Title: Response Probability Functions
Description: The purpose of this package is to factor out logic
and math common to Item Factor Analysis fitting, diagnostics, and
analysis. It is envisioned as core support code suitable for more
specialized IRT packages to build upon. Complete access to optimized C
functions are made available with R_RegisterCCallable().
This software is described in Pritikin & Falk (2020) <doi:10.1177/0146621620929431>.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 1.0.5 dated 2020-09-16 and 1.0.7 dated 2021-04-29
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- R/gpcmp.R | 2 +- R/lmp.R | 2 +- build/partial.rdb |only build/rpf.pdf |binary build/vignette.rds |binary inst/doc/diagnostics.html | 42 +++++++++++++++++++++--------------------- man/rpf.gpcmp.Rd | 2 +- man/rpf.lmp.Rd | 2 +- src/ba81quad.cpp | 14 +++++++------- tools/rox | 2 +- 12 files changed, 49 insertions(+), 48 deletions(-)
Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science
research. The package (<doi:10.1021/acs.jproteome.0c00684>) converts 1D
or 2D data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, are replaced by positive values. All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>
Diff between mrbin versions 1.5.1 dated 2021-04-22 and 1.5.2 dated 2021-04-29
DESCRIPTION | 9 +- MD5 | 19 +++--- NAMESPACE | 1 NEWS.md | 10 +++ R/mrbin.R | 162 +++++++++++++++++++++++++++++++++++++++++++--------- README.md | 6 + inst/doc/mrbin.R | 8 +- inst/doc/mrbin.Rnw | 18 +++++ inst/doc/mrbin.pdf |binary man/mrbinrun.Rd |only vignettes/mrbin.Rnw | 18 +++++ 11 files changed, 202 insertions(+), 49 deletions(-)
Title: Tools for Survival Analysis and Data Science
Description: Collection of functions to improve work-flow in survival analysis and data science.
The package features include: the generation of balanced datasets, live retrieval of
protein coding genes from two public databases, generation of random
matrix based on covariance matrix, cache function to store function results.
This work was supported by two grants from the Portuguese Foundation for Science
and technology, and the EU Commission under SOUND project.
Author: André Veríssimo [aut, cre],
Susana Vinga [aut]
Maintainer: André Veríssimo <andre.verissimo@tecnico.ulisboa.pt>
Diff between loose.rock versions 1.1.1 dated 2021-03-11 and 1.2.0 dated 2021-04-29
DESCRIPTION | 7 - MD5 | 27 ++-- NAMESPACE | 2 NEWS.md | 12 + R/balanced_data.R | 102 ++++++++++++++++ R/coding.genes.R | 6 README.md |only build/vignette.rds |binary inst/doc/Overview.Rmd | 2 inst/doc/Overview.html | 89 ++++++-------- man/balanced.cv.folds.from.vector.Rd |only man/balanced.train.and.test.from.vector.Rd |only tests/testthat/test-coding.genes.R | 109 ++++++++++++++---- tests/testthat/test_balanced_data.R | 11 + tests/testthat/test_balanced_data_from_vector.R |only tests/testthat/test_balanced_train_data_from_vector.R |only vignettes/Overview.Rmd | 2 17 files changed, 282 insertions(+), 87 deletions(-)
Title: Plot a Correlogram
Description: Calculates correlation of variables and displays the results
graphically. Included panel functions can display points, shading, ellipses, and
correlation values with confidence intervals. See Friendly (2002) <doi:10.1198/000313002533>.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between corrgram versions 1.13 dated 2018-07-09 and 1.14 dated 2021-04-29
DESCRIPTION | 17 - MD5 | 42 +-- NAMESPACE | 2 NEWS.md |only R/corrgram.R | 96 ++++--- build/vignette.rds |binary inst/doc/corrgram_cov2cor.R | 17 - inst/doc/corrgram_cov2cor.Rmd | 40 +-- inst/doc/corrgram_cov2cor.html | 237 ++++++++++++------- inst/doc/corrgram_examples.Rmd | 10 inst/doc/corrgram_examples.html | 463 ++++++++++++++++++++++---------------- man/auto.Rd | 6 man/baseball.Rd | 6 man/corrgram.Rd | 51 +++- man/figures |only man/vote.Rd | 4 tests/testthat/test_bounds.R | 4 tests/testthat/test_misc.R | 6 tests/testthat/test_order.R | 2 tests/testthat/test_outerlabels.R | 20 - vignettes/corrgram_cov2cor.Rmd | 40 +-- vignettes/corrgram_examples.Rmd | 10 22 files changed, 631 insertions(+), 442 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] (<https://orcid.org/0000-0002-9807-4686>),
Edwin de Jonge [aut] (<https://orcid.org/0000-0002-6580-4718>),
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.0.2 dated 2021-03-30 and 1.0.4 dated 2021-04-29
validate-1.0.2/validate/man/occurs.Rd |only validate-1.0.4/validate/DESCRIPTION | 8 - validate-1.0.4/validate/MD5 | 23 +--- validate-1.0.4/validate/NAMESPACE | 1 validate-1.0.4/validate/NEWS | 4 validate-1.0.4/validate/R/parse.R | 2 validate-1.0.4/validate/R/syntax.R | 78 +++++++------- validate-1.0.4/validate/build/vignette.rds |binary validate-1.0.4/validate/inst/doc/JSS_3483.pdf |binary validate-1.0.4/validate/inst/doc/cookbook.html | 34 +++--- validate-1.0.4/validate/inst/tinytest/test_genericrules.R | 23 ++-- validate-1.0.4/validate/inst/tinytest/test_syntax.R | 6 - validate-1.0.4/validate/man/voptions.Rd | 2 13 files changed, 92 insertions(+), 89 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>),
Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>),
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 2.0.0 dated 2021-03-09 and 2.1.0 dated 2021-04-29
