Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-04 0.1.1
2015-08-03 0.1.0
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Title: Bootstrapping the ARDL Tests for Cointegration
Description: The bootstrap ARDL tests for cointegration is the main functionality of this package. It also acts as a wrapper of the most commond ARDL testing procedures for cointegration: the bound tests of Pesaran, Shin and Smith (PSS; 2001 - <doi:10.1002/jae.616>) and the asymptotic test on the independent variables of Sam, McNown and Goh (SMG: 2019 - <doi:10.1016/j.econmod.2018.11.001>). Bootstrap and bound tests are performed under both the conditional and unconditional ARDL models.
Author: Gianmarco Vacca, Stefano Bertelli
Maintainer: Gianmarco Vacca <gianmarco.vacca@unicatt.it>
Diff between bootCT versions 1.1 dated 2022-07-18 and 1.1.1 dated 2022-09-27
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/boot_ardl.R | 5 +++++ R/sim_vecm_ardl.R | 5 ++--- R/sysdata.rda |binary man/sim_vecm_ardl.Rd | 2 +- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
RStudio, PBC [cph],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.41 dated 2022-08-16 and 0.42 dated 2022-09-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/install.R | 22 +++++++++++++++------- 3 files changed, 20 insertions(+), 12 deletions(-)
Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is
an open source distributed SQL query engine for running interactive
analytic queries against data sources of all sizes ranging from
gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut],
Sergey Goder [aut],
Jarod G.R. Meng [aut, cre],
Thomas J. Leeper [ctb],
John Myles White [ctb]
Maintainer: Jarod G.R. Meng <jarodm@fb.com>
Diff between RPresto versions 1.3.7 dated 2021-09-04 and 1.4.0 dated 2022-09-27
RPresto-1.3.7/RPresto/R/PrestoCursor.R |only RPresto-1.3.7/RPresto/R/RcppExports.R |only RPresto-1.3.7/RPresto/R/copy.to.src.presto.R |only RPresto-1.3.7/RPresto/R/db.data.type.PrestoConnection.R |only RPresto-1.3.7/RPresto/R/db.explain.PrestoConnection.R |only RPresto-1.3.7/RPresto/R/db.query.rows.PrestoConnection.R |only RPresto-1.3.7/RPresto/R/db_desc.PrestoConnection.R |only RPresto-1.3.7/RPresto/R/db_query_fields.R |only RPresto-1.3.7/RPresto/R/dbplyr_compatible.R |only RPresto-1.3.7/RPresto/R/description_from_info.R |only RPresto-1.3.7/RPresto/R/extract.data.R |only RPresto-1.3.7/RPresto/R/help.R |only RPresto-1.3.7/RPresto/R/json.tabular.to.data.frame.R |only RPresto-1.3.7/RPresto/R/parse.response.R |only RPresto-1.3.7/RPresto/R/sql_escape_date.R |only RPresto-1.3.7/RPresto/R/sql_escape_datetime.R |only RPresto-1.3.7/RPresto/R/sql_translate_env.R |only RPresto-1.3.7/RPresto/R/src.presto.R |only RPresto-1.3.7/RPresto/R/tbl.src.presto.R |only RPresto-1.3.7/RPresto/R/utility_functions.R |only RPresto-1.3.7/RPresto/man/PrestoCursor-class.Rd |only RPresto-1.3.7/RPresto/man/RPresto.Rd |only RPresto-1.3.7/RPresto/man/json.tabular.to.data.frame.Rd |only RPresto-1.3.7/RPresto/src |only RPresto-1.3.7/RPresto/tests/testthat/test-PrestoCursor.R |only RPresto-1.3.7/RPresto/tests/testthat/test-extract.data.R |only RPresto-1.3.7/RPresto/tests/testthat/test-json_tabular_to_data_frame.R |only RPresto-1.4.0/RPresto/DESCRIPTION | 67 - RPresto-1.4.0/RPresto/LICENSE | 4 RPresto-1.4.0/RPresto/MD5 | 237 ++-- RPresto-1.4.0/RPresto/NAMESPACE | 161 +-- RPresto-1.4.0/RPresto/NEWS.md | 55 + RPresto-1.4.0/RPresto/R/Presto.R | 6 RPresto-1.4.0/RPresto/R/PrestoConnection.R | 71 - RPresto-1.4.0/RPresto/R/PrestoDriver.R | 20 RPresto-1.4.0/RPresto/R/PrestoQuery.R |only RPresto-1.4.0/RPresto/R/PrestoResult.R | 64 - RPresto-1.4.0/RPresto/R/PrestoSession.R | 120 +- RPresto-1.4.0/RPresto/R/RPresto-package.R |only RPresto-1.4.0/RPresto/R/create.dummy.tables.R |only RPresto-1.4.0/RPresto/R/cte.R |only RPresto-1.4.0/RPresto/R/dbClearResult.R | 24 RPresto-1.4.0/RPresto/R/dbConnect.R | 141 ++ RPresto-1.4.0/RPresto/R/dbCreateTable.R |only RPresto-1.4.0/RPresto/R/dbCreateTableAs.R |only RPresto-1.4.0/RPresto/R/dbDataType.R | 165 +-- RPresto-1.4.0/RPresto/R/dbDisconnect.R | 12 RPresto-1.4.0/RPresto/R/dbExistsTable.R | 27 RPresto-1.4.0/RPresto/R/dbFetch.R | 168 +-- RPresto-1.4.0/RPresto/R/dbGetInfo.R | 79 - RPresto-1.4.0/RPresto/R/dbGetQuery.R | 53 - RPresto-1.4.0/RPresto/R/dbGetRowCount.R | 7 RPresto-1.4.0/RPresto/R/dbGetRowsAffected.R |only RPresto-1.4.0/RPresto/R/dbGetStatement.R | 5 RPresto-1.4.0/RPresto/R/dbHasCompleted.R | 7 RPresto-1.4.0/RPresto/R/dbIsValid.R | 7 RPresto-1.4.0/RPresto/R/dbListFields.R | 25 RPresto-1.4.0/RPresto/R/dbListTables.R | 21 RPresto-1.4.0/RPresto/R/dbReadTable.R |only RPresto-1.4.0/RPresto/R/dbRemoveTable.R |only RPresto-1.4.0/RPresto/R/dbSendQuery.R | 56 - RPresto-1.4.0/RPresto/R/dbUnloadDriver.R | 8 RPresto-1.4.0/RPresto/R/dbWriteTable.R |only RPresto-1.4.0/RPresto/R/dbplyr-db.R |only RPresto-1.4.0/RPresto/R/dbplyr-sql.R |only RPresto-1.4.0/RPresto/R/dbplyr-src.R |only RPresto-1.4.0/RPresto/R/default.R |only RPresto-1.4.0/RPresto/R/fetch.R | 16 RPresto-1.4.0/RPresto/R/presto.field.R |only RPresto-1.4.0/RPresto/R/presto.field_utilities.R |only RPresto-1.4.0/RPresto/R/request_headers.R | 36 RPresto-1.4.0/RPresto/R/sqlCreateTable.R |only RPresto-1.4.0/RPresto/R/sqlCreateTableAs.R |only RPresto-1.4.0/RPresto/R/zzz.R |only RPresto-1.4.0/RPresto/README.md | 412 ++++++- RPresto-1.4.0/RPresto/build |only RPresto-1.4.0/RPresto/inst |only RPresto-1.4.0/RPresto/man/Presto.Rd | 65 - RPresto-1.4.0/RPresto/man/PrestoConnection-class.Rd | 133 ++ RPresto-1.4.0/RPresto/man/PrestoQuery-class.Rd |only RPresto-1.4.0/RPresto/man/PrestoResult-class.Rd | 28 RPresto-1.4.0/RPresto/man/PrestoSession-class.Rd | 27 RPresto-1.4.0/RPresto/man/RPresto-package.Rd |only RPresto-1.4.0/RPresto/man/dbCreateTableAs.Rd |only RPresto-1.4.0/RPresto/man/dbDataType.Rd | 10 RPresto-1.4.0/RPresto/man/dbGetInfo.Rd | 58 - RPresto-1.4.0/RPresto/man/dbplyr-db.Rd |only RPresto-1.4.0/RPresto/man/dbplyr-sql.Rd |only RPresto-1.4.0/RPresto/man/dbplyr_edition.PrestoConnection.Rd |only RPresto-1.4.0/RPresto/man/dbplyr_function_implementations.Rd |only RPresto-1.4.0/RPresto/man/dplyr_function_implementations.Rd | 61 - RPresto-1.4.0/RPresto/man/dplyr_source_function_implementations.Rd |only RPresto-1.4.0/RPresto/man/dummy_tables.Rd |only RPresto-1.4.0/RPresto/man/figures |only RPresto-1.4.0/RPresto/man/presto_has_default.Rd |only RPresto-1.4.0/RPresto/man/sqlCreateTableAs.Rd |only RPresto-1.4.0/RPresto/man/src_presto.Rd | 54 - RPresto-1.4.0/RPresto/tests/testthat.R | 2 RPresto-1.4.0/RPresto/tests/testthat/credentials.dcf |only RPresto-1.4.0/RPresto/tests/testthat/test-PrestoQuery.R |only RPresto-1.4.0/RPresto/tests/testthat/test-bigint_handling.R | 69 + RPresto-1.4.0/RPresto/tests/testthat/test-check.status.code.R | 48 RPresto-1.4.0/RPresto/tests/testthat/test-copy_to.src_presto.R |only RPresto-1.4.0/RPresto/tests/testthat/test-cte.R |only RPresto-1.4.0/RPresto/tests/testthat/test-data_types.R | 246 ++-- RPresto-1.4.0/RPresto/tests/testthat/test-dbClearResult.R | 76 - RPresto-1.4.0/RPresto/tests/testthat/test-dbConnect.R | 185 ++- RPresto-1.4.0/RPresto/tests/testthat/test-dbCreateTable.R |only RPresto-1.4.0/RPresto/tests/testthat/test-dbCreateTableAs.R |only RPresto-1.4.0/RPresto/tests/testthat/test-dbDataType.R | 152 +- RPresto-1.4.0/RPresto/tests/testthat/test-dbDisconnect.R | 10 RPresto-1.4.0/RPresto/tests/testthat/test-dbExecute.R |only RPresto-1.4.0/RPresto/tests/testthat/test-dbExistsTable.R | 54 - RPresto-1.4.0/RPresto/tests/testthat/test-dbFetch.R | 516 +++++----- RPresto-1.4.0/RPresto/tests/testthat/test-dbGetInfo.R | 108 +- RPresto-1.4.0/RPresto/tests/testthat/test-dbGetQuery.R | 201 +-- RPresto-1.4.0/RPresto/tests/testthat/test-dbGetRowCount.R | 58 - RPresto-1.4.0/RPresto/tests/testthat/test-dbGetStatement.R | 62 - RPresto-1.4.0/RPresto/tests/testthat/test-dbHasCompleted.R | 55 - RPresto-1.4.0/RPresto/tests/testthat/test-dbIsValid.R | 232 ++-- RPresto-1.4.0/RPresto/tests/testthat/test-dbListFields.R | 458 ++++---- RPresto-1.4.0/RPresto/tests/testthat/test-dbListTables.R | 55 - RPresto-1.4.0/RPresto/tests/testthat/test-dbReadTable.R |only RPresto-1.4.0/RPresto/tests/testthat/test-dbRemoveTable.R |only RPresto-1.4.0/RPresto/tests/testthat/test-dbSendQuery.R | 240 ++-- RPresto-1.4.0/RPresto/tests/testthat/test-dbUnloadDriver.R | 6 RPresto-1.4.0/RPresto/tests/testthat/test-dbWriteTable.R |only RPresto-1.4.0/RPresto/tests/testthat/test-db_explain.R | 46 RPresto-1.4.0/RPresto/tests/testthat/test-db_query_fields.R | 251 ++-- RPresto-1.4.0/RPresto/tests/testthat/test-dbplyr-sql.R |only RPresto-1.4.0/RPresto/tests/testthat/test-dplyr.integration.R | 88 - RPresto-1.4.0/RPresto/tests/testthat/test-dplyr_as_type.R | 104 -- RPresto-1.4.0/RPresto/tests/testthat/test-extra.credential.R |only RPresto-1.4.0/RPresto/tests/testthat/test-fetch.R | 148 -- RPresto-1.4.0/RPresto/tests/testthat/test-get.state.R | 33 RPresto-1.4.0/RPresto/tests/testthat/test-integration.R | 40 RPresto-1.4.0/RPresto/tests/testthat/test-presto_field.R |only RPresto-1.4.0/RPresto/tests/testthat/test-response.to.content.R | 90 - RPresto-1.4.0/RPresto/tests/testthat/test-session.property.R | 32 RPresto-1.4.0/RPresto/tests/testthat/test-session.timezone.R | 57 - RPresto-1.4.0/RPresto/tests/testthat/test-sql_escape_date.R | 22 RPresto-1.4.0/RPresto/tests/testthat/test-sql_escape_datetime.R | 27 RPresto-1.4.0/RPresto/tests/testthat/test-stop.with.error.message.R | 28 RPresto-1.4.0/RPresto/tests/testthat/test-tbl.src_presto.R | 50 RPresto-1.4.0/RPresto/tests/testthat/test-translate_sql.R | 260 ++--- RPresto-1.4.0/RPresto/tests/testthat/utilities.R | 510 ++++++--- RPresto-1.4.0/RPresto/vignettes |only 147 files changed, 4072 insertions(+), 3057 deletions(-)
Title: Statistical Inference for Box-Cox Based Receiver Operating
Characteristic Curves
Description: Generation of Box-Cox based ROC curves and several aspects of inferences and hypothesis testing. Can be used when inferences for one biomarker (Bantis LE, Nakas CT, Reiser B. (2018) <doi:10.1002/bimj.201700107>) are of interest or when comparisons of two correlated biomarkers (Bantis LE, Nakas CT, Reiser B. (2021) <doi:10.1002/bimj.202000128>) are of interest. Provides inferences and comparisons around the AUC, the Youden index, the sensitivity at a given specificity level (and vice versa), the optimal operating point of the ROC curve (in the Youden sense), and the Youden based cutoff.
Author: Leonidas Bantis [aut],
Benjamin Brewer [cre, ctb],
Christos Nakas [ctb],
Benjamin Reiser [ctb]
Maintainer: Benjamin Brewer <tennisbenj@gmail.com>
Diff between rocbc versions 0.1.0 dated 2022-09-20 and 0.1.1 dated 2022-09-27
DESCRIPTION | 18 ++++++++++----- MD5 | 10 ++++---- inst/doc/documentation_rocbc.R | 1 inst/doc/documentation_rocbc.Rmd | 43 ++++++++++++++------------------------ inst/doc/documentation_rocbc.html | 43 +++++++++++++++----------------------- vignettes/documentation_rocbc.Rmd | 43 ++++++++++++++------------------------ 6 files changed, 68 insertions(+), 90 deletions(-)
Title: Tools for Multimodal Network Analysis
Description: A set of tools for analysing multimodal networks.
All functions operate with matrices, edge lists,
and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
It includes functions for measuring
centrality, centralization, cohesion, closure, and constraint,
as well as for network block-modelling and regression.
The package is released as a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book in addition to other network data.
Author: James Hollway [cre, aut, ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 0.11.3 dated 2022-09-13 and 0.12.0 dated 2022-09-27
migraph-0.11.3/migraph/inst/doc/p1data.R |only migraph-0.11.3/migraph/man/figures/isonnetworkers.pdf |only migraph-0.11.3/migraph/man/figures/isonnetworkers.png |only migraph-0.11.3/migraph/man/graph_census.Rd |only migraph-0.12.0/migraph/DESCRIPTION | 8 migraph-0.12.0/migraph/MD5 | 213 - migraph-0.12.0/migraph/NAMESPACE | 34 migraph-0.12.0/migraph/NEWS.md | 1161 ++++------ migraph-0.12.0/migraph/R/class_measures.R | 8 migraph-0.12.0/migraph/R/class_motifs.R | 8 migraph-0.12.0/migraph/R/data_ison.R | 1 migraph-0.12.0/migraph/R/make_create.R | 4 migraph-0.12.0/migraph/R/make_generate.R | 14 migraph-0.12.0/migraph/R/manip_add.R | 14 migraph-0.12.0/migraph/R/manip_as.R | 4 migraph-0.12.0/migraph/R/manip_grab.R | 30 migraph-0.12.0/migraph/R/manip_to.R | 10 migraph-0.12.0/migraph/R/mark_is.R | 8 migraph-0.12.0/migraph/R/mark_nodes.R | 2 migraph-0.12.0/migraph/R/mark_ties.R | 2 migraph-0.12.0/migraph/R/measure_centrality.R | 28 migraph-0.12.0/migraph/R/measure_closure.R | 28 migraph-0.12.0/migraph/R/measure_cohesion.R | 44 migraph-0.12.0/migraph/R/measure_diversity.R | 28 migraph-0.12.0/migraph/R/measure_features.R | 54 migraph-0.12.0/migraph/R/member_community.R | 2 migraph-0.12.0/migraph/R/member_core.R | 8 migraph-0.12.0/migraph/R/member_equivalence.R | 8 migraph-0.12.0/migraph/R/migraph-defunct.R | 306 ++ migraph-0.12.0/migraph/R/model_cluster.R | 2 migraph-0.12.0/migraph/R/model_regression.R | 2 migraph-0.12.0/migraph/R/model_tests.R | 20 migraph-0.12.0/migraph/R/motif_census.R | 28 migraph-0.12.0/migraph/R/viz_autographr.R | 2 migraph-0.12.0/migraph/R/viz_gglineage.R | 2 migraph-0.12.0/migraph/R/viz_layout_partition.R | 5 migraph-0.12.0/migraph/README.md | 43 migraph-0.12.0/migraph/build/vignette.rds |binary migraph-0.12.0/migraph/inst/doc/p1data.Rmd | 374 +-- migraph-0.12.0/migraph/inst/doc/p1data.html | 560 ++-- migraph-0.12.0/migraph/inst/doc/p2visualisation.R |only migraph-0.12.0/migraph/inst/doc/p2visualisation.Rmd |only migraph-0.12.0/migraph/inst/doc/p2visualisation.html |only migraph-0.12.0/migraph/inst/doc/p3centrality.R | 32 migraph-0.12.0/migraph/inst/doc/p3centrality.Rmd | 110 migraph-0.12.0/migraph/inst/doc/p3centrality.html | 137 - migraph-0.12.0/migraph/inst/doc/p5equivalence.R | 28 migraph-0.12.0/migraph/inst/doc/p5equivalence.Rmd | 96 migraph-0.12.0/migraph/inst/doc/p5equivalence.html | 147 - migraph-0.12.0/migraph/inst/doc/p7linearmodel.R | 56 migraph-0.12.0/migraph/inst/doc/p7linearmodel.Rmd | 118 - migraph-0.12.0/migraph/inst/doc/p7linearmodel.html | 166 - migraph-0.12.0/migraph/man/centralisation.Rd | 38 migraph-0.12.0/migraph/man/closure.Rd | 36 migraph-0.12.0/migraph/man/cohesion.Rd | 56 migraph-0.12.0/migraph/man/core-periphery.Rd | 2 migraph-0.12.0/migraph/man/defunct.Rd | 170 + migraph-0.12.0/migraph/man/diversity.Rd | 34 migraph-0.12.0/migraph/man/features.Rd | 50 migraph-0.12.0/migraph/man/figures/README-layout-comparison-1.png |only migraph-0.12.0/migraph/man/grab.Rd | 44 migraph-0.12.0/migraph/man/ison_networkers.Rd | 2 migraph-0.12.0/migraph/man/network_census.Rd |only migraph-0.12.0/migraph/man/node_census.Rd | 2 migraph-0.12.0/migraph/man/tests.Rd | 4 migraph-0.12.0/migraph/tests/testthat/test-make_create.R | 2 migraph-0.12.0/migraph/tests/testthat/test-manip_as.R | 8 migraph-0.12.0/migraph/tests/testthat/test-manip_grab.R | 26 migraph-0.12.0/migraph/tests/testthat/test-manip_to.R | 12 migraph-0.12.0/migraph/tests/testthat/test-mark_nodes.R | 8 migraph-0.12.0/migraph/tests/testthat/test-mark_ties.R | 6 migraph-0.12.0/migraph/tests/testthat/test-measure_centrality.R | 42 migraph-0.12.0/migraph/tests/testthat/test-measure_closure.R | 42 migraph-0.12.0/migraph/tests/testthat/test-measure_cohesion.R | 20 migraph-0.12.0/migraph/tests/testthat/test-measure_diversity.R | 12 migraph-0.12.0/migraph/tests/testthat/test-measure_features.R | 38 migraph-0.12.0/migraph/tests/testthat/test-measure_holes.R | 16 migraph-0.12.0/migraph/tests/testthat/test-member_community.R | 2 migraph-0.12.0/migraph/tests/testthat/test-member_equivalence.R | 16 migraph-0.12.0/migraph/tests/testthat/test-model_tests.R | 12 migraph-0.12.0/migraph/tests/testthat/test-motif_census.R | 30 migraph-0.12.0/migraph/vignettes/p1data.Rmd | 374 +-- migraph-0.12.0/migraph/vignettes/p1data.Rmd.orig | 7 migraph-0.12.0/migraph/vignettes/p2visualisation.Rmd |only migraph-0.12.0/migraph/vignettes/p2visualisation.Rmd.orig |only migraph-0.12.0/migraph/vignettes/p3centrality.Rmd | 110 migraph-0.12.0/migraph/vignettes/p3centrality.Rmd.orig | 17 migraph-0.12.0/migraph/vignettes/p5equivalence.Rmd | 96 migraph-0.12.0/migraph/vignettes/p5equivalence.Rmd.orig | 1 migraph-0.12.0/migraph/vignettes/p7linearmodel.Rmd | 118 - migraph-0.12.0/migraph/vignettes/p7linearmodel.Rmd.orig | 31 migraph-0.12.0/migraph/vignettes/teaching/addingnames-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/blaugroups-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/blaugroups-2.png |binary migraph-0.12.0/migraph/vignettes/teaching/constraintplot-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/cugqap-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/find-se-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/ggid-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/ggid-2.png |binary migraph-0.12.0/migraph/vignettes/teaching/ggid-3.png |binary migraph-0.12.0/migraph/vignettes/teaching/ggid-4.png |binary migraph-0.12.0/migraph/vignettes/teaching/ggrapheg-1.png |only migraph-0.12.0/migraph/vignettes/teaching/intro-eies-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/layoutseg-1.png |only migraph-0.12.0/migraph/vignettes/teaching/migrapheg-1.png |only migraph-0.12.0/migraph/vignettes/teaching/migraphexample2-1.png |only migraph-0.12.0/migraph/vignettes/teaching/multiplot-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/patchwork-1.png |only migraph-0.12.0/migraph/vignettes/teaching/patchwork-2.png |only migraph-0.12.0/migraph/vignettes/teaching/perm-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/qap-interp-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/rando-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/separatingnets-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/strplot-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/structblock-1.png |binary migraph-0.12.0/migraph/vignettes/teaching/unnamed-chunk-2-1.png |binary 116 files changed, 2792 insertions(+), 2647 deletions(-)
Title: For Writing Geneva Graduate Institute Documents
Description: A set of tools for writing documents
according to Geneva Graduate Institute conventions and regulations.
The most common use is for writing and compiling theses or thesis
chapters, as drafts or for examination with correct preamble formatting.
However, the package also offers users to create HTML presentation
slides with 'xaringan', complete problem sets, format posters, and,
for course instructors, prepare a syllabus.
The package includes additional functions for institutional color palettes,
an institutional 'ggplot' theme, a function for counting manuscript words,
and a bibliographical analysis toolkit.
Author: James Hollway [aut, cre, cph] ,
Bernhard Bieri [ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between iheiddown versions 0.9.3 dated 2022-05-13 and 0.9.5 dated 2022-09-27
iheiddown-0.9.3/iheiddown/vignettes/images/poster/1-Select_Template.png |only iheiddown-0.9.5/iheiddown/DESCRIPTION | 21 +++-- iheiddown-0.9.5/iheiddown/MD5 | 36 +++++----- iheiddown-0.9.5/iheiddown/NEWS.md | 19 +++++ iheiddown-0.9.5/iheiddown/R/bibfix.R | 1 iheiddown-0.9.5/iheiddown/R/bibstats.R | 32 ++++++-- iheiddown-0.9.5/iheiddown/R/poster_html.R | 10 ++ iheiddown-0.9.5/iheiddown/R/theme.R | 2 iheiddown-0.9.5/iheiddown/build/vignette.rds |binary iheiddown-0.9.5/iheiddown/inst/doc/poster.R | 4 - iheiddown-0.9.5/iheiddown/inst/doc/poster.Rmd | 4 - iheiddown-0.9.5/iheiddown/inst/doc/poster.html | 4 - iheiddown-0.9.5/iheiddown/inst/doc/presentations.html | 17 +++- iheiddown-0.9.5/iheiddown/inst/doc/problemset.html | 17 +++- iheiddown-0.9.5/iheiddown/inst/doc/syllabus.html | 4 - iheiddown-0.9.5/iheiddown/inst/doc/thesis.html | 4 - iheiddown-0.9.5/iheiddown/inst/rmarkdown/templates/thesis_pdf/resources/template.tex | 18 ++++- iheiddown-0.9.5/iheiddown/tests/testthat/test-bibstats.R | 10 +- iheiddown-0.9.5/iheiddown/vignettes/images/poster/select_template.png |only iheiddown-0.9.5/iheiddown/vignettes/poster.Rmd | 4 - 20 files changed, 137 insertions(+), 70 deletions(-)
Title: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry
Data)
Description: A tiny parser to extract mass spectra data and metadata table of MS acquisition properties from mzML, mzXML and netCDF mass spectrometry files.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.MXP versions 1.5 dated 2022-07-07 and 1.6 dated 2022-09-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/MXP_locate_regex.Rd | 4 ++-- man/getScanTable.Rd | 4 ++-- man/getSpectra.Rd | 4 ++-- man/peak2list.Rd | 4 ++-- 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract signals of organic compounds. The package performs isotope pairing, peak detection, alignment, RT correction, gap filling, peak annotation and visualization of extracted ion chromatograms (EIC) and total ion chromatograms (TIC).
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.IPA versions 2.2 dated 2022-09-09 and 2.3 dated 2022-09-27
DESCRIPTION | 6 - MD5 | 50 ++++++----- R/IPA_CompoundsAnnotation.R | 30 ++++-- R/IPA_GapFiller.R | 28 +++++- R/IPA_IsotopePairing.R | 18 +++- R/IPA_PeakAlignment.R | 40 +++++---- R/IPA_PeakAnalyzer.R | 16 +++ R/IPA_PeaklistAnnotation.R | 28 ++++-- R/IPA_TargetedAnalysis.R | 15 +-- R/IPA_Workflow.R | 173 +++++++++++++++++++++++++++------------ R/IPA_gsub.R |only R/IPA_logRecorder.R |only R/IPA_xlsxAnalyzer.R | 5 - R/global.R | 2 R/plot_mz_eic.R | 2 R/plot_simple_tic.R | 2 build/partial.rdb |binary inst/extdata/IPA_parameters.xlsx |binary man/IPA_CompoundsAnnotation.Rd | 2 man/IPA_GapFiller.Rd | 2 man/IPA_IsotopePairing.Rd | 2 man/IPA_PeakAlignment.Rd | 2 man/IPA_PeakAnalyzer.Rd | 2 man/IPA_PeaklistAnnotation.Rd | 2 man/IPA_TargetedAnalysis.Rd | 2 man/IPA_Workflow.Rd | 2 man/IPA_gsub.Rd |only man/IPA_logRecorder.Rd |only 28 files changed, 285 insertions(+), 146 deletions(-)
Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre],
Silvia Grieder [aut],
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.4.1 dated 2022-04-24 and 0.4.2 dated 2022-09-27
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 14 + R/PARALLEL.R | 5 R/helper.R | 2 build/vignette.rds |binary inst/doc/EFAtools.html | 299 ++++++++++++++++++------------------- inst/doc/Replicate_SPSS_psych.html | 31 ++- tests/testthat/test-HULL.R | 26 +-- tests/testthat/test-N_FACTORS.R | 26 +-- tests/testthat/test-PARALLEL.R | 24 ++ tests/testthat/test-SMT.R | 24 +- tests/testthat/test-helper.R | 4 13 files changed, 272 insertions(+), 215 deletions(-)
Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications.
