRIPTION | 14 markets-1.1.5/markets/LICENSE | 2 markets-1.1.5/markets/MD5 | 38 markets-1.1.5/markets/NEWS.md | 4 markets-1.1.5/markets/README.md | 175 markets-1.1.5/markets/build/partial.rdb |binary markets-1.1.5/markets/build/vignette.rds |binary markets-1.1.5/markets/configure | 1965 ++++------ markets-1.1.5/markets/inst/CITATION | 24 markets-1.1.5/markets/inst/WORDLIST | 2 markets-1.1.5/markets/inst/doc/basic_usage.R | 2 markets-1.1.5/markets/inst/doc/basic_usage.html | 991 ++--- markets-1.1.5/markets/inst/doc/market_clearing_assessment.R | 2 markets-1.1.5/markets/inst/doc/market_clearing_assessment.html | 823 ++-- markets-1.1.5/markets/inst/doc/model_details.R | 2 markets-1.1.5/markets/inst/doc/model_details.html | 445 +- markets-1.1.5/markets/inst/doc/package.Rmd | 2 markets-1.1.5/markets/inst/doc/package.html | 31 markets-1.1.5/markets/vignettes/package.Rmd | 2 22 files changed, 2258 insertions(+), 2266 deletions(-)
Title: Automatic Construction of Forced-Choice Tests
Description: Forced-choice (FC) response has gained increasing popularity
and interest for its resistance to faking when well-designed (Cao &
Drasgow, 2019 <doi:10.1037/apl0000414>). To established well-designed
FC scales, typically each item within a block should measure different
trait and have similar level of social desirability (Zhang et al.,
2020 <doi:10.1177/1094428119836486>). Recent study also suggests the
importance of high inter-item agreement of social desirability between
items within a block (Pavlov et al., 2021 <doi:10.31234/osf.io/hmnrc>).
In addition to this, FC developers may
also need to maximize factor loading differences (Brown &
Maydeu-Olivares, 2011 <doi:10.1177/0013164410375112>) or minimize item
location differences (Cao & Drasgow, 2019 <doi:10.1037/apl0000414>)
depending on scoring models. Decision of which items should be
assigned to the same block, termed item pairing, is thus critical to
the quality of an FC test. This pairing p [...truncated...]
Author: Mengtong Li [cre, aut] ,
Tianjun Sun [aut] ,
Bo Zhang [aut]
Maintainer: Mengtong Li <ml70@illinois.edu>
Diff between autoFC versions 0.1.2 dated 2021-06-07 and 0.2.0.1001 dated 2024-02-17
DESCRIPTION | 65 ++- MD5 | 50 ++ NAMESPACE | 26 + R/HEXACO_example_data.R |only R/RMSE_range.R |only R/build_TIRT_var_names.R |only R/build_scale_with_blueprint.R |only R/cal_block_energy_with_iia.R | 295 ++++++++-------- R/construct_blueprint.R |only R/convert_to_TIRT_response.R |only R/empirical_reliability.R |only R/fit_TIRT_model.R |only R/fit_TIRT_mplus_new.R |only R/get_CFA_estimates.R |only R/get_TIRT_long_data.R |only R/get_simulation_matrices.R |only R/make_mplus_code_new.R |only R/plot_scores.R |only R/predict_scores.R |only R/sa_pairing_generalized.R | 2 R/triplet_block_info.R |only R/triplet_example_data.R |only README.md | 143 ++++--- build/vignette.rds |binary data |only inst/CITATION |only inst/doc/autoFC.html | 690 +++++++++++++++++++++++++++++--------- man/HEXACO_example_data.Rd |only man/RMSE_range.Rd |only man/build_TIRT_var_names.Rd |only man/build_scale_with_blueprint.Rd |only man/construct_blueprint.Rd |only man/convert_to_TIRT_response.Rd |only man/empirical_reliability.Rd |only man/fit_TIRT_model.Rd |only man/get_CFA_estimates.Rd |only man/get_TIRT_long_data.Rd |only man/get_simulation_matrices.Rd |only man/plot_scores.Rd |only man/predict_scores.Rd |only man/triplet_block_info.Rd |only man/triplet_example_data.Rd |only 42 files changed, 895 insertions(+), 376 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-23 2.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-14 2.0.2
2017-08-06 1.0.3
2017-05-08 1.0.2
2015-10-13 0.1.4
2015-09-07 0.1.3
2015-09-02 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-23 1.0.4
2021-07-01 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-02 0.5.7
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between performance versions 0.10.8 dated 2023-10-30 and 0.10.9 dated 2024-02-17