opalr-2.0.0/opalr/R/datashield.admin.r |only opalr-2.0.0/opalr/R/opal.admin.r |only opalr-2.0.0/opalr/R/opal.annotations.r |only opalr-2.0.0/opalr/R/opal.assign.r |only opalr-2.0.0/opalr/R/opal.command.r |only opalr-2.0.0/opalr/R/opal.datasource.r |only opalr-2.0.0/opalr/R/opal.execute.r |only opalr-2.0.0/opalr/R/opal.file.r |only opalr-2.0.0/opalr/R/opal.project.r |only opalr-2.0.0/opalr/R/opal.r |only opalr-2.0.0/opalr/R/opal.report.r |only opalr-2.0.0/opalr/R/opal.resource.r |only opalr-2.0.0/opalr/R/opal.symbol.r |only opalr-2.0.0/opalr/R/opal.task.r |only opalr-2.0.0/opalr/R/opal.taxonomy.r |only opalr-2.0.0/opalr/R/opal.workspace.r |only opalr-2.0.0/opalr/R/utils.r |only opalr-2.1.0/opalr/DESCRIPTION | 13 opalr-2.1.0/opalr/MD5 | 363 +++++------ opalr-2.1.0/opalr/NAMESPACE | 9 opalr-2.1.0/opalr/R/datashield.admin.R |only opalr-2.1.0/opalr/R/dictionary.R | 6 opalr-2.1.0/opalr/R/opal.R |only opalr-2.1.0/opalr/R/opal.admin.R |only opalr-2.1.0/opalr/R/opal.annotations.R |only opalr-2.1.0/opalr/R/opal.assign.R |only opalr-2.1.0/opalr/R/opal.command.R |only opalr-2.1.0/opalr/R/opal.datasource.R |only opalr-2.1.0/opalr/R/opal.execute.R |only opalr-2.1.0/opalr/R/opal.file.R |only opalr-2.1.0/opalr/R/opal.project.R |only opalr-2.1.0/opalr/R/opal.report.R |only opalr-2.1.0/opalr/R/opal.resource.R |only opalr-2.1.0/opalr/R/opal.sql.R |only opalr-2.1.0/opalr/R/opal.symbol.R |only opalr-2.1.0/opalr/R/opal.task.R |only opalr-2.1.0/opalr/R/opal.taxonomy.R |only opalr-2.1.0/opalr/R/opal.token.R |only opalr-2.1.0/opalr/R/opal.workspace.R |only opalr-2.1.0/opalr/R/utils.R |only opalr-2.1.0/opalr/inst/doc/opal-files.html | 13 opalr-2.1.0/opalr/inst/doc/opal-projects.html | 13 opalr-2.1.0/opalr/inst/doc/opal-rsession.html | 13 opalr-2.1.0/opalr/man/dot-aclsToDataFrame.Rd | 2 opalr-2.1.0/opalr/man/dot-as.zeroOne.Rd | 2 opalr-2.1.0/opalr/man/dot-authorizationHeader.Rd | 2 opalr-2.1.0/opalr/man/dot-deparse.Rd | 2 opalr-2.1.0/opalr/man/dot-extractJsonField.Rd | 2 opalr-2.1.0/opalr/man/dot-extractLabel.Rd | 2 opalr-2.1.0/opalr/man/dot-extractOpalSessionId.Rd | 2 opalr-2.1.0/opalr/man/dot-getContent.Rd | 2 opalr-2.1.0/opalr/man/dot-getPEMFilePath.Rd | 2 opalr-2.1.0/opalr/man/dot-getRSessionId.Rd | 2 opalr-2.1.0/opalr/man/dot-getSessions.Rd | 2 opalr-2.1.0/opalr/man/dot-handleError.Rd | 2 opalr-2.1.0/opalr/man/dot-handleResponse.Rd | 2 opalr-2.1.0/opalr/man/dot-handleResponseLocation.Rd | 2 opalr-2.1.0/opalr/man/dot-handleResponseOrCallback.Rd | 2 opalr-2.1.0/opalr/man/dot-is.verbose.Rd | 2 opalr-2.1.0/opalr/man/dot-isContentEmpty.Rd | 2 opalr-2.1.0/opalr/man/dot-listToJson.Rd | 2 opalr-2.1.0/opalr/man/dot-newProgress.Rd | 2 opalr-2.1.0/opalr/man/dot-newSession.Rd | 2 opalr-2.1.0/opalr/man/dot-opal.login.Rd | 2 opalr-2.1.0/opalr/man/dot-rmOpalSession.Rd | 2 opalr-2.1.0/opalr/man/dot-rmRSession.Rd | 2 opalr-2.1.0/opalr/man/dot-select.Rd | 2 opalr-2.1.0/opalr/man/dot-tickProgress.Rd | 2 opalr-2.1.0/opalr/man/dot-tokenHeader.Rd | 2 opalr-2.1.0/opalr/man/dot-url.Rd | 2 opalr-2.1.0/opalr/man/dot-verbose.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.get_method.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.get_methods.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.get_options.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.install_github_package.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.install_local_package.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.install_package.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.installed_package.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.package_description.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.package_descriptions.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.perm.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.perm_add.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.perm_delete.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.remove_package.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.rm_method.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.rm_methods.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.rm_option.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.rm_package_methods.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.set_method.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.set_option.Rd | 2 opalr-2.1.0/opalr/man/dsadmin.set_package_methods.Rd | 2 opalr-2.1.0/opalr/man/oadmin.install_bioconductor_package.Rd | 2 opalr-2.1.0/opalr/man/oadmin.install_devtools.Rd | 2 opalr-2.1.0/opalr/man/oadmin.install_github_package.Rd | 2 opalr-2.1.0/opalr/man/oadmin.install_local_package.Rd | 2 opalr-2.1.0/opalr/man/oadmin.install_package.Rd | 2 opalr-2.1.0/opalr/man/oadmin.installed_devtools.Rd | 2 opalr-2.1.0/opalr/man/oadmin.installed_package.Rd | 2 opalr-2.1.0/opalr/man/oadmin.installed_packages.Rd | 2 opalr-2.1.0/opalr/man/oadmin.package_description.Rd | 2 opalr-2.1.0/opalr/man/oadmin.perm.Rd | 2 opalr-2.1.0/opalr/man/oadmin.perm_add.Rd | 2 opalr-2.1.0/opalr/man/oadmin.perm_delete.Rd | 2 opalr-2.1.0/opalr/man/oadmin.remove_package.Rd | 2 opalr-2.1.0/opalr/man/opal.annotate.Rd | 2 