Title: Statistical Methods for Microbiome Compositional Data
Description: A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects (Zhou et al. (2021)<arXiv:2104.00242>). The methods can be applied to the analysis of other (high-dimensional) compositional data arising from sequencing experiments.
Author: Xianyang Zhang [aut],
Jun Chen [aut, cre],
Huijuan Zhou [ctb]
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between MicrobiomeStat versions 1.0 dated 2021-11-19 and 1.1 dated 2022-01-23
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 3 ++- R/linda.R | 10 +++++++++- man/linda.Rd | 7 ++++++- man/linda.plot.Rd | 2 +- 6 files changed, 28 insertions(+), 14 deletions(-)
More information about MicrobiomeStat at CRAN
Permanent link
Title: Data Validation and Organization of Metadata for Local and
Remote Tables
Description: Validate data in data frames, 'tibble' objects, 'Spark'
'DataFrames', and database tables. Validation pipelines can be made using
easily-readable, consecutive validation steps. Upon execution of the
validation plan, several reporting options are available. User-defined
thresholds for failure rates allow for the determination of appropriate
reporting actions. Many other workflows are available including an
information management workflow, where the aim is to record, collect, and
generate useful information on data tables.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>),
Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Richard Iannone <riannone@me.com>
Diff between pointblank versions 0.9.0 dated 2021-10-28 and 0.10.0 dated 2022-01-23
pointblank-0.10.0/pointblank/DESCRIPTION | 10 pointblank-0.10.0/pointblank/LICENSE | 2 pointblank-0.10.0/pointblank/MD5 | 357 ++--- pointblank-0.10.0/pointblank/NAMESPACE | 9 pointblank-0.10.0/pointblank/NEWS.md | 28 pointblank-0.10.0/pointblank/R/col_exists.R | 3 pointblank-0.10.0/pointblank/R/col_is_character.R | 4 pointblank-0.10.0/pointblank/R/col_is_date.R | 23 pointblank-0.10.0/pointblank/R/col_is_factor.R | 23 pointblank-0.10.0/pointblank/R/col_is_integer.R | 4 pointblank-0.10.0/pointblank/R/col_is_logical.R | 9 pointblank-0.10.0/pointblank/R/col_is_numeric.R | 23 pointblank-0.10.0/pointblank/R/col_is_posix.R | 23 pointblank-0.10.0/pointblank/R/col_schema_match.R | 33 pointblank-0.10.0/pointblank/R/col_vals_between.R | 8 pointblank-0.10.0/pointblank/R/col_vals_decreasing.R | 90 + pointblank-0.10.0/pointblank/R/col_vals_expr.R | 4 pointblank-0.10.0/pointblank/R/col_vals_gte.R | 4 pointblank-0.10.0/pointblank/R/col_vals_in_set.R | 6 pointblank-0.10.0/pointblank/R/col_vals_increasing.R | 75 + pointblank-0.10.0/pointblank/R/col_vals_lte.R | 4 pointblank-0.10.0/pointblank/R/col_vals_make_set.R | 20 pointblank-0.10.0/pointblank/R/col_vals_make_subset.R | 10 pointblank-0.10.0/pointblank/R/col_vals_not_equal.R | 6 pointblank-0.10.0/pointblank/R/col_vals_not_in_set.R | 5 pointblank-0.10.0/pointblank/R/col_vals_not_null.R | 2 pointblank-0.10.0/pointblank/R/col_vals_null.R | 2 pointblank-0.10.0/pointblank/R/col_vals_regex.R | 2 pointblank-0.10.0/pointblank/R/col_vals_within_spec.R | 6 pointblank-0.10.0/pointblank/R/conjointly.R | 4 pointblank-0.10.0/pointblank/R/create_agent.R | 154 -- pointblank-0.10.0/pointblank/R/create_informant.R | 182 +- pointblank-0.10.0/pointblank/R/create_multiagent.R | 4 pointblank-0.10.0/pointblank/R/datasets.R | 11 pointblank-0.10.0/pointblank/R/draft_validation.R | 29 pointblank-0.10.0/pointblank/R/emailing.R | 18 pointblank-0.10.0/pointblank/R/get_agent_report.R | 124 + pointblank-0.10.0/pointblank/R/get_data_extracts.R | 2 pointblank-0.10.0/pointblank/R/get_informant_report.R | 8 pointblank-0.10.0/pointblank/R/get_multiagent_report.R | 2 pointblank-0.10.0/pointblank/R/get_sundered_data.R | 2 pointblank-0.10.0/pointblank/R/has_columns.R | 6 pointblank-0.10.0/pointblank/R/incorporate.R | 57 pointblank-0.10.0/pointblank/R/info_add.R | 48 pointblank-0.10.0/pointblank/R/interrogate.R | 710 +++++----- pointblank-0.10.0/pointblank/R/logging.R | 74 + pointblank-0.10.0/pointblank/R/object_ops.R | 364 +---- pointblank-0.10.0/pointblank/R/print.R | 329 ++++ pointblank-0.10.0/pointblank/R/remove_deactivate.R | 21 pointblank-0.10.0/pointblank/R/row_count_match.R |only pointblank-0.10.0/pointblank/R/rows_complete.R | 85 - pointblank-0.10.0/pointblank/R/rows_distinct.R | 89 - pointblank-0.10.0/pointblank/R/serially.R | 6 pointblank-0.10.0/pointblank/R/specially.R | 139 + pointblank-0.10.0/pointblank/R/steps_and_briefs.R | 35 pointblank-0.10.0/pointblank/R/table_transformers.R | 2 pointblank-0.10.0/pointblank/R/tbl_from_db.R | 27 pointblank-0.10.0/pointblank/R/tbl_from_file.R | 40 pointblank-0.10.0/pointblank/R/tbl_match.R |only pointblank-0.10.0/pointblank/R/tbl_store.R | 36 pointblank-0.10.0/pointblank/R/utils.R | 154 ++ pointblank-0.10.0/pointblank/R/validate_rmd.R | 88 - pointblank-0.10.0/pointblank/R/write_testthat_file.R | 22 pointblank-0.10.0/pointblank/R/yaml_exec.R | 2 pointblank-0.10.0/pointblank/R/yaml_read_agent.R | 55 pointblank-0.10.0/pointblank/R/yaml_read_informant.R | 34 pointblank-0.10.0/pointblank/R/yaml_write.R | 