Credentials are stored in an encrypted 'SQLite' database. Source code of main application
is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre],
Victor Perrier [aut]
Maintainer: Benoit Thieurmel <bthieurmel@gmail.com>
Diff between shinymanager versions 1.0.400 dated 2021-06-16 and 1.0.410 dated 2022-09-27
DESCRIPTION | 12 - MD5 | 77 ++++-- NEWS.md | 15 + R/credentials-db.R | 12 - R/fab_button.R | 2 R/language.R | 355 +++++++++++++++++++++++++----- R/module-admin.R | 246 ++++++++++++-------- R/module-auth.R | 60 +++-- R/module-pwd.R | 17 + R/modules-logs.R | 26 +- R/secure-app.R | 43 ++- R/shiny-utils.R | 17 + R/utils.R | 117 +++++++++ README.md | 89 +++++++ build/vignette.rds |binary inst/article |only inst/assets/fab-button/fab-button.min.css | 2 inst/assets/fab-button/mfb.scss | 2 inst/assets/shiny-utils.js | 4 inst/demo_app |only inst/doc/SQLite_Admin.html | 250 +++++++++++++++++++-- man/create_db.Rd | 11 man/fab_button.Rd | 2 man/figures/custom.png |only man/figures/shinymanager_ds.jpg |only man/module-authentication.Rd | 8 man/secure-app.Rd | 20 + tests/testthat/test-credentials-db.R | 2 tests/testthat/test-language.R | 2 tests/testthat/test-tokens.R | 2 30 files changed, 1136 insertions(+), 257 deletions(-)
Title: Identify Distributions that Match Reported Sample Parameters
(SPRITE)
Description: The SPRITE algorithm creates possible distributions of discrete responses
based on reported sample parameters, such as mean, standard deviation and range
(Heathers et al., 2018, <doi:10.7287/peerj.preprints.26968v1>). This package implements it,
drawing heavily on the code for Nick Brown's 'rSPRITE' Shiny app <https://shiny.ieis.tue.nl/sprite/>.
In addition, it supports the modeling of distributions based on multi-item (Likert-type)
scales and the use of restrictions on the frequency of particular responses.
Author: Lukas Wallrich [aut, cre] ,
Aurelien Allard [ctb]
Maintainer: Lukas Wallrich <lukas.wallrich@gmail.com>
Diff between rsprite2 versions 0.1.0 dated 2021-09-22 and 0.2.0 dated 2022-09-27
DESCRIPTION | 21 +- MD5 | 31 +-- NAMESPACE | 1 NEWS.md | 7 R/core-functions.R | 215 +++++++++++++++++++++-- README.md | 15 + build/partial.rdb |binary inst/REFERENCES.bib | 10 + man/GRIMMER_test.Rd |only man/GRIM_test.Rd | 88 ++++----- man/find_possible_distribution.Rd | 70 +++---- man/find_possible_distributions.Rd | 92 ++++----- man/plot_distributions.Rd | 92 ++++----- man/rsprite2-package.Rd | 60 +++--- man/set_parameters.Rd | 163 ++++++++--------- tests/testthat/_snaps/core-and-plot-functions.md | 82 ++++---- tests/testthat/test-core-and-plot-functions.R | 15 + 17 files changed, 595 insertions(+), 367 deletions(-)
Title: Automatic Colors for Multi-Dimensional Data
Description: Assign distinct colors to arbitrary multi-dimensional data, considering its structure.
Author: Oren Ben-Kiki [aut, cre],
Weizmann Institute of Science [cph]
Maintainer: Oren Ben-Kiki <oren@ben-kiki.org>
Diff between chameleon versions 0.2-1 dated 2022-07-13 and 0.2-3 dated 2022-09-27
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 2 +- R/chameleon.R | 29 +++++++++++++++-------------- inst/doc/examples.html | 19 +++++++++++++------ 5 files changed, 38 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-13 1.3.2
Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings.
The 'rsurveycto' R package uses the 'SurveyCTO' REST API
<https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html>
to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's
and to download file attachments. The package also has limited support to
write datasets to a server.
Author: Jake Hughey [aut, cre],
Robert On [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between rsurveycto versions 0.0.5 dated 2022-09-08 and 0.1.0 dated 2022-09-26
DESCRIPTION | 12 +- MD5 | 35 ++++--- NAMESPACE | 9 ++ R/scto_auth.R | 41 ++++++++- R/scto_get_attachments.R | 1 R/scto_meta.R |only R/scto_read.R | 129 +++++++++++------------------ R/scto_read_utils.R |only R/scto_write.R | 49 ++++++++--- R/utils.R | 71 +++++++++++---- man/scto_auth.Rd | 3 man/scto_meta.Rd |only man/scto_quiet.Rd |only man/scto_read.Rd | 26 ++++- man/scto_write.Rd | 31 +++++- tests/testthat/test-scto-auth.R | 11 ++ tests/testthat/test-scto-get-attachments.R | 4 tests/testthat/test-scto-meta.R |only tests/testthat/test-scto-read.R | 15 ++- tests/testthat/test-scto-write.R | 56 +++++++++--- tests/testthat/test-utils.R | 11 -- 21 files changed, 320 insertions(+), 184 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 1.0-0 dated 2022-08-25 and 1.1-0 dated 2022-09-26
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- NAMESPACE | 2 - R/documentation.R | 26 +++++++++++++++++++++ inst/NEWS.Rd | 9 +++++++ man/documentation.Rd | 40 ++++++++++++++++++++++----------- tests/documentation-tests.R | 53 +++++++++++++++++++++++++++++++++++++------- 7 files changed, 118 insertions(+), 32 deletions(-)
Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a
correlation matrix using 'ggplot2'. It provides a solution for
reordering the correlation matrix and displays the significance level
on the plot. It also includes a function for computing a matrix of
correlation p-values.
Author: Alboukadel Kassambara [aut, cre],
Indrajeet Patil [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggcorrplot versions 0.1.3 dated 2019-05-19 and 0.1.4 dated 2022-09-26
DESCRIPTION | 48 ++++++++++++++-------- MD5 | 37 +++++++++-------- NEWS.md | 69 ++++++++++++++++++++++++++------ R/ggcorrplot.R | 78 +++++++++++++++++++++++-------------- README.md | 66 ++++++++++++++++++++----------- inst/WORDLIST | 11 ++++- man/ggcorrplot.Rd | 53 ++++++++++++++++++------- tests/spelling.R | 5 +- tests/testthat |only tests/testthat.R |only tools/README-demo-ggcorrplot-1.png |binary tools/README-demo-ggcorrplot-2.png |binary tools/README-demo-ggcorrplot-3.png |binary tools/README-demo-ggcorrplot-4.png |binary tools/README-demo-ggcorrplot-5.png |binary tools/README-demo-ggcorrplot-6.png |binary tools/README-demo-ggcorrplot-7.png |binary tools/README-demo-ggcorrplot-8.png |binary tools/README-demo-ggcorrplot-9.png |binary 19 files changed, 250 insertions(+), 117 deletions(-)
Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran <j.curran@auckland.ac.nz>
Diff between relSim versions 0.3-3 dated 2022-09-15 and 0.3-4 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/concatProfiles.R |only R/readProfiles.R | 20 ++++++++++++++++---- man/readProfiles.Rd | 2 +- src/relSim.cpp | 17 ++++++++++------- 6 files changed, 36 insertions(+), 20 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Christophe Dervieux [ctb] ,
Atsushi Yasumoto [ctb] ,
RStudio, PBC [cph],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.18 dated 2022-04-26 and 0.19 dated 2022-09-26
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/chrome.R | 2 +- inst/resources/css/default.css | 2 +- man/chrome_print.Rd | 2 +- 7 files changed, 18 insertions(+), 14 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word', 'Microsoft PowerPoint'
documents from 'R Markdown' and as 'Grid Graphics' objects. Functions are provided to let users
create tables, modify and format their content. It also extends package 'officer' that does
not contain any feature for customized tabular reporting.
Author: David Gohel [aut, cre],
Clementine Jager [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] ,
Titouan Robert [ctb],
Michael Barrowman [ctb] ,
Atsushi Yasumoto [ctb] ,
Paul Julian [ctb] ,
Sean Browning [ctb] ,
Remi Theriaul [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.8.1 dated 2022-09-19 and 0.8.2 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/as_flextable_tabulator.R | 2 +- man/tabulator_colnames.Rd | 10 +++++----- tests/testthat/test-captions-rmd.R | 2 ++ 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for some new multivariate frailty models.
This version includes the gamma, inverse Gaussian and weighted Lindley as the distribution
for the frailty terms.
For the basal model, it is considered a parametric approach based on the Weibull distribution
and a semiparametric approach. For details, see Gallardo and Bourguignon (2022)
<arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between extrafrail versions 1.1 dated 2022-08-06 and 1.2 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/summary.extrafrail.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] ,
Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>
Diff between netrankr versions 1.1.1 dated 2021-12-21 and 1.2.0 dated 2022-09-26
netrankr-1.1.1/netrankr/man/figures |only netrankr-1.2.0/netrankr/DESCRIPTION | 8 netrankr-1.2.0/netrankr/LICENSE | 4 netrankr-1.2.0/netrankr/MD5 | 73 - netrankr-1.2.0/netrankr/NEWS.md | 5 netrankr-1.2.0/netrankr/R/approximate.ranks.R | 4 netrankr-1.2.0/netrankr/R/get.rankings.R | 2 netrankr-1.2.0/netrankr/R/indirect.relations.R | 8 netrankr-1.2.0/netrankr/R/mcmc.rank.R | 6 netrankr-1.2.0/netrankr/R/rank.analysis.R | 20 netrankr-1.2.0/netrankr/R/utils.R | 10 netrankr-1.2.0/netrankr/README.md | 12 netrankr-1.2.0/netrankr/build/vignette.rds |binary netrankr-1.2.0/netrankr/inst/CITATION | 13 netrankr-1.2.0/netrankr/inst/doc/benchmarks.Rmd | 12 netrankr-1.2.0/netrankr/inst/doc/benchmarks.html | 308 +++++++ netrankr-1.2.0/netrankr/inst/doc/centrality_indices.html | 284 ++++++- netrankr-1.2.0/netrankr/inst/doc/indirect_relations.html | 276 ++++++ netrankr-1.2.0/netrankr/inst/doc/neighborhood_inclusion.html | 310 +++++++ netrankr-1.2.0/netrankr/inst/doc/partial_centrality.Rmd | 2 netrankr-1.2.0/netrankr/inst/doc/partial_centrality.html | 267 ++++++ netrankr-1.2.0/netrankr/inst/doc/positional_dominance.html | 272 ++++++ netrankr-1.2.0/netrankr/inst/doc/probabilistic_cent.html | 319 +++++++ netrankr-1.2.0/netrankr/inst/doc/threshold_graph.html | 329 +++++++- netrankr-1.2.0/netrankr/inst/doc/use_case.html | 439 +++++++++-- netrankr-1.2.0/netrankr/man/exact_rank_prob.Rd | 2 netrankr-1.2.0/netrankr/man/get_rankings.Rd | 2 netrankr-1.2.0/netrankr/src/checkPairs.cpp | 8 netrankr-1.2.0/netrankr/src/listingIdeals.cpp | 2 netrankr-1.2.0/netrankr/vignettes/benchmarks.Rmd | 12 netrankr-1.2.0/netrankr/vignettes/mcmc_samples_exp.png |binary netrankr-1.2.0/netrankr/vignettes/mcmc_samples_rel.png |binary netrankr-1.2.0/netrankr/vignettes/partial_centrality.Rmd | 2 netrankr-1.2.0/netrankr/vignettes/quality_expected_mse.png |binary netrankr-1.2.0/netrankr/vignettes/quality_relative_mse.png |binary netrankr-1.2.0/netrankr/vignettes/runtimes_exact.png |binary 36 files changed, 2677 insertions(+), 334 deletions(-)
Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time
('hms') vectors. Date/times are considered discrete and are floored
whenever encountered. Times are wrapped and time zones are maintained
unless explicitly altered by the user.
Author: Joe Thorley [aut] ,
Ayla Pearson [aut, cre] ,
Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between dttr2 versions 0.4.1 dated 2022-08-26 and 0.4.2 dated 2022-09-26
DESCRIPTION | 26 +++++++++++++------------- MD5 | 8 ++++---- NEWS.md | 15 +++++++++++++++ man/dttr2-package.Rd | 7 ++++++- tests/testthat/test-check.R | 2 +- 5 files changed, 39 insertions(+), 19 deletions(-)
Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods:
integration by a cubature method and integration on a grid of points.
Annie Bouvier, Kien Kieu, Kasia Adamczyk and Herve Monod (2009)
<doi:10.1016/j.envsoft.2008.11.006>.
Author: Annie Bouvier [aut, cph],
Kien Kieu [aut, cph],
Kasia Adamczyk [aut, cph],
Herve Monod [aut, cph],
Jean-Francois Rey [cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between RCALI versions 0.3.3 dated 2022-08-12 and 0.3.4 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/intersection.cc | 4 ++-- src/readPoly.cc | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: A Multi-Process 'dplyr' Backend
Description: Partition a data frame across multiple worker processes to
provide simple multicore parallelism.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between multidplyr versions 0.1.1 dated 2021-12-01 and 0.1.2 dated 2022-09-26
DESCRIPTION | 36 ++-- MD5 | 20 +- NEWS.md | 5 R/cluster-call.R | 85 ++++++++-- README.md | 24 +- build/vignette.rds |binary inst/doc/multidplyr.html | 288 ++++++++++++++++++++-------------- man/cluster_call.Rd | 18 +- man/multidplyr-package.Rd | 2 tests/testthat/_snaps/cluster-call.md | 34 +++- tests/testthat/test-cluster-call.R | 34 +++- 11 files changed, 366 insertions(+), 180 deletions(-)
Title: Create Constraints for Small Test Assembly Problems
Description: Provides simple functions to create constraints for small test assembly problems
(e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently,
'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from
any mainstream repository; see <https://www.gurobi.com/downloads/>.
Author: Benjamin Becker [aut, cre],
Dries Debeer [aut]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatATA versions 1.0.0 dated 2021-07-06 and 1.1.0 dated 2022-09-26
eatATA-1.0.0/eatATA/man/calculateExpectedRT.Rd |only eatATA-1.1.0/eatATA/DESCRIPTION | 8 eatATA-1.1.0/eatATA/MD5 | 116 eatATA-1.1.0/eatATA/NAMESPACE | 6 eatATA-1.1.0/eatATA/NEWS.md | 11 eatATA-1.1.0/eatATA/R/appendSolution.R | 2 eatATA-1.1.0/eatATA/R/calculateExpectedRT.R | 82 eatATA-1.1.0/eatATA/R/get_mean_var_3PLN.R |only eatATA-1.1.0/eatATA/R/inspectSolution.R | 2 eatATA-1.1.0/eatATA/R/itemCategoryMinMaxConstraint.R | 224 eatATA-1.1.0/eatATA/R/itemTuples.R | 3 eatATA-1.1.0/eatATA/R/itemValuesConstraint.R | 8 eatATA-1.1.0/eatATA/R/itemValuesMinMaxConstraint.R | 220 eatATA-1.1.0/eatATA/R/objectives.R | 4 eatATA-1.1.0/eatATA/README.md | 16 eatATA-1.1.0/eatATA/build/eatATA.pdf | 5761 +++++----- eatATA-1.1.0/eatATA/build/partial.rdb |only eatATA-1.1.0/eatATA/inst/doc/minimal_example.html | 359 eatATA-1.1.0/eatATA/inst/doc/overview.Rmd | 2 eatATA-1.1.0/eatATA/inst/doc/overview.html | 402 eatATA-1.1.0/eatATA/inst/doc/use_case_pilot_study.html | 495 eatATA-1.1.0/eatATA/man/acrossFormsConstraint.Rd | 156 eatATA-1.1.0/eatATA/man/analyzeBlockExclusion.Rd | 138 eatATA-1.1.0/eatATA/man/analyzeComplexBlockExclusion.Rd | 88 eatATA-1.1.0/eatATA/man/appendSolution.Rd | 88 eatATA-1.1.0/eatATA/man/autoItemValuesMinMaxConstraint.Rd | 102 eatATA-1.1.0/eatATA/man/calculateIIF.Rd | 86 eatATA-1.1.0/eatATA/man/cappedMaximinObjective.Rd | 100 eatATA-1.1.0/eatATA/man/combineConstraints.Rd | 52 eatATA-1.1.0/eatATA/man/computeTargetValues.Rd | 252 eatATA-1.1.0/eatATA/man/depletePoolConstraint.Rd | 52 eatATA-1.1.0/eatATA/man/dummiesToFactor.Rd | 68 eatATA-1.1.0/eatATA/man/getMean3PLN.Rd |only eatATA-1.1.0/eatATA/man/get_mean_3PLN.Rd |only eatATA-1.1.0/eatATA/man/inspectSolution.Rd | 114 eatATA-1.1.0/eatATA/man/itemCategoryConstraint.Rd | 108 eatATA-1.1.0/eatATA/man/itemCategoryRangeConstraint.Rd | 226 eatATA-1.1.0/eatATA/man/itemExclusionConstraint.Rd | 164 eatATA-1.1.0/eatATA/man/itemTuples.Rd | 78 eatATA-1.1.0/eatATA/man/itemUsageConstraint.Rd | 142 eatATA-1.1.0/eatATA/man/itemValuesConstraint.Rd | 132 eatATA-1.1.0/eatATA/man/itemValuesRangeConstraint.Rd | 210 eatATA-1.1.0/eatATA/man/itemsPerFormConstraint.Rd | 98 eatATA-1.1.0/eatATA/man/items_diao.Rd | 54 eatATA-1.1.0/eatATA/man/items_lsa.Rd | 54 eatATA-1.1.0/eatATA/man/items_mini.Rd | 44 eatATA-1.1.0/eatATA/man/items_pilot.Rd | 48 eatATA-1.1.0/eatATA/man/items_vera.Rd | 48 eatATA-1.1.0/eatATA/man/matrixExclusionTuples.Rd | 68 eatATA-1.1.0/eatATA/man/maxObjective.Rd | 84 eatATA-1.1.0/eatATA/man/maximinObjective.Rd | 94 eatATA-1.1.0/eatATA/man/minObjective.Rd | 84 eatATA-1.1.0/eatATA/man/minimaxObjective.Rd | 94 eatATA-1.1.0/eatATA/man/stemInclusionTuples.Rd | 72 eatATA-1.1.0/eatATA/man/useSolver.Rd | 130 eatATA-1.1.0/eatATA/tests/testthat/test_acrossFormsConstraint.R | 130 eatATA-1.1.0/eatATA/tests/testthat/test_calculateExpectedRT.R | 43 eatATA-1.1.0/eatATA/tests/testthat/test_get_mean_var_3PLN.R |only eatATA-1.1.0/eatATA/tests/testthat/test_itemTuples.R | 12 eatATA-1.1.0/eatATA/tests/testthat/test_itemValuesConstraint.R | 5 eatATA-1.1.0/eatATA/tests/testthat/test_stemInclusionTuples.R | 11 eatATA-1.1.0/eatATA/vignettes/overview.Rmd | 2 62 files changed, 6215 insertions(+), 5037 deletions(-)
Title: Climate Variability Indices for Ecological Modelling
Description: Supports analysis of trends in climate change,
ecological and crop modelling.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [ctb, ths] ,
Svein O. Solberg [ctb, ths]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between climatrends versions 0.2 dated 2022-02-24 and 0.4 dated 2022-09-26
DESCRIPTION | 15 - LICENSE | 4 MD5 | 20 +- NEWS.md | 5 R/get_timeseries.R | 17 -- R/internal_functions.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.html | 374 +++++++++++++++++++++++++++++++++++++++++----- man/climatrends.Rd | 2 vignettes/climatrends.bib | 1 11 files changed, 374 insertions(+), 66 deletions(-)
Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>
Diff between basemaps versions 0.0.4 dated 2022-09-08 and 0.0.5 dated 2022-09-26
DESCRIPTION | 15 +- MD5 | 26 ++- NAMESPACE | 36 ++--- NEWS.md | 20 +++ R/basemap.R | 178 +++++++++++++++------------ R/internal.R | 270 +++++++++++++++++++++++++---------------- R/plot.R |only README.md | 187 ++++++++++++++++------------ man/basemap.Rd | 45 ++++-- man/plot.Rd |only tests/testthat/helper-vars.R | 19 ++ tests/testthat/test-basemap.R | 56 +++++--- tests/testthat/test-cache.R |only tests/testthat/test-draw_ext.R | 5 tests/testthat/test-internal.R | 13 + tests/testthat/test-plot.R |only 16 files changed, 532 insertions(+), 338 deletions(-)
Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications and R
Markdown documents.
Author: Winston Chang [aut, cre],
Yihui Xie [ctb],
Francois Guillem [ctb],
Barret Schloerke [ctb],
Nicolas Perriault [ctb]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between webshot versions 0.5.3 dated 2022-04-14 and 0.5.4 dated 2022-09-26
DESCRIPTION | 9 +++++---- MD5 | 10 ++++++---- NEWS.md | 5 +++++ R/utils.R | 2 +- README.md | 7 +++---- tests |only 6 files changed, 20 insertions(+), 13 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R,
the 'targets' package brings together function-oriented programming and
'Make'-like declarative workflows.
It analyzes the dependency relationships among the tasks of a workflow,
skips steps that are already up to date, runs the necessary
computation with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between targets versions 0.13.4 dated 2022-09-15 and 0.13.5 dated 2022-09-26
DESCRIPTION | 6 - MD5 | 116 ++++++++++++++--------------- NEWS.md | 6 + R/tar_built.R | 4 - R/tar_canceled.R | 4 - R/tar_delete.R | 2 R/tar_errored.R | 4 - R/tar_glimpse.R | 2 R/tar_invalidate.R | 2 R/tar_load.R | 4 - R/tar_load_raw.R | 2 R/tar_make.R | 4 - R/tar_manifest.R | 4 - R/tar_meta.R | 6 - R/tar_network.R | 2 R/tar_newer.R | 4 - R/tar_objects.R | 4 - R/tar_older.R | 4 - R/tar_outdated.R | 2 R/tar_process.R | 2 R/tar_progress.R | 4 - R/tar_sitrep.R | 4 - R/tar_skipped.R | 4 - R/tar_started.R | 4 - R/tar_visnetwork.R | 2 R/tar_watch_server.R | 2 inst/run/run.R | 2 man/tar_built.Rd | 4 - man/tar_canceled.Rd | 4 - man/tar_delete.Rd | 2 man/tar_errored.Rd | 4 - man/tar_glimpse.Rd | 4 - man/tar_invalidate.Rd | 2 man/tar_load.Rd | 4 - man/tar_load_raw.Rd | 2 man/tar_make.Rd | 4 - man/tar_make_clustermq.Rd | 4 - man/tar_make_future.Rd | 4 - man/tar_manifest.Rd | 4 - man/tar_mermaid.Rd | 2 man/tar_meta.Rd | 6 - man/tar_network.Rd | 2 man/tar_newer.Rd | 4 - man/tar_objects.Rd | 4 - man/tar_older.Rd | 4 - man/tar_outdated.Rd | 2 man/tar_process.Rd | 2 man/tar_progress.Rd | 4 - man/tar_sitrep.Rd | 4 - man/tar_skipped.Rd | 4 - man/tar_started.Rd | 4 - man/tar_visnetwork.Rd | 4 - tests/interactive/test-tar_poll.R | 2 tests/interactive/test-time.R | 12 +-- tests/testthat/test-class_file.R | 2 tests/testthat/test-tar_manifest.R | 4 - tests/testthat/test-tar_newer.R | 2 tests/testthat/test-tar_older.R | 2 tests/testthat/test-tar_progress_summary.R | 2 59 files changed, 164 insertions(+), 156 deletions(-)
Title: Nonparametric Spearman's Correlation for Survival Data
Description: Nonparametric estimation of Spearman's rank correlation with bivariate survival (right-censored) data as described in Eden, S.K., Li, C., Shepherd B.E. (2021), Nonparametric Estimation of Spearman's Rank Correlation with Bivariate Survival Data, Biometrics (under revision). The package also provides functions that visualize bivariate survival data and bivariate probability mass function.
Author: Svetlana Eden [aut, cre],
Chun Li [aut, anl],
Bryan Shepherd [aut, anl]
Maintainer: Svetlana Eden <svetlana.k.eden.1@vumc.org>
Diff between survSpearman versions 1.0.0 dated 2021-01-29 and 1.0.1 dated 2022-09-26
DESCRIPTION | 6 MD5 | 6 NEWS.md | 3 inst/doc/survSpearman.html | 1066 +++++++++++++++++++++------------------------ 4 files changed, 523 insertions(+), 558 deletions(-)
Title: Statistical Inference in High Dimensional Regression
Description: Inference procedures in the high-dimensional setting for
(1) linear functionals in generalized linear regression ('Cai et al.' (2019) <arXiv:1904.12891>, 'Guo et al.' (2020) <arXiv:2012.07133>, 'Cai et al.' (2021)),
(2) individual treatment effects in generalized linear regression,
(3) quadratic functionals in generalized linear regression ('Guo et al.' (2019) <arXiv:1909.01503>).
Author: Prabrisha Rakshit, Zhenyu Wang, Tony Cai, Zijian Guo
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>
Diff between SIHR versions 1.0.1 dated 2022-08-10 and 1.1.0 dated 2022-09-26
SIHR-1.0.1/SIHR/R/Projection_Directions.R |only SIHR-1.0.1/SIHR/inst |only SIHR-1.1.0/SIHR/DESCRIPTION | 10 - SIHR-1.1.0/SIHR/MD5 | 26 +- SIHR-1.1.0/SIHR/NAMESPACE | 46 ++-- SIHR-1.1.0/SIHR/R/ITE.R | 133 +++++++------ SIHR-1.1.0/SIHR/R/LF.R | 251 ++++++++++++++----------- SIHR-1.1.0/SIHR/R/Methods.R | 28 +- SIHR-1.1.0/SIHR/R/QF.R | 291 ++++++++++++++++++------------ SIHR-1.1.0/SIHR/R/check.R | 55 ++--- SIHR-1.1.0/SIHR/R/helpers.R | 112 ++++++++++- SIHR-1.1.0/SIHR/README.md | 273 +++++++++++++++++----------- SIHR-1.1.0/SIHR/man/ITE.Rd | 102 +++++----- SIHR-1.1.0/SIHR/man/LF.Rd | 80 +++----- SIHR-1.1.0/SIHR/man/QF.Rd | 94 ++++----- 15 files changed, 871 insertions(+), 630 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
RStudio [cph, fnd],
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between shinytest2 versions 0.1.1 dated 2022-09-06 and 0.2.0 dated 2022-09-26
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Title: Reactivity Visualizer for 'shiny'
Description: Building interactive web applications with R is incredibly easy
with 'shiny'. Behind the scenes, 'shiny' builds a reactive graph that can
quickly become intertwined and difficult to debug. 'reactlog'
(Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into
that black box of 'shiny' reactivity by constructing a directed dependency
graph of the application's reactive state at any time point in a reactive
recording.
Author: Barret Schloerke [aut, cre] ,
Joe Cheng [ctb],
RStudio [cph, fnd]
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between reactlog versions 1.1.0 dated 2020-09-12 and 1.1.1 dated 2022-09-26
DESCRIPTION | 14 MD5 | 22 - NEWS.md | 10 R/shinyModule.R | 2 R/showReactLog.R | 2 README.md | 6 build/vignette.rds |binary inst/doc/reactlog.R | 4 inst/doc/reactlog.Rmd | 8 inst/doc/reactlog.html | 615 +++++++++++++++++++++++--------- inst/reactlog/reactlogAsset/reactlog.js | 16 vignettes/reactlog.Rmd | 8 12 files changed, 494 insertions(+), 213 deletions(-)
Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create
linked micromap plots for a collection of geographic areas.
Linked micromap plots are visualizations of geo-referenced data
that link statistical graphics to an organized series of small
maps or graphic images. The Help description contains examples
of how to use the 'micromapST' function. Contained in this
package are border group datasets to support creating linked
micromap plots for the 50 U.S. states and District of Columbia
(51 areas), the U. S. 20 Seer Registries, the 105 counties in
the state of Kansas, the 62 counties of New York, the 24
counties of Maryland, the 29 counties of Utah, the 32
administrative areas in China, the 218 administrative areas in
the UK and Ireland (for testing only), the 25 districts in the
city of Seoul South Korea, and the 52 counties on the Africa
continent.
A border group dataset contains the boundaries related to the
data level areas, a second layer boundaries, a top or third
layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph],
Dan Carr [aut, cph],
Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>
Diff between micromapST versions 2.0.0 dated 2022-08-20 and 2.0.1 dated 2022-09-26
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Title: Decision Analytic Modelling in Health Economics
Description: Classes and functions for modelling health care interventions
using decision trees and semi-Markov models. Mechanisms are provided for
associating an uncertainty distribution with each source variable and for
ensuring transparency of the mathematical relationships between variables.