opalr-2.1.0/opalr/man/opal.annotations.Rd | 2 opalr-2.1.0/opalr/man/opal.as_md_table.Rd | 2 opalr-2.1.0/opalr/man/opal.assign.Rd | 2 opalr-2.1.0/opalr/man/opal.assign.data.Rd | 2 opalr-2.1.0/opalr/man/opal.assign.resource.Rd | 2 opalr-2.1.0/opalr/man/opal.assign.script.Rd | 2 opalr-2.1.0/opalr/man/opal.assign.table.Rd | 2 opalr-2.1.0/opalr/man/opal.assign.table.tibble.Rd | 2 opalr-2.1.0/opalr/man/opal.attribute_values.Rd | 2 opalr-2.1.0/opalr/man/opal.command.Rd | 2 opalr-2.1.0/opalr/man/opal.command_result.Rd | 2 opalr-2.1.0/opalr/man/opal.command_rm.Rd | 2 opalr-2.1.0/opalr/man/opal.commands.Rd | 2 opalr-2.1.0/opalr/man/opal.commands_rm.Rd | 2 opalr-2.1.0/opalr/man/opal.datasource.Rd | 2 opalr-2.1.0/opalr/man/opal.datasources.Rd | 2 opalr-2.1.0/opalr/man/opal.delete.Rd | 2 opalr-2.1.0/opalr/man/opal.execute.Rd | 2 opalr-2.1.0/opalr/man/opal.execute.source.Rd | 2 opalr-2.1.0/opalr/man/opal.file.Rd | 2 opalr-2.1.0/opalr/man/opal.file_cp.Rd | 2 opalr-2.1.0/opalr/man/opal.file_download.Rd | 2 opalr-2.1.0/opalr/man/opal.file_ls.Rd | 2 opalr-2.1.0/opalr/man/opal.file_mkdir.Rd | 2 opalr-2.1.0/opalr/man/opal.file_mkdir_tmp.Rd | 2 opalr-2.1.0/opalr/man/opal.file_mv.Rd | 2 opalr-2.1.0/opalr/man/opal.file_read.Rd | 2 opalr-2.1.0/opalr/man/opal.file_rm.Rd | 2 opalr-2.1.0/opalr/man/opal.file_upload.Rd | 2 opalr-2.1.0/opalr/man/opal.file_write.Rd | 2 opalr-2.1.0/opalr/man/opal.get.Rd | 2 opalr-2.1.0/opalr/man/opal.load_package.Rd | 2 opalr-2.1.0/opalr/man/opal.login.Rd | 2 opalr-2.1.0/opalr/man/opal.logout.Rd | 2 opalr-2.1.0/opalr/man/opal.post.Rd | 2 opalr-2.1.0/opalr/man/opal.project.Rd | 3 opalr-2.1.0/opalr/man/opal.project_create.Rd | 3 opalr-2.1.0/opalr/man/opal.project_delete.Rd | 3 opalr-2.1.0/opalr/man/opal.project_exists.Rd | 3 opalr-2.1.0/opalr/man/opal.project_perm.Rd | 2 opalr-2.1.0/opalr/man/opal.project_perm_add.Rd | 2 opalr-2.1.0/opalr/man/opal.project_perm_delete.Rd | 2 opalr-2.1.0/opalr/man/opal.projects.Rd | 3 opalr-2.1.0/opalr/man/opal.put.Rd | 2 opalr-2.1.0/opalr/man/opal.report.Rd | 2 opalr-2.1.0/opalr/man/opal.report_md.Rd | 2 opalr-2.1.0/opalr/man/opal.resource.Rd | 3 opalr-2.1.0/opalr/man/opal.resource_create.Rd | 3 opalr-2.1.0/opalr/man/opal.resource_delete.Rd | 2 opalr-2.1.0/opalr/man/opal.resource_exists.Rd | 3 opalr-2.1.0/opalr/man/opal.resource_extension_create.Rd |only opalr-2.1.0/opalr/man/opal.resource_get.Rd | 3 opalr-2.1.0/opalr/man/opal.resource_perm.Rd | 2 opalr-2.1.0/opalr/man/opal.resource_perm_add.Rd | 2 opalr-2.1.0/opalr/man/opal.resource_perm_delete.Rd | 2 opalr-2.1.0/opalr/man/opal.resources.Rd | 3 opalr-2.1.0/opalr/man/opal.resources_perm.Rd | 2 opalr-2.1.0/opalr/man/opal.resources_perm_add.Rd | 2 opalr-2.1.0/opalr/man/opal.resources_perm_delete.Rd | 2 opalr-2.1.0/opalr/man/opal.rm.Rd | 2 opalr-2.1.0/opalr/man/opal.sql.Rd |only opalr-2.1.0/opalr/man/opal.sql_history.Rd |only opalr-2.1.0/opalr/man/opal.symbol_import.Rd | 2 opalr-2.1.0/opalr/man/opal.symbol_rm.Rd | 2 opalr-2.1.0/opalr/man/opal.symbol_save.Rd | 2 opalr-2.1.0/opalr/man/opal.symbols.Rd | 2 opalr-2.1.0/opalr/man/opal.table.Rd | 2 opalr-2.1.0/opalr/man/opal.tables.Rd | 2 opalr-2.1.0/opalr/man/opal.tables_perm.Rd | 2 opalr-2.1.0/opalr/man/opal.tables_perm_add.Rd | 2 opalr-2.1.0/opalr/man/opal.tables_perm_delete.Rd | 2 opalr-2.1.0/opalr/man/opal.task.Rd | 2 opalr-2.1.0/opalr/man/opal.task_cancel.Rd | 2 opalr-2.1.0/opalr/man/opal.task_wait.Rd | 2 opalr-2.1.0/opalr/man/opal.tasks.Rd | 2 opalr-2.1.0/opalr/man/opal.taxonomies.Rd | 2 opalr-2.1.0/opalr/man/opal.taxonomy.Rd | 2 opalr-2.1.0/opalr/man/opal.taxonomy_delete.Rd | 2 opalr-2.1.0/opalr/man/opal.taxonomy_download.Rd | 2 opalr-2.1.0/opalr/man/opal.taxonomy_upload.Rd | 2 opalr-2.1.0/opalr/man/opal.terms.Rd | 2 opalr-2.1.0/opalr/man/opal.token.Rd |only opalr-2.1.0/opalr/man/opal.token_datashield_create.Rd |only opalr-2.1.0/opalr/man/opal.token_delete.Rd |only opalr-2.1.0/opalr/man/opal.token_r_create.Rd |only opalr-2.1.0/opalr/man/opal.token_sql_create.Rd |only opalr-2.1.0/opalr/man/opal.tokens.Rd |only opalr-2.1.0/opalr/man/opal.unload_package.Rd | 2 opalr-2.1.0/opalr/man/opal.valueset.Rd | 2 opalr-2.1.0/opalr/man/opal.variable.Rd | 2 opalr-2.1.0/opalr/man/opal.variables.Rd | 2 opalr-2.1.0/opalr/man/opal.version_compare.Rd | 2 opalr-2.1.0/opalr/man/opal.vocabularies.Rd | 2 opalr-2.1.0/opalr/man/opal.vocabulary.Rd | 2 opalr-2.1.0/opalr/man/opal.workspace_rm.Rd | 2 opalr-2.1.0/opalr/man/opal.workspace_save.Rd | 8 opalr-2.1.0/opalr/man/opal.workspaces.Rd | 2 opalr-2.1.0/opalr/tests/testthat/helper-setup.R | 2 opalr-2.1.0/opalr/tests/testthat/test-dictionary.R | 53 + opalr-2.1.0/opalr/tests/testthat/test-sql.R |only opalr-2.1.0/opalr/tests/testthat/test-token.R |only 206 files changed, 457 insertions(+), 344 deletions(-)
Title: Algorithm to Compute Monitor Independent Movement Summary Unit
(MIMS-Unit)
Description: The MIMS-unit algorithm is developed to compute Monitor Independent
Movement Summary Unit, a measurement to summarize raw accelerometer data
while ensuring harmonized results across different devices. It also includes
scripts to reproduce results in the related publication
(John, D., Tang. Q., Albinali, F. and Intille, S. (2019) <doi:10.1123/jmpb.2018-0068>).