69 pointblank-0.10.0/pointblank/R/zzz.R | 14 pointblank-0.10.0/pointblank/README.md | 4 pointblank-0.10.0/pointblank/inst/img/function_icons/row_count_match.png |only pointblank-0.10.0/pointblank/inst/img/function_icons/row_count_match.svg |only pointblank-0.10.0/pointblank/inst/img/function_icons/tbl_match.png |only pointblank-0.10.0/pointblank/inst/img/function_icons/tbl_match.svg |only pointblank-0.10.0/pointblank/inst/rmarkdown/templates/pointblank-validation/skeleton/skeleton.Rmd | 8 pointblank-0.10.0/pointblank/inst/text/translations_built |binary pointblank-0.10.0/pointblank/inst/yaml/agent-small_table.yml | 2 pointblank-0.10.0/pointblank/inst/yaml/informant-small_table.yml | 2 pointblank-0.10.0/pointblank/man/activate_steps.Rd | 7 pointblank-0.10.0/pointblank/man/col_exists.Rd | 6 pointblank-0.10.0/pointblank/man/col_is_character.Rd | 8 pointblank-0.10.0/pointblank/man/col_is_date.Rd | 26 pointblank-0.10.0/pointblank/man/col_is_factor.Rd | 26 pointblank-0.10.0/pointblank/man/col_is_integer.Rd | 8 pointblank-0.10.0/pointblank/man/col_is_logical.Rd | 12 pointblank-0.10.0/pointblank/man/col_is_numeric.Rd | 26 pointblank-0.10.0/pointblank/man/col_is_posix.Rd | 26 pointblank-0.10.0/pointblank/man/col_schema.Rd | 11 pointblank-0.10.0/pointblank/man/col_schema_match.Rd | 5 pointblank-0.10.0/pointblank/man/col_vals_between.Rd | 12 pointblank-0.10.0/pointblank/man/col_vals_decreasing.Rd | 95 + pointblank-0.10.0/pointblank/man/col_vals_equal.Rd | 4 pointblank-0.10.0/pointblank/man/col_vals_expr.Rd | 8 pointblank-0.10.0/pointblank/man/col_vals_gt.Rd | 4 pointblank-0.10.0/pointblank/man/col_vals_gte.Rd | 8 pointblank-0.10.0/pointblank/man/col_vals_in_set.Rd | 10 pointblank-0.10.0/pointblank/man/col_vals_increasing.Rd | 80 + pointblank-0.10.0/pointblank/man/col_vals_lt.Rd | 4 pointblank-0.10.0/pointblank/man/col_vals_lte.Rd | 8 pointblank-0.10.0/pointblank/man/col_vals_make_set.Rd | 24 pointblank-0.10.0/pointblank/man/col_vals_make_subset.Rd | 14 pointblank-0.10.0/pointblank/man/col_vals_not_between.Rd | 4 pointblank-0.10.0/pointblank/man/col_vals_not_equal.Rd | 10 pointblank-0.10.0/pointblank/man/col_vals_not_in_set.Rd | 9 pointblank-0.10.0/pointblank/man/col_vals_not_null.Rd | 6 pointblank-0.10.0/pointblank/man/col_vals_null.Rd | 6 pointblank-0.10.0/pointblank/man/col_vals_regex.Rd | 6 pointblank-0.10.0/pointblank/man/col_vals_within_spec.Rd | 10 pointblank-0.10.0/pointblank/man/conjointly.Rd | 8 pointblank-0.10.0/pointblank/man/create_agent.Rd | 45 pointblank-0.10.0/pointblank/man/create_informant.Rd | 53 pointblank-0.10.0/pointblank/man/create_multiagent.Rd | 4 pointblank-0.10.0/pointblank/man/db_tbl.Rd | 29 pointblank-0.10.0/pointblank/man/deactivate_steps.Rd | 14 pointblank-0.10.0/pointblank/man/email_blast.Rd | 8 pointblank-0.10.0/pointblank/man/email_create.Rd | 6 pointblank-0.10.0/pointblank/man/export_report.Rd | 9 pointblank-0.10.0/pointblank/man/file_tbl.Rd | 29 pointblank-0.10.0/pointblank/man/from_github.Rd | 7 pointblank-0.10.0/pointblank/man/game_revenue_info.Rd | 5 pointblank-0.10.0/pointblank/man/get_agent_report.Rd | 78 - pointblank-0.10.0/pointblank/man/get_data_extracts.Rd | 2 pointblank-0.10.0/pointblank/man/get_informant_report.Rd | 8 pointblank-0.10.0/pointblank/man/get_multiagent_report.Rd | 2 pointblank-0.10.0/pointblank/man/get_sundered_data.Rd | 2 pointblank-0.10.0/pointblank/man/has_columns.Rd | 6 pointblank-0.10.0/pointblank/man/incorporate.Rd | 2 pointblank-0.10.0/pointblank/man/info_columns.Rd | 4 pointblank-0.10.0/pointblank/man/info_columns_from_tbl.Rd | 18 pointblank-0.10.0/pointblank/man/info_section.Rd | 8 pointblank-0.10.0/pointblank/man/info_snippet.Rd | 2 pointblank-0.10.0/pointblank/man/info_tabular.Rd | 4 pointblank-0.10.0/pointblank/man/log4r_step.Rd | 76 + pointblank-0.10.0/pointblank/man/print.read_fn.Rd | 4 pointblank-0.10.0/pointblank/man/remove_steps.Rd | 9 pointblank-0.10.0/pointblank/man/row_count_match.Rd |only pointblank-0.10.0/pointblank/man/rows_complete.Rd | 71 - pointblank-0.10.0/pointblank/man/rows_distinct.Rd | 71 - pointblank-0.10.0/pointblank/man/serially.Rd | 10 pointblank-0.10.0/pointblank/man/set_tbl.Rd | 36 pointblank-0.10.0/pointblank/man/small_table_sqlite.Rd | 6 pointblank-0.10.0/pointblank/man/snip_highest.Rd | 4 pointblank-0.10.0/pointblank/man/snip_list.Rd | 4 pointblank-0.10.0/pointblank/man/snip_lowest.Rd | 2 pointblank-0.10.0/pointblank/man/snip_stats.Rd | 2 pointblank-0.10.0/pointblank/man/specially.Rd | 143 +- pointblank-0.10.0/pointblank/man/stock_msg_body.Rd | 2 pointblank-0.10.0/pointblank/man/stock_msg_footer.Rd | 2 pointblank-0.10.0/pointblank/man/tbl_get.Rd | 4 pointblank-0.10.0/pointblank/man/tbl_match.Rd |only pointblank-0.10.0/pointblank/man/tbl_source.Rd | 14 pointblank-0.10.0/pointblank/man/tbl_store.Rd | 16 pointblank-0.10.0/pointblank/man/tt_summary_stats.Rd | 2 pointblank-0.10.0/pointblank/man/validate_rmd.Rd | 26 pointblank-0.10.0/pointblank/man/write_testthat_file.Rd | 19 pointblank-0.10.0/pointblank/man/x_read_disk.Rd | 14 pointblank-0.10.0/pointblank/man/x_write_disk.Rd | 20 pointblank-0.10.0/pointblank/man/yaml_agent_interrogate.Rd | 6 pointblank-0.10.0/pointblank/man/yaml_agent_show_exprs.Rd | 2 pointblank-0.10.0/pointblank/man/yaml_agent_string.Rd | 2 pointblank-0.10.0/pointblank/man/yaml_informant_incorporate.Rd | 12 pointblank-0.10.0/pointblank/man/yaml_read_agent.Rd | 28 pointblank-0.10.0/pointblank/man/yaml_write.Rd | 21 pointblank-0.10.0/pointblank/tests/testthat/_snaps/draft_validation.md | 126 - pointblank-0.10.0/pointblank/tests/testthat/test-create_agent.R | 64 pointblank-0.10.0/pointblank/tests/testthat/test-create_informant.R | 66 pointblank-0.10.0/pointblank/tests/testthat/test-create_multiagent.R | 8 pointblank-0.10.0/pointblank/tests/testthat/test-create_validation_steps.R | 82 + pointblank-0.10.0/pointblank/tests/testthat/test-draft_validation.R | 2 pointblank-0.10.0/pointblank/tests/testthat/test-expectation_fns.R | 110 + pointblank-0.10.0/pointblank/tests/testthat/test-get_informant_report.R | 4 pointblank-0.10.0/pointblank/tests/testthat/test-get_multiagent_report.R | 8 pointblank-0.10.0/pointblank/tests/testthat/test-incorporate_with_informant.R | 37 pointblank-0.10.0/pointblank/tests/testthat/test-interrogate_simple.R | 224 ++- pointblank-0.10.0/pointblank/tests/testthat/test-interrogate_with_agent.R | 45 pointblank-0.10.0/pointblank/tests/testthat/test-object_ops.R | 100 + pointblank-0.10.0/pointblank/tests/testthat/test-remove_deactivate.R | 4 pointblank-0.10.0/pointblank/tests/testthat/test-tbl_store.R | 6 pointblank-0.10.0/pointblank/tests/testthat/test-test_fns.R | 89 + pointblank-0.10.0/pointblank/tests/testthat/test-util_functions.R | 4 pointblank-0.10.0/pointblank/tests/testthat/test-write_testthat_file.R | 2 pointblank-0.10.0/pointblank/tests/testthat/test-yaml.R | 22 pointblank-0.10.0/pointblank/tests/testthat/test-yaml_read_informant.R | 4 pointblank-0.9.0/pointblank/man/remove_read_fn.Rd |only pointblank-0.9.0/pointblank/man/remove_tbl.Rd |only pointblank-0.9.0/pointblank/man/set_read_fn.Rd |only 185 files changed, 4148 insertions(+), 2180 deletions(-)
Title: Match One Sample using Two Criteria
Description: Multivariate matching in observational studies typically has two goals: 1. to construct
treated and control groups that have similar distribution of observed covariates and 2. to produce
matched pairs or sets that are homogeneous in a few priority variables. This packages implements a
network-flow-based method built around a tripartite graph that can simultaneously achieve both goals.
A detailed explanation of the workflow and numerous examples are given in the vignette.
Author: Bo Zhang [aut, cre]
Maintainer: Bo Zhang <bozhan@wharton.upenn.edu>
Diff between match2C versions 1.1.1 dated 2021-05-09 and 1.2.1 dated 2022-01-23
DESCRIPTION | 10 MD5 | 26 NAMESPACE | 5 R/check_balance_template.R |only R/construct_outcome_template.R |only R/stitch_two_nets_template.R |only R/template_match.R |only R/treated_control_net.R | 3 build/vignette.rds |binary inst/doc/tutorial.R | 67 + inst/doc/tutorial.Rmd | 200 +++++ inst/doc/tutorial.html | 1440 +++++++++++++++++++------------------- man/check_balance_template.Rd |only man/construct_outcome_template.Rd |only man/stitch_two_nets_template.Rd |only man/template_match.Rd |only src/RcppExports.cpp | 5 vignettes/tutorial.Rmd | 200 +++++ 18 files changed, 1234 insertions(+), 722 deletions(-)
Title: Mixture Autoregressive Models
Description: Model time series using mixture autoregressive (MAR)
models. Implemented are frequentist (EM) and Bayesian
methods for estimation, prediction and model
evaluation. See Wong and Li (2002)
<doi:10.1111/1467-9868.00222>, Boshnakov (2009)
<doi:10.1016/j.spl.2009.04.009>), and the extensive
references in the documentation.
Author: Georgi N. Boshnakov [aut, cre],
Davide Ravagli [aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between mixAR versions 0.22.5 dated 2021-01-04 and 0.22.6 dated 2022-01-23
DESCRIPTION | 10 - MD5 | 66 +++++---- NAMESPACE | 6 NEWS.md | 18 ++ R/00marmath.R | 12 + R/dist.R | 41 +++++- R/emGaussian.R | 26 ++- R/emgen.R | 235 ++++++++++++++++++++++++----------- R/mixAR.R | 74 +++++++++-- R/mixAR_diag.R | 108 ---------------- R/mixComp.R | 3 R/predict.R | 49 +++++-- R/tsdiag.R | 41 ++++-- README.md | 9 - build/partial.rdb |binary inst/REFERENCES.bib | 10 + inst/test-mixVAR.RData |only man/PortfolioData1.Rd | 2 man/fit_mixAR-methods.Rd | 28 +++- man/mixARExperiment.Rd | 1 man/mixAR_diag.Rd | 13 + man/mix_hatk.Rd | 2 man/mix_pdf-methods.Rd | 11 + man/mix_qf-methods.Rd |only man/multiStep_dist-methods.Rd | 17 +- man/predict_coef.Rd | 36 ++++- man/stdnormmoment.Rd | 5 man/test_unswitch.Rd | 3 man/unswitch.Rd | 14 -- tests/testthat/test-dist.R |only tests/testthat/test-fit_mixAR.R |only tests/testthat/test-mixAR.R | 65 +++------ tests/testthat/test-mixAR_diag.R | 17 +- tests/testthat/test-mixARnoise_sim.R |only tests/testthat/test-mixARreg.R | 57 ++++---- tests/testthat/test-predict.R | 16 ++ tests/testthat/test-unswitch.R |only 37 files changed, 600 insertions(+), 395 deletions(-)
Title: Managing, Querying and Analyzing Tokenized Text
Description: Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations).
Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences),
similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages,
and the possibility to reconstruct original text from tokens to facilitate interpretation.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between corpustools versions 0.4.8 dated 2021-06-25 and 0.4.9 dated 2022-01-23
corpustools-0.4.8/corpustools/R/compare_documents_dtm.r |only corpustools-0.4.8/corpustools/R/deprecated.r |only corpustools-0.4.9/corpustools/DESCRIPTION | 10 corpustools-0.4.9/corpustools/MD5 | 72 corpustools-0.4.9/corpustools/NAMESPACE | 2 corpustools-0.4.9/corpustools/R/1_tcorpus.r | 38 corpustools-0.4.9/corpustools/R/adjacency_functions.r | 2 corpustools-0.4.9/corpustools/R/aggregate.r | 4 corpustools-0.4.9/corpustools/R/create_tcorpus.r | 137 corpustools-0.4.9/corpustools/R/data.r | 2 corpustools-0.4.9/corpustools/R/document_term_matrix.r | 10 corpustools-0.4.9/corpustools/R/feature_associations.r | 4 corpustools-0.4.9/corpustools/R/feature_information.r | 2 corpustools-0.4.9/corpustools/R/import_tcorpus.r | 10 corpustools-0.4.9/corpustools/R/kwic.r | 2 corpustools-0.4.9/corpustools/R/lda.r | 4 corpustools-0.4.9/corpustools/R/merge_tcorpus.r | 2 corpustools-0.4.9/corpustools/R/plot_words.r | 2 corpustools-0.4.9/corpustools/R/preprocessing.r | 9 corpustools-0.4.9/corpustools/R/print_text.r | 2 corpustools-0.4.9/corpustools/R/rsyntax.r | 4 corpustools-0.4.9/corpustools/R/search.r | 8 corpustools-0.4.9/corpustools/R/search_dictionary.r | 14 corpustools-0.4.9/corpustools/R/search_results.r | 9 corpustools-0.4.9/corpustools/R/semnet.r | 10 corpustools-0.4.9/corpustools/R/semnet_plotting.r | 2 corpustools-0.4.9/corpustools/R/subset_tcorpus.r | 4 corpustools-0.4.9/corpustools/R/tokenize.r | 22 corpustools-0.4.9/corpustools/R/udpipe_coref.r | 1 corpustools-0.4.9/corpustools/R/untokenize.r |only corpustools-0.4.9/corpustools/R/util.r | 2 corpustools-0.4.9/corpustools/build/vignette.rds |binary corpustools-0.4.9/corpustools/data/sotu_texts.rda |binary corpustools-0.4.9/corpustools/inst/doc/corpustools.html | 1505 ++++------ corpustools-0.4.9/corpustools/man/create_tcorpus.Rd | 12 corpustools-0.4.9/corpustools/man/export_span_annotations.Rd |only corpustools-0.4.9/corpustools/man/untokenize.Rd |only corpustools-0.4.9/corpustools/src/RcppExports.cpp | 5 corpustools-0.4.9/corpustools/tests/testthat/test_compare_documents.r | 3 corpustools-0.4.9/corpustools/tests/testthat/test_remember_space.r |only 40 files changed, 903 insertions(+), 1012 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] (<https://orcid.org/0000-0003-0363-3180>),
Yujing Jiang [aut],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between clusrank versions 1.0-1 dated 2021-07-26 and 1.0-2 dated 2022-01-23
DESCRIPTION | 8 ++++---- MD5 | 26 ++++++++++++++------------ NEWS.md |only R/amd.R | 2 +- R/clusWilcox.R | 24 +++++++----------------- R/clusranksum.R | 2 +- R/clussignrank.R | 6 ++++-- R/crd.R | 2 +- R/crdstr.R | 2 +- R/crsd.R | 2 +- R/crsdunb.R | 2 +- R/print.R | 2 +- R/recodeFun.R | 2 +- R/special.R | 2 +- README.md |only 15 files changed, 38 insertions(+), 44 deletions(-)
Title: Weighted Metrics, Scoring Functions and Performance Measures for
Machine Learning
Description: Provides weighted versions of several metrics, scoring
functions and performance measures used in machine learning, including
average unit deviances of the Bernoulli, Tweedie, Poisson, and Gamma
distributions, see Jorgensen B. (1997, ISBN: 978-0412997112). The
package also contains a weighted version of generalized R-squared, see
e.g. Cohen, J. et al. (2002, ISBN: 978-0805822236). Furthermore,
'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph],
Christian Lorentzen [ctb, rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between MetricsWeighted versions 0.5.3 dated 2021-06-06 and 0.5.4 dated 2022-01-23
MetricsWeighted-0.5.3/MetricsWeighted/man/figures |only MetricsWeighted-0.5.4/MetricsWeighted/DESCRIPTION | 17 - MetricsWeighted-0.5.4/MetricsWeighted/MD5 | 109 +++--- MetricsWeighted-0.5.4/MetricsWeighted/NAMESPACE | 88 ++--- MetricsWeighted-0.5.4/MetricsWeighted/NEWS.md | 7 MetricsWeighted-0.5.4/MetricsWeighted/README.md | 2 MetricsWeighted-0.5.4/MetricsWeighted/build/vignette.rds |binary MetricsWeighted-0.5.4/MetricsWeighted/inst/doc/MetricsWeighted.Rmd | 2 MetricsWeighted-0.5.4/MetricsWeighted/inst/doc/MetricsWeighted.html | 6 MetricsWeighted-0.5.4/MetricsWeighted/man/AUC.Rd | 70 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/accuracy.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/classification_error.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/deviance_bernoulli.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/deviance_gamma.Rd | 66 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/deviance_normal.Rd | 66 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/deviance_poisson.Rd | 72 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/deviance_tweedie.Rd | 76 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/elementary_score.Rd | 116 +++--- MetricsWeighted-0.5.4/MetricsWeighted/man/f1_score.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/gini_coefficient.Rd | 62 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/logLoss.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/mae.Rd | 54 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/mape.Rd | 54 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/medae.Rd | 54 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/mse.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/multi_metric.Rd | 78 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/murphy_diagram.Rd | 108 +++--- MetricsWeighted-0.5.4/MetricsWeighted/man/performance.Rd | 170 +++++----- MetricsWeighted-0.5.4/MetricsWeighted/man/precision.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/prop_within.Rd | 66 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/r_squared.Rd | 116 +++--- MetricsWeighted-0.5.4/MetricsWeighted/man/r_squared_bernoulli.Rd | 72 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/r_squared_gamma.Rd | 70 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/r_squared_poisson.Rd | 72 ++-- MetricsWeighted-0.5.4/MetricsWeighted/man/recall.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/rmse.Rd | 60 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/weighted_cor.Rd | 64 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/weighted_mean.Rd | 58 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/weighted_median.Rd | 58 +-- MetricsWeighted-0.5.4/MetricsWeighted/man/weighted_quantile.Rd | 102 +++--- MetricsWeighted-0.5.4/MetricsWeighted/man/weighted_var.Rd | 70 ++-- MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-accuracy-error.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-deviance.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-elescore.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-interface.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-mae.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-mape.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-medae.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-mse.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-performance-multimetric.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-precision-recall-f1.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-probabilities.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-prop-within.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-rsquared.R | 8 MetricsWeighted-0.5.4/MetricsWeighted/tests/testthat/test-stats.R | 2 MetricsWeighted-0.5.4/MetricsWeighted/vignettes/MetricsWeighted.Rmd | 2 56 files changed, 1290 insertions(+), 1311 deletions(-)
More information about MetricsWeighted at CRAN
Permanent link
Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for
Analysis and Visualization
Description: Provides a consistent API to pull United States Department of
Agriculture census and survey data from the National Agricultural
Statistics Service (NASS) QuickStats service.