The package terminology follows Briggs "Decision Modelling for Health
Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Author: Andrew Sims [aut, cre] ,
Kim Fairbairn [aut] ,
Paola Cognigni [aut]
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>
Diff between rdecision versions 1.1.2 dated 2022-09-07 and 1.1.3 dated 2022-09-26
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rdecision-1.1.3/rdecision/R/ExprModVar.R | 165 +- rdecision-1.1.3/rdecision/R/GammaDistribution.R | 97 - rdecision-1.1.3/rdecision/R/GammaModVar.R | 11 rdecision-1.1.3/rdecision/R/Graph.R | 106 - rdecision-1.1.3/rdecision/R/LeafNode.R | 7 rdecision-1.1.3/rdecision/R/LogNormDistribution.R | 105 - rdecision-1.1.3/rdecision/R/LogNormModVar.R | 11 rdecision-1.1.3/rdecision/R/MarkovState.R | 8 rdecision-1.1.3/rdecision/R/ModVar.R | 96 - rdecision-1.1.3/rdecision/R/Node.R | 25 rdecision-1.1.3/rdecision/R/NormModVar.R | 8 rdecision-1.1.3/rdecision/R/NormalDistribution.R | 71 - rdecision-1.1.3/rdecision/R/Reaction.R | 105 - rdecision-1.1.3/rdecision/R/SemiMarkovModel.R | 431 ++---- rdecision-1.1.3/rdecision/R/Stack.R | 16 rdecision-1.1.3/rdecision/R/Transition.R | 57 rdecision-1.1.3/rdecision/R/data.R | 3 rdecision-1.1.3/rdecision/R/utils.R | 64 rdecision-1.1.3/rdecision/README.md | 46 rdecision-1.1.3/rdecision/inst/CITATION | 3 rdecision-1.1.3/rdecision/inst/NEWS.md | 30 rdecision-1.1.3/rdecision/inst/doc/DT00-DecisionTreeTutorial.R | 108 - rdecision-1.1.3/rdecision/inst/doc/DT00-DecisionTreeTutorial.Rmd | 112 - rdecision-1.1.3/rdecision/inst/doc/DT00-DecisionTreeTutorial.html | 241 +-- rdecision-1.1.3/rdecision/inst/doc/DT01-Sumatriptan.R | 10 rdecision-1.1.3/rdecision/inst/doc/DT01-Sumatriptan.Rmd | 10 rdecision-1.1.3/rdecision/inst/doc/DT01-Sumatriptan.html | 20 rdecision-1.1.3/rdecision/inst/doc/DT02-Tegaderm.R | 212 +-- rdecision-1.1.3/rdecision/inst/doc/DT02-Tegaderm.Rmd | 212 +-- rdecision-1.1.3/rdecision/inst/doc/DT02-Tegaderm.html | 327 ++-- rdecision-1.1.3/rdecision/inst/doc/DT03-ShaleGas.R | 52 rdecision-1.1.3/rdecision/inst/doc/DT03-ShaleGas.Rmd | 53 rdecision-1.1.3/rdecision/inst/doc/DT03-ShaleGas.html | 46 rdecision-1.1.3/rdecision/inst/doc/GT01-NewScientistPuzzle.R | 110 - rdecision-1.1.3/rdecision/inst/doc/GT01-NewScientistPuzzle.Rmd | 118 + rdecision-1.1.3/rdecision/inst/doc/GT01-NewScientistPuzzle.html | 52 rdecision-1.1.3/rdecision/inst/doc/SM01-HIV.R | 171 +- rdecision-1.1.3/rdecision/inst/doc/SM01-HIV.Rmd | 173 +- rdecision-1.1.3/rdecision/inst/doc/SM01-HIV.html | 152 +- rdecision-1.1.3/rdecision/man/Action.Rd | 26 rdecision-1.1.3/rdecision/man/Arborescence.Rd | 6 rdecision-1.1.3/rdecision/man/Arrow.Rd | 6 rdecision-1.1.3/rdecision/man/BriggsEx47.Rd | 3 rdecision-1.1.3/rdecision/man/DecisionTree.Rd | 32 rdecision-1.1.3/rdecision/man/Digraph.Rd | 4 rdecision-1.1.3/rdecision/man/DiracDistribution.Rd | 50 rdecision-1.1.3/rdecision/man/Distribution.Rd | 27 rdecision-1.1.3/rdecision/man/ExprModVar.Rd | 4 rdecision-1.1.3/rdecision/man/GammaModVar.Rd | 2 rdecision-1.1.3/rdecision/man/Graph.Rd | 2 rdecision-1.1.3/rdecision/man/ModVar.Rd | 2 rdecision-1.1.3/rdecision/man/Reaction.Rd | 22 rdecision-1.1.3/rdecision/man/SemiMarkovModel.Rd | 7 rdecision-1.1.3/rdecision/man/Stack.Rd | 3 rdecision-1.1.3/rdecision/man/Transition.Rd | 6 rdecision-1.1.3/rdecision/man/figures/README-sb.gv |only rdecision-1.1.3/rdecision/man/figures/README-sb.png |only rdecision-1.1.3/rdecision/tests/testthat.R | 1 rdecision-1.1.3/rdecision/tests/testthat/setup.R | 13 rdecision-1.1.3/rdecision/tests/testthat/test-Action.R | 33 rdecision-1.1.3/rdecision/tests/testthat/test-Arborescence.R | 178 +- rdecision-1.1.3/rdecision/tests/testthat/test-Arrow.R | 20 rdecision-1.1.3/rdecision/tests/testthat/test-BetaDistribution.R | 60 rdecision-1.1.3/rdecision/tests/testthat/test-BetaModVar.R | 84 - rdecision-1.1.3/rdecision/tests/testthat/test-ChanceNode.R | 6 rdecision-1.1.3/rdecision/tests/testthat/test-ConstModVar.R | 64 rdecision-1.1.3/rdecision/tests/testthat/test-DecisionNode.R | 15 rdecision-1.1.3/rdecision/tests/testthat/test-DecisionTree.R | 429 +++--- rdecision-1.1.3/rdecision/tests/testthat/test-Digraph.R | 133 + rdecision-1.1.3/rdecision/tests/testthat/test-DiracDistribution.R | 30 rdecision-1.1.3/rdecision/tests/testthat/test-DirichletDistribution.R | 157 +- rdecision-1.1.3/rdecision/tests/testthat/test-Distribution.R | 73 - rdecision-1.1.3/rdecision/tests/testthat/test-Edge.R | 10 rdecision-1.1.3/rdecision/tests/testthat/test-EmpiricalDistribution.R | 67 rdecision-1.1.3/rdecision/tests/testthat/test-ExprModVar.R | 265 +-- rdecision-1.1.3/rdecision/tests/testthat/test-GammaDistribution.R | 28 rdecision-1.1.3/rdecision/tests/testthat/test-GammaModVar.R | 36 rdecision-1.1.3/rdecision/tests/testthat/test-Graph.R | 115 - rdecision-1.1.3/rdecision/tests/testthat/test-LeafNode.R | 28 rdecision-1.1.3/rdecision/tests/testthat/test-LogNormDistribution.R | 63 rdecision-1.1.3/rdecision/tests/testthat/test-LogNormModVar.R | 85 - rdecision-1.1.3/rdecision/tests/testthat/test-MarkovState.R | 40 rdecision-1.1.3/rdecision/tests/testthat/test-ModVar.R | 69 rdecision-1.1.3/rdecision/tests/testthat/test-Node.R | 6 rdecision-1.1.3/rdecision/tests/testthat/test-NormModVar.R | 64 rdecision-1.1.3/rdecision/tests/testthat/test-NormalDistribution.R | 37 rdecision-1.1.3/rdecision/tests/testthat/test-Reaction.R | 43 rdecision-1.1.3/rdecision/tests/testthat/test-SemiMarkovModel.R | 359 ++--- rdecision-1.1.3/rdecision/tests/testthat/test-Stack.R | 42 rdecision-1.1.3/rdecision/tests/testthat/test-Transition.R | 50 rdecision-1.1.3/rdecision/tests/testthat/test-utils.R | 131 + rdecision-1.1.3/rdecision/vignettes/DT00-DecisionTreeTutorial.Rmd | 112 - rdecision-1.1.3/rdecision/vignettes/DT01-Sumatriptan.Rmd | 10 rdecision-1.1.3/rdecision/vignettes/DT02-Tegaderm.Rmd | 212 +-- rdecision-1.1.3/rdecision/vignettes/DT03-ShaleGas.Rmd | 53 rdecision-1.1.3/rdecision/vignettes/GT01-NewScientistPuzzle.Rmd | 118 + rdecision-1.1.3/rdecision/vignettes/SM01-HIV.Rmd | 173 +- 118 files changed, 4825 insertions(+), 4631 deletions(-)
Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre],
Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>
Diff between MCM versions 0.1.6 dated 2022-09-25 and 0.1.7 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mcm.R | 4 ++-- tests/mcm_package_test.R | 6 ++++++ 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Fuzzy Set Ordination
Description: Fuzzy set ordination is a multivariate analysis used in ecology to
relate the composition of samples to possible explanatory variables. While
differing in theory and method, in practice, the use is similar to 'constrained
ordination.' The package contains plotting and summary functions as well as
the analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>
Diff between fso versions 2.1-1 dated 2018-06-01 and 2.1-2 dated 2022-09-26
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- R/fso.R | 42 +++++++++++++++++++----------------------- inst/ChangeLog | 9 ++++++++- man/fso.Rd | 3 +-- man/mfso.Rd | 2 -- man/plot.fso.Rd | 3 --- man/plot.mfso.Rd | 1 - man/step.mfso.Rd | 1 - 9 files changed, 40 insertions(+), 46 deletions(-)
Title: Computing Comorbidity Scores
Description: Computing comorbidity indices and scores such as the weighted Charlson
score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser
comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>)
using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Australian and Swedish modifications of the Charlson Comorbidity Index are available
as well (Sundararajan, 2004 <doi:10.1016/j.jclinepi.2004.03.012> and Ludvigsson, 2021
<doi:10.2147/CLEP.S282475>).
Author: Alessandro Gasparini [aut, cre]
,
Hojjat Salmasian [ctb] ,
Jonathan Williman [ctb] ,
Sing Yi Chia [ctb] ,
Edmund Teo [ctb]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>
Diff between comorbidity versions 1.0.3 dated 2022-07-12 and 1.0.5 dated 2022-09-26
DESCRIPTION | 13 +-- MD5 | 34 ++++---- NEWS.md | 18 ++++ R/comorbidity-package.R | 7 + R/comorbidity.R | 44 +++++++--- R/score.R | 30 +++++-- R/zzz.R | 4 README.md | 6 - inst/doc/A-introduction.Rmd | 2 inst/doc/A-introduction.html | 157 ++++++++++++++++++------------------- inst/doc/B-comorbidity-scores.html | 18 ++-- man/comorbidity-package.Rd | 7 + man/comorbidity.Rd | 42 +++++++-- man/figures/hex.png |binary man/score.Rd | 32 ++++++- tests/testthat/test-#55.R | 22 ++--- tests/testthat/test-comorbidity.R | 6 - vignettes/A-introduction.Rmd | 2 18 files changed, 275 insertions(+), 169 deletions(-)
Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data.
Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU),
and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters
can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized
in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>,
Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>,
Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>,
Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, and
Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanović [aut, cre],
Jason D. Vescovi [dtc]
Maintainer: Mladen Jovanović <coach.mladen.jovanovic@gmail.com>
Diff between shorts versions 2.0.0 dated 2022-07-07 and 2.1.0 dated 2022-09-26
DESCRIPTION | 8 MD5 | 47 ++-- NAMESPACE | 6 NEWS.md | 10 R/find-functions.R | 329 +++++++++++++++++++++++++++++- R/format-splits.R | 14 - R/make-FV-profile.R | 37 +++ R/model-tether.R |only R/predict-functions.R | 23 ++ R/shorts-S3.R | 2 R/shorts-constructors.R | 16 + README.md | 248 ++++++++++++++-------- inst/CITATION | 8 man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-22-1.png |only man/figures/README-unnamed-chunk-24-1.png |only man/find_functions.Rd | 104 +++++++++ man/format_splits.Rd | 1 man/make_FV_profile.Rd | 13 + man/model_tether.Rd |only man/predict_kinematics.Rd | 7 27 files changed, 743 insertions(+), 130 deletions(-)
Title: Colorful Data Frames in R Terminal
Description: Colorful Data Frames in the terminal. The new class does
change the behaviour of any of the objects, but adds a style
definition and a print method. Using ANSI escape codes, it
colors the terminal output of data frames. Some column types
(such as p-values and identifiers) are automatically
recognized.
Author: January Weiner [aut, cre]
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between colorDF versions 0.1.5 dated 2022-09-25 and 0.1.7 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/definitions.R |only R/print.R | 12 ++++++++++++ R/styles.R | 2 +- R/summary.R | 18 ++++++++---------- R/themes.R | 10 +++++----- inst/doc/colorDF.R | 5 ----- inst/doc/colorDF.Rmd | 29 ----------------------------- inst/doc/colorDF.html | 50 ++++++++++++++++++++------------------------------ vignettes/colorDF.Rmd | 29 ----------------------------- 11 files changed, 59 insertions(+), 121 deletions(-)
Title: Estimating Dynamic Heritability and Twin Model Comparison
Description: Twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He
Maintainer: Liang He <lianghe@health.sdu.dk>
Diff between ACEt versions 1.8.1 dated 2020-10-21 and 1.8.2 dated 2022-09-26
DESCRIPTION | 30 ++++++++++++++---------------- MD5 | 31 +++++++++++++++++++------------ NAMESPACE | 3 ++- R/acetp_mcmc.R | 15 +++++++++------ R/plot_AtCtEt.R | 3 ++- R/plot_AtCtEt_h.R | 9 ++++++--- R/plot_AtCtEtp.R | 3 ++- R/plot_acet.R | 15 ++++----------- build |only data/data_ace.rda |binary inst |only man/ACEt-package.Rd | 6 +++--- src/AtCtEt.cpp | 36 ++++++++++++------------------------ src/AtCtEtp.cpp | 48 ++++++++++++++++-------------------------------- src/AtEtp.cpp | 48 ++++++++++++++++-------------------------------- vignettes |only 16 files changed, 105 insertions(+), 142 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 0.109.6 dated 2022-07-08 and 0.110.2 dated 2022-09-26
rgl-0.109.6/rgl/inst/htmlwidgets/lib/rglClass/rglClass.min.js |only rgl-0.110.2/rgl/DESCRIPTION | 8 rgl-0.110.2/rgl/MD5 | 105 +-- rgl-0.110.2/rgl/NAMESPACE | 2 rgl-0.110.2/rgl/NEWS.md | 50 + rgl-0.110.2/rgl/R/as.mesh3d.default.R | 12 rgl-0.110.2/rgl/R/axes.R | 74 +- rgl-0.110.2/rgl/R/buffer.R | 88 ++- rgl-0.110.2/rgl/R/enum.R | 10 rgl-0.110.2/rgl/R/internal.R | 6 rgl-0.110.2/rgl/R/material.R | 25 rgl-0.110.2/rgl/R/obj.R | 20 rgl-0.110.2/rgl/R/persp3d.R | 2 rgl-0.110.2/rgl/R/plotmath3d.R | 2 rgl-0.110.2/rgl/R/r3d.rgl.R | 7 rgl-0.110.2/rgl/R/rglwidget.R | 4 rgl-0.110.2/rgl/R/scene.R | 265 ++++------ rgl-0.110.2/rgl/R/shapelist3d.R | 2 rgl-0.110.2/rgl/R/triangulate.R | 20 rgl-0.110.2/rgl/R/zzz.R | 2 rgl-0.110.2/rgl/inst/doc/WebGL.html | 91 +-- rgl-0.110.2/rgl/inst/doc/pkgdown.html | 20 rgl-0.110.2/rgl/inst/doc/rgl.Rmd | 2 rgl-0.110.2/rgl/inst/doc/rgl.html | 136 ++--- rgl-0.110.2/rgl/inst/doc/transparency.html | 27 - rgl-0.110.2/rgl/inst/htmlwidgets/lib/rglClass/draw.src.js | 29 - rgl-0.110.2/rgl/inst/htmlwidgets/lib/rglClass/init.src.js | 5 rgl-0.110.2/rgl/man/Buffer.Rd | 150 +++-- rgl-0.110.2/rgl/man/bg.Rd | 2 rgl-0.110.2/rgl/man/gltfTypes.Rd | 2 rgl-0.110.2/rgl/man/material.Rd | 38 + rgl-0.110.2/rgl/man/polygon3d.Rd | 5 rgl-0.110.2/rgl/man/rglShared.Rd | 7 rgl-0.110.2/rgl/man/rglwidget.Rd | 7 rgl-0.110.2/rgl/src/BBoxDeco.cpp | 5 rgl-0.110.2/rgl/src/Material.cpp | 18 rgl-0.110.2/rgl/src/Material.h | 1 rgl-0.110.2/rgl/src/Texture.cpp | 6 rgl-0.110.2/rgl/src/api.cpp | 41 - rgl-0.110.2/rgl/src/api.h | 2 rgl-0.110.2/rgl/src/geom.cpp | 21 rgl-0.110.2/rgl/src/gui.cpp | 3 rgl-0.110.2/rgl/src/init.cpp | 3 rgl-0.110.2/rgl/src/subscene.cpp | 8 rgl-0.110.2/rgl/src/x11gui.cpp | 5 rgl-0.110.2/rgl/tests/testthat/testdata/mergeVertices.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/obj.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/qmesh3d.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/r3d.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/shade3detc.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/subscenes.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/tmesh3d.rds |binary rgl-0.110.2/rgl/tests/testthat/testdata/transformations.rds |binary rgl-0.110.2/rgl/vignettes/rgl.Rmd | 2 54 files changed, 800 insertions(+), 540 deletions(-)
Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>
Diff between dsfa versions 0.0.3 dated 2022-09-07 and 1.0.0 dated 2022-09-26
dsfa-0.0.3/dsfa/R/cop_utility.R |only dsfa-0.0.3/dsfa/man/dcop_copula.Rd |only dsfa-0.0.3/dsfa/man/erfcinv.Rd |only dsfa-1.0.0/dsfa/DESCRIPTION | 8 dsfa-1.0.0/dsfa/MD5 | 77 +- dsfa-1.0.0/dsfa/NAMESPACE | 8 dsfa-1.0.0/dsfa/NEWS.md |only dsfa-1.0.0/dsfa/R/OwenT.R |only dsfa-1.0.0/dsfa/R/chainrule.R | 62 +- dsfa-1.0.0/dsfa/R/comperr.R | 68 +- dsfa-1.0.0/dsfa/R/comperr_mv.R | 121 ++-- dsfa-1.0.0/dsfa/R/comperr_mv_mgcv.R | 134 +++-- dsfa-1.0.0/dsfa/R/cop.R | 907 +++++++++++++++++++++------------- dsfa-1.0.0/dsfa/R/cop_mgcv.R | 195 +++++-- dsfa-1.0.0/dsfa/R/dsfa.R | 95 ++- dsfa-1.0.0/dsfa/R/efficiency.R | 2 dsfa-1.0.0/dsfa/R/elasticity.R | 2 dsfa-1.0.0/dsfa/R/erf.R |only dsfa-1.0.0/dsfa/R/normexp.R | 18 dsfa-1.0.0/dsfa/R/normexp_mgcv.R | 13 dsfa-1.0.0/dsfa/R/normhnorm.R | 56 -- dsfa-1.0.0/dsfa/R/normhnorm_mgcv.R | 13 dsfa-1.0.0/dsfa/R/reparametrize.R | 24 dsfa-1.0.0/dsfa/R/utility_functions.R | 89 --- dsfa-1.0.0/dsfa/R/zeta.R |only dsfa-1.0.0/dsfa/build/partial.rdb |binary dsfa-1.0.0/dsfa/inst/REFERENCES.bib | 21 dsfa-1.0.0/dsfa/man/OwenT.Rd |only dsfa-1.0.0/dsfa/man/chainrule.Rd | 4 dsfa-1.0.0/dsfa/man/comperr_mv.Rd | 29 - dsfa-1.0.0/dsfa/man/cop.Rd | 47 + dsfa-1.0.0/dsfa/man/dcomperr.Rd | 31 - dsfa-1.0.0/dsfa/man/dcomperr_mv.Rd | 84 +-- dsfa-1.0.0/dsfa/man/dcop.Rd | 66 +- dsfa-1.0.0/dsfa/man/dnormexp.Rd | 6 dsfa-1.0.0/dsfa/man/dnormhnorm.Rd | 10 dsfa-1.0.0/dsfa/man/dsfa.Rd | 92 ++- dsfa-1.0.0/dsfa/man/efficiency.Rd | 2 dsfa-1.0.0/dsfa/man/elasticity.Rd | 2 dsfa-1.0.0/dsfa/man/erf.Rd |only dsfa-1.0.0/dsfa/man/normexp.Rd | 9 dsfa-1.0.0/dsfa/man/normhnorm.Rd | 9 dsfa-1.0.0/dsfa/man/pos_eigen.Rd |only dsfa-1.0.0/dsfa/man/reparametrize.Rd | 12 dsfa-1.0.0/dsfa/man/zeta.Rd |only 45 files changed, 1374 insertions(+), 942 deletions(-)
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut]
,
Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.UFAx versions 1.5 dated 2022-09-09 and 1.6 dated 2022-09-26
DESCRIPTION | 6 ++-- MD5 | 9 +++--- R/UFAx_score_coefficient_corrector.R | 46 +++++++++++++++++++++-------------- inst/CITATION |only inst/extdata/UFAx_parameters.xlsx |binary man/UFAx_workflow.Rd | 7 ++--- 6 files changed, 39 insertions(+), 29 deletions(-)
Title: Plot Data on Oceanographic Maps using 'ggplot2'
Description: Allows plotting data on bathymetric maps using 'ggplot2'. Plotting
oceanographic spatial data is made as simple as feasible, but also flexible
for custom modifications. Data that contain geographic information from
anywhere around the globe can be plotted on maps generated by the basemap()
or qmap() functions using 'ggplot2' layers separated by the '+' operator. The
package uses spatial shapefiles stored in the 'ggOceanMapsData' package,
geospatial packages for R to manipulate, and the 'ggspatial' package to help
to plot these shapefiles. High-resolution shapefiles for detailed maps are
stored on GitHub and downloaded automatically when needed.
Author: Mikko Vihtakari [aut, cre] ,
Yves Reecht [ctb] ,
Hadley Wickham [ctb],
Simon O'Hanlon [ctb],
Roger Bivand [ctb]
Maintainer: Mikko Vihtakari <mikko.vihtakari@hi.no>
Diff between ggOceanMaps versions 1.3.0 dated 2022-09-20 and 1.3.4 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/basemap.R | 21 +++++++++++---------- R/basemap_data.R | 15 ++++++++++++--- R/datasets-docs.R | 6 ++++++ R/dist2land.R | 3 +++ R/qmap.R | 6 ++---- R/reorder_layers.R | 2 ++ R/shapefile_list.R | 8 ++++++++ man/basemap.Rd | 19 +++++++++---------- man/dist2land.Rd | 3 +++ man/fdir_main_areas.Rd | 2 ++ man/fdir_sub_areas.Rd | 2 ++ man/ices_areas.Rd | 2 ++ man/qmap.Rd | 6 ++---- man/reorder_layers.Rd | 2 ++ 16 files changed, 85 insertions(+), 50 deletions(-)
Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between calculus versions 0.3.4 dated 2022-08-20 and 1.0.0 dated 2022-09-26
DESCRIPTION | 8 - MD5 | 155 +++++++++++++++++------------------ NEWS.md | 4 R/contraction.R | 2 R/delta.R | 2 R/derivative.R | 2 R/einstein.R | 2 R/epsilon.R | 2 R/evaluate.R | 2 R/hermite.R | 2 R/integral.R | 2 R/mxdet.R | 2 R/mxinv.R | 2 R/mxtr.R | 2 R/ode.R | 2 R/operators.R | 32 +++---- R/partitions.R | 2 R/taylor.R | 2 R/utils.R | 10 +- README.md | 21 ++-- build/partial.rdb |only inst/CITATION | 23 ++--- inst/doc/derivatives.Rmd | 21 ++-- inst/doc/derivatives.html | 24 ++--- inst/doc/differential-operators.Rmd | 21 ++-- inst/doc/differential-operators.html | 24 ++--- inst/doc/einstein.Rmd | 21 ++-- inst/doc/einstein.html | 24 ++--- inst/doc/hermite.Rmd | 21 ++-- inst/doc/hermite.html | 24 ++--- inst/doc/integrals.Rmd | 24 ++--- inst/doc/integrals.html | 24 ++--- inst/doc/ode.Rmd | 22 ++-- inst/doc/ode.html | 24 ++--- inst/doc/taylor.Rmd | 21 ++-- inst/doc/taylor.html | 24 ++--- man/c2e.Rd | 2 man/calculus-package.Rd | 2 man/contraction.Rd | 2 man/cross.Rd | 2 man/curl.Rd | 2 man/delta.Rd | 2 man/derivative.Rd | 2 man/diagonal.Rd | 2 man/divergence.Rd | 2 man/e2c.Rd | 2 man/einstein.Rd | 2 man/epsilon.Rd | 2 man/evaluate.Rd | 2 man/gradient.Rd | 2 man/grapes-diff-grapes.Rd | 2 man/grapes-div-grapes.Rd | 2 man/grapes-dot-grapes.Rd | 2 man/grapes-inner-grapes.Rd | 2 man/grapes-kronecker-grapes.Rd | 2 man/grapes-outer-grapes.Rd | 2 man/grapes-prod-grapes.Rd | 2 man/grapes-sum-grapes.Rd | 2 man/hermite.Rd | 2 man/hessian.Rd | 2 man/index.Rd | 2 man/integral.Rd | 2 man/jacobian.Rd | 2 man/laplacian.Rd | 2 man/mx.Rd | 2 man/mxdet.Rd | 2 man/mxinv.Rd | 2 man/mxtr.Rd | 2 man/ode.Rd | 2 man/partitions.Rd | 2 man/taylor.Rd | 2 man/wrap.Rd | 2 vignettes/derivatives.Rmd | 21 ++-- vignettes/differential-operators.Rmd | 21 ++-- vignettes/einstein.Rmd | 21 ++-- vignettes/hermite.Rmd | 21 ++-- vignettes/integrals.Rmd | 24 ++--- vignettes/ode.Rmd | 22 ++-- vignettes/taylor.Rmd | 21 ++-- 79 files changed, 425 insertions(+), 398 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph]
,
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.4.0 dated 2022-08-13 and 0.4.1 dated 2022-09-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/zzz.R | 7 +++++-- inst/CITATION | 6 ++++-- inst/doc/tidytree.html | 4 ++-- 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph]
,
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.1.2 dated 2022-08-16 and 2.1.3 dated 2022-09-26
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++-------------- NEWS.md | 6 +++++ R/Rogue-package.R | 4 +-- R/stability.R | 35 ++++++++++++++++------------- R/utilities.R | 2 - R/zz_RogueNaRok.R | 20 ++++++++-------- R/zzz.R | 12 ---------- build/partial.rdb |binary inst/doc/Bayesian.html | 4 +-- man/Rogue-package.Rd | 4 +-- man/RogueTaxa.Rd | 10 ++++---- man/TipInstability.Rd | 23 +++++++++++++++---- man/TipVolatility.Rd | 6 ++--- tests/testthat.R | 4 +-- tests/testthat/test-RogueNaRok.R | 24 ++++++++++---------- tests/testthat/test-RogueTaxa.R | 46 +++++++++++++++++++-------------------- tests/testthat/test-stability.R | 10 ++++---- 18 files changed, 131 insertions(+), 119 deletions(-)
Title: The Multivariate Normal and t Distributions, and Their Truncated
Versions
Description: Functions are provided for computing the density and the
distribution function of d-dimensional normal and "t" random variables,
possibly truncated (on one side or two sides), and for generating random
vectors sampled from these distributions, except sampling from the truncated
"t". Moments of arbitrary order of a multivariate truncated normal are
computed, and converted to cumulants up to order 4.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.
Author: Adelchi Azzalini [aut, cre],
Alan Genz [aut] ,
Alan Miller [ctb] ,
Michael J. Wichura [ctb] ,
G. W. Hill [ctb] ,
Yihong Ge [ctb] .
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 2.1.0 dated 2022-06-07 and 2.1.1 dated 2022-09-26
mnormt-2.1.0/mnormt/NEWS |only mnormt-2.1.1/mnormt/DESCRIPTION | 8 +++---- mnormt-2.1.1/mnormt/INDEX |only mnormt-2.1.1/mnormt/MD5 | 21 +++++++++--------- mnormt-2.1.1/mnormt/R/mnormt.R | 34 +++++++++++++++++++----------- mnormt-2.1.1/mnormt/R/truncNorm.R | 9 ++++--- mnormt-2.1.1/mnormt/build/partial.rdb |binary mnormt-2.1.1/mnormt/inst/NEWS.Rd |only mnormt-2.1.1/mnormt/man/mnorm.Rd | 28 ++++++++++++++---------- mnormt-2.1.1/mnormt/man/mom.mtruncnorm.Rd | 25 +++++++++++++--------- mnormt-2.1.1/mnormt/man/mt.Rd | 28 +++++++++++++----------- mnormt-2.1.1/mnormt/man/mtruncnorm.Rd | 23 +++++++++++--------- mnormt-2.1.1/mnormt/man/recintab.Rd | 3 ++ 13 files changed, 104 insertions(+), 75 deletions(-)
Title: Intensity Analysis of Spatial Point Patterns on Complex Networks
Description: Tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks.
This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.