Author: Qu Tang [aut, cre] (<https://orcid.org/0000-0001-5415-0205>),
Dinesh John [aut],
Stephen Intille [aut],
mHealth Research Group [cph] (https://www.mhealthgroup.org)
Maintainer: Qu Tang <tang.q@northeastern.edu>
Diff between MIMSunit versions 0.9.2 dated 2020-07-31 and 0.10.0 dated 2021-04-29
MIMSunit-0.10.0/MIMSunit/DESCRIPTION | 24 ++--- MIMSunit-0.10.0/MIMSunit/MD5 | 42 +++++----- MIMSunit-0.10.0/MIMSunit/NEWS.md | 26 +++++- MIMSunit-0.10.0/MIMSunit/R/data.R | 12 +- MIMSunit-0.10.0/MIMSunit/R/export_data.R | 4 MIMSunit-0.10.0/MIMSunit/R/extrapolate.R | 2 MIMSunit-0.10.0/MIMSunit/R/helper.R | 7 - MIMSunit-0.10.0/MIMSunit/R/import_data.R | 40 +++------ MIMSunit-0.10.0/MIMSunit/R/mims_unit.R | 5 - MIMSunit-0.10.0/MIMSunit/README.md | 34 ++++---- MIMSunit-0.10.0/MIMSunit/inst/app/server.R | 2 MIMSunit-0.10.0/MIMSunit/inst/pkgdown |only MIMSunit-0.10.0/MIMSunit/man/conceptual_diagram_data.Rd | 2 MIMSunit-0.10.0/MIMSunit/man/cv_different_algorithms.Rd | 2 MIMSunit-0.10.0/MIMSunit/man/edge_case.Rd | 2 MIMSunit-0.10.0/MIMSunit/man/import_actigraph_csv.Rd | 25 +---- MIMSunit-0.10.0/MIMSunit/man/import_actigraph_csv_chunked.Rd | 12 +- MIMSunit-0.10.0/MIMSunit/man/import_actigraph_meta.Rd | 2 MIMSunit-0.10.0/MIMSunit/man/measurements_different_devices.Rd | 2 MIMSunit-0.10.0/MIMSunit/man/mims_unit.Rd | 5 - MIMSunit-0.10.0/MIMSunit/man/rest_on_table.Rd | 2 MIMSunit-0.10.0/MIMSunit/man/sample_raw_accel_data.Rd | 2 MIMSunit-0.9.2/MIMSunit/inst/extdata/actigraph.csv |only 23 files changed, 130 insertions(+), 124 deletions(-)
Title: Create Complex UpSet Plots Using 'ggplot2' Components
Description: UpSet plots are an improvement over Venn Diagram for set overlap visualizations.
Striving to bring the best of the 'UpSetR' and 'ggplot2', this package offers a way to create
complex overlap visualisations, using simple and familiar tools, i.e. geoms of 'ggplot2'.
For introduction to UpSet concept, see Lex et al. (2014) <doi:10.1109/TVCG.2014.2346248>.
Author: Michał Krassowski [aut, cre] (<https://orcid.org/0000-0002-9638-7785>)
Maintainer: Michał Krassowski <krassowski.michal+r@gmail.com>
Diff between ComplexUpset versions 1.2.0 dated 2021-04-04 and 1.2.1 dated 2021-04-29
ComplexUpset-1.2.0/ComplexUpset/vignettes/Examples_R_files |only ComplexUpset-1.2.1/ComplexUpset/DESCRIPTION | 6 ComplexUpset-1.2.1/ComplexUpset/LICENSE | 2 ComplexUpset-1.2.1/ComplexUpset/MD5 | 142 ComplexUpset-1.2.1/ComplexUpset/R/venn.R | 10 ComplexUpset-1.2.1/ComplexUpset/README.md | 9 ComplexUpset-1.2.1/ComplexUpset/inst/doc/Examples_R.Rmd | 144 ComplexUpset-1.2.1/ComplexUpset/inst/doc/Examples_R.html | 2818 +++++++--- ComplexUpset-1.2.1/ComplexUpset/vignettes/Examples_R.Rmd | 144 ComplexUpset-1.2.1/ComplexUpset/vignettes/Files_for_Examples_R |only 10 files changed, 2215 insertions(+), 1060 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
data.table team [cph] (Radix sort based on data.table's forder() and
their contribution to R's order()),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.3.7 dated 2021-03-29 and 0.3.8 dated 2021-04-29
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 5 +++++ R/aaa.R | 28 ++++++++++++++++++++++++++++ R/register-s3.R | 47 ++++++++++++++++++++++++++--------------------- R/zzz.R | 2 ++ inst/doc/s3-vector.html | 2 +- inst/doc/stability.html | 4 ++-- inst/doc/type-size.html | 8 +++++--- man/s3_register.Rd | 3 --- src/version.c | 2 +- 11 files changed, 83 insertions(+), 44 deletions(-)
Title: Pedigree Inference from SNPs
Description: Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 2.0.7 dated 2020-05-18 and 2.3.2 dated 2021-04-29