Author: Brad Lindblad [aut, cre],
Michael Thomas [ctb],
Alex Mindeman [ctb]
Maintainer: Brad Lindblad <me@bradlindblad.com>
Diff between tidyUSDA versions 0.3.2 dated 2021-08-01 and 0.3.3 dated 2022-01-23
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 5 README.md | 2 inst/doc/using_tidyusda.R | 48 ++--- inst/doc/using_tidyusda.Rmd | 18 +- inst/doc/using_tidyusda.html | 366 ------------------------------------------- vignettes/using_tidyusda.Rmd | 18 +- 8 files changed, 69 insertions(+), 408 deletions(-)
Title: Global and Individual Tests for Direct Effects
Description: Functions evaluate global and individual tests for direct effects in Mendelian randomization studies. Methods used in the package refer to J. Y. Dai, U. Peters, X. Wang, J. Kocarnik et al. (2018) <doi:10.1093/aje/kwy177>.
Author: James Dai [aut, cre],
Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Diff between GLIDE versions 1.0.3 dated 2021-11-09 and 1.0.4 dated 2022-01-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/GLIDE.pdf |binary src/Makevars.in | 1 - src/Makevars.win | 1 - src/glide.c | 1 - src/glide.h | 2 +- 7 files changed, 11 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-05 0.1.3
2022-01-03 0.1.2
2021-11-19 0.1.0
2021-11-19 0.1.1
Title: Exact Bayesian Model Selection Methods for the Sparse Normal
Sequence Model
Description: Contains fast functions to calculate the exact Bayes posterior
for the Sparse Normal Sequence Model, implementing the algorithms
described in Van Erven and Szabo (2021,
<doi:10.1214/20-BA1227>). For general hierarchical
priors, sample sizes up to 10,000 are feasible within half an hour
on a standard laptop. For beta-binomial spike-and-slab priors, a
faster algorithm is provided, which can handle sample sizes of
100,000 in half an hour. In the implementation, special care has
been taken to assure numerical stability of the methods even for
such large sample sizes.
Author: Steven de Rooij [aut],
Tim van Erven [cre, aut],
Botond Szabo [aut]
Maintainer: Tim van Erven <tim@timvanerven.nl>
Diff between SequenceSpikeSlab versions 0.1.1 dated 2020-01-08 and 1.0.0 dated 2022-01-23
DESCRIPTION | 34 - MD5 | 22 - NAMESPACE | 1 NEWS | 9 R/SequenceSpikeSlab.R | 1 build/vignette.rds |binary inst/CITATION | 17 inst/doc/SequenceSpikeSlab-vignette.Rmd | 4 inst/doc/SequenceSpikeSlab-vignette.html | 679 +++++++++++++++++-------------- src/RcppExports.cpp | 5 vignettes/SequenceSpikeSlab-vignette.Rmd | 4 vignettes/sss.bib | 19 12 files changed, 467 insertions(+), 328 deletions(-)
More information about SequenceSpikeSlab at CRAN
Permanent link
Title: Multivariate Normal Variance Mixtures
Description: Functions for working with (grouped) multivariate normal variance mixture
distributions (evaluation of distribution functions and densities,
random number generation and parameter estimation), including
Student's t distribution for non-integer degrees-of-freedom as well as the grouped t
distribution and copula with multiple degrees-of-freedom parameters.
Author: Marius Hofert [aut, cre],
Erik Hintz [aut],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between nvmix versions 0.0-7 dated 2022-01-04 and 0.0-8 dated 2022-01-23
DESCRIPTION | 10 ++--- MD5 | 16 ++++----- inst/doc/nvmix_functionality.html | 4 +- inst/doc/nvmix_riskmeasures.html | 4 +- man/dgnvmix.Rd | 64 +++++++++++++++++++------------------- man/fitnvmix.Rd | 63 +++++++++++++++++++------------------ man/gammamix.Rd | 16 ++++++--- man/pnvmix.Rd | 24 +++++++------- man/rgnvmix.Rd | 32 +++++++++---------- 9 files changed, 121 insertions(+), 112 deletions(-)
Title: Hyperband for 'mlr3'
Description: Implements hyperband method for hyperparameter
tuning. Various termination criteria can be set and combined. The
class 'AutoTuner' provides a convenient way to perform nested
resampling in combination with 'mlr3'. The hyperband algorithm was
proposed by Lisha Li, Kevin Jamieson, Giulia DeSalvo, Afshin
Rostamizadeh and Ameet Talwalkar (2018) <arXiv:1603.06560>.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>),
Sebastian Gruber [aut] (<https://orcid.org/0000-0002-8544-3470>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Julia Moosbauer [aut] (<https://orcid.org/0000-0002-0000-9297>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3hyperband versions 0.2.0 dated 2021-09-13 and 0.3.0 dated 2022-01-23
mlr3hyperband-0.2.0/mlr3hyperband/R/nds_selection.R |only mlr3hyperband-0.2.0/mlr3hyperband/man/nds_selection.Rd |only mlr3hyperband-0.3.0/mlr3hyperband/DESCRIPTION | 16 mlr3hyperband-0.3.0/mlr3hyperband/MD5 | 39 - mlr3hyperband-0.3.0/mlr3hyperband/NAMESPACE | 3 mlr3hyperband-0.3.0/mlr3hyperband/NEWS.md | 10 mlr3hyperband-0.3.0/mlr3hyperband/R/OptimizerHyperband.R | 344 +++------- mlr3hyperband-0.3.0/mlr3hyperband/R/OptimizerSuccessiveHalving.R | 90 +- mlr3hyperband-0.3.0/mlr3hyperband/R/TunerHyperband.R | 37 - mlr3hyperband-0.3.0/mlr3hyperband/R/TunerSuccessiveHalving.R | 27 mlr3hyperband-0.3.0/mlr3hyperband/R/helper.R |only mlr3hyperband-0.3.0/mlr3hyperband/inst |only mlr3hyperband-0.3.0/mlr3hyperband/man/hyperband_budget.Rd |only mlr3hyperband-0.3.0/mlr3hyperband/man/hyperband_n_configs.Rd |only mlr3hyperband-0.3.0/mlr3hyperband/man/hyperband_schedule.Rd |only mlr3hyperband-0.3.0/mlr3hyperband/man/mlr3hyperband-package.Rd | 7 mlr3hyperband-0.3.0/mlr3hyperband/man/mlr_optimizers_hyperband.Rd | 73 -- mlr3hyperband-0.3.0/mlr3hyperband/man/mlr_optimizers_successive_halving.Rd | 29 mlr3hyperband-0.3.0/mlr3hyperband/man/mlr_tuners_hyperband.Rd | 29 mlr3hyperband-0.3.0/mlr3hyperband/man/mlr_tuners_successive_halving.Rd | 12 mlr3hyperband-0.3.0/mlr3hyperband/tests/testthat/helper.R | 212 ++---- mlr3hyperband-0.3.0/mlr3hyperband/tests/testthat/test_TunerHyperband.R | 211 ++++-- mlr3hyperband-0.3.0/mlr3hyperband/tests/testthat/test_TunerSuccessiveHalving.R | 61 + mlr3hyperband-0.3.0/mlr3hyperband/tests/testthat/test_nds_selection.R | 2 24 files changed, 568 insertions(+), 634 deletions(-)
Title: Bayesian and Classical Audit Sampling
Description: Implements the audit sampling workflow as discussed in Derks et al. (2019) <doi:10.31234/osf.io/9f6ub>. The package makes it easy for an auditor to plan a statistical sample, select the sample from the population, and evaluate the misstatement in the sample compliant with the International Standards on Auditing. Next to classical audit sampling methodology, the package implements Bayesian equivalents of these methods whose statistical underpinnings are described in Derks et al. (2021) <doi:10.1111/ijau.12240> and Derks et al. (2021) <doi:10.31234/osf.io/kzqp5>.