Author: Pol Llagostera [aut, cre],
Matthias Eckardt [aut]
Maintainer: Pol Llagostera <pol.llagostera@udl.cat>
Diff between intensitynet versions 1.3.0 dated 2022-05-16 and 1.3.1 dated 2022-09-26
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.6.0 dated 2021-10-17 and 3.7.0 dated 2022-09-26
rcdk-3.6.0/rcdk/NEWS |only rcdk-3.7.0/rcdk/DESCRIPTION | 12 rcdk-3.7.0/rcdk/MD5 | 63 +- rcdk-3.7.0/rcdk/NEWS.md |only rcdk-3.7.0/rcdk/R/atoms.R | 66 +- rcdk-3.7.0/rcdk/R/desc.R | 2 rcdk-3.7.0/rcdk/R/formula.R | 10 rcdk-3.7.0/rcdk/R/io.R | 27 rcdk-3.7.0/rcdk/R/props.R | 7 rcdk-3.7.0/rcdk/R/smsd.R | 2 rcdk-3.7.0/rcdk/R/visual.R | 8 rcdk-3.7.0/rcdk/build/vignette.rds |binary rcdk-3.7.0/rcdk/inst/cont/rcdk.jar |binary rcdk-3.7.0/rcdk/inst/doc/molform.html | 431 ++++++++++++--- rcdk-3.7.0/rcdk/inst/doc/using-rcdk.Rmd | 6 rcdk-3.7.0/rcdk/inst/doc/using-rcdk.html | 706 ++++++++++++++++++++----- rcdk-3.7.0/rcdk/inst/unitTests/runit.formula.R |only rcdk-3.7.0/rcdk/inst/unitTests/runit.rcdk.R | 2 rcdk-3.7.0/rcdk/man/Atoms.Rd | 2 rcdk-3.7.0/rcdk/man/get.atom.index.Rd | 8 rcdk-3.7.0/rcdk/man/get.atomic.number.Rd | 2 rcdk-3.7.0/rcdk/man/get.charge.Rd | 8 rcdk-3.7.0/rcdk/man/get.connected.atoms.Rd | 7 rcdk-3.7.0/rcdk/man/get.formal.charge.Rd | 7 rcdk-3.7.0/rcdk/man/get.hydrogen.count.Rd | 9 rcdk-3.7.0/rcdk/man/get.point2d.Rd | 9 rcdk-3.7.0/rcdk/man/get.point3d.Rd | 9 rcdk-3.7.0/rcdk/man/get.properties.Rd | 2 rcdk-3.7.0/rcdk/man/get.symbol.Rd | 6 rcdk-3.7.0/rcdk/man/is.aliphatic.Rd | 8 rcdk-3.7.0/rcdk/man/is.aromatic.Rd | 8 rcdk-3.7.0/rcdk/man/is.in.ring.Rd | 8 rcdk-3.7.0/rcdk/man/set.atom.types.Rd | 10 rcdk-3.7.0/rcdk/vignettes/using-rcdk.Rmd | 6 34 files changed, 1066 insertions(+), 385 deletions(-)
Title: Hidden Markov Models with Discrete Non-Parametric Observation
Distributions
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. The observations may
be univariate or bivariate. Simulates data from such models.
Finds most probable underlying hidden states, the most
probable sequences of such states, and the log likelihood
of a collection of observations given the parameters of
the model. Auxiliary predictors are accommodated in the
univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between hmm.discnp versions 3.0-7 dated 2022-02-08 and 3.0-9 dated 2022-09-26
hmm.discnp-3.0-7/hmm.discnp/R/fix.tpm.R |only hmm.discnp-3.0-9/hmm.discnp/ChangeLog | 44 ++ hmm.discnp-3.0-9/hmm.discnp/DESCRIPTION | 8 hmm.discnp-3.0-9/hmm.discnp/MD5 | 80 ++-- hmm.discnp-3.0-9/hmm.discnp/R/First.R | 14 hmm.discnp-3.0-9/hmm.discnp/R/checkStartVal.R | 13 hmm.discnp-3.0-9/hmm.discnp/R/ffun.R | 24 - hmm.discnp-3.0-9/hmm.discnp/R/hmmLM.R | 3 hmm.discnp-3.0-9/hmm.discnp/R/hmmNumOpt.R | 7 hmm.discnp-3.0-9/hmm.discnp/R/hmmSD.R | 3 hmm.discnp-3.0-9/hmm.discnp/R/hmmUV.R | 20 - hmm.discnp-3.0-9/hmm.discnp/R/lmstep.R | 2 hmm.discnp-3.0-9/hmm.discnp/R/makeDat.R | 2 hmm.discnp-3.0-9/hmm.discnp/R/revise.rho.R | 4 hmm.discnp-3.0-9/hmm.discnp/R/steepest.R | 21 - hmm.discnp-3.0-9/hmm.discnp/R/suffices.R |only hmm.discnp-3.0-9/hmm.discnp/data/Bovine.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Cryptosporidiosis.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Downloads.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/EricssonB_Jul2.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/FattyLiver.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/FattyLiver2.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Hanta.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/IPs.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/InfantEEGsleepstates.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/LegionnairesDisease.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/OffshoreRigcountsAlaska.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/PriceStability.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/Strikes.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/SydColDisc.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/WoodPeweeSong.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/ccprSim.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/ftLiardFlows.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/goldparticle380.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/lesionCount.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/linLandFlows.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/portMannFlows.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/portMannSedCon.rda |binary hmm.discnp-3.0-9/hmm.discnp/data/portMannSedLoads.rda |binary hmm.discnp-3.0-9/hmm.discnp/man/hmm.Rd | 196 +++++++++-- hmm.discnp-3.0-9/hmm.discnp/man/hmm.discnp-internal.Rd | 6 hmm.discnp-3.0-9/hmm.discnp/man/viterbi.Rd | 7 42 files changed, 341 insertions(+), 113 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 1.0.6 dated 2021-06-22 and 1.0.7 dated 2022-09-26
DESCRIPTION | 12 - MD5 | 178 +++++++++---------- R/Plotting_with_ggplot.R | 2 README.md | 27 +- build/partial.rdb |binary data/HData.RData |binary man/Age_Pyramids_2014.Rd | 44 ++-- man/Agronomique.Rd | 46 ++-- man/BLOOD.Rd | 40 ++-- man/BloodBRITO.Rd | 42 ++-- man/Center.cell.MatH-methods.Rd | 50 ++--- man/DouglasPeucker.Rd | 44 ++-- man/HTS-class.Rd | 42 ++-- man/HTS.exponential.smoothing.Rd | 66 +++---- man/HTS.moving.averages.Rd | 74 +++---- man/HTS.predict.knn.Rd | 80 ++++---- man/HistDAWass-package.Rd | 120 ++++++------ man/MatH-class.Rd | 190 ++++++++++---------- man/OzoneFull.Rd | 42 ++-- man/OzoneH.Rd | 42 ++-- man/ShortestDistance.Rd | 44 ++-- man/TMatH-class.Rd | 60 +++--- man/TdistributionH-class.Rd | 78 ++++---- man/WH.1d.PCA.Rd | 132 +++++++------- man/WH.MultiplePCA.Rd | 64 +++--- man/WH.SSQ-methods.Rd | 68 +++---- man/WH.SSQ2-methods.Rd | 78 ++++---- man/WH.bind-methods.Rd | 76 ++++---- man/WH.bind.col-methods.Rd | 56 +++--- man/WH.bind.row-methods.Rd | 56 +++--- man/WH.correlation-methods.Rd | 80 ++++---- man/WH.correlation2-methods.Rd | 78 ++++---- man/WH.mat.prod-methods.Rd | 74 +++---- man/WH.mat.sum-methods.Rd | 62 +++--- man/WH.plot_multiple_Spanish.funs.Rd | 94 +++++----- man/WH.plot_multiple_indivs.Rd | 140 +++++++-------- man/WH.regression.GOF.Rd | 66 +++---- man/WH.regression.two.components.Rd | 94 +++++----- man/WH.regression.two.components.predict.Rd | 62 +++--- man/WH.var.covar-methods.Rd | 80 ++++---- man/WH.var.covar2-methods.Rd | 78 ++++---- man/WH.vec.mean-methods.Rd | 66 +++---- man/WH.vec.sum-methods.Rd | 68 +++---- man/WH_2d_Adaptive_Kohonen_maps.Rd | 260 ++++++++++++++-------------- man/WH_2d_Kohonen_maps.Rd | 202 ++++++++++----------- man/WH_MAT_DIST.Rd | 64 +++--- man/WH_adaptive.kmeans.Rd | 172 +++++++++--------- man/WH_adaptive_fcmeans.Rd | 130 +++++++------- man/WH_fcmeans.Rd | 104 +++++------ man/WH_hclust.Rd | 108 +++++------ man/WH_kmeans.Rd | 136 +++++++------- man/WassSqDistH-methods.Rd | 92 ++++----- man/checkEmptyBins-methods.Rd | 68 +++---- man/compP-methods.Rd | 62 +++--- man/compQ-methods.Rd | 76 ++++---- man/crwtransform-methods.Rd | 82 ++++---- man/data2hist.Rd | 110 +++++------ man/distributionH-class.Rd | 172 +++++++++--------- man/dotpW-methods.Rd | 116 ++++++------ man/extract-methods.Rd | 62 +++--- man/get.MatH.main.info-methods.Rd | 64 +++--- man/get.MatH.stats-methods.Rd | 116 ++++++------ man/get.MatH.varnames-methods.Rd | 40 ++-- man/get.cell.MatH-methods.Rd | 56 +++--- man/get.distr-methods.Rd | 48 ++--- man/get.histo-methods.Rd | 48 ++--- man/get.m-methods.Rd | 48 ++--- man/get.s-methods.Rd | 48 ++--- man/is.registeredMH-methods.Rd | 106 +++++------ man/kurtH-methods.Rd | 64 +++--- man/meanH-methods.Rd | 62 +++--- man/minus.Rd | 60 +++--- man/plot-HTS.Rd | 74 +++---- man/plot-MatH.Rd | 72 +++---- man/plot-TdistributionH.Rd | 50 ++--- man/plot-distributionH.Rd | 74 +++---- man/plotPredVsObs.Rd | 80 ++++---- man/plot_errors.Rd | 78 ++++---- man/plus-methods.Rd | 62 +++--- man/rQQ-methods.Rd | 80 ++++---- man/register-methods.Rd | 118 ++++++------ man/registerMH-methods.Rd | 146 +++++++-------- man/set.cell.MatH-methods.Rd | 62 +++--- man/show-MatH-methods.Rd | 44 ++-- man/show-distributionH-methods.Rd | 46 ++-- man/skewH-methods.Rd | 62 +++--- man/stdH-methods.Rd | 64 +++--- man/subsetHTS-methods.Rd | 54 ++--- man/times-methods.Rd | 54 ++--- src/RcppExports.cpp | 5 90 files changed, 3454 insertions(+), 3442 deletions(-)
Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Robert Krause [aut]
Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo@tudublin.ie>
Diff between Bergm versions 5.0.4 dated 2022-08-15 and 5.0.5 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/CITATION | 53 +++++++++++++++++++++++++++++++++++------------------ 3 files changed, 41 insertions(+), 24 deletions(-)
Title: Multiple Imputation with Automated Machine Learning
Description: Machine learning algorithms have been used for performing
single missing data imputation and most recently, multiple imputations.
However, this is the first attempt for using automated machine learning algorithms
for performing both
single and multiple imputation. Automated machine learning is a procedure for
fine-tuning the model automatic, performing a random search for a model that
results in less error, without overfitting the data. The main idea is
to allow the model to set its own parameters for imputing each variable seperately
instead of setting fixed predefined parameters to impute all variables
of the dataset.
Using automated machine learning, the package fine-tunes an Elastic
Net (default) or Gradient Boosting, Random Forest, Deep Learning, Extreme Gradient Boosting,
or Stacked Ensemble machine learning model (from one or a combination of other
supported algorithms) for imputing the missing
observations. This procedure has been implemented for the
first time by this package [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>
Diff between mlim versions 0.0.9 dated 2022-09-07 and 0.2.0 dated 2022-09-26
DESCRIPTION | 38 LICENSE | 4 MD5 | 101 +- NAMESPACE | 70 - R/addNA.R | 44 - R/algoSelector.R | 144 +-- R/bootstrapWeight.R |only R/charity.R | 30 R/checkNconvert.R | 266 +++--- R/extractMetrics.R | 108 +- R/getDigits.R | 27 R/getMetrics.R | 48 - R/h2o.check.R | 78 - R/init.R | 115 +- R/is.imbalanced.R | 52 - R/is.valid.R | 52 - R/iterate.R | 1251 ++++++++++++++++++----------- R/iterationNextVar.R |only R/iteration_loop.R | 544 +++++++----- R/javaServer.R |only R/manifest.R | 200 ++-- R/matching.R | 88 +- R/meanmode.R | 70 - R/miss_per_class_error.R | 80 - R/missclass.R | 40 R/missrank.R | 48 - R/mlim.R | 1280 +++++++++++++++--------------- R/mlim.error.R | 408 ++++----- R/mlim.mids.R | 94 +- R/mlim.na.R | 154 +-- R/mlim.postimpute.R | 152 +-- R/mlim.preimpute.R | 124 +- R/mlim.summarize.R | 156 +-- R/normalize.R | 20 R/nrmse.R | 48 - R/selectVariables.R | 112 +- R/server.check.R | 78 - R/stoppingCriteria.R | 253 ++--- R/syntaxProcessing.R | 188 ++-- R/threeDots.R | 32 R/zzz.R | 16 README.md | 376 ++++---- man/charity.Rd | 52 - man/figures/flowchart_base.drawio |only man/figures/flowchart_base.png |only man/figures/flowchart_optimization.drawio |only man/figures/flowchart_optimization.png |only man/figures/procedure5.drawio |only man/figures/procedure5.png |only man/manifest.Rd | 190 ++-- man/mlim.Rd | 496 ++++++----- man/mlim.error.Rd | 174 ++-- man/mlim.mids.Rd | 88 +- man/mlim.na.Rd | 126 +- man/mlim.preimpute.Rd | 92 +- man/mlim.summarize.Rd | 72 - 56 files changed, 4415 insertions(+), 3864 deletions(-)
Title: Generate Activity Counts from Raw Accelerometer Data
Description: A tool to obtain activity counts, originally a translation of the
'python' package 'agcounts' <https://github.com/actigraph/agcounts>. This tool
allows the processing of data from any accelerometer brand, with a more flexible
approach to handle different sampling frequencies.
Author: Jairo Hidalgo Migueles
Maintainer: Jairo Hidalgo Migueles <jairo.hidalgo.migueles@gmail.com>
Diff between actilifecounts versions 1.0.0 dated 2022-05-30 and 1.1.0 dated 2022-09-26
actilifecounts-1.0.0/actilifecounts/NEWS.md |only actilifecounts-1.1.0/actilifecounts/DESCRIPTION | 13 +++---- actilifecounts-1.1.0/actilifecounts/MD5 | 18 +++++----- actilifecounts-1.1.0/actilifecounts/R/bpf_filter.R | 5 +- actilifecounts-1.1.0/actilifecounts/R/get_counts.R | 7 ++- actilifecounts-1.1.0/actilifecounts/R/resample_30hz.R | 3 + actilifecounts-1.1.0/actilifecounts/README.md | 9 +++-- actilifecounts-1.1.0/actilifecounts/inst/NEWS.Rd |only actilifecounts-1.1.0/actilifecounts/man/get_counts.Rd | 4 +- actilifecounts-1.1.0/actilifecounts/tests/testthat/test-get_counts.R | 6 +-- actilifecounts-1.1.0/actilifecounts/tests/testthat/test-pipeline.R | 6 +++ 11 files changed, 43 insertions(+), 28 deletions(-)
More information about actilifecounts at CRAN
Permanent link
Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a
model formula or recipe from 'recipes', can often be challenging. The
goal of 'workflows' is to streamline this process by bundling the
model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut],
Simon Couch [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between workflows versions 1.0.0 dated 2022-07-05 and 1.1.0 dated 2022-09-26
DESCRIPTION | 17 +++++---- MD5 | 30 ++++++++-------- NEWS.md | 22 +++++++++++ R/broom.R | 17 +++++++++ R/butcher.R | 9 ++++ R/fit-action-model.R | 14 +++++++ R/pre-action-formula.R | 22 +++++++++++ inst/doc/stages.html | 14 +++---- man/workflows-package.Rd | 7 +++ tests/testthat/_snaps/fit-action-model.md | 9 ++++ tests/testthat/_snaps/pre-action-formula.md | 9 ++++ tests/testthat/test-broom.R | 52 ++++++++++++++++++++++++++++ tests/testthat/test-butcher.R | 27 ++++++++++++++ tests/testthat/test-fit-action-model.R | 30 ++++++++++++++++ tests/testthat/test-pre-action-formula.R | 19 ++++++++++ vignettes/extras/getting-started.Rmd | 26 ++++++-------- 16 files changed, 280 insertions(+), 44 deletions(-)
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2022.09.13 dated 2022-09-17 and 2022.09.23 dated 2022-09-26
riskRegression-2022.09.13/riskRegression/src/getInfluenceFunctionBrierCVCensoringKM.cpp |only riskRegression-2022.09.23/riskRegression/DESCRIPTION | 6 riskRegression-2022.09.23/riskRegression/MD5 | 37 riskRegression-2022.09.23/riskRegression/R/AUC.competing.risks.R | 98 riskRegression-2022.09.23/riskRegression/R/AUC.survival.R | 26 riskRegression-2022.09.23/riskRegression/R/Brier.competing.risks.R | 59 riskRegression-2022.09.23/riskRegression/R/Brier.survival.R | 64 riskRegression-2022.09.23/riskRegression/R/RcppExports.R | 16 riskRegression-2022.09.23/riskRegression/R/Score.R | 1497 +++++----- riskRegression-2022.09.23/riskRegression/R/computePerformance.R | 3 riskRegression-2022.09.23/riskRegression/R/crossvalPerf.R | 412 ++ riskRegression-2022.09.23/riskRegression/R/getInfluenceCurve.R | 144 riskRegression-2022.09.23/riskRegression/man/Score.Rd | 3 riskRegression-2022.09.23/riskRegression/src/RcppExports.cpp | 57 riskRegression-2022.09.23/riskRegression/src/arma-wrap.cpp | 34 riskRegression-2022.09.23/riskRegression/src/arma-wrap.h | 3 riskRegression-2022.09.23/riskRegression/src/getInfluenceFunctionAUC.cpp | 391 -- riskRegression-2022.09.23/riskRegression/src/getInfluenceFunctionBrier.cpp | 161 - riskRegression-2022.09.23/riskRegression/vignettes/IFAUC.Rmd | 110 riskRegression-2022.09.23/riskRegression/vignettes/IFBrier.Rmd | 29 20 files changed, 1417 insertions(+), 1733 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network
Reconstruction
Description: Provides an implementation of Regularized LS-TreeBoost & LAD-TreeBoost algorithm for Regulatory Network inference from any type of expression data (Microarray/RNA-seq etc).
Author: Raghvendra Mall [aut, cre],
Khalid Kunji [aut],
Melissa O'Neill [ctb]
Maintainer: Raghvendra Mall <raghvendra5688@gmail.com>
Diff between RGBM versions 1.0-9 dated 2022-08-11 and 1.0-10 dated 2022-09-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/train_regression_stump.cpp | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: A Framework for Robust Shiny Applications
Description: An opinionated framework for building a production-ready
'Shiny' application. This package contains a series of tools for
building a robust 'Shiny' application from start to finish.
Author: Colin Fay [cre, aut] ,
Vincent Guyader [aut] ,
Sebastien Rochette [aut] ,
Cervan Girard [aut] ,
Novica Nakov [ctb],
David Granjon [ctb],
Arthur Breant [ctb],
Antoine Languillaume [ctb],
ThinkR [cph]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between golem versions 0.3.3 dated 2022-07-13 and 0.3.4 dated 2022-09-26
DESCRIPTION | 10 +++---- MD5 | 34 ++++++++++++------------- R/add_dockerfiles.R | 10 +++---- R/add_r_files.R | 1 R/modules_fn.R | 1 R/test_helpers.R | 5 --- R/with_opt.R | 42 +++++++++++++++---------------- inst/doc/a_start.html | 4 +- inst/doc/b_dev.html | 4 +- inst/doc/c_deploy.html | 4 +- inst/doc/d_js.html | 4 +- inst/doc/e_config.html | 2 - man/dockerfiles.Rd | 10 +++---- man/get_golem_options.Rd | 42 +++++++++++++++---------------- man/testhelpers.Rd | 4 -- tests/testthat/test-add_deploy_helpers.R | 5 ++- tests/testthat/test-extra_sysreqs.R | 3 ++ tests/testthat/test-renv_stuff.R | 4 ++ 18 files changed, 93 insertions(+), 96 deletions(-)
Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggridges versions 0.5.3 dated 2021-01-08 and 0.5.4 dated 2022-09-26
DESCRIPTION | 13 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 5 R/geoms-gradient.R | 13 R/geoms.R | 14 R/geomsv.R | 14 R/ggridges.R | 1 R/position.R | 9 R/stats.R | 5 R/utils.R | 1 README.md | 36 +- build/vignette.rds |binary inst/doc/gallery.html | 288 ++++++++++---------- inst/doc/introduction.html | 648 +++++++++++++++++++++++++++------------------ man/ggridges.Rd | 1 man/position_raincloud.Rd | 10 man/reduce.Rd | 1 man/stat_binline.Rd | 17 - 19 files changed, 655 insertions(+), 458 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between conos versions 1.4.7 dated 2022-09-04 and 1.4.8 dated 2022-09-26
DESCRIPTION | 14 ++-- MD5 | 25 ++++---- NAMESPACE | 2 R/RcppExports.R | 4 + R/communities.R | 1 R/integrations.R | 93 ++++++++++++++++++++++++++++++ README.md | 2 man/Conos.Rd | 90 ++++++++++++++--------------- man/armaCor.Rd |only man/filter.genes.by.cluster.expression.Rd |only man/plotEmbeddings.Rd | 10 --- man/plotSamples.Rd | 10 --- man/velocityInfoConos.Rd |only src/RcppExports.cpp | 12 +++ src/spcov.cpp | 17 +++++ 15 files changed, 198 insertions(+), 82 deletions(-)
Title: Implements the Leiden Algorithm via an R Interface
Description: An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
Author: Peter Kharchenko [aut],
Viktor Petukhov [aut],
V.A. Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Minh Van Nguyen [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between leidenAlg versions 1.0.3 dated 2022-04-11 and 1.0.4 dated 2022-09-25
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 1 - R/communities.R | 1 - man/exampleGraph.Rd | 2 +- src/RcppExports.cpp | 1 - src/leiden.cpp | 5 +++++ src/leidenalg/RBConfigurationVertexPartition.cpp | 5 +++++ 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre],
Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>
Diff between MCM versions 0.1.5 dated 2022-01-04 and 0.1.6 dated 2022-09-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/mcm.R | 41 +++++++++++++++++++++++++++++++++++------ man/mcm.Rd | 8 +++++--- tests/mcm_package_test.R | 1 + 5 files changed, 49 insertions(+), 17 deletions(-)
Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables.
For comparing two independent proportions, performs Barnard's test (1945)
<doi:10.1038/156177a0> using the original CSM test (Barnard, 1947 <doi:10.1093/biomet/34.1-2.123>),
using Fisher's p-value referred to as Boschloo's test (1970) <doi:10.1111/j.1467-9574.1970.tb00104.x>,
or using a Z-statistic (Suissa and Shuster, 1985, <doi:10.2307/2981892>).
For comparing two binary proportions, performs unconditional exact test using McNemar's
Z-statistic (Berger and Sidik, 2003, <doi:10.1191/0962280203sm312ra>),
using McNemar's conditional p-value, using McNemar's Z-statistic with continuity correction,
or using CSM test. Calculates confidence intervals for the difference in proportion.
This package interacts with pre-computed data available through the ExactData R package,
which is available in a 'drat' repository.
Install the ExactData R package from GitHub at <https://pcal [...truncated...]
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between Exact versions 3.1 dated 2021-11-26 and 3.2 dated 2022-09-25
Exact-3.1/Exact/R/multinomialCode.R |only Exact-3.2/Exact/DESCRIPTION | 8 +++---- Exact-3.2/Exact/MD5 | 31 ++++++++++++++++-------------- Exact-3.2/Exact/NAMESPACE | 2 - Exact-3.2/Exact/R/binomialCode.R | 6 +++-- Exact-3.2/Exact/R/checkParam.R | 5 ++++ Exact-3.2/Exact/R/confInt.R | 6 +++-- Exact-3.2/Exact/R/exact.reject.region.R | 2 - Exact-3.2/Exact/R/exact.test.R | 2 - Exact-3.2/Exact/R/maxPvalueMultinom.R |only Exact-3.2/Exact/R/moreExtreme.R | 10 ++++----- Exact-3.2/Exact/R/multinom.R |only Exact-3.2/Exact/R/multinomCode.R |only Exact-3.2/Exact/R/searchMaxProbMultinom.R |only Exact-3.2/Exact/R/zunpooled_TX.R | 4 +-- Exact-3.2/Exact/build/partial.rdb |binary Exact-3.2/Exact/inst/NEWS.Rd | 9 ++++++++ Exact-3.2/Exact/man/Exact-package.Rd | 2 + Exact-3.2/Exact/man/exact.test.Rd | 4 +-- 19 files changed, 57 insertions(+), 34 deletions(-)
Title: The CDK Libraries Packaged for R
Description: An R interface to the Chemistry Development Kit, a Java library
for chemoinformatics. Given the size of the library itself, this package is
not expected to change very frequently. To make use of the CDK within R, it is
suggested that you use the 'rcdk' package. Note that it is possible to directly
interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more
idiomatic way. The CDK library itself is released as LGPL and the sources can be
obtained from <https://github.com/cdk/cdk>.
Author: Rajarshi Guha [aut],
Zachary Charlop-Powers [cre],
CDK Project [ctb, cph]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdklibs versions 2.3 dated 2020-03-08 and 2.8 dated 2022-09-25
rcdklibs-2.3/rcdklibs/NEWS |only rcdklibs-2.3/rcdklibs/inst/cont/cdk-2.3.jar |only rcdklibs-2.8/rcdklibs/DESCRIPTION | 12 - rcdklibs-2.8/rcdklibs/MD5 | 97 +++++++++- rcdklibs-2.8/rcdklibs/NEWS.md |only rcdklibs-2.8/rcdklibs/README.md |only rcdklibs-2.8/rcdklibs/inst/cont/beam-core-1.3.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/beam-func-1.3.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-atomtype-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-charges-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-cip-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-control-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-core-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-ctab-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-data-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-datadebug-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-depict-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-dict-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-diff-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-extra-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-fingerprint-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-forcefield-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-formula-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-fragment-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-group-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-hash-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-inchi-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-interfaces-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-io-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-ioformats-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-ionpot-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-isomorphism-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-jniinchi-support-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-legacy-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-libiocml-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-libiomd-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-model-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-pcore-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-pdb-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-pdbcml-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsar-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsaratomic-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarbond-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarcml-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarionpot-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarmolecular-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-qsarprotein-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-reaction-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-render-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-renderawt-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-renderbasic-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-renderextra-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-sdg-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-signature-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-silent-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-smarts-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-smiles-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-standard-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-structgen-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-tautomer-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cdk-valencycheck-2.8.jar |only rcdklibs-2.8/rcdklibs/inst/cont/cmlxom-4.3.jar |only rcdklibs-2.8/rcdklibs/inst/cont/commons-io-2.11.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/commons-lang3-3.12.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/commons-math-2.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/euclid-2.3.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-graphics2d-2.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-graphicsbase-2.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-graphicsio-2.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-graphicsio-pdf-2.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-graphicsio-ps-2.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-graphicsio-tests-2.4.jar |only rcdklibs-2.8/rcdklibs/inst/cont/freehep-io-2.2.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jama-1.0.3.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jgrapht-0.6.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-5.10.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-api-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-core-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-darwin-aarch64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-darwin-x86-64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-linux-arm-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-linux-x86-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-linux-x86-64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-win32-x86-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/jna-inchi-win32-x86-64-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/joda-time-2.11.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/log4j-1.2-api-2.18.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/log4j-api-2.18.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/log4j-core-2.18.0.jar |only rcdklibs-2.8/rcdklibs/inst/cont/serializer-2.7.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/signatures-1.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/tagsoup-1.2.1.jar |only rcdklibs-2.8/rcdklibs/inst/cont/vecmath-1.5.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xalan-2.7.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xercesImpl-2.12.2.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xml-apis-1.4.01.jar |only rcdklibs-2.8/rcdklibs/inst/cont/xom-1.3.7.jar |only 97 files changed, 100 insertions(+), 9 deletions(-)
Title: Interface to the 'Open Science Framework' ('OSF')
Description: An interface for interacting with 'OSF' (<https://osf.io>). 'osfr'
enables you to access open research materials and data, or create and
manage your own private or public projects.