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sequoia-2.3.2/sequoia/R/SNPstats.R | 121 sequoia-2.3.2/sequoia/R/SeqListSummary.R | 346 sequoia-2.3.2/sequoia/R/Sequoia_F90wrappers.R | 457 sequoia-2.3.2/sequoia/R/Sequoia_Main.R | 613 sequoia-2.3.2/sequoia/R/Simulate.R | 213 sequoia-2.3.2/sequoia/R/Utils.R | 341 sequoia-2.3.2/sequoia/R/WriteToFiles.R | 106 sequoia-2.3.2/sequoia/R/getAssignable.R | 128 sequoia-2.3.2/sequoia/R/getRelM.R |only sequoia-2.3.2/sequoia/build/vignette.rds |binary sequoia-2.3.2/sequoia/data/FieldMums_griffin.txt |only sequoia-2.3.2/sequoia/data/LH_griffin.txt |only sequoia-2.3.2/sequoia/data/SeqOUT_griffin.RData |binary sequoia-2.3.2/sequoia/inst/doc/PedComp.R |only sequoia-2.3.2/sequoia/inst/doc/PedComp.Rmd |only sequoia-2.3.2/sequoia/inst/doc/PedComp.html |only sequoia-2.3.2/sequoia/inst/doc/flowchart.pdf |only sequoia-2.3.2/sequoia/inst/doc/flowchart.pdf.asis |only sequoia-2.3.2/sequoia/inst/doc/quick_start_example1.R |only sequoia-2.3.2/sequoia/inst/doc/quick_start_example1.html |only sequoia-2.3.2/sequoia/inst/doc/quick_start_example1.rmd |only sequoia-2.3.2/sequoia/inst/doc/vignette-age.R |only sequoia-2.3.2/sequoia/inst/doc/vignette-age.Rmd |only sequoia-2.3.2/sequoia/inst/doc/vignette-age.pdf |only sequoia-2.3.2/sequoia/inst/doc/vignette-main.R |only sequoia-2.3.2/sequoia/inst/doc/vignette-main.Rmd |only sequoia-2.3.2/sequoia/inst/doc/vignette-main.pdf |only sequoia-2.3.2/sequoia/inst/extdata/Inherit.csv |only sequoia-2.3.2/sequoia/man/CalcBYprobs.Rd |only sequoia-2.3.2/sequoia/man/CalcChi2.Rd | 10 sequoia-2.3.2/sequoia/man/CalcCorners.Rd |only sequoia-2.3.2/sequoia/man/CalcMaxMismatch.Rd | 23 sequoia-2.3.2/sequoia/man/CalcOHLLR.Rd | 189 sequoia-2.3.2/sequoia/man/CalcPairLL.Rd |only sequoia-2.3.2/sequoia/man/CalcRped.Rd |only sequoia-2.3.2/sequoia/man/CheckAP.Rd |only sequoia-2.3.2/sequoia/man/CheckGeno.Rd | 46 sequoia-2.3.2/sequoia/man/CheckLH.Rd | 28 sequoia-2.3.2/sequoia/man/CheckParams.Rd |only sequoia-2.3.2/sequoia/man/ComparePairs.Rd | 241 sequoia-2.3.2/sequoia/man/CountAgeDif.Rd |only sequoia-2.3.2/sequoia/man/DoErrors.Rd | 8 sequoia-2.3.2/sequoia/man/DuplicateCheck.Rd | 43 sequoia-2.3.2/sequoia/man/DyadCompare.Rd | 17 sequoia-2.3.2/sequoia/man/ErrToM.Rd | 9 sequoia-2.3.2/sequoia/man/EstConf.Rd | 351 sequoia-2.3.2/sequoia/man/EstErr.Rd | 10 sequoia-2.3.2/sequoia/man/FieldMums_griffin.Rd |only sequoia-2.3.2/sequoia/man/FindFamilies.Rd | 2 sequoia-2.3.2/sequoia/man/FoldSibGPs.Rd |only sequoia-2.3.2/sequoia/man/FortifyPairs.Rd |only sequoia-2.3.2/sequoia/man/GenoConvert.Rd | 91 sequoia-2.3.2/sequoia/man/GetDummifiable.Rd |only sequoia-2.3.2/sequoia/man/GetLLRAge.Rd |only sequoia-2.3.2/sequoia/man/GetMaybeRel.Rd | 151 sequoia-2.3.2/sequoia/man/GetRelA.Rd |only sequoia-2.3.2/sequoia/man/GetRelM.Rd |only sequoia-2.3.2/sequoia/man/LHConvert.Rd | 18 sequoia-2.3.2/sequoia/man/LH_HSg5.Rd | 13 sequoia-2.3.2/sequoia/man/LH_griffin.Rd |only sequoia-2.3.2/sequoia/man/LLRplot.Rd |only sequoia-2.3.2/sequoia/man/MakeAgePrior.Rd | 200 sequoia-2.3.2/sequoia/man/MergeFill.Rd | 8 sequoia-2.3.2/sequoia/man/MkFortParams.Rd |only sequoia-2.3.2/sequoia/man/MkGenoErrors.Rd | 10 sequoia-2.3.2/sequoia/man/NumToID.Rd |only sequoia-2.3.2/sequoia/man/ParamToSpecs.Rd |only sequoia-2.3.2/sequoia/man/PedCompare.Rd | 81 sequoia-2.3.2/sequoia/man/PedPolish.Rd | 51 sequoia-2.3.2/sequoia/man/PedStripFID.Rd | 10 sequoia-2.3.2/sequoia/man/PedToNum.Rd |only sequoia-2.3.2/sequoia/man/Ped_HSg5.Rd | 4 sequoia-2.3.2/sequoia/man/Ped_griffin.Rd | 8 sequoia-2.3.2/sequoia/man/PlotAgePrior.Rd | 32 sequoia-2.3.2/sequoia/man/PlotPairLL.Rd |only sequoia-2.3.2/sequoia/man/PlotPedComp.Rd |only sequoia-2.3.2/sequoia/man/PlotRelPairs.Rd |only sequoia-2.3.2/sequoia/man/SeqOUT_griffin.Rd | 15 sequoia-2.3.2/sequoia/man/SeqParSib.Rd | 42 sequoia-2.3.2/sequoia/man/SimGeno.Rd | 67 sequoia-2.3.2/sequoia/man/SnpStats.Rd | 40 sequoia-2.3.2/sequoia/man/SpecsToParam.Rd |only sequoia-2.3.2/sequoia/man/SummarySeq.Rd | 48 sequoia-2.3.2/sequoia/man/VennSquares.Rd |only 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sequoia-2.3.2/sequoia/vignettes/sequoia_refs.bib |only sequoia-2.3.2/sequoia/vignettes/vignette-age.Rmd |only sequoia-2.3.2/sequoia/vignettes/vignette-main.Rmd |only sequoia-2.3.2/sequoia/vignettes/vignette-main.html |only 170 files changed, 11257 insertions(+), 7526 deletions(-)
Title: Get Facts and Data from Wikipedia and Wikidata
Description: Query Wikidata and get facts from current and historic Wikipedia main pages.