Author: Koen Derks [aut, cre] (<https://orcid.org/0000-0002-5533-9349>)
Maintainer: Koen Derks <k.derks@nyenrode.nl>
Diff between jfa versions 0.6.1 dated 2021-11-18 and 0.6.2 dated 2022-01-23
DESCRIPTION | 10 - MD5 | 68 ++++++------ NAMESPACE | 4 NEWS.md | 11 + R/BuildIt-data.R | 15 ++ R/auditPrior.R | 106 +++++++------------ R/carrier-data.R | 15 ++ R/evaluation.R | 96 ++++++----------- R/jfa_internal.R | 18 +++ R/jfa_methods.R | 81 +++----------- R/methods.R | 27 +++- R/planning.R | 89 ++++++--------- R/report.R | 15 ++ R/selection.R | 17 ++- README.md | 3 build/vignette.rds |binary inst/CITATION | 6 - inst/doc/v3_prior_distributions.html | 6 - inst/doc/v6_testing_misstatement.html | 14 +- inst/doc/v7_bayes_factors_summary_statistics.html | 6 - man/auditPrior.Rd | 2 man/jfa-methods.Rd | 14 -- tests/testthat/test-consistency-auditPrior.R | 15 ++ tests/testthat/test-consistency-evaluation.R | 23 +++- tests/testthat/test-consistency-other.R | 15 ++ tests/testthat/test-consistency-planning.R | 19 +++ tests/testthat/test-consistency-selection.R | 15 ++ tests/testthat/test-consistency-statistical-tables.R | 15 ++ tests/testthat/test-consistency-workflow.R | 15 ++ tests/testthat/test-validation-MUS.R | 15 ++ tests/testthat/test-validation-appendix-a.R | 15 ++ tests/testthat/test-validation-appendix-c.R | 15 ++ tests/testthat/test-validation-audit-sampler.R | 15 ++ tests/testthat/test-validation-smash21.R | 15 ++ tests/testthat/test-validation-touwhoogduin.R | 15 ++ 35 files changed, 507 insertions(+), 323 deletions(-)
Title: Algorithms for Bundling Edges in Networks and Visualizing Flow
and Metro Maps
Description: Implements several algorithms for bundling edges in networks and flow and metro map layouts. This includes force directed edge bundling <doi:10.1111/j.1467-8659.2009.01450.x>, a flow algorithm based on Steiner trees<doi:10.1080/15230406.2018.1437359> and a multicriteria optimization method for metro map layouts <doi:10.1109/TVCG.2010.24>.
Author: David Schoch [aut, cre] (<https://orcid.org/0000-0003-2952-4812>)
Maintainer: David Schoch <david@schochastics.net>
Diff between edgebundle versions 0.3.0 dated 2021-10-30 and 0.3.1 dated 2022-01-23
DESCRIPTION | 15 +++++++++------ MD5 | 6 +++--- NEWS.md | 4 ++++ README.md | 1 + 4 files changed, 17 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-21 1.0.0
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'declared', 'DDIwR', 'mixed',
'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum
of Products expressions, for both binary and multi-value crisp sets, and
extracts information (set names, set values) from those expressions. Other
functions perform various other checks if possibly numeric (even if all
numbers reside in a character vector) and coerce to numeric, or check if the
numbers are whole. It also offers, among many others, a highly flexible
recoding routine and a more flexible alternative to the base function
'with()'.
Some of the functions in this package use related functions from package
'QCA'. Users are encouraged to install that package despite not being listed
in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.22 dated 2022-01-08 and 0.23 dated 2022-01-23
DESCRIPTION | 8 +- MD5 | 26 ++++----- NAMESPACE | 3 + R/compute.R | 3 - R/equality.R | 138 +++++++++++++++++++++++++++++++++++++++++--------- R/mvSOP.R | 3 + R/possibleNumeric.R | 8 ++ R/string.R | 29 +++++++--- R/translate.R | 3 + R/wholeNumeric.R | 25 +++------ build/partial.rdb |binary inst/ChangeLog | 10 +++ man/admisc.package.Rd | 4 - man/equality.Rd | 32 ++++++----- 14 files changed, 212 insertions(+), 80 deletions(-)
Title: Visualization Methods for Raster Data
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut]
(<https://orcid.org/0000-0002-4134-7196>),
Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@upm.es>
Diff between rasterVis versions 0.51.1 dated 2021-11-20 and 0.51.2 dated 2022-01-23
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++----------- R/gplot.R | 5 +--- R/histogram.R | 47 +++++++++++++++++++++++++-------------------- R/horizonplot.R | 12 +++-------- R/xyplot.R | 19 ++++++++++++------ build/partial.rdb |binary man/chooseRegion.Rd | 2 - man/densityplot-methods.Rd | 1 man/histogram-methods.Rd | 2 - man/hovmoller-methods.Rd | 3 +- man/vectorplot.Rd | 6 ++--- 12 files changed, 68 insertions(+), 57 deletions(-)
Title: Visualizes a Matrix as Heatmap
Description: Visualizes a matrix object plainly as heatmap. It provides S3 functions to plot simple matrices and loading matrices.
Author: Sigbert Klinke [aut, cre],
Frédéric Chevalier [ctb]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between plot.matrix versions 1.6 dated 2021-04-26 and 1.6.1 dated 2022-01-23
DESCRIPTION | 13 ++-- MD5 | 18 +++--- R/plot.matrix.R | 9 +++ README.md | 1 build/vignette.rds |binary inst/doc/plot.matrix.R | 32 ++++++++++++ inst/doc/plot.matrix.Rmd | 49 ++++++++++++++++++ inst/doc/plot.matrix.html | 120 ++++++++++++++++++++++++++++++++-------------- man/plot.matrix.Rd | 9 +++ vignettes/plot.matrix.Rmd | 49 ++++++++++++++++++ 10 files changed, 250 insertions(+), 50 deletions(-)
Title: FROC Analysis by Bayesian Approaches
Description: Provides new methods for the so-called Free-response Receiver Operating Characteristic (FROC) analysis. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), ..., etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI, CT, PET, ... , etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. References: Dev Chakraborty (1989) Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data.