Author: Aaron Wolen [aut, cre] ,
Chris Hartgerink [aut] ,
Timothy York [ctb] ,
Ryan Hafen [ctb],
Brian Richards [ctb],
Courtney Soderberg [ctb] ,
Carl Boettiger [rev] ,
Heidi Seibold [rev]
Maintainer: Aaron Wolen <aaron@wolen.com>
Diff between osfr versions 0.2.8 dated 2020-02-17 and 0.2.9 dated 2022-09-25
DESCRIPTION | 21 - MD5 | 145 +++++-- NAMESPACE | 1 NEWS.md | 24 + R/osf_auth.R | 2 R/osf_create.R | 4 R/osf_download.R | 77 +-- R/osf_retrieve.R | 2 R/osf_tbl.R | 2 R/osf_upload.R | 12 R/osfr-package.R | 2 R/utils-accessors.R | 14 R/utils-wb-files.R | 18 README.md | 93 ++-- build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/auth.html | 165 +++++--- inst/doc/getting_started.Rmd | 104 ++--- inst/doc/getting_started.html | 506 +++++++++++++++---------- man/osf_auth.Rd | 8 man/osf_create.Rd | 4 man/osf_download.Rd | 6 man/osf_retrieve.Rd | 2 man/osf_upload.Rd | 26 - man/osfr-package.Rd | 4 tests/testthat.R | 4 tests/testthat/cassettes |only tests/testthat/helper-vcr.R |only tests/testthat/helpers-test-files.R |only tests/testthat/test-directories.R | 67 ++- tests/testthat/test-downloading.R | 19 tests/testthat/test-files.R | 186 +++++---- tests/testthat/test-html-entity-encoding.R | 24 - tests/testthat/test-nodes.R | 54 ++ tests/testthat/test-uploading-multiple-files.R | 138 ++++-- tests/testthat/test-uploading.R | 86 +++- vignettes/getting_started.Rmd | 104 ++--- vignettes/getting_started.Rmd.orig | 38 - 38 files changed, 1256 insertions(+), 709 deletions(-)
Title: A GraphQL Query Parser
Description: Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL syntax
and exports the AST in JSON format.
Author: Jeroen Ooms [cre, aut],
Barret Schloerke [ctb],
Scott Wolchok [ctb],
Facebook, Inc [aut, cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between graphql versions 1.5 dated 2018-12-01 and 1.5.1 dated 2022-09-25
DESCRIPTION | 10 ++++---- MD5 | 10 ++++---- NEWS | 3 ++ src/RcppExports.cpp | 5 ++++ src/libgraphqlparser/lexer.cpp | 46 ++++++++++++++++++++--------------------- src/libgraphqlparser/lexer.lpp | 6 ++--- 6 files changed, 44 insertions(+), 36 deletions(-)
Title: Bibtex Parser
Description: Utility to parse a bibtex file.
Author: Romain Francois [aut, cph] ,
James Joseph Balamuta [ctb, cre]
,
Diego Hernangomez [aut] ,
Scott Chamberlain [ctb] ,
Kurt Hornik [ctb] ,
Brian Ripley [ctb] ,
Michael Koohafkan [ctb],
Mathew W. McLean [ctb]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between bibtex versions 0.4.2.3 dated 2020-09-19 and 0.5.0 dated 2022-09-25
bibtex-0.4.2.3/bibtex/inst/bibparse.output |only bibtex-0.4.2.3/bibtex/inst/clean-bibtex.R |only bibtex-0.4.2.3/bibtex/inst/grammar |only bibtex-0.4.2.3/bibtex/inst/grammar.output |only bibtex-0.4.2.3/bibtex/inst/include |only bibtex-0.4.2.3/bibtex/inst/objects.output |only bibtex-0.4.2.3/bibtex/src |only bibtex-0.5.0/bibtex/DESCRIPTION | 81 + bibtex-0.5.0/bibtex/MD5 | 76 + bibtex-0.5.0/bibtex/NAMESPACE | 2 bibtex-0.5.0/bibtex/R/bibtex-package.R |only bibtex-0.5.0/bibtex/R/bibtex.R | 563 +++++++------ bibtex-0.5.0/bibtex/R/utils.R |only bibtex-0.5.0/bibtex/R/zzz.R |only bibtex-0.5.0/bibtex/README.md | 38 bibtex-0.5.0/bibtex/inst/bib/issue15.bib |only bibtex-0.5.0/bibtex/inst/bib/issue17.bib |only bibtex-0.5.0/bibtex/inst/bib/issue18.bib |only bibtex-0.5.0/bibtex/inst/bib/issue23.bib |only bibtex-0.5.0/bibtex/inst/bib/issue6.bib |only bibtex-0.5.0/bibtex/inst/bib/issue7.bib |only bibtex-0.5.0/bibtex/inst/bib/issue9.bib |only bibtex-0.5.0/bibtex/inst/bib/multiline_string.bib |only bibtex-0.5.0/bibtex/inst/bib/unable_recover_42.bib |only bibtex-0.5.0/bibtex/inst/bib/unbalanced_braces.bib |only bibtex-0.5.0/bibtex/inst/bib/xampl_message.bib |only bibtex-0.5.0/bibtex/inst/bib/xampl_mod.bib |only bibtex-0.5.0/bibtex/inst/bib/xampl_multiline.bib |only bibtex-0.5.0/bibtex/inst/bib/xampl_preamble.bib |only bibtex-0.5.0/bibtex/inst/bib/xampl_single.bib |only bibtex-0.5.0/bibtex/inst/bib/xampl_standard.bib |only bibtex-0.5.0/bibtex/man/bibtex-package.Rd |only bibtex-0.5.0/bibtex/man/do_read_bib.Rd | 2 bibtex-0.5.0/bibtex/man/read.bib.Rd | 38 bibtex-0.5.0/bibtex/man/write.bib.Rd | 12 bibtex-0.5.0/bibtex/tests/testthat.R | 5 bibtex-0.5.0/bibtex/tests/testthat/_snaps |only bibtex-0.5.0/bibtex/tests/testthat/test-authors.R | 10 bibtex-0.5.0/bibtex/tests/testthat/test-bibtex.R | 64 - bibtex-0.5.0/bibtex/tests/testthat/test-deprecated.R |only bibtex-0.5.0/bibtex/tests/testthat/test-do_read_bib.R |only bibtex-0.5.0/bibtex/tests/testthat/test-examples.R |only bibtex-0.5.0/bibtex/tests/testthat/test-fatal-errors.R |only bibtex-0.5.0/bibtex/tests/testthat/test-full_xampl.R |only bibtex-0.5.0/bibtex/tests/testthat/test-multiline.R |only bibtex-0.5.0/bibtex/tests/testthat/test-preamble.R |only bibtex-0.5.0/bibtex/tests/testthat/test-previous-issues.R |only bibtex-0.5.0/bibtex/tests/testthat/test-read.R |only bibtex-0.5.0/bibtex/tests/testthat/test-standard-entries.R |only bibtex-0.5.0/bibtex/tests/testthat/test-utils.R |only bibtex-0.5.0/bibtex/tests/testthat/test-write.R |only 51 files changed, 557 insertions(+), 334 deletions(-)
Title: TAP-Compliant Unit Testing
Description: Concise TAP <http://testanything.org/> compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut, cre],
Anthony Hennessey [aut]
Maintainer: Jamie Lentin <jm@ravingmantis.com>
Diff between unittest versions 1.5-1 dated 2022-09-07 and 1.5-3 dated 2022-09-25
ChangeLog | 12 ++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README.md | 2 +- build/vignette.rds |binary tests/test_ut_cmp.R | 7 +++++-- 6 files changed, 27 insertions(+), 12 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.4.0 dated 2022-09-08 and 1.4.1 dated 2022-09-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/archive.R | 2 +- R/ichimoku-package.R | 2 +- R/oanda.R | 9 ++++----- src/shikokuchuo.c | 38 +++++++++++++++++++++++++------------- 7 files changed, 46 insertions(+), 29 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 2.2.5 dated 2022-05-10 and 2.2.9 dated 2022-09-25
DESCRIPTION | 8 ++++---- MD5 | 38 ++++++++++++++++++++------------------ R/df2latex.R | 42 ++++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary data/Athenstaedt.rda |binary data/msqR.rda |binary data/zola.rda |only inst/CITATION | 4 ++-- inst/NEWS.Rd | 16 ++++++++++++++-- inst/doc/factor.pdf |binary inst/doc/mediation.pdf |binary inst/doc/omega.pdf |binary inst/doc/overview.pdf |binary man/Athenstaedt.Rd | 9 +++++++-- man/GERAS.Rd | 5 +++-- man/df2latex.Rd | 21 +++++++++++++++++++-- man/eminence.Rd | 2 +- man/msqR.rd | 3 ++- man/read.clipboard.Rd | 36 ++++++++++++++++++++++++++++++++++++ man/zola.Rd |only 21 files changed, 142 insertions(+), 42 deletions(-)
Title: Letter Value 'Boxplots'
Description: Implements the letter value 'boxplot' which extends the
standard 'boxplot' to deal with both larger and smaller number of data
points by dynamically selecting the appropriate number of letter
values to display.
Author: Hadley Wickham [aut, cre],
Heike Hofmann [aut]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between lvplot versions 0.2.0 dated 2016-05-01 and 0.2.1 dated 2022-09-25
lvplot-0.2.0/lvplot/data/datalist |only lvplot-0.2.1/lvplot/DESCRIPTION | 24 +++--- lvplot-0.2.1/lvplot/MD5 | 31 ++++---- lvplot-0.2.1/lvplot/NAMESPACE | 1 lvplot-0.2.1/lvplot/NEWS.md | 11 +++ lvplot-0.2.1/lvplot/R/data.r | 2 lvplot-0.2.1/lvplot/R/geom-lv.r | 34 ++++----- lvplot-0.2.1/lvplot/R/lvplot-package.R |only lvplot-0.2.1/lvplot/R/stat-lv.r | 1 lvplot-0.2.1/lvplot/README.md | 11 +-- lvplot-0.2.1/lvplot/man/LVboxplot.Rd | 42 +++++++++--- lvplot-0.2.1/lvplot/man/census.Rd | 7 +- lvplot-0.2.1/lvplot/man/determineDepth.Rd | 1 lvplot-0.2.1/lvplot/man/drawLVplot.Rd | 17 ++++ lvplot-0.2.1/lvplot/man/geom_lv.Rd | 105 +++++++++++++++++++----------- lvplot-0.2.1/lvplot/man/lvplot-package.Rd |only lvplot-0.2.1/lvplot/man/lvtable.Rd | 1 lvplot-0.2.1/lvplot/man/ontime.Rd | 9 +- 18 files changed, 185 insertions(+), 112 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr2 versions 0.2.1 dated 2022-05-10 and 0.2.2 dated 2022-09-25
DESCRIPTION | 8 +- MD5 | 50 ++++++------- NEWS.md | 21 +++++ R/curl.R | 2 R/oauth-flow-device.R | 2 R/oauth-flow-refresh.R | 10 +- R/oauth-token.R | 5 + R/oauth.R | 2 R/parse.R | 6 + R/req-options.R | 3 R/req-url.R | 5 - R/url.R | 12 ++- README.md | 61 +++++++-------- build/vignette.rds |binary inst/doc/httr2.html | 146 +++++++++++++++++++------------------- man/oauth_flow_refresh.Rd | 4 - man/req_body.Rd | 4 - man/req_oauth_refresh.Rd | 6 - man/req_options.Rd | 1 man/req_url.Rd | 9 +- man/url_parse.Rd | 2 tests/testthat/test-curl.R | 7 + tests/testthat/test-parse.R | 2 tests/testthat/test-req-options.R | 6 + tests/testthat/test-req-url.R | 5 + tests/testthat/test-url.R | 4 + 26 files changed, 223 insertions(+), 160 deletions(-)
Title: 'GLCM' Texture Features
Description: Two 'Gray Level Co-occurrence Matrix' ('GLCM') implementations are included: The first is a fast 'GLCM' feature texture computation based on 'Python' 'Numpy' arrays ('Github' Repository, <https://github.com/tzm030329/GLCM>). The second is a fast 'GLCM' 'RcppArmadillo' implementation which is parallelized (using 'OpenMP') with the option to return all 'GLCM' features at once. For more information, see "Artifact-Free Thin Cloud Removal Using Gans" by Toizumi Takahiro, Zini Simone, Sagi Kazutoshi, Kaneko Eiji, Tsukada Masato, Schettini Raimondo (2019), IEEE International Conference on Image Processing (ICIP), pp. 3596-3600, <doi:10.1109/ICIP.2019.8803652>.
Author: Lampros Mouselimis [aut, cre] ,
Takahiro Toizumi [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fastGLCM versions 1.0.1 dated 2022-09-04 and 1.0.2 dated 2022-09-25
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 5 +++++ README.md | 2 +- inst/doc/fastGLCM_Functionality.html | 13 ++++++++++--- man/fastglcm.Rd | 18 +++++++++--------- src/fastglcm.cpp | 2 +- 7 files changed, 37 insertions(+), 25 deletions(-)
Title: Import Public Health Ontario's Ontario Marginalization Index
Description: The Ontario Marginalization Index is a socioeconomic model that is built on Statistics Canada census data.
The model consists of four dimensions: Residential Instability, Material Deprivation, Dependency and Ethnic Concentration.
Each of these dimensions are imported for a variety of geographic levels (DA, CD, etc.) for both the 2011 and 2016 administrations of the census (2021 pending).
These data sets contribute to community analysis of equity with respect to Ontario's Anti-Racism Act.
The Ontario Marginalization Index data is retrieved from the Public Health Ontario website: <https://www.publichealthontario.ca/en/data-and-analysis/health-equity/ontario-marginalization-index>.
The shapefile data is retrieved from the Statistics Canada website: <https://www12.statcan.gc.ca/census-recensement/2011/geo/bound-limit/bound-limit-eng.cfm>.
Author: William Conley [aut, cre]
Maintainer: William Conley <william@cconley.ca>
Diff between onmaRg versions 0.1.1 dated 2022-09-18 and 0.1.2 dated 2022-09-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/om_geo.R | 2 +- inst/doc/demo.R | 1 - inst/doc/demo.Rmd | 1 - man/om_geo.Rd | 2 +- vignettes/demo.Rmd | 1 - 7 files changed, 11 insertions(+), 14 deletions(-)
Title: Download 'nflverse' Data
Description: A minimal package for downloading data from 'GitHub'
repositories of the 'nflverse' project.
Author: Tan Ho [aut, cre, cph] ,
Sebastian Carl [aut],
John Edwards [ctb],
Ben Baldwin [ctb],
Thomas Mock [ctb],
Lee Sharpe [ctb],
Pranav Rajaram [ctb]
Maintainer: Tan Ho <tan@tanho.ca>
Diff between nflreadr versions 1.3.0 dated 2022-08-06 and 1.3.1 dated 2022-09-25
DESCRIPTION | 12 ++-- MD5 | 89 +++++++++++++++--------------- NAMESPACE | 4 - NEWS.md | 30 +++++++++- R/from_url.R | 52 +---------------- R/load_participation.R | 10 ++- R/load_pbp.R | 2 R/load_pfr_advstats.R | 2 R/load_player_stats.R | 2 R/load_snap_counts.R | 8 +- R/load_teams.R | 4 - R/utils.R | 7 +- R/utils_date.R | 9 +++ R/utils_download_nflverse.R | 26 +++++--- R/utils_gameid.R |only R/utils_name_cleaning.R | 23 ++++--- R/utils_progressively.R |only data/player_name_mapping.rda |binary inst/doc/dictionary_espn_qbr.html | 4 - inst/doc/dictionary_ff_opportunity.html | 4 - inst/doc/dictionary_pbp.html | 4 - inst/doc/dictionary_player_stats.html | 4 - inst/doc/dictionary_rosters.html | 4 - inst/doc/dictionary_schedules.html | 4 - inst/doc/exporting_nflreadr.R | 2 inst/doc/exporting_nflreadr.Rmd | 2 inst/doc/exporting_nflreadr.html | 2 man/clean_player_names.Rd | 2 man/csv_from_url.Rd | 2 man/get_current_week.Rd | 5 + man/latest_season.Rd | 3 + man/load_pbp.Rd | 2 man/load_pfr_passing.Rd | 2 man/load_player_stats.Rd | 2 man/load_snap_counts.Rd | 4 - man/load_teams.Rd | 2 man/nflverse_download.Rd | 5 + man/nflverse_game_id.Rd |only man/nflverse_releases.Rd | 5 + man/progressively.Rd | 18 +++--- man/raw_from_url.Rd | 4 + man/rds_from_url.Rd | 2 tests/testthat/test-from_url.R | 16 +++-- tests/testthat/test-nflverse.R | 42 +++++++++++++- tests/testthat/test-utils_date.R | 4 + tests/testthat/test-utils_name_cleaning.R | 2 vignettes/exporting_nflreadr.Rmd | 2 47 files changed, 254 insertions(+), 180 deletions(-)
Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google
Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>
Diff between ngramr versions 1.8.2 dated 2022-09-20 and 1.8.3 dated 2022-09-25
DESCRIPTION | 6 +- MD5 | 14 ++-- NEWS.md | 6 +- R/ggram.R | 4 + R/ngram.R | 127 +++++++++++++++++++++++++++++++------------ R/ngramw.R | 1 man/ngram.Rd | 7 +- tests/testthat/test-ngramr.R | 1 8 files changed, 119 insertions(+), 47 deletions(-)
Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://activinsights.com/technology/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing.
Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut],
Aimee Gott [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre],
Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@springhead-data.com>
Diff between GENEAclassify versions 1.5.2 dated 2021-01-05 and 1.5.3 dated 2022-09-25
GENEAclassify-1.5.2/GENEAclassify/inst/vignettes |only GENEAclassify-1.5.3/GENEAclassify/DESCRIPTION | 12 GENEAclassify-1.5.3/GENEAclassify/MD5 | 61 GENEAclassify-1.5.3/GENEAclassify/NAMESPACE | 1 GENEAclassify-1.5.3/GENEAclassify/R/changeTimes.R | 1 GENEAclassify-1.5.3/GENEAclassify/R/classifyGENEA.R | 5 GENEAclassify-1.5.3/GENEAclassify/R/getGENEAsegments.R | 15 GENEAclassify-1.5.3/GENEAclassify/R/segmentation.R | 128 - GENEAclassify-1.5.3/GENEAclassify/R/statistics.R | 39 GENEAclassify-1.5.3/GENEAclassify/R/stepCounter.R | 50 GENEAclassify-1.5.3/GENEAclassify/build/vignette.rds |binary GENEAclassify-1.5.3/GENEAclassify/inst/doc/GENEAclassifyDemo.html | 727 ++++++---- GENEAclassify-1.5.3/GENEAclassify/inst/doc/GENEAclassifyDemo.rmd | 6 GENEAclassify-1.5.3/GENEAclassify/man/CirDisp.Rd | 48 GENEAclassify-1.5.3/GENEAclassify/man/CirKurt.Rd | 48 GENEAclassify-1.5.3/GENEAclassify/man/CirSD.Rd | 48 GENEAclassify-1.5.3/GENEAclassify/man/CirSkew.Rd | 48 GENEAclassify-1.5.3/GENEAclassify/man/CirVar.Rd | 48 GENEAclassify-1.5.3/GENEAclassify/man/GENEAclassify-package.Rd | 32 GENEAclassify-1.5.3/GENEAclassify/man/GENEAcount.Rd | 52 GENEAclassify-1.5.3/GENEAclassify/man/GENEAskew.Rd | 17 GENEAclassify-1.5.3/GENEAclassify/man/MeanDir.Rd | 48 GENEAclassify-1.5.3/GENEAclassify/man/classifyGENEA.Rd | 3 GENEAclassify-1.5.3/GENEAclassify/man/createGENEAmodel.Rd | 3 GENEAclassify-1.5.3/GENEAclassify/man/getGENEAsegments.Rd | 7 GENEAclassify-1.5.3/GENEAclassify/man/impact.Rd | 50 GENEAclassify-1.5.3/GENEAclassify/man/radians.Rd | 56 GENEAclassify-1.5.3/GENEAclassify/man/segmentation.Rd | 7 GENEAclassify-1.5.3/GENEAclassify/man/sod.Rd |only GENEAclassify-1.5.3/GENEAclassify/man/stepCounter.Rd | 6 GENEAclassify-1.5.3/GENEAclassify/man/sumdiff.Rd | 1 GENEAclassify-1.5.3/GENEAclassify/vignettes/GENEAclassifyDemo.rmd | 6 32 files changed, 911 insertions(+), 662 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.50 dated 2022-07-01 and 2.0.52 dated 2022-09-25
DESCRIPTION | 8 - MD5 | 20 +-- NEWS | 18 ++ R/epi.2by2.R | 2 R/zRRscore.R | 190 ++++++++++++++++------------- build/vignette.rds |binary inst/doc/epiR_descriptive.html | 34 ++--- inst/doc/epiR_measures_of_association.html | 56 ++++---- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 64 ++++----- man/epi.2by2.Rd | 10 + 11 files changed, 230 insertions(+), 176 deletions(-)
Title: Event Detection Using Confidence Bounds
Description: Detects sustained change in digital bio-marker data using
simultaneous confidence bands. Accounts for noise using an auto-regressive
model. Based on Buehlmann (1998) "Sieve bootstrap for smoothing in
nonstationary time series" <doi:10.1214/aos/1030563978>.
Author: Zheng Chen Man [aut, cre]
Maintainer: Zheng Chen Man <zheng.chen.man@alumni.ethz.ch>
Diff between edecob versions 1.1.0 dated 2022-05-27 and 1.2.0 dated 2022-09-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/edecob.R | 27 +++++++++++++-------------- man/bt_smoother.Rd | 4 ++-- man/detect_event.Rd | 2 +- man/edecob.Rd | 25 ++++++++++++------------- 6 files changed, 36 insertions(+), 38 deletions(-)
Title: Google's Compact Language Detector 2
Description: Bindings to Google's C++ library Compact Language Detector 2
(see <https://github.com/cld2owners/cld2#readme> for more information). Probabilistically
detects over 80 languages in plain text or HTML. For mixed-language input it returns the
top three detected languages and their approximate proportion of the total classified
text bytes (e.g. 80% English and 20% French out of 1000 bytes). There is also a 'cld3'
package on CRAN which uses a neural network model instead.
Author: Jeroen Ooms [aut, cre] ,
Dirk Sites [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between cld2 versions 1.2.1 dated 2020-12-15 and 1.2.2 dated 2022-09-25
DESCRIPTION | 7 +++---- MD5 | 8 ++++---- NEWS | 3 +++ src/RcppExports.cpp | 5 +++++ src/libcld2/internal/scoreonescriptspan.h | 12 ++++++------ 5 files changed, 21 insertions(+), 14 deletions(-)
Title: Analyse Biological Time-Series Data
Description: Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007&g [...truncated...]
Author: Lakshman Abhilash [aut, cre]
Maintainer: Lakshman Abhilash <labhilash@gc.cuny.edu>
Diff between phase versions 1.2.1 dated 2021-08-16 and 1.2.2 dated 2022-09-25
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 2 R/CoM.R | 65 +++-------- R/peakIdentifier.R | 65 +++++++---- R/sleepData.R | 125 ++++++++++++++++------ R/sleepStat.R | 275 ++++++++++++++++++++------------------------------ man/CoM.Rd | 2 man/peakIdentifier.Rd | 6 - man/sleepStat.Rd | 14 +- 10 files changed, 294 insertions(+), 284 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.10-0 dated 2022-06-21 and 2.11 dated 2022-09-25
DESCRIPTION | 16 +--- MD5 | 50 +++++++------- R/importAURNCsv.R | 29 +------- R/importTraj.R | 6 - R/importUKAQ.R | 23 ++++-- R/polarPlot.R | 3 R/quickText.R | 6 - R/summaryPlot.R | 14 +++- R/timeAverage.R | 6 - R/timePlot.R | 1 R/timeProp.R | 154 ++++++++++++-------------------------------- R/timeVariation.R | 24 +++++- R/trajCluster.R | 14 ++-- R/trajLevel.R | 44 ++++++++---- R/windRose.R | 12 ++- README.md | 86 ++++++++++++------------ man/importAURN.Rd | 10 +- man/importAURNCsv.Rd | 27 +------ man/importTraj.Rd | 6 - man/timeProp.Rd | 11 --- man/timeVariation.Rd | 5 + man/trajCluster.Rd | 2 man/trajLevel.Rd | 7 ++ man/windRose.Rd | 8 ++ tools/unnamed-chunk-6-1.png |binary tools/unnamed-chunk-7-1.png |binary 26 files changed, 260 insertions(+), 304 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to easily manipulate, clean, transform,
and prepare your data for analysis. It also forms the data wrangling
backend for the packages in the 'easystats' ecosystem.
Author: Indrajeet Patil [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Etienne Bacher [aut] ,
Remi Theriault [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between datawizard versions 0.6.0 dated 2022-09-15 and 0.6.1 dated 2022-09-25
datawizard-0.6.0/datawizard/R/backports.R |only datawizard-0.6.1/datawizard/DESCRIPTION | 10 - datawizard-0.6.1/datawizard/MD5 | 87 ++++++------- datawizard-0.6.1/datawizard/NAMESPACE | 2 datawizard-0.6.1/datawizard/NEWS.md | 4 datawizard-0.6.1/datawizard/R/adjust.R | 4 datawizard-0.6.1/datawizard/R/categorize.R | 20 +- datawizard-0.6.1/datawizard/R/center.R | 4 datawizard-0.6.1/datawizard/R/convert_na_to.R | 16 +- datawizard-0.6.1/datawizard/R/convert_to_na.R | 20 +- datawizard-0.6.1/datawizard/R/data_arrange.R | 4 datawizard-0.6.1/datawizard/R/data_find.R | 4 datawizard-0.6.1/datawizard/R/data_match.R | 16 +- datawizard-0.6.1/datawizard/R/data_merge.R | 30 +--- datawizard-0.6.1/datawizard/R/data_partition.R | 17 +- datawizard-0.6.1/datawizard/R/data_rename.R | 8 - datawizard-0.6.1/datawizard/R/data_rescale.R | 8 - datawizard-0.6.1/datawizard/R/data_reshape.R | 24 +-- datawizard-0.6.1/datawizard/R/data_reverse.R | 4 datawizard-0.6.1/datawizard/R/data_rotate.R | 2 datawizard-0.6.1/datawizard/R/data_select.R | 2 datawizard-0.6.1/datawizard/R/demean.R | 12 - datawizard-0.6.1/datawizard/R/describe_distribution.R | 5 datawizard-0.6.1/datawizard/R/descriptives.R | 30 ++-- datawizard-0.6.1/datawizard/R/normalize.R | 8 - datawizard-0.6.1/datawizard/R/recode_values.R | 8 - datawizard-0.6.1/datawizard/R/rescale_weights.R | 13 - datawizard-0.6.1/datawizard/R/select_helpers.R | 24 +-- datawizard-0.6.1/datawizard/R/skewness_kurtosis.R | 21 --- datawizard-0.6.1/datawizard/R/slide.R | 4 datawizard-0.6.1/datawizard/R/standardize.R | 2 datawizard-0.6.1/datawizard/R/standardize.models.R | 73 +++------- datawizard-0.6.1/datawizard/R/to_factor.R | 4 datawizard-0.6.1/datawizard/R/to_numeric.R | 23 ++- datawizard-0.6.1/datawizard/R/unnormalize.R | 2 datawizard-0.6.1/datawizard/R/utils.R | 4 datawizard-0.6.1/datawizard/R/utils_data.R | 30 +--- datawizard-0.6.1/datawizard/R/utils_standardize_center.R | 28 ++-- datawizard-0.6.1/datawizard/R/winsorize.R | 23 +-- datawizard-0.6.1/datawizard/README.md | 7 + datawizard-0.6.1/datawizard/inst/doc/selection_syntax.R | 2 datawizard-0.6.1/datawizard/inst/doc/selection_syntax.Rmd | 2 datawizard-0.6.1/datawizard/inst/doc/selection_syntax.html | 2 datawizard-0.6.1/datawizard/tests/testthat.R | 7 + datawizard-0.6.1/datawizard/vignettes/selection_syntax.Rmd | 2 45 files changed, 294 insertions(+), 328 deletions(-)
Title: Meta-Analysis of Diagnosis and Prognosis Research Studies
Description: Facilitate frequentist and Bayesian meta-analysis of diagnosis and prognosis research studies. It includes functions to summarize multiple estimates of prediction model discrimination and calibration performance (Debray et al., 2019) <doi:10.1177/0962280218785504>. It also includes functions to evaluate funnel plot asymmetry (Debray et al., 2018) <doi:10.1002/jrsm.1266>. Finally, the package provides functions for developing multivariable prediction models from datasets with clustering (de Jong et al., 2021) <doi:10.1002/sim.8981>.