Author: Keith McNulty [aut, cre] (<https://orcid.org/0000-0002-2332-1654>),
Petr Kajzar [ctb]
Maintainer: Keith McNulty <keith.mcnulty@gmail.com>
Diff between wikifacts versions 0.4.1 dated 2020-11-24 and 0.4.2 dated 2021-04-29
DESCRIPTION | 9 +-- MD5 | 14 +++--- NEWS.md | 7 +++ R/wiki_define.R |only R/wiki_search.R | 2 README.md | 72 +++++++++++++++++++++---------- man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/wiki_define.Rd |only 9 files changed, 69 insertions(+), 35 deletions(-)
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Andrea Gilardi [ctb],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@opengeohub.org>
Diff between plotKML versions 0.8-0 dated 2021-04-12 and 0.8-1 dated 2021-04-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/AAAA.R | 2 +- build/partial.rdb |binary inst/doc/jss1079.pdf |binary 5 files changed, 8 insertions(+), 8 deletions(-)
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Diego Hernangómez [ctb] (<https://orcid.org/0000-0001-8457-4658>),
Hugues Pecout [ctb],
Ian Fellows [cph] (No overlap algorithm for labels, from wordcloud
package),
Jim Lemon [cph] (Arc drawing algorithm for annotations, from plotrix
package),
Florian Zenoni [cph] (Orthographic projection visualisation)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 0.1.1 dated 2021-03-01 and 0.2.0 dated 2021-04-29
mapsf-0.1.1/mapsf/inst/img |only mapsf-0.1.1/mapsf/inst/tinytest/test_leg.R |only mapsf-0.1.1/mapsf/man/figures/logox.png |only mapsf-0.1.1/mapsf/man/figures/mtq.svg |only mapsf-0.1.1/mapsf/vignettes/fig/mf_grad-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_init-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_label-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_map_c-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_map_pc-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_map_pt-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_map_t-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/mf_prop-1.png |only mapsf-0.1.1/mapsf/vignettes/fig/poly_d.svg |only mapsf-0.1.1/mapsf/vignettes/fig/poly_dd.svg |only mapsf-0.2.0/mapsf/DESCRIPTION | 9 - mapsf-0.2.0/mapsf/MD5 | 131 +++++++++----------- mapsf-0.2.0/mapsf/NAMESPACE | 1 mapsf-0.2.0/mapsf/NEWS.md |only mapsf-0.2.0/mapsf/R/compassboard.R |only mapsf-0.2.0/mapsf/R/mf_credits.R | 58 +++++++- mapsf-0.2.0/mapsf/R/mf_doc_utils.R | 12 + mapsf-0.2.0/mapsf/R/mf_export.R |only mapsf-0.2.0/mapsf/R/mf_init.R | 104 ++------------- mapsf-0.2.0/mapsf/R/mf_inset.R | 1 mapsf-0.2.0/mapsf/R/mf_layout.R | 4 mapsf-0.2.0/mapsf/R/mf_leg_c.R | 1 mapsf-0.2.0/mapsf/R/mf_leg_p_utils.R | 3 mapsf-0.2.0/mapsf/R/mf_leg_s.R | 1 mapsf-0.2.0/mapsf/R/mf_leg_t.R | 2 mapsf-0.2.0/mapsf/R/mf_legend.R | 6 mapsf-0.2.0/mapsf/R/mf_map.R | 21 +-- mapsf-0.2.0/mapsf/R/mf_map_b.R | 21 +-- mapsf-0.2.0/mapsf/R/mf_map_c.R | 20 +-- mapsf-0.2.0/mapsf/R/mf_map_g.R | 16 +- mapsf-0.2.0/mapsf/R/mf_map_p.R | 19 +- mapsf-0.2.0/mapsf/R/mf_map_pc.R | 27 ++-- mapsf-0.2.0/mapsf/R/mf_map_pt.R | 27 ++-- mapsf-0.2.0/mapsf/R/mf_map_r.R | 21 +-- mapsf-0.2.0/mapsf/R/mf_map_s.R | 15 +- mapsf-0.2.0/mapsf/R/mf_map_sc.R | 19 +- mapsf-0.2.0/mapsf/R/mf_map_t.R | 20 +-- mapsf-0.2.0/mapsf/R/mf_map_utils.R | 62 ++++++++- mapsf-0.2.0/mapsf/R/mf_pkg_utils.R | 8 - mapsf-0.2.0/mapsf/R/mf_shadow.R | 2 mapsf-0.2.0/mapsf/R/mf_theme.R | 50 +++---- mapsf-0.2.0/mapsf/R/mf_title.R | 2 mapsf-0.2.0/mapsf/R/mf_worldmap.R | 7 - mapsf-0.2.0/mapsf/README.md | 33 ++--- mapsf-0.2.0/mapsf/build/vignette.rds |binary mapsf-0.2.0/mapsf/inst/doc/mapsf.R | 1 mapsf-0.2.0/mapsf/inst/doc/mapsf.Rmd | 3 mapsf-0.2.0/mapsf/inst/doc/mapsf.html | 22 +-- mapsf-0.2.0/mapsf/inst/gpkg/world.gpkg |binary mapsf-0.2.0/mapsf/inst/tinytest/test_export.R |only mapsf-0.2.0/mapsf/inst/tinytest/test_init.R | 19 -- mapsf-0.2.0/mapsf/inst/tinytest/test_map_pc.R | 12 + mapsf-0.2.0/mapsf/inst/tinytest/test_map_s.R |only mapsf-0.2.0/mapsf/inst/tinytest/test_raster.R | 2 mapsf-0.2.0/mapsf/inst/tinytest/test_theme.R | 5 mapsf-0.2.0/mapsf/man/figures/README-example1-1.png |binary mapsf-0.2.0/mapsf/man/figures/README-example4-1.png |binary mapsf-0.2.0/mapsf/man/figures/mtq.png |only mapsf-0.2.0/mapsf/man/mf_choro.Rd | 5 mapsf-0.2.0/mapsf/man/mf_credits.Rd | 11 + mapsf-0.2.0/mapsf/man/mf_export.Rd |only mapsf-0.2.0/mapsf/man/mf_grad.Rd | 2 mapsf-0.2.0/mapsf/man/mf_init.Rd | 27 ---- mapsf-0.2.0/mapsf/man/mf_legend.Rd | 2 mapsf-0.2.0/mapsf/man/mf_map.Rd | 6 mapsf-0.2.0/mapsf/man/mf_prop.Rd | 2 mapsf-0.2.0/mapsf/man/mf_prop_choro.Rd | 7 - mapsf-0.2.0/mapsf/man/mf_prop_typo.Rd | 7 - mapsf-0.2.0/mapsf/man/mf_symb.Rd | 5 mapsf-0.2.0/mapsf/man/mf_symb_choro.Rd | 7 - mapsf-0.2.0/mapsf/man/mf_theme.Rd | 14 -- mapsf-0.2.0/mapsf/man/mf_typo.Rd | 5 mapsf-0.2.0/mapsf/vignettes/mapsf.Rmd | 3 77 files changed, 484 insertions(+), 406 deletions(-)
Title: Tools for Working with ...
Description: The ellipsis is a powerful tool for extending functions. Unfortunately
this power comes at a cost: misspelled arguments will be silently ignored.