Author: Issei Tsunoda [aut, cre]
Maintainer: Issei Tsunoda <tsunoda.issei1111@gmail.com>
Diff between BayesianFROC versions 0.5.0 dated 2021-10-27 and 1.0.0 dated 2022-01-23
BayesianFROC-0.5.0/BayesianFROC/R/p_value_visualization.R |only BayesianFROC-0.5.0/BayesianFROC/R/ppp.R |only BayesianFROC-0.5.0/BayesianFROC/man/p_value_visualization.Rd |only BayesianFROC-0.5.0/BayesianFROC/man/ppp.Rd |only BayesianFROC-0.5.0/BayesianFROC/man/ppp_MRMC.Rd |only BayesianFROC-0.5.0/BayesianFROC/man/ppp_srsc.Rd |only BayesianFROC-1.0.0/BayesianFROC/DESCRIPTION | 13 BayesianFROC-1.0.0/BayesianFROC/MD5 | 202 - BayesianFROC-1.0.0/BayesianFROC/NAMESPACE | 5 BayesianFROC-1.0.0/BayesianFROC/NEWS.md | 81 BayesianFROC-1.0.0/BayesianFROC/R/AFROC.R | 14 BayesianFROC-1.0.0/BayesianFROC/R/BayesianFROC.R | 3 BayesianFROC-1.0.0/BayesianFROC/R/DrawCurves.R | 2 BayesianFROC-1.0.0/BayesianFROC/R/StartupMessage.R | 75 BayesianFROC-1.0.0/BayesianFROC/R/chi_square_goodness_of_fit.R | 14 BayesianFROC-1.0.0/BayesianFROC/R/demo_Bayesian_FROC.R | 3 BayesianFROC-1.0.0/BayesianFROC/R/demo_Bayesian_FROC_without_pause.R | 6 BayesianFROC-1.0.0/BayesianFROC/R/document_dataset_srsc.R | 120 BayesianFROC-1.0.0/BayesianFROC/R/explanation_about_package_BayesianFROC.R | 199 + BayesianFROC-1.0.0/BayesianFROC/R/fffaaabbb.R | 12 BayesianFROC-1.0.0/BayesianFROC/R/fit_Bayesian_FROC.R | 25 BayesianFROC-1.0.0/BayesianFROC/R/fit_GUI_Shiny.R | 1333 ++++++---- BayesianFROC-1.0.0/BayesianFROC/R/fut_GUI_MRMC_shiny.R | 17 BayesianFROC-1.0.0/BayesianFROC/R/hit_rate_adjusted_from_the_vector_p.R | 2 BayesianFROC-1.0.0/BayesianFROC/R/is_na_list.R |only BayesianFROC-1.0.0/BayesianFROC/R/plot_FPF_and_TPF_from_a_dataset.R | 2 BayesianFROC-1.0.0/BayesianFROC/R/ppp_vectorization.R | 42 BayesianFROC-1.0.0/BayesianFROC/R/show_codes_in_my_manuscript.R | 3 BayesianFROC-1.0.0/BayesianFROC/R/size_of_return_value.R | 2 BayesianFROC-1.0.0/BayesianFROC/R/snippet_for_BayesianFROC.R | 2 BayesianFROC-1.0.0/BayesianFROC/R/stanfitExtended.R | 1 BayesianFROC-1.0.0/BayesianFROC/R/validation_error_srsc.R | 134 - BayesianFROC-1.0.0/BayesianFROC/build/vignette.rds |binary BayesianFROC-1.0.0/BayesianFROC/data/data_generate_NaN_in_fit_with_iteration1111_seed1234.rda |only BayesianFROC-1.0.0/BayesianFROC/inst/doc/Implemented_Models.Rmd | 3 BayesianFROC-1.0.0/BayesianFROC/inst/doc/Implemented_Models.html | 595 +++- BayesianFROC-1.0.0/BayesianFROC/inst/doc/References.pdf |binary BayesianFROC-1.0.0/BayesianFROC/inst/extdata/Model_srsc_multinomial.stan | 18 BayesianFROC-1.0.0/BayesianFROC/inst/extdata/SBCver2.stan | 56 BayesianFROC-1.0.0/BayesianFROC/man/AFROC.Rd | 9 BayesianFROC-1.0.0/BayesianFROC/man/Author_vs_classic_for_AUC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/BayesianFROC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Chi_square_goodness_of_fit_in_case_of_MRMC_Posterior_Mean.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/DrawCurves.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/DrawCurves_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/DrawCurves_MRMC_pairwise.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/DrawCurves_MRMC_pairwise_BlackWhite.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/DrawCurves_MRMC_pairwise_col.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/DrawCurves_srsc.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Draw_a_simulated_data_set.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Draw_a_simulated_data_set_and_Draw_posterior_samples.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Draw_an_area_of_AUC_for_srsc.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Simulation_Based_Calibration_histogram.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Simulation_Based_Calibration_single_reader_single_modality_via_rstan_sbc.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/Test_Null_Hypothesis_that_all_modalities_are_same.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/check_rhat.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/chi_square_at_replicated_data_and_MCMC_samples_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/chi_square_goodness_of_fit.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/chi_square_goodness_of_fit_from_input_all_param.Rd | 12 BayesianFROC-1.0.0/BayesianFROC/man/data_generate_NaN_in_fit_with_iteration1111_seed1234.Rd |only BayesianFROC-1.0.0/BayesianFROC/man/data_low_p_value.Rd | 3 BayesianFROC-1.0.0/BayesianFROC/man/draw_ROC_Curve.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/draw_ROC_Curve_from_fitted_model.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/draw_latent_noise_distribution.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/draw_latent_signal_distribution.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/error_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/error_message_on_imaging_device_rhat_values.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/error_srsc.Rd | 37 BayesianFROC-1.0.0/BayesianFROC/man/extractAUC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/extract_EAP_by_array.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/extract_estimates_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/extract_parameters_from_replicated_models.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/fffaaabbb.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/fit_Bayesian_FROC.Rd | 9 BayesianFROC-1.0.0/BayesianFROC/man/fit_GUI_Shiny.Rd | 60 BayesianFROC-1.0.0/BayesianFROC/man/fit_MRMC.Rd | 4 BayesianFROC-1.0.0/BayesianFROC/man/fit_MRMC_casewise.Rd | 4 BayesianFROC-1.0.0/BayesianFROC/man/fit_MRMC_versionTWO.Rd | 4 BayesianFROC-1.0.0/BayesianFROC/man/fit_Null_hypothesis_model_to_.Rd | 4 BayesianFROC-1.0.0/BayesianFROC/man/fit_srsc.Rd | 6 BayesianFROC-1.0.0/BayesianFROC/man/fit_srsc_ROC.Rd | 4 BayesianFROC-1.0.0/BayesianFROC/man/get_posterior_variance.