Author: Thomas Debray [aut, cre] ,
Valentijn de Jong [aut]
Maintainer: Thomas Debray <thomas.debray@gmail.com>
Diff between metamisc versions 0.2.5 dated 2021-09-20 and 0.4.0 dated 2022-09-25
DESCRIPTION | 18 +-- MD5 | 69 +++++++-------- NEWS.md |only R/basics.r | 8 - R/bugs_utils.r | 36 +++++-- R/ccalc.r | 5 - R/fat.r | 70 +++++++-------- R/metapred.R | 4 R/metapred_recal.R | 12 +- R/metapred_utils.R | 17 +++ R/oecalc.R | 2 R/uvmeta.r | 36 ++++--- R/valmeta.r | 151 ++++++++++++++++++++------------- README.md |only build |only data/Collins.rda |binary data/DVTipd.rda |binary data/DVTmodels.rda |binary data/Daniels.rda |binary data/EuroSCORE.rda |binary data/Fibrinogen.rda |binary data/Framingham.rda |binary data/Kertai.rda |binary data/Roberts.rda |binary data/Scheidler.rda |binary data/Zhang.rda |binary data/impact.rda |binary man/ccalc.Rd | 3 man/fat.Rd | 70 +++++++-------- man/metamisc-package.Rd | 4 man/uvmeta.Rd | 35 ++++--- man/valmeta.Rd | 151 ++++++++++++++++++++------------- tests/testthat/Rplots.pdf |binary tests/testthat/test_formula.R | 31 +++--- tests/testthat/test_metapred_1_utils.R | 20 ++++ tests/testthat/test_metapred_2_fit.R | 53 ++++++++++- tests/testthat/test_valmeta_6_plots.R | 19 ++-- 37 files changed, 504 insertions(+), 310 deletions(-)
Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre]
,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between WDI versions 2.7.7 dated 2022-07-16 and 2.7.8 dated 2022-09-25
DESCRIPTION | 12 +-- MD5 | 16 ++-- NAMESPACE | 1 NEWS.md | 5 + R/WDI.R | 149 +++++++++++++++++++++++---------------------- data/WDI_data.RData |binary man/WDI.Rd | 4 - man/wdi.query.Rd | 4 - tests/testthat/test-main.R | 25 +++---- 9 files changed, 112 insertions(+), 104 deletions(-)
Title: Import Data from Our World in Data
Description: Search and download the data used in over 3,000 Our World in Data charts.
Author: Piers York
Maintainer: Piers York <piersyork@gmail.com>
Diff between owidR versions 1.3.1 dated 2022-08-07 and 1.4.0 dated 2022-09-25
owidR-1.3.1/owidR/inst/images/map-1.png |only owidR-1.3.1/owidR/inst/images/owid_plot-1.png |only owidR-1.3.1/owidR/inst/images/owid_plot2-1.png |only owidR-1.4.0/owidR/DESCRIPTION | 17 +-- owidR-1.4.0/owidR/MD5 | 38 ++++--- owidR-1.4.0/owidR/NAMESPACE | 1 owidR-1.4.0/owidR/NEWS.md | 4 owidR-1.4.0/owidR/R/owidR-package.R |only owidR-1.4.0/owidR/R/owid_map.R | 20 ++- owidR-1.4.0/owidR/R/owid_plot.R | 32 +++-- owidR-1.4.0/owidR/R/theme_owid.R | 52 +++------ owidR-1.4.0/owidR/README.md | 51 ++------- owidR-1.4.0/owidR/inst/doc/example-analysis.html | 123 ++++++++++++----------- owidR-1.4.0/owidR/inst/images/plot-1.png |only owidR-1.4.0/owidR/man/figures |only owidR-1.4.0/owidR/man/owidR-package.Rd |only owidR-1.4.0/owidR/man/owid_map.Rd | 11 -- owidR-1.4.0/owidR/man/owid_plot.Rd | 27 ++--- owidR-1.4.0/owidR/man/scale_owid.Rd | 38 ------- owidR-1.4.0/owidR/man/theme_owid.Rd | 4 20 files changed, 196 insertions(+), 222 deletions(-)
Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Description: Compute and plot adjusted predictions, contrasts, marginal effects, and marginal means for over 65 classes of statistical models in R. Conduct linear and non-linear hypothesis tests using the delta method.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Marcio Augusto Diniz [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.7.0 dated 2022-08-06 and 0.7.1 dated 2022-09-25
marginaleffects-0.7.0/marginaleffects/inst/doc/elasticity.R |only marginaleffects-0.7.0/marginaleffects/inst/doc/elasticity.Rmd |only marginaleffects-0.7.0/marginaleffects/inst/doc/elasticity.html |only marginaleffects-0.7.0/marginaleffects/vignettes/elasticity.Rmd |only marginaleffects-0.7.1/marginaleffects/DESCRIPTION | 70 +- marginaleffects-0.7.1/marginaleffects/MD5 | 251 +++---- marginaleffects-0.7.1/marginaleffects/NAMESPACE | 6 marginaleffects-0.7.1/marginaleffects/NEWS.md | 21 marginaleffects-0.7.1/marginaleffects/R/backtransform.R | 11 marginaleffects-0.7.1/marginaleffects/R/by.R |only marginaleffects-0.7.1/marginaleffects/R/comparisons.R | 100 +- marginaleffects-0.7.1/marginaleffects/R/datagrid.R | 17 marginaleffects-0.7.1/marginaleffects/R/deltamethod.R | 3 marginaleffects-0.7.1/marginaleffects/R/find_categorical.R | 6 marginaleffects-0.7.1/marginaleffects/R/get_coef.R | 2 marginaleffects-0.7.1/marginaleffects/R/get_contrast_data.R | 9 marginaleffects-0.7.1/marginaleffects/R/get_contrast_data_character.R | 6 marginaleffects-0.7.1/marginaleffects/R/get_contrast_data_numeric.R | 21 marginaleffects-0.7.1/marginaleffects/R/get_contrasts.R | 312 ++++----- marginaleffects-0.7.1/marginaleffects/R/get_hypothesis.R | 235 +++++- marginaleffects-0.7.1/marginaleffects/R/get_se_delta.R | 8 marginaleffects-0.7.1/marginaleffects/R/get_vcov.R | 4 marginaleffects-0.7.1/marginaleffects/R/glance.R | 6 marginaleffects-0.7.1/marginaleffects/R/marginaleffects.R | 27 marginaleffects-0.7.1/marginaleffects/R/marginalmeans.R | 171 ++++ marginaleffects-0.7.1/marginaleffects/R/methods_MASS.R | 4 marginaleffects-0.7.1/marginaleffects/R/methods_aod.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_betareg.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_brms.R | 6 marginaleffects-0.7.1/marginaleffects/R/methods_crch.R | 4 marginaleffects-0.7.1/marginaleffects/R/methods_fixest.R | 53 + marginaleffects-0.7.1/marginaleffects/R/methods_gamlss.R |only marginaleffects-0.7.1/marginaleffects/R/methods_glmmTMB.R | 64 + marginaleffects-0.7.1/marginaleffects/R/methods_glmx.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_lme4.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_mclogit.R | 9 marginaleffects-0.7.1/marginaleffects/R/methods_nnet.R | 46 + marginaleffects-0.7.1/marginaleffects/R/methods_pscl.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_robustlmm.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_sampleSelection.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_scam.R | 2 marginaleffects-0.7.1/marginaleffects/R/methods_stats.R | 4 marginaleffects-0.7.1/marginaleffects/R/methods_survival.R | 2 marginaleffects-0.7.1/marginaleffects/R/modelarchive.R |only marginaleffects-0.7.1/marginaleffects/R/package.R | 69 +- marginaleffects-0.7.1/marginaleffects/R/plot.R | 1 marginaleffects-0.7.1/marginaleffects/R/plot_cap.R | 8 marginaleffects-0.7.1/marginaleffects/R/plot_cco.R | 5 marginaleffects-0.7.1/marginaleffects/R/plot_cme.R | 31 marginaleffects-0.7.1/marginaleffects/R/posteriordraws.R | 59 + marginaleffects-0.7.1/marginaleffects/R/predictions.R | 285 ++++---- marginaleffects-0.7.1/marginaleffects/R/sanitize_hypothesis.R | 2 marginaleffects-0.7.1/marginaleffects/R/sanitize_newdata.R | 61 + marginaleffects-0.7.1/marginaleffects/R/sanitize_transform_pre.R | 28 marginaleffects-0.7.1/marginaleffects/R/sanitize_type.R | 14 marginaleffects-0.7.1/marginaleffects/R/sanitize_variables.R | 19 marginaleffects-0.7.1/marginaleffects/R/sanity_by.R |only marginaleffects-0.7.1/marginaleffects/R/sanity_dots.R | 3 marginaleffects-0.7.1/marginaleffects/R/sanity_model.R | 34 marginaleffects-0.7.1/marginaleffects/R/set_coef.R | 4 marginaleffects-0.7.1/marginaleffects/R/summary.R | 24 marginaleffects-0.7.1/marginaleffects/R/tidy.R | 323 --------- marginaleffects-0.7.1/marginaleffects/R/tidy.comparisons.R |only marginaleffects-0.7.1/marginaleffects/R/tidy.predictions.R |only marginaleffects-0.7.1/marginaleffects/R/type_dictionary.R | 27 marginaleffects-0.7.1/marginaleffects/README.md | 122 +-- marginaleffects-0.7.1/marginaleffects/build/vignette.rds |binary marginaleffects-0.7.1/marginaleffects/inst/COPYRIGHTS | 10 marginaleffects-0.7.1/marginaleffects/inst/WORDLIST | 58 + marginaleffects-0.7.1/marginaleffects/inst/doc/documentation.Rmd | 6 marginaleffects-0.7.1/marginaleffects/inst/doc/documentation.html | 8 marginaleffects-0.7.1/marginaleffects/inst/tinytest/helpers.R | 10 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-by.R | 58 + marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-comparisons-interaction.R | 2 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-contrast.R | 2 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-counterfactual.R | 2 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-datagrid.R | 1 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-hypothesis.R | 21 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-interaction.R | 21 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-marginalmeans.R | 47 - marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-newdata.R | 1 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-betareg.R | 7 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-brms.R | 246 +++++-- marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-fixest.R | 95 ++ marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-gamlss.R |only marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-glmmTMB.R | 50 + marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-mclogit.R | 42 + marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-mgcv.R | 18 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-nnet.R | 42 + marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-ordinal.R | 18 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-quantreg.R | 2 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-rstanarm.R | 1 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-pkg-stats.R | 8 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-plot_cap.R | 12 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-predictions.R | 28 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-transform_pre.R | 12 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-typical.R | 4 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-variables.R | 4 marginaleffects-0.7.1/marginaleffects/inst/tinytest/test-weights.R | 26 marginaleffects-0.7.1/marginaleffects/man/comparisons.Rd | 56 + marginaleffects-0.7.1/marginaleffects/man/datagrid.Rd | 5 marginaleffects-0.7.1/marginaleffects/man/datagridcf.Rd | 5 marginaleffects-0.7.1/marginaleffects/man/deltamethod.Rd | 7 marginaleffects-0.7.1/marginaleffects/man/get_coef.Rd | 16 marginaleffects-0.7.1/marginaleffects/man/get_group_names.Rd | 4 marginaleffects-0.7.1/marginaleffects/man/get_predict.Rd | 23 marginaleffects-0.7.1/marginaleffects/man/get_vcov.Rd | 8 marginaleffects-0.7.1/marginaleffects/man/glance.marginaleffects.Rd | 14 marginaleffects-0.7.1/marginaleffects/man/marginaleffects.Rd | 24 marginaleffects-0.7.1/marginaleffects/man/marginalmeans.Rd | 87 +- marginaleffects-0.7.1/marginaleffects/man/meffects.Rd | 24 marginaleffects-0.7.1/marginaleffects/man/plot.marginaleffects.Rd | 7 marginaleffects-0.7.1/marginaleffects/man/plot_cap.Rd | 11 marginaleffects-0.7.1/marginaleffects/man/plot_cco.Rd | 13 marginaleffects-0.7.1/marginaleffects/man/plot_cme.Rd | 11 marginaleffects-0.7.1/marginaleffects/man/predictions.Rd | 88 +- marginaleffects-0.7.1/marginaleffects/man/reexports.Rd | 14 marginaleffects-0.7.1/marginaleffects/man/sanity_model_specific.Rd | 14 marginaleffects-0.7.1/marginaleffects/man/set_coef.Rd | 51 - marginaleffects-0.7.1/marginaleffects/man/summary.comparisons.Rd | 16 marginaleffects-0.7.1/marginaleffects/man/summary.marginaleffects.Rd | 14 marginaleffects-0.7.1/marginaleffects/man/summary.marginalmeans.Rd | 18 marginaleffects-0.7.1/marginaleffects/man/summary.predictions.Rd | 20 marginaleffects-0.7.1/marginaleffects/man/tidy.comparisons.Rd | 18 marginaleffects-0.7.1/marginaleffects/man/tidy.deltamethod.Rd | 14 marginaleffects-0.7.1/marginaleffects/man/tidy.marginaleffects.Rd | 14 marginaleffects-0.7.1/marginaleffects/man/tidy.marginalmeans.Rd | 18 marginaleffects-0.7.1/marginaleffects/man/tidy.predictions.Rd | 20 marginaleffects-0.7.1/marginaleffects/vignettes/contrasts.html |only marginaleffects-0.7.1/marginaleffects/vignettes/documentation.Rmd | 6 marginaleffects-0.7.1/marginaleffects/vignettes/logistic_contrasts.html |only marginaleffects-0.7.1/marginaleffects/vignettes/marginalmeans.html |only marginaleffects-0.7.1/marginaleffects/vignettes/predictions.html | 344 +++++----- marginaleffects-0.7.1/marginaleffects/vignettes/sandwich.html |only 134 files changed, 2876 insertions(+), 1583 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Handling an Inconsistently Coded Categorical Variable in a Panel
Dataset
Description: Unifying of an inconsistently coded categorical variable between two different time points in accordance with a mapping table.
The main rule is to replicate the observation if it could be assign to a few categories.
Then using simple frequencies or statistical methods to approximate probabilities of being assign to each of them.
This procedure was invented and implemented in the paper by (Nasinski, Majchrowska and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>).
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between cat2cat versions 0.4.4 dated 2022-08-31 and 0.4.5 dated 2022-09-25
DESCRIPTION | 6 MD5 | 74 +++--- NEWS.md | 7 R/cat2cat.R | 269 +++++++++++++++++++------ R/cat2cat_agg.R | 28 +- R/cat2cat_utils.R | 130 ++++++++---- R/data.R | 60 ++++- R/lms.R | 30 +- R/mapping.R | 67 ++++-- R/plot_cat2cat.R | 46 +++- R/read_eq.R | 2 inst/doc/cat2cat.R | 104 ++++++--- inst/doc/cat2cat.Rmd | 104 ++++++--- inst/doc/cat2cat.html | 386 +++++++++++++++++++----------------- man/cat2cat.Rd | 105 ++++++--- man/cat2cat_agg.Rd | 13 - man/cat2cat_ml.Rd | 3 man/cat_apply_freq.Rd | 26 +- man/cross_c2c.Rd | 32 +- man/dummy_c2c.Rd | 14 - man/get_freqs.Rd | 22 +- man/get_mappings.Rd | 17 - man/occup.Rd | 21 + man/occup_small.Rd | 23 +- man/plot_c2c.Rd | 12 - man/prune_c2c.Rd | 42 ++- man/resolve_frequencies.Rd | 6 man/summary_c2c.Rd | 30 +- man/trans.Rd | 9 man/validate_cover_cats.Rd | 3 man/verticals2.Rd | 10 tests/testthat.R | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test-cat2cat.R | 148 ++++++++++--- tests/testthat/test-multi-cat2cat.R | 85 ++++++- tests/testthat/test-plot.R | 6 tests/testthat/test-utils.R | 46 +++- vignettes/cat2cat.Rmd | 104 ++++++--- 38 files changed, 1422 insertions(+), 674 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-26 2.2
2015-09-04 2.1
2015-01-13 2.0
2014-10-23 1.1
2014-10-17 1.0
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb],
Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 2.0 dated 2022-09-21 and 2.0.1 dated 2022-09-25
DESCRIPTION | 10 +++++----- MD5 | 41 ++++++++++++++++++++++------------------- NAMESPACE | 4 ++++ NEWS.md | 13 +++++++++++++ R/helpers.R |only README.md | 10 +++++----- data/advantage_details.rda |binary data/advantage_movement.rda |binary data/boot_mapping.rda |binary data/castaway_details.rda |binary data/castaways.rda |binary data/challenge_results.rda |binary data/confessionals.rda |binary data/jury_votes.rda |binary data/season_palettes.rda |binary data/season_summary.rda |binary data/survivor_auction.rda |binary data/tribe_colours.rda |binary data/tribe_mapping.rda |binary data/viewers.rda |binary data/vote_history.rda |binary man/get_castaway_image.Rd |only man/show_palette.Rd |only 23 files changed, 49 insertions(+), 29 deletions(-)
Title: Open Population Capture-Recapture
Description: Non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between openCR versions 2.2.4 dated 2022-07-01 and 2.2.5 dated 2022-09-25
DESCRIPTION | 13 - MD5 | 40 ++-- NAMESPACE | 2 NEWS | 8 R/derived.openCR.r | 5 R/modelAverage.R | 352 +++++++++++++++++++++--------------------- R/ucare.R |only R/utility.R | 5 inst/doc/openCR-vignette.R | 4 inst/doc/openCR-vignette.Rmd | 26 +-- inst/doc/openCR-vignette.pdf |binary man/cumMove.Rd | 10 + man/expected.d.Rd | 8 man/kernel.Rd | 4 man/microtus.Rd | 2 man/movementmodels.Rd | 4 man/openCR-defunct.Rd | 7 man/openCR-package.Rd | 10 - man/pkernel.Rd | 8 man/ucare.Rd |only src/utils.cpp | 2 vignettes/openCR-vignette.Rmd | 26 +-- 22 files changed, 294 insertions(+), 242 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-30 0.9.9
2015-03-24 0.9.7
2015-03-19 0.9.6
Title: Converts 'MultiQC' Reports into Tidy Data Frames
Description: Provides the means to convert 'multiqc_data.json' files,
produced by the wonderful 'MultiQC' tool, into tidy data frames for downstream
analysis in R. This analysis might involve cohort analysis, quality control visualisation,
change-point detection, statistical process control, clustering, or any other
type of quality analysis.
Author: Michael Milton
Maintainer: Michael Milton <michael.r.milton@gmail.com>
Diff between TidyMultiqc versions 1.0.2 dated 2022-02-10 and 1.0.3 dated 2022-09-24
DESCRIPTION | 6 MD5 | 18 NEWS.md | 34 R/multiqc.R | 2 build/vignette.rds |binary inst/doc/TidyMultiqc.Rmd | 4 inst/doc/TidyMultiqc.html | 1489 +++++++++++++++++++++++++++- inst/extdata/general_list/multiqc_data.json | 41 tests/testthat/test-edge-cases.R | 2 vignettes/TidyMultiqc.Rmd | 4 10 files changed, 1552 insertions(+), 48 deletions(-)
Title: Bayesian Mediation Analysis
Description: We perform general mediation analysis in the Bayesian setting using the methods described in Yu and Li (2022, ISBN:9780367365479). With the package, the mediation analysis can be performed on different types of outcomes (e.g., continuous, binary, categorical, or time-to-event), with default or user-defined priors and predictive models. The Bayesian estimates and credible sets of mediation effects are reported as analytic results.
Author: Qingzhao Yu [aut, cre, cph],
Bin Li [aut]
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between BayesianMediationA versions 1.0 dated 2022-08-18 and 1.0.1 dated 2022-09-24
DESCRIPTION | 15 ++++++++++----- MD5 | 24 +++++++++++++++++++++--- build |only inst |only man/BayesianMediationA-package.Rd | 4 +++- man/data_org.Rd | 4 ++-- vignettes |only 7 files changed, 36 insertions(+), 11 deletions(-)
More information about BayesianMediationA at CRAN
Permanent link
Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP,
setup a secure tunnel, or run a command or script on the host while
streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between ssh versions 0.8.0 dated 2021-05-03 and 0.8.1 dated 2022-09-24
DESCRIPTION | 6 MD5 | 18 NEWS | 3 R/connect.R | 2 build/vignette.rds |binary configure | 2 inst/doc/intro.html | 1526 +++++++++++++++++++++++++++++++++++++++++++++++----- src/myssh.h | 10 src/scp.c | 2 src/tunnel.c | 3 10 files changed, 1433 insertions(+), 139 deletions(-)
Title: Semi-Automatic Preprocessing of Messy Data with Change Tracking
for Dataset Cleaning
Description: Tools for assessing data quality, performing exploratory analysis, and
semi-automatic preprocessing of messy data with change tracking for integral dataset cleaning.
Author: David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.8.0 dated 2021-08-10 and 0.8.3 dated 2022-09-24
DESCRIPTION | 8 +-- MD5 | 33 ++++++++------- NAMESPACE | 1 NEWS | 10 ++++ R/fix_functions.R | 95 +++++++++++++++++++++++++++++++++++++++------- man/bivariate_outliers.Rd | 48 +++++++++++------------ man/f_replace.Rd |only man/fix_NA.Rd | 54 +++++++++++++------------- man/fix_all.Rd | 34 ++++++++-------- man/fix_concat.Rd | 50 ++++++++++++------------ man/fix_dates.Rd | 89 ++++++++++++++++++++++--------------------- man/fix_factors.Rd | 60 +++++++++++++++-------------- man/fix_levels.Rd | 86 ++++++++++++++++++++--------------------- man/fix_numerics.Rd | 64 +++++++++++++++--------------- man/manual_fix.Rd | 48 +++++++++++------------ man/nice_names.Rd | 6 ++ man/remove_empty.Rd | 46 ++++++++++++---------- man/text_date.Rd | 32 +++++++-------- 18 files changed, 430 insertions(+), 334 deletions(-)
Title: Record Linkage Toolkit
Description: Functions to assist in performing probabilistic record linkage and
deduplication: generating pairs, comparing records, em-algorithm for
estimating m- and u-probabilities
(I. Fellegi & A. Sunter (1969) <doi:10.1080/01621459.1969.10501049>,
T.N. Herzog, F.J. Scheuren, & W.E. Winkler (2007),
"Data Quality and Record Linkage Techniques", ISBN:978-0-387-69502-0),
forcing one-to-one matching. Can also be
used for pre- and post-processing for machine learning methods for record
linkage. Focus is on memory, CPU performance and flexibility.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between reclin2 versions 0.1.1 dated 2022-01-07 and 0.2.0 dated 2022-09-24
DESCRIPTION | 8 MD5 | 53 - NAMESPACE | 5 NEWS |only R/cluster_collect.R | 2 R/cluster_merge_pairs.R |only R/cluster_pair.R | 5 R/cluster_pair_blocking.R | 5 R/cluster_pair_minsim.R | 3 R/distribute_over_cluster.R |only R/merge_pairs.R |only R/pair_minsim.R | 10 R/set_seed.R |only R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/deduplication.html | 546 +++++++-------- inst/doc/introduction.html | 665 +++++++++--------- inst/doc/record_linkage_using_machine_learning.html | 589 ++++++++-------- inst/doc/using_a_cluster_for_record_linkage.html | 717 ++++++++++---------- man/cluster_pair.Rd | 2 man/cluster_pair_blocking.Rd | 2 man/merge_pairs.Rd |only man/pair_minsim.Rd | 7 tests/test_cluster_pair.R | 16 tests/test_cluster_pair_blocking.R | 8 tests/test_cluster_pair_minsim.R | 8 tests/test_distribute_over_cluster.R |only tests/test_merge_pairs.R |only tests/test_pair_minsim.R | 10 tests/test_set_seed.R |only vignettes/style.css | 20 32 files changed, 1416 insertions(+), 1267 deletions(-)
Title: Exploration of Multiple Biomarker Responses using Effect Size
Description: Summarize multiple biomarker responses of aquatic organisms to
contaminants using Cliff’s delta, as described in Pham & Sokolova (2022)
<doi:10.1002/ieam.4676>.
Author: Duy Nghia Pham [aut, cre] ,
Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between mbRes versions 0.1.4 dated 2022-08-24 and 0.1.5 dated 2022-09-24
DESCRIPTION | 14 +++++++------- MD5 | 7 ++++--- R/mbRes-package.R | 5 +++-- inst |only man/mbRes-package.Rd | 5 +++-- 5 files changed, 17 insertions(+), 14 deletions(-)
Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces.
Playing surfaces are drawn pursuant to rule-book specifications.
This package should be used as a baseline plot for displaying any type of
tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>
Diff between sportyR versions 2.0.0 dated 2022-08-15 and 2.0.1 dated 2022-09-24
sportyR-2.0.0/sportyR/LICENSE |only sportyR-2.0.1/sportyR/DESCRIPTION | 12 - sportyR-2.0.1/sportyR/MD5 | 27 +- sportyR-2.0.1/sportyR/NEWS.md | 69 +++++- sportyR-2.0.1/sportyR/R/features-curling.R | 25 +- sportyR-2.0.1/sportyR/R/geom-curling.R | 23 +- sportyR-2.0.1/sportyR/R/geom-football.R | 4 sportyR-2.0.1/sportyR/R/geom-hockey.R | 70 +++++- sportyR-2.0.1/sportyR/inst/doc/animating-tracking-data.html | 111 +++++------ sportyR-2.0.1/sportyR/inst/doc/customize-plot.html | 111 +++++------ sportyR-2.0.1/sportyR/inst/doc/plotting-tracking-data.html | 111 +++++------ sportyR-2.0.1/sportyR/inst/doc/sportyR.Rmd | 6 sportyR-2.0.1/sportyR/inst/doc/sportyR.html | 121 +++++------- sportyR-2.0.1/sportyR/man/curling_end.Rd | 3 sportyR-2.0.1/sportyR/vignettes/sportyR.Rmd | 6 15 files changed, 403 insertions(+), 296 deletions(-)
Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut],
Samuel Bosch [aut],
Ward Appeltans [ctb],
OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Diff between robis versions 2.8.2 dated 2021-10-13 and 2.11.3 dated 2022-09-24
DESCRIPTION | 12 - MD5 | 40 ++- NAMESPACE | 5 NEWS.md | 24 ++ R/dataset.R | 8 R/dna.R | 43 --- R/mof.R | 43 --- R/occurrence.R | 13 - R/robis.R | 4 R/util.R | 91 ++++++++ README.md | 2 build/vignette.rds |binary inst/doc/getting-started.R | 58 ----- inst/doc/getting-started.Rmd | 8 inst/doc/getting-started.html | 406 +++++++------------------------------ man/dataset.Rd | 5 man/figures |only man/generate_citation.Rd |only man/occurrence.Rd | 11 - man/unnest_extension.Rd |only tests/testthat/test_measurements.R | 6 vignettes/getting-started.Rmd | 8 22 files changed, 268 insertions(+), 519 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging, a distance based on global alignment kernels,
and the soft-DTW distance and centroid routines are also provided.
All included distance functions have custom loops optimized for the
calculation of cross-distance matrices, including parallelization support.
Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 5.5.10 dated 2022-04-14 and 5.5.11 dated 2022-09-24
DESCRIPTION | 14 +-- MD5 | 34 +++---- NAMESPACE | 1 R/CLUSTERING-cvi-evaluators.R | 16 ++- R/CLUSTERING-ddist2.R | 2 R/GENERICS-cvi.R | 2 R/S4-Distmat.R | 3 R/S4-tsclustFamily.R | 22 +++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 5 - inst/doc/dtwclust.pdf |binary inst/doc/parallelization-considerations.html | 124 ++++++++++++++------------- inst/doc/timing-experiments.html | 32 +++--- man/compare_clusterings.Rd | 6 - man/cvi.Rd | 2 man/cvi_evaluators.Rd | 3 man/tsclustFamily-class.Rd | 25 +++-- 18 files changed, 161 insertions(+), 130 deletions(-)
Title: Methods for Partial Linear Single Index Model
Description: Estimation, hypothesis tests, and variable selection in partially linear single-index models. Please see H. (2010) at <doi:10.1214/10-AOS835> for more details.