The ellipsis package provides a collection of functions to catch problems
and alert the user.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between ellipsis versions 0.3.1 dated 2020-05-15 and 0.3.2 dated 2021-04-29
DESCRIPTION | 11 +++++------ LICENSE |only MD5 | 18 ++++++++++-------- NEWS.md | 6 ++++++ R/aaa.R |only R/check.R | 12 ++++++++++++ R/ellipsis-package.R | 4 ++++ README.md | 6 +++--- man/check_dots_empty.Rd | 5 +---- man/check_dots_unnamed.Rd | 5 +---- man/check_dots_used.Rd | 5 +---- 11 files changed, 43 insertions(+), 29 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6.9 dated 2021-03-09 and 4.6.10 dated 2021-04-29
doBy-4.6.10/doBy/DESCRIPTION | 12 doBy-4.6.10/doBy/MD5 | 55 + doBy-4.6.10/doBy/NAMESPACE | 10 doBy-4.6.10/doBy/NEWS.md |only doBy-4.6.10/doBy/R/NAMESPACE.R | 14 doBy-4.6.10/doBy/R/by-lmBy.R | 3 doBy-4.6.10/doBy/R/dobyxtabs.R | 120 ++-- doBy-4.6.10/doBy/R/restrict_env.R |only doBy-4.6.10/doBy/R/taylor.R | 2 doBy-4.6.10/doBy/build/vignette.rds |binary doBy-4.6.10/doBy/inst/doc/doby.R | 150 +++-- doBy-4.6.10/doBy/inst/doc/doby.Rnw | 293 +++++++--- doBy-4.6.10/doBy/inst/doc/doby.pdf |binary doBy-4.6.10/doBy/man/doBy-internal.Rd | 1 doBy-4.6.10/doBy/man/restrict.Rd |only doBy-4.6.10/doBy/tests |only doBy-4.6.10/doBy/vignettes/doby.Rnw | 293 +++++++--- doBy-4.6.10/doBy/vignettes/doby.bib | 754 +++++++++++++-------------- doBy-4.6.10/doBy/vignettes/figures |only doBy-4.6.9/doBy/NEWS |only doBy-4.6.9/doBy/R/specialize.R |only doBy-4.6.9/doBy/inst/doc/linest-lsmeans.R |only doBy-4.6.9/doBy/inst/doc/linest-lsmeans.Rnw |only doBy-4.6.9/doBy/inst/doc/linest-lsmeans.pdf |only doBy-4.6.9/doBy/vignettes/linest-lsmeans.Rnw |only 25 files changed, 1029 insertions(+), 678 deletions(-)
Title: Manipulation of Linear Systems of (in)Equalities
Description: Variable elimination (Gaussian elimination, Fourier-Motzkin elimination),
Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution,
projecting a vector on the convex polytope described by a system of (in)equations,
simplify systems by removing spurious columns and rows and collapse implied equalities,
test if a matrix is totally unimodular, compute variable ranges implied by linear
(in)equalities.
Author: Mark van der Loo [aut, cre],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between lintools versions 0.1.3 dated 2019-12-05 and 0.1.5 dated 2021-04-29
DESCRIPTION | 10 - MD5 | 32 ++-- NEWS | 4 R/compact.R | 19 +- R/eliminate.R | 17 +- R/lintools-pkg.R | 7 build/vignette.rds |binary inst/doc/project.R | 14 - inst/doc/project.html | 333 +++++++++++++++++++++++++++++++++++-------- inst/tinytest/test_compact.R | 79 +++++++--- man/compact.Rd | 15 + man/eliminate.Rd | 12 + man/is_feasible.Rd | 3 man/lintools.Rd | 17 -- man/project.Rd | 11 + man/sparse_constraints.Rd | 3 man/sparse_project.Rd | 12 + 17 files changed, 439 insertions(+), 149 deletions(-)
Title: Modify Data Using Externally Defined Modification Rules
Description: Data cleaning scripts typically contain a lot of 'if this change that'
type of statements. Such statements are typically condensed expert knowledge.
With this package, such 'data modifying rules' are taken out of the code and
become in stead parameters to the work flow. This allows one to maintain, document,
and reason about data modification rules as separate entities.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between dcmodify versions 0.1.2 dated 2018-07-30 and 0.1.5 dated 2021-04-29
dcmodify-0.1.2/dcmodify/tests/testthat |only dcmodify-0.1.2/dcmodify/tests/testthat.R |only dcmodify-0.1.2/dcmodify/vignettes/simple_log.csv |only dcmodify-0.1.5/dcmodify/DESCRIPTION | 10 dcmodify-0.1.5/dcmodify/MD5 | 23 - dcmodify-0.1.5/dcmodify/NEWS | 10 dcmodify-0.1.5/dcmodify/R/modify.R | 8 dcmodify-0.1.5/dcmodify/build/vignette.rds |binary dcmodify-0.1.5/dcmodify/inst/doc/introduction.R | 14 dcmodify-0.1.5/dcmodify/inst/doc/introduction.html | 426 ++++++++++++++++----- dcmodify-0.1.5/dcmodify/inst/tinytest |only dcmodify-0.1.5/dcmodify/man/dcmodify.Rd | 6 dcmodify-0.1.5/dcmodify/man/modify.Rd | 1 dcmodify-0.1.5/dcmodify/tests/tinytest.R |only 14 files changed, 368 insertions(+), 130 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-16 dated 2021-02-08 and 1.4-17 dated 2021-04-29
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/helpers.R | 2 +- R/print.R | 4 ++-- build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary inst/NEWS | 8 +++++++- inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.pdf |binary man/mmm.Rd | 3 ++- tests/Examples/multcomp-Ex.Rout.save | 11 ++++++----- 13 files changed, 34 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-04 1.4
2016-02-10 1.3
2015-09-28 1.2
2015-09-25 1.1
2015-09-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-07 0.1.6
2019-03-16 0.1.5
2018-04-19 0.1.4
2017-07-31 0.1.3
2017-04-06 0.1.2
2016-11-19 0.1.1
2016-04-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-19 1.4.12
2020-11-13 1.4.11
2020-05-12 1.4.10
2020-03-02 1.4.9
2019-03-27 1.4.8
2019-03-16 1.4.7
2019-01-27 1.4.6
2017-11-24 1.4.5
2017-09-01 1.4.4
2017-06-08 1.4.3
2017-04-09 1.4.2
2017-04-06 1.4.1
2017-04-03 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-06 0.2.12
2020-05-13 0.2.10
2020-03-06 0.2.9
2019-12-17 0.2.8
2019-03-15 0.2.7
2018-08-15 0.2.6
2018-06-23 0.2.5
2018-03-28 0.2.4
2018-03-03 0.2.3
2017-09-27 0.2.2
2017-09-22 0.2.1
2017-09-17 0.2.0
2017-07-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-22 1.0.1
2017-06-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-08 1.9.4
2021-04-03 1.9.1
2020-09-01 1.8.3
2019-02-07 1.1.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-29 1.3.3
2014-06-27 1.3.2
2014-01-03 1.3
2012-11-10 1.2-1