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/get_samples_from_Posterior_Predictive_distribution.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/get_treedepth_threshold.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/ggplotFROC.EAP.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/ggplotFROC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/grapes-greater-than-greater-than-grapes.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/hit_rate_adjusted_from_the_vector_p.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/is_na_list.Rd |only BayesianFROC-1.0.0/BayesianFROC/man/make_true_parameter_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/metadata_to_DrawCurve_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/name_of_param_whose_Rhat_is_maximal.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/p_value_of_the_Bayesian_sense_for_chi_square_goodness_of_fit.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/pairs_plot_if_divergent_transition_occurred.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/plot_curve_and_hit_rate_and_false_rate_simultaneously.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/plot_dataset_of_ppp.Rd | 17 BayesianFROC-1.0.0/BayesianFROC/man/plot_dataset_of_ppp_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/replicate_model_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/sortAUC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/stan_trace_of_max_rhat.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/stanfitExtended.Rd | 4 BayesianFROC-1.0.0/BayesianFROC/man/stanfit_from_its_inherited_class.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/summarize_MRMC.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/summary_EAP_CI_srsc.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/trace_Plot.Rd | 2 BayesianFROC-1.0.0/BayesianFROC/man/validation.dataset_srsc.Rd | 88 BayesianFROC-1.0.0/BayesianFROC/vignettes/Implemented_Models.Rmd | 3 107 files changed, 2373 insertions(+), 979 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-17 1.1.4
2021-06-29 1.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-03 1.6.5
2021-07-22 1.6.4
2021-07-21 1.6.3
2021-07-08 1.6.2
2021-04-16 1.6.1
2021-04-14 1.6
2021-02-06 1.5-1
2021-02-03 1.5
2020-10-04 1.4
2020-03-29 1.3
2020-02-20 1.2
2019-12-03 1.1
2019-08-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-29 0.2.0
2021-09-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-01-13 0.3
2005-09-10 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-02 0.6-3
2015-01-09 0.6-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-22 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-27 1.1.2-1
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters). It specifies basic functions that allow many visual field tests to be constructed. As of October 2017 it is fully implemented on the Octopus 900 and partially on the Heidelberg Edge Perimeter, the Kowa AP 7000, the CrewT imo and the Centervue Compass. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph],
David Lawson [ctb, cph],
Matthias Muller [ctb],
Jonathan Dennis [ctb, cph],
Astrid Zeman [ctb],
Ivan Marin-Franch [ctb]
Maintainer: Andrew Turpin <aturpin@unimelb.edu.au>
Diff between OPI versions 2.9 dated 2019-09-19 and 2.10.0 dated 2022-01-23
OPI-2.10.0/OPI/DESCRIPTION | 32 - OPI-2.10.0/OPI/MD5 | 98 +-- OPI-2.10.0/OPI/NAMESPACE | 129 ++-- OPI-2.10.0/OPI/NEWS.md | 7 OPI-2.10.0/OPI/R/OPI-package.r |only OPI-2.10.0/OPI/R/compassClient.r | 134 ++++- OPI-2.10.0/OPI/R/data-RtDbUnits.r |only OPI-2.10.0/OPI/R/data-RtSigmaUnits.r |only OPI-2.10.0/OPI/R/daydreamClient.r | 509 +++++++++++-------- OPI-2.10.0/OPI/R/dbTocd.r | 40 + OPI-2.10.0/OPI/R/displayClient.r |only OPI-2.10.0/OPI/R/fourTwo.r | 163 ++++-- OPI-2.10.0/OPI/R/full_threshold.r | 335 ++++++++++++ OPI-2.10.0/OPI/R/imoClient.r | 766 ++++++++++++++++++++--------- OPI-2.10.0/OPI/R/kowaAP7000Client.r | 99 +++ OPI-2.10.0/OPI/R/mocs.r | 190 +++++++ OPI-2.10.0/OPI/R/octopus600.r | 103 +++ OPI-2.10.0/OPI/R/octopus900Client.r | 776 ++++++++++++++++++------------ OPI-2.10.0/OPI/R/opi.r | 260 +++++++++- OPI-2.10.0/OPI/R/opiKineticStimulus.r |only OPI-2.10.0/OPI/R/opiStaticStimulus.r |only OPI-2.10.0/OPI/R/opiTemporalStimulus.r |only OPI-2.10.0/OPI/R/pix2deg.r | 30 - OPI-2.10.0/OPI/R/simDisplay.r | 4 OPI-2.10.0/OPI/R/simG.r | 69 ++ OPI-2.10.0/OPI/R/simH.r | 144 +++++ OPI-2.10.0/OPI/R/simH_RT.r | 72 ++ OPI-2.10.0/OPI/R/simNo.r | 22 OPI-2.10.0/OPI/R/simYes.r | 21 OPI-2.10.0/OPI/R/zest.r | 381 ++++++++++---- OPI-2.10.0/OPI/README.md | 25 OPI-2.10.0/OPI/man/MOCS.Rd | 365 ++++++-------- OPI-2.10.0/OPI/man/OPI.Rd |only OPI-2.10.0/OPI/man/RtDbUnits.Rd | 55 +- OPI-2.10.0/OPI/man/RtSigmaUnits.Rd | 58 +- OPI-2.10.0/OPI/man/ZEST.Rd | 425 +++++++--------- OPI-2.10.0/OPI/man/chooseOpi.Rd | 106 +--- OPI-2.10.0/OPI/man/dbTocd.Rd | 74 +- OPI-2.10.0/OPI/man/fourTwo.Rd | 254 ++++----- OPI-2.10.0/OPI/man/full_threshold.Rd |only OPI-2.10.0/OPI/man/opiClose.Rd | 99 ++- OPI-2.10.0/OPI/man/opiDistributor.Rd |only OPI-2.10.0/OPI/man/opiGetParams.Rd |only OPI-2.10.0/OPI/man/opiInitialize.Rd | 632 +++++++++++++++--------- OPI-2.10.0/OPI/man/opiKineticStimulus.Rd | 146 ++--- OPI-2.10.0/OPI/man/opiPresent.Rd | 609 +++++++++++++---------- OPI-2.10.0/OPI/man/opiQueryDevice.Rd | 153 +++-- OPI-2.10.0/OPI/man/opiSetBackground.Rd | 442 ++++++++++++----- OPI-2.10.0/OPI/man/opiStaticStimulus.Rd | 202 +++---- OPI-2.10.0/OPI/man/opiTemporalStimulus.Rd | 123 ++-- OPI-2.10.0/OPI/man/pixTodeg.Rd | 23 OPI-2.10.0/OPI/tests/5.R | 2 OPI-2.9/OPI/R/full_threshold_state.r |only OPI-2.9/OPI/R/multiLocation.r |only OPI-2.9/OPI/man/FT.Rd |only OPI-2.9/OPI/man/OPI-package.Rd |only OPI-2.9/OPI/man/cdTodb.Rd |only OPI-2.9/OPI/man/degTopix.Rd |only OPI-2.9/OPI/tests/k_test.r |only 59 files changed, 5297 insertions(+), 2880 deletions(-)