Author: Shunyao Wu, Qi Zhang, Zhiruo Li, Hua Liang
Maintainer: Shunyao Wu <wushunyao@qdu.edu.cn>
Diff between PLSiMCpp versions 1.0.3 dated 2022-08-20 and 1.0.4 dated 2022-09-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plsim.MAVE.r | 2 -- R/plsim.vs.hard.r | 2 +- 4 files changed, 8 insertions(+), 10 deletions(-)
Title: Reproducible Input-Output Economics Analysis, Economic and
Environmental Impact Assessment with Empirical Data
Description: Pre-processing and basic analytical tasks related to working
with Eurostat's symmetric input-output tables and provide basic
input-output economics calculations. The package is part of rOpenGov
<http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal [aut, cre] ,
Kasia Kulma [ctb] ,
Pyry Kantanen [ctb]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>
Diff between iotables versions 0.9 dated 2022-02-10 and 0.9.1 dated 2022-09-24
DESCRIPTION | 12 MD5 | 118 +-- NEWS.md | 11 R/airpol_get.R | 2 R/check_digits.R | 14 R/coefficient_matrix_create.R | 2 R/data-croatia_2010_1700.R | 2 R/data-croatia_2010_1800.R | 2 R/data-croatia_2010_1900.R | 2 R/data-employment_metadata.R | 6 R/data-uk_2010_data.R | 2 R/employment_get.R | 93 +- R/indirect_effects_create.R | 24 R/input_indicator_create.R | 2 R/iotable_get.R | 906 +++++++++++++------------- R/iotable_year_get.R | 20 R/iotables.R | 2 R/iotables_read_tempdir.R | 5 R/output_get.R | 3 R/primary_input_get.R | 3 R/round_table.R | 12 R/sysdata.rda |binary README.md | 32 build/vignette.rds |binary data/employment_metadata.rda |only data/germany_1995.rda |binary data/germany_airpol.rda |binary inst/WORDLIST |only inst/doc/environmental_impact.Rmd | 5 inst/doc/environmental_impact.html | 335 ++++++++- inst/doc/intro.Rmd | 7 inst/doc/intro.html | 534 ++++++++++++--- inst/doc/united_kingdom_2010.Rmd | 4 inst/doc/united_kingdom_2010.html | 525 ++++++++++++++- inst/doc/working_with_eurostat.Rmd | 16 inst/doc/working_with_eurostat.html | 404 ++++++++++- man/airpol_get.Rd | 2 man/check_digits.Rd | 6 man/coefficient_matrix_create.Rd | 2 man/croatia_2010_1700.Rd | 2 man/croatia_2010_1800.Rd | 2 man/croatia_2010_1900.Rd | 2 man/employment_get.Rd | 8 man/employment_metadata.Rd | 2 man/figures/logo.png |binary man/figures/logo20.png |binary man/figures/logo_old.png |only man/indirect_effects_create.Rd | 4 man/input_indicator_create.Rd | 2 man/iotables.Rd | 2 man/iotables_read_tempdir.Rd | 25 man/output_get.Rd | 7 man/primary_input_get.Rd | 7 man/uk_2010_data.Rd | 2 tests/testthat/test-backward_linkages.R | 3 tests/testthat/test-indirect_effects_create.R |only tests/testthat/test-iotable_get.R | 9 tests/testthat/test-iotable_year_get.R | 15 vignettes/environmental_impact.Rmd | 5 vignettes/intro.Rmd | 7 vignettes/united_kingdom_2010.Rmd | 4 vignettes/working_with_eurostat.Rmd | 16 62 files changed, 2312 insertions(+), 927 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 1.0.5 dated 2022-08-31 and 1.0.6 dated 2022-09-24
rlang-1.0.5/rlang/R/rlang.R |only rlang-1.0.6/rlang/DESCRIPTION | 6 - rlang-1.0.6/rlang/MD5 | 78 +++++++++--------- rlang-1.0.6/rlang/NAMESPACE | 1 rlang-1.0.6/rlang/NEWS.md | 21 ++++ rlang-1.0.6/rlang/R/arg.R | 2 rlang-1.0.6/rlang/R/cnd-abort.R | 44 +++++++--- rlang-1.0.6/rlang/R/cnd-handlers.R | 14 +-- rlang-1.0.6/rlang/R/cnd-last.R | 27 +----- rlang-1.0.6/rlang/R/cnd-signal.R | 2 rlang-1.0.6/rlang/R/compat-cli.R | 41 +++++++-- rlang-1.0.6/rlang/R/compat-downstream-deps.R | 17 +-- rlang-1.0.6/rlang/R/compat-obj-type.R | 24 +++-- rlang-1.0.6/rlang/R/compat-rlang.R | 21 ++-- rlang-1.0.6/rlang/R/compat-s3-register.R | 17 +-- rlang-1.0.6/rlang/R/compat-types-check.R | 68 ++++++++------- rlang-1.0.6/rlang/R/deparse.R | 6 - rlang-1.0.6/rlang/R/fn.R | 1 rlang-1.0.6/rlang/R/rlang-package.R |only rlang-1.0.6/rlang/R/session.R | 4 rlang-1.0.6/rlang/R/utils.R | 15 +++ rlang-1.0.6/rlang/man/abort.Rd | 2 rlang-1.0.6/rlang/man/format_error_call.Rd | 19 +++- rlang-1.0.6/rlang/man/rlang-package.Rd | 2 rlang-1.0.6/rlang/man/rmd/topic-error-chaining.Rmd | 2 rlang-1.0.6/rlang/man/topic-data-mask-programming.Rd | 3 rlang-1.0.6/rlang/man/topic-data-mask.Rd | 2 rlang-1.0.6/rlang/man/topic-error-chaining.Rd | 6 - rlang-1.0.6/rlang/man/try_fetch.Rd | 12 +- rlang-1.0.6/rlang/src/rlang/vec-lgl.c | 65 +++++++++++---- rlang-1.0.6/rlang/src/version.c | 2 rlang-1.0.6/rlang/tests/testthat/_snaps/arg.md | 3 rlang-1.0.6/rlang/tests/testthat/_snaps/c-api.md | 6 - rlang-1.0.6/rlang/tests/testthat/_snaps/cnd-abort.md | 15 ++- rlang-1.0.6/rlang/tests/testthat/_snaps/compat-cli.md | 36 ++++---- rlang-1.0.6/rlang/tests/testthat/_snaps/session.md | 12 ++ rlang-1.0.6/rlang/tests/testthat/_snaps/trace.md | 16 +-- rlang-1.0.6/rlang/tests/testthat/test-c-api.R | 15 ++- rlang-1.0.6/rlang/tests/testthat/test-deparse.R | 4 rlang-1.0.6/rlang/tests/testthat/test-fn.R | 7 + rlang-1.0.6/rlang/tests/testthat/test-session.R | 39 ++++----- 41 files changed, 407 insertions(+), 270 deletions(-)
Title: Pin, Discover and Share Resources
Description: Publish data sets, models, and other R objects, making it
easy to share them across projects and with your colleagues. You can
pin objects to a variety of "boards", including local folders (to
share on a networked drive or with 'DropBox'), 'RStudio' connect,
Amazon S3, and more.
Author: Julia Silge [cre, aut] ,
Hadley Wickham [aut] ,
Javier Luraschi [aut],
RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between pins versions 1.0.2 dated 2022-08-23 and 1.0.3 dated 2022-09-24
DESCRIPTION | 23 ++++++---- MD5 | 51 ++++++++++++------------ NEWS.md | 17 +++++++- R/board_rsconnect.R | 8 ++- R/board_rsconnect_bundle.R | 4 + R/board_s3.R | 26 ++++++++---- R/meta.R | 2 R/pin-read-write.R | 15 ++++++- README.md | 4 - inst/doc/pins-update.Rmd | 2 inst/doc/pins-update.html | 18 ++++---- inst/doc/pins.Rmd | 2 inst/doc/pins.html | 22 +++++----- inst/doc/rsc.R | 3 - inst/doc/rsc.Rmd | 3 - man/board_s3.Rd | 8 +++ man/pins-package.Rd | 3 - tests/testthat/_snaps/board_azure_adls2.md |only tests/testthat/_snaps/board_azure_blob.md |only tests/testthat/_snaps/board_azure_file.md |only tests/testthat/_snaps/board_rsconnect_bundle.md | 2 tests/testthat/test-board_rsconnect.R | 1 tests/testthat/test-board_rsconnect_server.R | 2 tests/testthat/test-pin-read-write.R | 2 tests/testthat/test-pin.R | 1 vignettes/pins-update.Rmd | 2 vignettes/pins.Rmd | 2 vignettes/rsc.Rmd | 3 - 28 files changed, 144 insertions(+), 82 deletions(-)
Title: Angular Distance Weighting Interpolation
Description: The irregularly-spaced data are interpolated onto regular latitude-longitude grids by weighting each station according to its distance and angle from the center of a search radius.
Author: Panfeng Zhang [aut, cre]
Maintainer: Panfeng Zhang <zhangpanfeng@cug.edu.cn>
Diff between adw versions 0.2.0 dated 2022-09-22 and 0.2.1 dated 2022-09-24
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS.md | 5 +++++ R/adw.R | 2 +- README.md |only man/adw.Rd | 2 +- 6 files changed, 16 insertions(+), 10 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package
supports the static site generator 'Hugo' (<https://gohugo.io>) best,
and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo'
(<https://hexo.io>).
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Alison Presmanes Hill [aut] ,
Amber Thomas [ctb],
Beilei Bian [ctb],
Brandon Greenwell [ctb],
Brian Barkley [ctb],
Deependra Dhakal [ctb],
Eric Nantz [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 1.12 dated 2022-09-15 and 1.13 dated 2022-09-24
blogdown-1.12/blogdown/tests/test-all.R |only blogdown-1.12/blogdown/tests/testit |only blogdown-1.13/blogdown/DESCRIPTION | 6 ++-- blogdown-1.13/blogdown/MD5 | 24 +++++++++-------- blogdown-1.13/blogdown/R/hugo.R | 42 ++++++++++++++++++++++--------- blogdown-1.13/blogdown/R/install.R | 11 ++++++-- blogdown-1.13/blogdown/R/utils.R | 12 +++++--- blogdown-1.13/blogdown/tests/test-ci |only blogdown-1.13/blogdown/tests/test-ci.R |only blogdown-1.13/blogdown/tests/test-cran |only blogdown-1.13/blogdown/tests/test-cran.R |only 11 files changed, 63 insertions(+), 32 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-22 3.1.1
2021-09-28 3.1.0
2021-07-13 3.0.1
2021-06-10 3.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-08 0.2.0
2021-09-07 0.1.0
Title: Multi-Objective Optimization in R
Description: The 'rmoo' package is a framework for multi- and many-objective
optimization, which allows researchers and users versatility
in parameter configuration, as well as tools for analysis, replication
and visualization of results. The 'rmoo' package was built as a fork of
the 'GA' package by Luca Scrucca(2017) <DOI:10.32614/RJ-2017-008> and
implementing the Non-Dominated Sorting Genetic Algorithms proposed
by K. Deb's.
Author: Francisco Benitez [aut, cre],
Diego Pinto Roa [aut]
Maintainer: Francisco Benitez <benitezfj94@gmail.com>
Diff between rmoo versions 0.1.8 dated 2022-08-11 and 0.2.0 dated 2022-09-23
rmoo-0.1.8/rmoo/R/nsga-class.R |only rmoo-0.1.8/rmoo/R/nsga2-class.R |only rmoo-0.1.8/rmoo/R/nsga3-class.R |only rmoo-0.1.8/rmoo/R/numberOrNAOrMatrix-class.R |only rmoo-0.1.8/rmoo/R/plotting.R |only rmoo-0.1.8/rmoo/man/heat_map.Rd |only rmoo-0.1.8/rmoo/man/pcp.Rd |only rmoo-0.1.8/rmoo/man/polar.Rd |only rmoo-0.1.8/rmoo/man/scatter.Rd |only rmoo-0.1.8/rmoo/man/summary.Rd |only rmoo-0.2.0/rmoo/DESCRIPTION | 38 - rmoo-0.2.0/rmoo/MD5 | 63 +- rmoo-0.2.0/rmoo/NAMESPACE | 18 rmoo-0.2.0/rmoo/R/AllClasses.R |only rmoo-0.2.0/rmoo/R/AllGenerics.R |only rmoo-0.2.0/rmoo/R/geneticoperator.R | 2 rmoo-0.2.0/rmoo/R/miscfun.R | 579 +++++++++++++++++++-- rmoo-0.2.0/rmoo/R/nsga.R | 129 ++++ rmoo-0.2.0/rmoo/R/nsga2.R | 86 ++- rmoo-0.2.0/rmoo/R/nsga3.R | 120 ++++ rmoo-0.2.0/rmoo/R/rmoo.R | 2 rmoo-0.2.0/rmoo/R/rmoo_func.R |only rmoo-0.2.0/rmoo/R/zzz.R | 22 rmoo-0.2.0/rmoo/README.md | 56 +- rmoo-0.2.0/rmoo/man/algorithm-class.Rd |only rmoo-0.2.0/rmoo/man/getCrowdingDistance-methods.Rd |only rmoo-0.2.0/rmoo/man/getDummyFitness-methods.Rd |only rmoo-0.2.0/rmoo/man/getFitness-methods.Rd |only rmoo-0.2.0/rmoo/man/getMetrics-methods.Rd |only rmoo-0.2.0/rmoo/man/getPopulation-methods.Rd |only rmoo-0.2.0/rmoo/man/nsga-class.Rd | 17 rmoo-0.2.0/rmoo/man/nsga.Rd | 2 rmoo-0.2.0/rmoo/man/nsga1-class.Rd |only rmoo-0.2.0/rmoo/man/nsga2-class.Rd | 64 -- rmoo-0.2.0/rmoo/man/nsga3-class.Rd | 65 -- rmoo-0.2.0/rmoo/man/numberOrNAOrMatrix-class.Rd | 4 rmoo-0.2.0/rmoo/man/plot-methods.Rd |only rmoo-0.2.0/rmoo/man/print-methods.Rd |only rmoo-0.2.0/rmoo/man/progress-methods.Rd |only rmoo-0.2.0/rmoo/man/rmoo-package.Rd | 4 rmoo-0.2.0/rmoo/man/rmoo_func.Rd |only rmoo-0.2.0/rmoo/man/summary-methods.Rd |only rmoo-0.2.0/rmoo/tests/testthat/test-nsga3.r | 2 rmoo-0.2.0/rmoo/tests/testthat/test-pcp.r | 8 rmoo-0.2.0/rmoo/tests/testthat/test-scatter.r | 12 45 files changed, 1001 insertions(+), 292 deletions(-)
Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric
objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and
calculate deviance residuals as well as 'R' translations of some
'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs
Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between extras versions 0.3.0 dated 2022-06-08 and 0.4.0 dated 2022-09-23
DESCRIPTION | 6 +-- MD5 | 35 ++++++++++--------- NAMESPACE | 3 + NEWS.md | 6 +++ R/bern.R |only R/odds.R | 35 +++++++++++++++++++ R/params.R | 4 ++ README.md | 4 +- build/partial.rdb |binary inst/WORDLIST | 1 man/bern.Rd |only man/inv_odds.Rd | 2 + man/log_odds-set.Rd |only man/log_odds.Rd |only man/log_odds_ratio.Rd | 2 + man/odds-set.Rd | 2 + man/odds.Rd | 2 + man/odds_ratio.Rd | 2 + man/params.Rd | 8 ++++ tests/testthat/test-bern.R |only tests/testthat/test-odds.R | 82 +++++++++++++++++++++++++++++++++++++++++++++ 21 files changed, 174 insertions(+), 20 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] ,
Ryan P. Browne [aut] ,
Paul D. McNicholas [aut, cre]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between mixture versions 2.0.4 dated 2021-04-19 and 2.0.5 dated 2022-09-23
ChangeLog | 4 DESCRIPTION | 20 - MD5 | 63 ++-- NAMESPACE | 1 R/RcppExports.R | 8 R/gh_mixture.R | 111 ++++++-- R/mixture.R | 69 ++++- R/pcm.R | 11 R/st_mixture.R | 82 +++++- R/t_mixture.R | 70 ++++- R/vg_mixture.R | 74 +++++ man/ghpcm.Rd | 1 man/gpcm.Rd | 1 man/main_loop_st.Rd | 7 man/main_loop_vg.Rd | 7 man/mixture.Rd | 4 man/pcm.Rd | 1 man/stpcm.Rd | 8 man/tpcm.Rd | 1 man/vgpcm.Rd | 7 src/Cluster_Error.hpp | 7 src/GH_Model/GH_Mixture_Model.h | 530 +++++++++++++++++++++++----------------- src/Random_GIG.hpp |only src/RcppExports.cpp | 23 + src/ST_Model/ST_Mixture_Model.h | 354 ++++++++++++++++++++++---- src/T_Model/General_Methods.hpp | 8 src/VG_Model/VG_Mixture_Model.h | 391 ++++++++++++++++++++++++----- src/ghpcm_arma.hpp | 267 ++++++++------------ src/gpcm_arma.hpp | 11 src/pcm.cpp | 3 src/stpcm_arma.hpp | 276 +++++++++----------- src/tpcm_arma.hpp | 11 src/vgpcm_arma.hpp | 261 ++++++++----------- 33 files changed, 1794 insertions(+), 898 deletions(-)
Title: Fast, Consistent Tokenization of Natural Language Text
Description: Convert natural language text into tokens. Includes tokenizers for
shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs,
characters, shingled characters, lines, tweets, Penn Treebank, regular
expressions, as well as functions for counting characters, words, and sentences,
and a function for splitting longer texts into separate documents, each with
the same number of words. The tokenizers have a consistent interface, and
the package is built on the 'stringi' and 'Rcpp' packages for fast
yet correct tokenization in 'UTF-8'.
Author: Lincoln Mullen [aut, cre] ,
Os Keyes [ctb] ,
Dmitriy Selivanov [ctb],
Jeffrey Arnold [ctb] ,
Kenneth Benoit [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between tokenizers versions 0.2.1 dated 2018-03-29 and 0.2.3 dated 2022-09-23
DESCRIPTION | 14 MD5 | 56 +-- NEWS.md | 5 R/basic-tokenizers.R | 9 R/chunk-text.R | 4 R/ngram-tokenizers.R | 6 R/ptb-tokenizer.R | 2 R/stem-tokenizers.R | 9 R/tokenize_tweets.R | 170 +++++---- R/utils.R | 2 README.md | 65 +-- build/vignette.rds |binary inst/doc/introduction-to-tokenizers.R | 28 - inst/doc/introduction-to-tokenizers.html | 544 +++++++++++++++++-------------- inst/doc/tif-and-tokenizers.R | 10 inst/doc/tif-and-tokenizers.Rmd | 2 inst/doc/tif-and-tokenizers.html | 334 +++++++++++-------- man/basic-tokenizers.Rd | 60 ++- man/mobydick.Rd | 4 man/ngram-tokenizers.Rd | 46 +- man/ptb-tokenizer.Rd | 14 man/shingle-tokenizers.Rd | 10 man/stem-tokenizers.Rd | 35 + man/tokenizers.Rd | 1 src/RcppExports.cpp | 5 src/shingle_ngrams.cpp | 2 tests/testthat/test-ptb.R | 2 tests/testthat/test-tokenize_tweets.R | 29 + vignettes/tif-and-tokenizers.Rmd | 2 29 files changed, 854 insertions(+), 616 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.9.1 dated 2022-08-22 and 0.9.2 dated 2022-09-23
DESCRIPTION | 12 MD5 | 96 ++--- NAMESPACE | 34 - R/ARMA.R | 154 ++++---- R/ARMA_optim.R | 97 ++--- R/Boost.R | 55 +-- R/Internal_Functions.R | 61 --- R/Mode.R |only R/Multivariate_Regression.R | 273 +++++++-------- R/NNS_Distance.R | 22 - R/NNS_VAR.R | 134 +++---- R/NNS_meboot.R | 15 R/Nowcast.R | 45 -- R/Partition_Map.R | 10 R/Regression.R | 223 ++++++------ R/Stack.R | 340 +++++++++---------- R/dy_d_wrt.R | 9 R/dy_dx.R | 8 R/gvload.R | 41 -- README.md | 4 build/partial.rdb |binary inst/doc/NNSvignette_Classification.R | 1 inst/doc/NNSvignette_Classification.Rmd | 1 inst/doc/NNSvignette_Classification.html | 62 --- inst/doc/NNSvignette_Clustering_and_Regression.R | 2 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 2 inst/doc/NNSvignette_Clustering_and_Regression.html | 54 +-- inst/doc/NNSvignette_Correlation_and_Dependence.R | 1 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 1 inst/doc/NNSvignette_Correlation_and_Dependence.html | 19 - inst/doc/NNSvignette_Forecasting.R | 1 inst/doc/NNSvignette_Forecasting.Rmd | 1 inst/doc/NNSvignette_Forecasting.html | 3 inst/doc/NNSvignette_Partial_Moments.Rmd | 3 inst/doc/NNSvignette_Partial_Moments.html | 6 man/NNS.ARMA.optim.Rd | 2 man/NNS.VAR.Rd | 13 man/NNS.boost.Rd | 7 man/NNS.distance.Rd | 2 man/NNS.mode.Rd |only man/NNS.nowcast.Rd | 14 man/NNS.reg.Rd | 5 man/NNS.stack.Rd | 7 tests/testthat/Rplots.pdf |binary tests/testthat/test_Partition_Map.R | 26 - vignettes/NNSvignette_Classification.Rmd | 1 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 2 vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 1 vignettes/NNSvignette_Forecasting.Rmd | 1 vignettes/NNSvignette_Partial_Moments.Rmd | 3 50 files changed, 845 insertions(+), 1029 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.8.0 dated 2022-07-05 and 1.9.0 dated 2022-09-23
DESCRIPTION | 8 MD5 | 72 ++-- NAMESPACE | 1 NEWS.md | 15 R/assert_package.R | 94 ++++-- R/model_get_model_matrix.R | 4 R/model_get_terms.R | 4 R/model_identify_variables.R | 9 R/model_list_variables.R | 4 R/select_utilities.R | 2 R/tidiers.R | 2 R/tidy_add_contrasts.R | 4 R/tidy_add_estimate_to_reference_rows.R | 4 R/tidy_add_header_rows.R | 10 R/tidy_add_reference_rows.R | 16 - R/tidy_add_term_labels.R | 2 R/tidy_add_variable_labels.R | 2 R/tidy_disambiguate_terms.R | 2 R/tidy_plus_plus.R | 2 build/vignette.rds |binary data/supported_models.rda |binary inst/doc/tidy.R | 5 inst/doc/tidy.Rmd | 5 inst/doc/tidy.html | 453 ++++++++++++++--------------- man/assert_package.Rd | 37 +- man/model_get_model_matrix.Rd | 4 man/model_get_terms.Rd | 4 man/model_list_variables.Rd | 2 man/tidy_add_estimate_to_reference_rows.Rd | 4 man/tidy_add_header_rows.Rd | 2 man/tidy_add_reference_rows.Rd | 2 man/tidy_disambiguate_terms.Rd | 2 man/tidy_parameters.Rd | 2 man/tidy_plus_plus.Rd | 2 tests/testthat/test-assert_package.R | 37 +- tests/testthat/test-tidy_plus_plus.R | 2 vignettes/tidy.Rmd | 5 37 files changed, 465 insertions(+), 360 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr],
Paul Bailey [aut, cre],
Claire Kelley [aut],
Trang Nguyen [aut],
Huade Huo [aut],
Eric Buehler [ctb],
Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.2.1 dated 2021-12-07 and 3.2.2 dated 2022-09-23
DESCRIPTION | 8 MD5 | 18 R/adaptiveQuad.R | 7 R/analyticSolve.R | 71 ++ R/helpers.R | 42 + build/vignette.rds |binary inst/NEWS.Rd | 17 inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |binary inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |binary tests/testthat/test-1-main.R | 286 ++++++++++- 10 files changed, 397 insertions(+), 52 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table',
giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Robert On [ctb],
Alexander Sevostianov [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.8.1 dated 2022-08-17 and 0.9.0 dated 2022-09-23
tidytable-0.8.1/tidytable/tests/testthat/test-lead..R |only tidytable-0.9.0/tidytable/DESCRIPTION | 43 tidytable-0.9.0/tidytable/MD5 | 522 ++++++---- tidytable-0.9.0/tidytable/NAMESPACE | 171 +++ tidytable-0.9.0/tidytable/NEWS.md | 32 tidytable-0.9.0/tidytable/R/across.R | 20 tidytable-0.9.0/tidytable/R/add_count.R | 45 tidytable-0.9.0/tidytable/R/arrange.R | 21 tidytable-0.9.0/tidytable/R/as_tidytable.R | 37 tidytable-0.9.0/tidytable/R/between.R | 19 tidytable-0.9.0/tidytable/R/bind.R | 25 tidytable-0.9.0/tidytable/R/c_across.R | 13 tidytable-0.9.0/tidytable/R/case.R | 9 tidytable-0.9.0/tidytable/R/case_match.R |only tidytable-0.9.0/tidytable/R/case_when.R | 25 tidytable-0.9.0/tidytable/R/coalesce.R | 13 tidytable-0.9.0/tidytable/R/complete.R | 32 tidytable-0.9.0/tidytable/R/consecutive_id.R | 9 tidytable-0.9.0/tidytable/R/count.R | 98 + tidytable-0.9.0/tidytable/R/crossing.R | 17 tidytable-0.9.0/tidytable/R/cur-context.R | 62 - tidytable-0.9.0/tidytable/R/desc.R | 12 tidytable-0.9.0/tidytable/R/distinct.R | 40 tidytable-0.9.0/tidytable/R/drop_na.R | 16 tidytable-0.9.0/tidytable/R/dt.R | 29 tidytable-0.9.0/tidytable/R/enframe.R | 9 tidytable-0.9.0/tidytable/R/expand.R | 53 - 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Title: Simple Geographical Operations (with OSGB36)
Description: Methods focused in performing the OSGB36/ETRS89 transformation
(Great Britain and the Isle of Man only) by using the Ordnance Survey's
OSTN15/OSGM15 transformation model. Calculation of distances and areas from
sets of points defined in any of the supported Coordinated Systems is also
available.
Author: Carlos Lozano Ruiz [aut, cre]
Maintainer: Carlos Lozano Ruiz <carloslozanoruiz@outlook.com>
Diff between sgo versions 0.9.1 dated 2021-12-11 and 0.9.2 dated 2022-09-23
sgo-0.9.1/sgo/man/sgo.Rd |only sgo-0.9.1/sgo/tests/testthat |only sgo-0.9.1/sgo/tests/testthat.R |only sgo-0.9.2/sgo/DESCRIPTION | 13 +-- sgo-0.9.2/sgo/MD5 | 86 +++++++++++++------------- sgo-0.9.2/sgo/NEWS.md | 9 ++ sgo-0.9.2/sgo/R/sgo.R | 8 +- sgo-0.9.2/sgo/R/sgo_area.R | 14 ++-- sgo-0.9.2/sgo/R/sgo_bng.R | 30 ++++----- sgo-0.9.2/sgo/R/sgo_distance.R | 31 ++++----- sgo-0.9.2/sgo/R/sgo_laea.R | 14 ++-- sgo-0.9.2/sgo/R/sgo_ngr.R | 28 ++------ sgo-0.9.2/sgo/R/sgo_points.R | 115 +++++++++++++++++++++++++++++++---- sgo-0.9.2/sgo/R/sgo_set_gcs.R | 28 +++----- sgo-0.9.2/sgo/R/sgo_transform.R | 6 - sgo-0.9.2/sgo/R/sgo_wgs84.R | 8 +- sgo-0.9.2/sgo/R/sysdata.rda |binary sgo-0.9.2/sgo/README.md | 41 +++++++++--- sgo-0.9.2/sgo/inst |only sgo-0.9.2/sgo/man/sgo-package.Rd |only sgo-0.9.2/sgo/man/sgo_area.Rd | 2 sgo-0.9.2/sgo/man/sgo_bng_lonlat.Rd | 12 +-- sgo-0.9.2/sgo/man/sgo_bng_ngr.Rd | 4 - sgo-0.9.2/sgo/man/sgo_cart_lonlat.Rd | 3 sgo-0.9.2/sgo/man/sgo_coordinates.Rd | 16 ++++ sgo-0.9.2/sgo/man/sgo_distance.Rd | 21 +++--- sgo-0.9.2/sgo/man/sgo_lonlat_bng.Rd | 4 - sgo-0.9.2/sgo/man/sgo_lonlat_cart.Rd | 3 sgo-0.9.2/sgo/man/sgo_ngr_bng.Rd | 4 - sgo-0.9.2/sgo/man/sgo_points.Rd | 2 sgo-0.9.2/sgo/man/sgo_set_gcs.Rd | 6 - sgo-0.9.2/sgo/man/sgo_transform.Rd | 2 sgo-0.9.2/sgo/man/sgo_wgs84_en.Rd | 2 sgo-0.9.2/sgo/tests/tinytest.R |only 34 files changed, 319 insertions(+), 193 deletions(-)
Title: Tools for Data Analysis in Experimental Agriculture
Description: Toolkit for a workflow to analyse experimental agriculture data,
from data synthesis to model selection and visualisation.
The package is named after W.S. Gosset aka ‘Student’, a pioneer
of modern statistics in small sample experimental design and analysis.
Author: Kaue de Sousa [aut, cre] ,
Jacob van Etten [aut] ,
David Brown [aut] ,
Jonathan Steinke [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>
Diff between gosset versions 0.4 dated 2022-06-28 and 0.5 dated 2022-09-23
DESCRIPTION | 16 ++++++------- MD5 | 23 +++++++++---------- NEWS.md | 7 +++++ R/kendallW.R | 17 -------------- R/reliability.R | 4 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.html | 2 - inst/paper/paper.Rmd | 59 ++++++++++++++++++++++++------------------------- inst/paper/paper.docx |only man/gosset.Rd | 2 - man/kendallW.Rd | 17 -------------- man/reliability.Rd | 4 ++- 13 files changed, 64 insertions(+), 87 deletions(-)
Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between EnrichIntersect versions 0.3 dated 2022-09-14 and 0.4 dated 2022-09-23
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/intersectSankey.R | 6 +++++- inst/doc/EnrichIntersect.Rmd | 2 +- inst/doc/EnrichIntersect.html | 2 +- vignettes/EnrichIntersect.Rmd | 2 +- 7 files changed, 24 insertions(+), 16 deletions(-)
More information about EnrichIntersect at CRAN
Permanent link
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education S [...truncated...]