2012-09-12 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-25 1.0.1
2012-09-04 0.9.5
2012-08-30 0.9.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-24 0.2.1
2020-11-17 0.2.0
2020-04-22 0.1.0
Title: The hse Distribution
Description: Deprecated.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between hse versions 0.0-26 dated 2021-01-06 and 0.0-28 dated 2021-04-29
hse-0.0-26/hse/R/aHess.R |only hse-0.0-26/hse/R/dhse.R |only hse-0.0-26/hse/R/expValHse.R |only hse-0.0-26/hse/R/expValHse.default.R |only hse-0.0-26/hse/R/expValHse.mleHse.R |only hse-0.0-26/hse/R/finfo.R |only hse-0.0-26/hse/R/gof.R |only hse-0.0-26/hse/R/gradHess.R |only hse-0.0-26/hse/R/llPlot.R |only hse-0.0-26/hse/R/logLik.mleHse.R |only hse-0.0-26/hse/R/mcCovMat.R |only hse-0.0-26/hse/R/meHse.R |only hse-0.0-26/hse/R/mleHse.R |only hse-0.0-26/hse/R/nHess.R |only hse-0.0-26/hse/R/ndata.R |only hse-0.0-26/hse/R/phse.R |only hse-0.0-26/hse/R/plot.mleHse.R |only hse-0.0-26/hse/R/plotHse.R |only hse-0.0-26/hse/R/qhse.R |only hse-0.0-26/hse/R/rhse.R |only hse-0.0-26/hse/R/simulate.mleHse.R |only hse-0.0-26/hse/R/varHse.R |only hse-0.0-26/hse/R/varHse.default.R |only hse-0.0-26/hse/R/varHse.mleHse.R |only hse-0.0-26/hse/R/vcov.mleHse.R |only hse-0.0-26/hse/man |only hse-0.0-28/hse/ChangeLog | 23 ++++++++++++++++ hse-0.0-28/hse/DESCRIPTION | 20 +++----------- hse-0.0-28/hse/MD5 | 50 ++--------------------------------- hse-0.0-28/hse/NAMESPACE | 15 ---------- hse-0.0-28/hse/R/First.R |only 31 files changed, 32 insertions(+), 76 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-01 0.10.2
2015-07-10 0.10.0
2015-06-09 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-03 0.0.5
2021-02-24 0.0.4
2020-11-26 0.0.1
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-13 dated 2020-07-06 and 1.0-4 dated 2021-04-29
DESCRIPTION | 10 MD5 | 193 ++++--- NEWS | 171 ++++--- R/0classes.R | 11 R/J.R | 19 R/call.R | 13 R/loader.R | 101 ++-- R/reflection.R | 61 +- inst/java/boot/RJavaClassLoader$RJavaObjectInputStream.class |binary inst/java/boot/RJavaClassLoader.class |binary inst/java/boot/RJavaClassLoader.java | 25 - inst/javadoc/ArrayDimensionException.html | 4 inst/javadoc/ArrayWrapper.html | 4 inst/javadoc/ArrayWrapper_Test.html | 4 inst/javadoc/DummyPoint.html | 4 inst/javadoc/FlatException.html | 4 inst/javadoc/NotAnArrayException.html | 4 inst/javadoc/NotComparableException.html | 4 inst/javadoc/ObjectArrayException.html | 4 inst/javadoc/PrimitiveArrayException.html | 4 inst/javadoc/RJavaArrayIterator.html | 4 inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 inst/javadoc/RJavaArrayTools.html | 4 inst/javadoc/RJavaArrayTools_Test.html | 4 inst/javadoc/RJavaClassLoader.html | 38 + inst/javadoc/RJavaComparator.html | 4 inst/javadoc/RJavaImport.html | 4 inst/javadoc/RJavaTools.html | 4 inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 inst/javadoc/RJavaTools_Test.TestException.html | 4 inst/javadoc/RJavaTools_Test.html | 4 inst/javadoc/RectangularArrayBuilder.html | 4 inst/javadoc/RectangularArrayBuilder_Test.html | 4 inst/javadoc/RectangularArrayExamples.html | 4 inst/javadoc/RectangularArraySummary.html | 4 inst/javadoc/TestException.html | 4 inst/javadoc/allclasses-frame.html | 4 inst/javadoc/allclasses-noframe.html | 4 inst/javadoc/constant-values.html | 4 inst/javadoc/deprecated-list.html | 4 inst/javadoc/help-doc.html | 4 inst/javadoc/index-all.html | 11 inst/javadoc/index.html | 2 inst/javadoc/overview-tree.html | 4 inst/javadoc/package-frame.html | 4 inst/javadoc/package-summary.html | 4 inst/javadoc/package-tree.html | 4 inst/javadoc/serialized-form.html | 4 inst/jri/JRIEngine.jar |binary inst/jri/REngine.jar |binary jri/REngine/Makefile | 2 jri/REngine/README.md |only jri/REngine/Rserve/RConnection.java | 54 +- jri/REngine/Rserve/pom.xml | 57 +- jri/REngine/Rserve/src/test/java/org/rosuda/rserve/RserveTest.java | 6 jri/REngine/Rserve/test/test.java | 17 jri/REngine/pom.xml | 33 + jri/Rengine.java | 84 +-- jri/configure | 17 jri/configure.ac | 22 jri/configure.win | 10 jri/src/Rcallbacks.c | 2 jri/src/Rcallbacks.h | 7 jri/src/Rinit.c | 2 jri/src/rjava.c | 19 jri/src/rjava.h | 3 jri/tools/getsp.class |binary jri/tools/getsp.java | 19 man/J.Rd | 4 man/accessOp.Rd | 10 man/jarray.Rd | 8 man/jcall.Rd | 20 man/jcastToArray.Rd | 6 man/jcheck.Rd | 8 man/jfield.Rd | 4 man/jfloat.Rd | 23 man/jmemprof.Rd | 4 man/jnew.Rd | 6 man/jnull.Rd | 2 man/jpackage.Rd | 44 + man/jrectRef-class.Rd | 28 - man/jreflection.Rd | 14 man/jserialize.Rd | 2 man/loader.Rd | 49 +- man/toJava.Rd | 2 man/with.Rd | 2 src/Rglue.c | 242 ++++++++-- src/callJNI.c | 6 src/fields.c | 178 ++++--- src/init.c | 89 +-- src/java/RJavaClassLoader$RJavaObjectInputStream.class |binary src/java/RJavaClassLoader.class |binary src/java/RJavaClassLoader.java | 25 - src/jri_glue.c | 8 src/otables.c | 109 ++-- src/rJava.c | 103 ---- src/rJava.h | 9 src/tools.c | 4 98 files changed, 1309 insertions(+), 845 deletions(-)
Title: Convert Data among QTL Mapping Packages
Description: Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2convert versions 0.22-7 dated 2020-07-01 and 0.24 dated 2021-04-29
DESCRIPTION | 11 +++++------ MD5 | 15 +++++++++------ NAMESPACE | 2 ++ NEWS.md | 18 +++++++++++++++++- R/cross2_do_to_genail8.R |only R/encode_geno.R | 2 +- README.md | 5 +++-- man/cross2_do_to_genail8.Rd |only man/qtl2convert-package.Rd | 2 +- tests/testthat/test-cross2_do_to_genail8.R |only 10 files changed, 38 insertions(+), 17 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-23 0.1.1
2021-04-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-22 1.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-16 1.2.5
2020-07-21 1.2.4
2020-06-02 1.2.3
2020-04-13 1.2.2
2020-03-19 1.2.1
2020-03-16 1.2.0
2019-10-30 1.0.1