DESCRIPTION | 34 ++--- MD5 | 126 ++++++++++--------- NAMESPACE | 8 + NEWS.md | 48 +++++++ R/binned_residuals.R | 27 ++-- R/check_clusterstructure.R | 21 +-- R/check_collinearity.R | 63 ++++++--- R/check_distribution.R | 19 -- R/check_factorstructure.R | 60 ++++----- R/check_heterogeneity_bias.R | 10 - R/check_heteroscedasticity.R | 2 R/check_itemscale.R | 78 ++++++++++-- R/check_model.R | 67 +++++----- R/check_model_diagnostics.R | 107 +++++++++------- R/check_outliers.R | 147 +++++++++++++++-------- R/check_singularity.R | 15 +- R/compare_performance.R | 20 +-- R/icc.R | 42 ++---- R/model_performance.bayesian.R | 8 - R/performance_aicc.R | 37 ++--- R/performance_pcp.R | 14 +- R/performance_score.R | 52 ++++---- R/r2.R | 85 ++++++++++++- R/r2_bayes.R | 62 +++------ R/r2_coxsnell.R | 41 +++++- R/r2_kl.R | 14 ++ R/r2_loo.R | 58 ++++----- R/r2_nagelkerke.R | 54 +++++++- R/r2_zeroinflated.R | 1 R/test_bf.R | 20 +-- R/test_likelihoodratio.R | 22 +-- R/test_performance.R | 16 +- R/test_vuong.R | 10 - R/test_wald.R | 24 +-- README.md | 19 +- build/partial.rdb |binary inst/WORDLIST | 1 man/check_itemscale.Rd | 20 ++- man/check_outliers.Rd | 11 + man/compare_performance.Rd | 3 man/figures/unnamed-chunk-14-1.png |binary man/figures/unnamed-chunk-20-1.png |binary man/model_performance.merMod.Rd | 3 man/model_performance.rma.Rd | 3 man/model_performance.stanreg.Rd | 8 - man/performance-package.Rd | 3 man/performance_aicc.Rd | 6 man/r2_bayes.Rd | 20 --- man/r2_kullback.Rd | 7 - tests/testthat/_snaps/windows |only tests/testthat/test-binned_residuals.R | 68 ++++++++++ tests/testthat/test-check_collinearity.R | 7 + tests/testthat/test-check_itemscale.R | 29 ++++ tests/testthat/test-check_model.R | 15 ++ tests/testthat/test-check_outliers.R | 46 +++++-- tests/testthat/test-check_singularity.R | 26 +++- tests/testthat/test-glmmPQL.R |only tests/testthat/test-icc.R | 3 tests/testthat/test-model_performance.bayesian.R | 4 tests/testthat/test-model_performance.merMod.R | 1 tests/testthat/test-performance_aic.R | 3 tests/testthat/test-pkg-fixest.R | 38 +++-- tests/testthat/test-r2.R | 72 +++++++++++ tests/testthat/test-r2_bayes.R | 2 tests/testthat/test-r2_kullback.R | 7 + 65 files changed, 1209 insertions(+), 628 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-27 0.3.1
2024-01-08 0.3.0
2023-12-08 0.2.7
2023-03-18 0.2.1
2022-12-14 0.2.0
2022-12-02 0.1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-02 1.4.1
2023-07-18 1.3.14.4
2023-07-08 1.3.14.3
2023-02-05 1.3.14.1
2022-11-04 1.3.14
2022-10-07 1.3.13
2021-11-15 1.3.0.1
2021-05-10 1.3.0
2020-01-12 1.2-23
2018-05-13 1.2-12
2017-09-08 1.2-3
2013-06-19 1.1-232
2012-03-30 1.1-212
2012-02-10 1.0.12.201
2012-02-04 1.0.12.198
2011-08-04 1.0.12.167
2011-05-17 1.0.12.146
2011-02-27 1.0.12.141
2010-11-14 1.0.11.125
2010-08-25 1.0.11.119
2010-07-03 1.0.11.110
2010-03-15 1.0.10
2010-02-09 1.0.9
2010-01-13 1.0.8
2009-08-19 1.0.5
2009-06-27 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-15 0.8.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-16 1.0.4
2021-05-19 1.0.2
2021-01-21 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-08 1.0.2
2022-08-07 1.0.1
2022-06-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-06 0.1.3
2023-06-22 0.1.2
Title: Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')
Description: Loads 'Blackrock' <https://blackrockneurotech.com> neural signal
data files into the memory, provides utility tools to extract the data into
common formats such as plain-text 'tsv' and 'HDF5'.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between readNSx versions 0.0.2 dated 2023-06-21 and 0.0.3 dated 2024-02-17
DESCRIPTION | 8 - MD5 | 27 ++++-- NAMESPACE | 7 + NEWS.md | 4 R/bci2000.R |only R/cpp11.R | 36 ++++++++ R/nev.R | 6 - R/nsx.R | 178 ++++++++++++++++++++++++++++++++----------- R/utils.R | 55 ++++++++++++- build/vignette.rds |binary inst/doc/read-nev-nsx-data.R | 2 inst/samples |only man/read_bci2000.Rd |only src/common.h |only src/cpp11.cpp | 92 ++++++++++++++++++++-- src/readBCI.h |only src/readBCI2R.cpp |only src/readNSxDataPacket.cpp |only 18 files changed, 343 insertions(+), 72 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.1.5 dated 2024-02-02 and 1.1.6 dated 2024-02-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/forestcox.R | 39 +++++++++++++++++---------------------- R/forestglm.R | 10 +++++++--- inst/doc/jstable.html | 30 +++++++++++++++--------------- 6 files changed, 52 insertions(+), 49 deletions(-)