Author: Paul Bailey [aut, cre],
Ahmad Emad [aut],
Huade Huo [aut],
Michael Lee [aut],
Yuqi Liao [aut],
Alex Lishinski [aut],
Trang Nguyen [aut],
Qingshu Xie [aut],
Jiao Yu [aut],
Ting Zhang [aut],
Eric Buehler [aut],
person,
person),
Jeppe Bundsgaard [ctb],
[...truncated...]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 2.7.1 dated 2021-10-05 and 3.0.0 dated 2022-09-23
DESCRIPTION | 15 MD5 | 195 +++--- NAMESPACE | 18 R/achievementLevels.R | 9 R/all.R | 9 R/cor.sdf.R | 49 - R/descriptionOfFile.R | 173 ++--- R/dim.edsurvey.data.frame.R | 2 R/downloadPIAAC.R | 2 R/downloadTIMSS.R | 6 R/drawPVs.sdf.R |only R/edsurvey.data.frame.R | 88 -- R/edsurveyTable.R | 11 R/gap.R | 20 R/getAttributes.R | 7 R/getData.R | 290 ++++----- R/getItems.R |only R/glm.sdf.R | 16 R/levelsSDF.R | 6 R/lm.sdf.R | 11 R/mergev.R |only R/mml.paramtabs.R | 194 ++++-- R/mml.scoreNAEP.R | 65 +- R/mml.scoreTIMSS.R | 54 + R/mml.sdf.R | 858 +++++++++++++-------------- R/mml.sdf.helpers.R | 48 + R/mvrlm.sdf.R | 8 R/percentile.R | 24 R/readELS.R | 2 R/readICCS.R | 305 ++++----- R/readNAEP.r | 880 +++++++++++++++++++--------- R/readPIAAC.R | 3 R/readPISA_YAFS.R | 2 R/readTIMSS.R | 867 ++++++++++++++++++++------- R/readUTILS.R | 47 + R/readUTILS_PRINT.R |only R/read_ePIRLS.R | 78 +- R/rebindAttributes.R | 2 R/rq.sdf.R | 10 R/sameSurvey.R | 9 R/setAttributes.R | 2 R/showPlausibleValues.R | 2 R/subset.edsurvey.data.frame.list.R | 37 - R/subset.light.edsurvey.data.frame.R | 38 - R/suggestWeights.R |only R/summary2.R | 4 R/utilities.R | 180 +++++ R/waldTest.R | 2 R/zzz.R | 3 build/vignette.rds |binary inst/NEWS.Rd | 21 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 13 inst/suggestWeights |only man/UnclassCols.Rd |only man/checkIdVar.Rd |only man/checkPsuStrata.Rd |only man/cor.sdf.Rd | 6 man/drawPVs.sdf.Rd |only man/edsurvey-class.Rd | 8 man/examples/getAllItems.R |only man/examples/readPIAAC.R | 18 man/examples/suggestWeights.R |only man/getAllItems.Rd |only man/mergev.Rd |only man/mml.sdf.Rd | 40 - man/readNAEP.Rd | 42 - man/readPIAAC.Rd | 18 man/scoreDefault.Rd |only man/scoreTIMSS.Rd | 5 man/setNAEPScoreCard.Rd |only man/suggestWeights.Rd |only man/summary2.Rd | 2 tests/testthat/NHESlm1.rds |only tests/testthat/PISAedTable1.rds |only tests/testthat/PISAgd0.rds |only tests/testthat/PISAgd1.rds |only tests/testthat/PISAgd2.rds |only tests/testthat/PISAgd3.rds |only tests/testthat/PISAgd4.rds |only tests/testthat/REF-0-main.R | 698 ++++++++++------------ tests/testthat/REF-11-NHES.R |only tests/testthat/REF-12-SSOCS.R | 2 tests/testthat/REF-2-esdfl.R | 12 tests/testthat/REF-3-TIMSS.R | 35 - tests/testthat/REF-6-ECLS_K.R | 2 tests/testthat/REF-7-ELS.R | 10 tests/testthat/TIMSSes1Fin.rds |only tests/testthat/TIMSSes1Fin4.rds |only tests/testthat/TIMSSes1USA.rds |only tests/testthat/TIMSSes1USA4.rds |only tests/testthat/TIMSSgap3d_varest.rds |only tests/testthat/TIMSSgap_AL1.rds |only tests/testthat/TIMSSgap_main_percentile.rds |only tests/testthat/TIMSSgap_percentage1.rds |only tests/testthat/TIMSSgd1.rds |only tests/testthat/TIMSSgd2.rds |only tests/testthat/TIMSSgd3.rds |only tests/testthat/TIMSSlm1.rds |only tests/testthat/TIMSSlm1_sum.rds |only tests/testthat/TIMSSlm1t.rds |only tests/testthat/TIMSSlm1t_sum.rds |only tests/testthat/TIMSSpct1.rds |only tests/testthat/gddat.rds |binary tests/testthat/lm1t.rds |binary tests/testthat/pisa_1re_REF.rds |only tests/testthat/test-05-mergev.R |only tests/testthat/test-10-main.R | 134 +++- tests/testthat/test-15-lesdf.R | 3 tests/testthat/test-20-esdfl.R | 5 tests/testthat/test-25-NHES.R |only tests/testthat/test-27-SSOCS.R | 4 tests/testthat/test-30-TIMSS.R | 92 ++ tests/testthat/test-40-ELS.R | 16 tests/testthat/test-45-HSLS.R | 22 tests/testthat/test-50-pisa.R | 12 tests/testthat/test-51-YAFS.R | 2 tests/testthat/test-60-ECLS_K.R | 4 tests/testthat/test-75-iccs.R | 4 vignettes/introduction.Rmd | 2 120 files changed, 3593 insertions(+), 2292 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al.
(2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
using both regional and local information. Functional Rarity combines both
the functional aspect of rarity as well as the extent aspect of rarity.
'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenie [aut, cre] ,
Pierre Denelle [aut] ,
Caroline Tucker [aut] ,
Francois Munoz [ths] ,
Cyrille Violle [ths]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>
Diff between funrar versions 1.4.1 dated 2020-04-20 and 1.5.0 dated 2022-09-23
funrar-1.4.1/funrar/inst/doc/rarity_indices.R |only funrar-1.4.1/funrar/inst/doc/rarity_indices.Rmd |only funrar-1.4.1/funrar/inst/doc/rarity_indices.html |only funrar-1.4.1/funrar/vignettes/rarity_indices.Rmd |only funrar-1.5.0/funrar/DESCRIPTION | 16 funrar-1.5.0/funrar/MD5 | 140 - funrar-1.5.0/funrar/NAMESPACE | 61 funrar-1.5.0/funrar/NEWS.md | 186 + funrar-1.5.0/funrar/R/check_functions.R | 498 ++--- funrar-1.5.0/funrar/R/compute_dist_matrix.R | 198 +- funrar-1.5.0/funrar/R/distinctiveness.R | 662 +++--- funrar-1.5.0/funrar/R/distinctiveness_alt.R | 217 +- funrar-1.5.0/funrar/R/distinctiveness_global.R | 127 - funrar-1.5.0/funrar/R/distinctiveness_range.R | 342 +-- funrar-1.5.0/funrar/R/funrar.R | 226 +- funrar-1.5.0/funrar/R/make_relative.R | 186 - funrar-1.5.0/funrar/R/rarity_dimensions.R | 271 +- funrar-1.5.0/funrar/R/restrictedness.R | 359 +-- funrar-1.5.0/funrar/R/scarcity.R | 368 +-- funrar-1.5.0/funrar/R/stack_matrix.R | 372 +-- funrar-1.5.0/funrar/R/uniqueness.R | 300 +-- funrar-1.5.0/funrar/README.md | 112 - funrar-1.5.0/funrar/build/vignette.rds |binary funrar-1.5.0/funrar/inst/CITATION | 46 funrar-1.5.0/funrar/inst/doc/funrar.R |only funrar-1.5.0/funrar/inst/doc/funrar.Rmd |only funrar-1.5.0/funrar/inst/doc/funrar.html |only funrar-1.5.0/funrar/inst/doc/new_distinctiveness.R | 366 +-- funrar-1.5.0/funrar/inst/doc/new_distinctiveness.Rmd | 854 ++++---- funrar-1.5.0/funrar/inst/doc/new_distinctiveness.pdf |binary funrar-1.5.0/funrar/inst/doc/other_functions.R |only funrar-1.5.0/funrar/inst/doc/other_functions.Rmd |only funrar-1.5.0/funrar/inst/doc/other_functions.html |only funrar-1.5.0/funrar/inst/doc/sparse_matrices.R | 186 - funrar-1.5.0/funrar/inst/doc/sparse_matrices.Rmd | 320 +-- funrar-1.5.0/funrar/inst/doc/sparse_matrices.html | 990 +++++----- funrar-1.5.0/funrar/man/combination_trait_dist.Rd | 44 funrar-1.5.0/funrar/man/compute_dist_matrix.Rd | 156 - funrar-1.5.0/funrar/man/distinctiveness.Rd | 170 - funrar-1.5.0/funrar/man/distinctiveness_alt.Rd | 141 - funrar-1.5.0/funrar/man/distinctiveness_com.Rd | 114 - funrar-1.5.0/funrar/man/distinctiveness_dimensions.Rd | 94 funrar-1.5.0/funrar/man/distinctiveness_global.Rd | 64 funrar-1.5.0/funrar/man/distinctiveness_range.Rd | 226 +- funrar-1.5.0/funrar/man/distinctiveness_stack.Rd | 174 - funrar-1.5.0/funrar/man/funrar.Rd | 90 funrar-1.5.0/funrar/man/funrar_stack.Rd | 98 funrar-1.5.0/funrar/man/is_relative.Rd | 79 funrar-1.5.0/funrar/man/make_relative.Rd | 59 funrar-1.5.0/funrar/man/matrix_to_stack.Rd | 98 funrar-1.5.0/funrar/man/restrictedness.Rd | 152 - funrar-1.5.0/funrar/man/restrictedness_stack.Rd | 104 - funrar-1.5.0/funrar/man/scarcity.Rd | 102 - funrar-1.5.0/funrar/man/scarcity_com.Rd | 96 funrar-1.5.0/funrar/man/scarcity_stack.Rd | 110 - funrar-1.5.0/funrar/man/stack_to_matrix.Rd | 108 - funrar-1.5.0/funrar/man/uniqueness.Rd | 128 - funrar-1.5.0/funrar/man/uniqueness_dimensions.Rd | 90 funrar-1.5.0/funrar/man/uniqueness_stack.Rd | 108 - funrar-1.5.0/funrar/tests/testthat.R | 8 funrar-1.5.0/funrar/tests/testthat/test-check_functions.R | 348 +-- funrar-1.5.0/funrar/tests/testthat/test-dist_matrix.R | 308 +-- funrar-1.5.0/funrar/tests/testthat/test-distinctiveness.R | 669 +++--- funrar-1.5.0/funrar/tests/testthat/test-distinctiveness_alt.R | 309 +-- funrar-1.5.0/funrar/tests/testthat/test-distinctiveness_global.R | 180 + funrar-1.5.0/funrar/tests/testthat/test-distinctiveness_range.R | 458 ++-- funrar-1.5.0/funrar/tests/testthat/test-funrar.R | 295 +- funrar-1.5.0/funrar/tests/testthat/test-rarity_dimensions.R | 322 +-- funrar-1.5.0/funrar/tests/testthat/test-rel_abund.R | 164 - funrar-1.5.0/funrar/tests/testthat/test-restrictedness.R | 106 - funrar-1.5.0/funrar/tests/testthat/test-scarcity.R | 313 +-- funrar-1.5.0/funrar/tests/testthat/test-tidy_matrix.R | 344 +-- funrar-1.5.0/funrar/tests/testthat/test-uniqueness.R | 159 - funrar-1.5.0/funrar/vignettes/funrar.Rmd |only funrar-1.5.0/funrar/vignettes/new_distinctiveness.Rmd | 854 ++++---- funrar-1.5.0/funrar/vignettes/other_functions.Rmd |only funrar-1.5.0/funrar/vignettes/sparse_matrices.Rmd | 320 +-- 77 files changed, 7646 insertions(+), 7519 deletions(-)
Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help
patients differently, personalized drug response predictions remain
challenging. Solutions based on single omics measurements have been proposed,
and networks provide means to incorporate molecular interactions into reasoning.
However, how to integrate the wealth of information contained in multiple omics
layers still poses a complex problem.
We present a novel network analysis pipeline, DrDimont, Drug response prediction
from Differential analysis of multi-omics networks. It allows for comparative
conclusions between two conditions and translates them into differential drug
response predictions. DrDimont focuses on molecular interactions. It establishes
condition-specific networks from correlation within an omics layer that are
then reduced and combined into heterogeneous, multi-omics molecular networks.
A novel semi-local, path-based integration step ensures integrative conclusions.
Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] ,
Pauline Hiort [aut] ,
Julian Hugo [aut] ,
Spoorthi Kashyap [aut] ,
Nataniel Mueller [aut] ,
Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@hpi.de>
Diff between DrDimont versions 0.1.3 dated 2022-05-17 and 0.1.4 dated 2022-09-23
DrDimont-0.1.3/DrDimont/vignettes/pipeline_bpmn.png |only DrDimont-0.1.3/DrDimont/vignettes/pipeline_overview.png |only DrDimont-0.1.4/DrDimont/DESCRIPTION | 43 DrDimont-0.1.4/DrDimont/MD5 | 138 DrDimont-0.1.4/DrDimont/R/checks.R | 725 +-- DrDimont-0.1.4/DrDimont/R/drug_targets.R | 2 DrDimont-0.1.4/DrDimont/R/graph_combination.R | 3 DrDimont-0.1.4/DrDimont/R/interaction_score.R | 72 DrDimont-0.1.4/DrDimont/R/network_generation.R | 3 DrDimont-0.1.4/DrDimont/R/network_reduction.R | 5 DrDimont-0.1.4/DrDimont/R/pipeline_functions.R | 2144 +++++----- DrDimont-0.1.4/DrDimont/R/settings.R | 129 DrDimont-0.1.4/DrDimont/R/utilities.R | 196 DrDimont-0.1.4/DrDimont/build/vignette.rds |binary DrDimont-0.1.4/DrDimont/data/combined_graphs_example.rda |binary DrDimont-0.1.4/DrDimont/data/correlation_matrices_example.rda |binary DrDimont-0.1.4/DrDimont/data/differential_graph_example.rda |binary DrDimont-0.1.4/DrDimont/data/drug_response_scores_example.rda |binary DrDimont-0.1.4/DrDimont/data/drug_target_edges_example.rda |binary DrDimont-0.1.4/DrDimont/data/individual_graphs_example.rda |binary DrDimont-0.1.4/DrDimont/data/interaction_score_graphs_example.rda |binary DrDimont-0.1.4/DrDimont/data/layers_example.rda |binary DrDimont-0.1.4/DrDimont/data/metabolite_data.rda |binary DrDimont-0.1.4/DrDimont/data/metabolite_protein_interactions.rda |binary DrDimont-0.1.4/DrDimont/inst/CITATION |only DrDimont-0.1.4/DrDimont/inst/doc/DrDimont_Vignette.R | 377 - DrDimont-0.1.4/DrDimont/inst/doc/DrDimont_Vignette.Rmd | 854 ++- DrDimont-0.1.4/DrDimont/inst/doc/DrDimont_Vignette.html | 2110 +++++---- DrDimont-0.1.4/DrDimont/inst/requirements_pip.txt | 2 DrDimont-0.1.4/DrDimont/man/calculate_interaction_score.Rd | 8 DrDimont-0.1.4/DrDimont/man/check_connection.Rd | 8 DrDimont-0.1.4/DrDimont/man/check_drug_target.Rd | 10 DrDimont-0.1.4/DrDimont/man/check_drug_targets_in_layers.Rd | 11 DrDimont-0.1.4/DrDimont/man/check_input.Rd | 24 DrDimont-0.1.4/DrDimont/man/check_layer.Rd | 14 DrDimont-0.1.4/DrDimont/man/check_sensible_connections.Rd | 29 DrDimont-0.1.4/DrDimont/man/chunk.Rd | 1 DrDimont-0.1.4/DrDimont/man/chunk_2gether.Rd | 1 DrDimont-0.1.4/DrDimont/man/combine_graphs.Rd | 1 DrDimont-0.1.4/DrDimont/man/compute_correlation_matrices.Rd | 23 DrDimont-0.1.4/DrDimont/man/compute_drug_response_scores.Rd | 12 DrDimont-0.1.4/DrDimont/man/corPvalueStudentParallel.Rd | 1 DrDimont-0.1.4/DrDimont/man/create_unique_layer_node_ids.Rd | 1 DrDimont-0.1.4/DrDimont/man/determine_drug_targets.Rd | 18 DrDimont-0.1.4/DrDimont/man/drdimont_settings.Rd | 112 DrDimont-0.1.4/DrDimont/man/find_targets.Rd | 1 DrDimont-0.1.4/DrDimont/man/generate_combined_graphs.Rd | 26 DrDimont-0.1.4/DrDimont/man/generate_differential_score_graph.Rd | 10 DrDimont-0.1.4/DrDimont/man/generate_individual_graphs.Rd | 26 DrDimont-0.1.4/DrDimont/man/generate_interaction_score_graphs.Rd | 38 DrDimont-0.1.4/DrDimont/man/generate_reduced_graph.Rd | 1 DrDimont-0.1.4/DrDimont/man/get_layer.Rd | 1 DrDimont-0.1.4/DrDimont/man/get_layer_setting.Rd | 1 DrDimont-0.1.4/DrDimont/man/graph_metrics.Rd | 12 DrDimont-0.1.4/DrDimont/man/install_python_dependencies.Rd | 16 DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_id.Rd | 1 DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_table.Rd | 1 DrDimont-0.1.4/DrDimont/man/load_interaction_score_output.Rd | 1 DrDimont-0.1.4/DrDimont/man/make_connection.Rd | 23 DrDimont-0.1.4/DrDimont/man/make_drug_target.Rd | 7 DrDimont-0.1.4/DrDimont/man/make_layer.Rd | 18 DrDimont-0.1.4/DrDimont/man/network_reduction_by_p_value.Rd | 1 DrDimont-0.1.4/DrDimont/man/network_reduction_by_pickHardThreshold.Rd | 1 DrDimont-0.1.4/DrDimont/man/return_errors.Rd | 26 DrDimont-0.1.4/DrDimont/man/run_pipeline.Rd | 44 DrDimont-0.1.4/DrDimont/man/sample_size.Rd | 1 DrDimont-0.1.4/DrDimont/man/set_cluster.Rd | 1 DrDimont-0.1.4/DrDimont/man/shutdown_cluster.Rd | 1 DrDimont-0.1.4/DrDimont/man/target_edge_list.Rd | 1 DrDimont-0.1.4/DrDimont/man/write_interaction_score_input.Rd | 1 DrDimont-0.1.4/DrDimont/vignettes/220401_overview.png |only DrDimont-0.1.4/DrDimont/vignettes/DrDimont_Vignette.Rmd | 854 ++- 72 files changed, 4189 insertions(+), 4002 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.3 dated 2022-03-17 and 0.1.4 dated 2022-09-23
DESCRIPTION | 8 - MD5 | 14 - R/wdnr.gis-package.R | 3 inst/doc/wdnr.gis-intro.Rmd | 2 inst/doc/wdnr.gis-intro.html | 273 +++++++++++++++++++++++++++++++++--- man/wdnr.gis-package.Rd | 3 tests/testthat/test-get-functions.R | 37 ++-- vignettes/wdnr.gis-intro.Rmd | 2 8 files changed, 291 insertions(+), 51 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.2-1 dated 2022-08-14 and 1.2-2 dated 2022-09-23
DESCRIPTION | 12 ++-- MD5 | 10 ++-- NEWS.md | 7 ++ R/memoiR.R | 14 +++++ inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 12 ++-- inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 25 +++++----- 6 files changed, 51 insertions(+), 29 deletions(-)
Title: Desparsified Lasso Inference for Time Series
Description: Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <arXiv:2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <arXiv:2209.03218>.
Author: Robert Adamek [cre, aut],
Stephan Smeekes [aut],
Ines Wilms [aut]
Maintainer: Robert Adamek <robertadamek94@gmail.com>
Diff between desla versions 0.1.0 dated 2021-11-11 and 0.2.0 dated 2022-09-23
DESCRIPTION | 15 MD5 | 33 NAMESPACE | 7 NEWS.md | 19 R/R_functions.R | 800 +++++++++++++++++------ R/RcppExports.R | 12 README.md | 184 +++++ build/partial.rdb |binary inst/REFERENCES.bib | 10 man/HDLP.Rd | 49 - man/coef.desla.Rd |only man/confint.desla.Rd |only man/create_state_dummies.Rd |only man/create_state_dummies_from_datamatrix.Rd |only man/create_state_dummies_from_vector.Rd |only man/desla.Rd | 116 --- man/plot.hdlp.Rd |only man/print.desla.Rd |only man/print.summary.desla.Rd |only man/summary.desla.Rd |only src/RcppExports.cpp | 46 + src/rcpp_functions.cpp | 954 ++++++++++++++++++++++------ 22 files changed, 1699 insertions(+), 546 deletions(-)
Title: 3D Volcano Plots and Polar Plots for Three-Class Data
Description: Generates interactive plots for analysing and visualising
three-class high dimensional data. It is particularly suited to visualising
differences in continuous attributes such as gene/protein/biomarker
expression levels between three groups. Differential gene/biomarker
expression analysis between two classes is typically shown as a volcano
plot. However, with three groups this type of visualisation is particularly
difficult to interpret. This package generates 3D volcano plots and 3-way
polar plots for easier interpretation of three-class data.
Author: Katriona Goldmann [aut, cre] ,
Myles Lewis [aut]
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>
Diff between volcano3D versions 2.0.0 dated 2022-07-05 and 2.0.8 dated 2022-09-23
DESCRIPTION | 12 +-- MD5 | 92 +++++++++++++++++------------ NAMESPACE | 30 +++++++++ NEWS.md | 19 ++++++ R/add_animation.R | 7 +- R/boxplot_trio.R | 67 +++++++++++---------- R/boxplot_trio_old.R | 1 R/deseq_2x3.R |only R/deseq_2x3_polar.R |only R/deseq_polar.R | 62 +++++++++++++------- R/forest_plot.R |only R/polar_coords.R | 133 ++++++++++++++++++++++++++++++++----------- R/polar_coords_2x3.R |only R/polar_grid.R | 7 +- R/radial_ggplot.R | 25 +++----- R/radial_ggplot_old.R | 1 R/radial_plotly.R | 52 +++++++++------- R/radial_plotly_old.R | 1 R/show_grid.R | 2 R/significance_subset.R | 8 +- R/volcano3D.R | 25 +++++--- R/volcano3D_old.R | 2 R/voom_polar.R | 46 ++++++++++---- build/vignette.rds |binary inst/WORDLIST | 42 ++++++------- inst/doc/Vignette.R | 5 + inst/doc/Vignette.html | 52 ++++++++++++---- inst/doc/Vignette.rmd | 47 ++++++++++++--- inst/doc/Vignette_2x3.R |only inst/doc/Vignette_2x3.Rmd |only inst/doc/Vignette_2x3.html |only man/add_animation.Rd | 17 +++-- man/boxplot_trio.Rd | 28 ++++----- man/calc_pvals.Rd | 6 - man/calc_stats_2x3.Rd |only man/deseq_2x3.Rd |only man/deseq_2x3_polar.Rd |only man/deseq_polar.Rd | 36 +++++++---- man/forest_plot.Rd |only man/polar_coords.Rd | 63 ++++++++++++-------- man/polar_coords_2x3.Rd |only man/polar_grid.Rd | 18 ++--- man/radial_ggplot.Rd | 21 +++--- man/radial_plotly.Rd | 42 ++++++++----- man/significance_subset.Rd | 6 - man/syn_example_meta.Rd | 4 - man/syn_example_rld.Rd | 4 - man/volc3d-class.Rd |only man/volcano3D.Rd | 24 ++++--- man/voom_polar.Rd | 32 +++++++--- vignettes/Vignette.rmd | 47 ++++++++++++--- vignettes/Vignette_2x3.Rmd |only vignettes/forest.png |only vignettes/radial_2x3_neg.png |only vignettes/radial_2x3_pos.png |only vignettes/volc3d_2x3.png |only 56 files changed, 715 insertions(+), 371 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph]
,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 0.2.3 dated 2022-08-15 and 0.3.0 dated 2022-09-23
cffr-0.2.3/cffr/R/cff.R |only cffr-0.2.3/cffr/man/cff.Rd |only cffr-0.2.3/cffr/tests/testthat/_snaps/cff.md |only cffr-0.2.3/cffr/tests/testthat/test-cff.R |only cffr-0.3.0/cffr/DESCRIPTION | 6 cffr-0.3.0/cffr/MD5 | 87 cffr-0.3.0/cffr/NAMESPACE | 1 cffr-0.3.0/cffr/NEWS.md | 8 cffr-0.3.0/cffr/R/cff_create.R | 57 cffr-0.3.0/cffr/R/cff_gha_update.R | 146 - cffr-0.3.0/cffr/R/cff_parse_citation.R | 863 ++++---- cffr-0.3.0/cffr/R/cff_parse_person.R | 468 ++-- cffr-0.3.0/cffr/R/cff_read.R |only cffr-0.3.0/cffr/R/cff_to_bibtex.R | 19 cffr-0.3.0/cffr/R/parse_citation.R | 602 +++--- cffr-0.3.0/cffr/R/write_bib.R | 206 +- cffr-0.3.0/cffr/README.md | 12 cffr-0.3.0/cffr/inst/doc/bibtex_cff.html | 13 cffr-0.3.0/cffr/inst/doc/cffr.html | 288 +- cffr-0.3.0/cffr/inst/doc/crosswalk.R | 4 cffr-0.3.0/cffr/inst/doc/crosswalk.Rmd | 4 cffr-0.3.0/cffr/inst/doc/crosswalk.html | 339 +-- cffr-0.3.0/cffr/inst/doc/paper.html | 13 cffr-0.3.0/cffr/inst/examples/DESCRIPTION_two_emails |only cffr-0.3.0/cffr/man/cff_create.Rd | 4 cffr-0.3.0/cffr/man/cff_parse_citation.Rd | 2 cffr-0.3.0/cffr/man/cff_parse_person.Rd | 4 cffr-0.3.0/cffr/man/cff_read.Rd |only cffr-0.3.0/cffr/man/cff_to_bibtex.Rd | 5 cffr-0.3.0/cffr/man/cff_validate.Rd | 4 cffr-0.3.0/cffr/man/cff_write.Rd | 4 cffr-0.3.0/cffr/man/write_bib.Rd | 7 cffr-0.3.0/cffr/tests/testthat/_snaps/bibtex2cff.md | 14 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_create.md | 70 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_description.md | 304 --- cffr-0.3.0/cffr/tests/testthat/_snaps/cff_parse_citation.md | 71 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_read.md |only cffr-0.3.0/cffr/tests/testthat/_snaps/cff_to_bibtex.md | 8 cffr-0.3.0/cffr/tests/testthat/_snaps/cff_write.md | 51 cffr-0.3.0/cffr/tests/testthat/_snaps/encoding.md | 51 cffr-0.3.0/cffr/tests/testthat/_snaps/merge_desc_cit.md | 64 cffr-0.3.0/cffr/tests/testthat/test-bibtex2cff.R | 1162 ++++++------ cffr-0.3.0/cffr/tests/testthat/test-cff_create.R | 168 - cffr-0.3.0/cffr/tests/testthat/test-cff_description.R | 1 cffr-0.3.0/cffr/tests/testthat/test-cff_parse_citation.R | 5 cffr-0.3.0/cffr/tests/testthat/test-cff_parse_person.R | 220 +- cffr-0.3.0/cffr/tests/testthat/test-cff_read.R |only cffr-0.3.0/cffr/tests/testthat/test-cff_to_bibtex.R | 11 cffr-0.3.0/cffr/vignettes/crosswalk.Rmd | 4 49 files changed, 2478 insertions(+), 2892 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Utils for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph]
,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.2.0 dated 2022-06-21 and 0.2.1 dated 2022-09-23
tidyterra-0.2.0/tidyterra/inst/doc/tidyterra.R |only tidyterra-0.2.1/tidyterra/DESCRIPTION | 15 tidyterra-0.2.1/tidyterra/MD5 | 58 tidyterra-0.2.1/tidyterra/NEWS.md | 118 + tidyterra-0.2.1/tidyterra/R/geom_spat_contour.R | 199 +-- tidyterra-0.2.1/tidyterra/R/geom_spat_contour_fill.R | 158 -- tidyterra-0.2.1/tidyterra/R/geom_spatraster.R | 20 tidyterra-0.2.1/tidyterra/R/geom_spatraster_rgb.R | 600 +++++----- tidyterra-0.2.1/tidyterra/R/sysdata.rda |binary tidyterra-0.2.1/tidyterra/README.md | 2 tidyterra-0.2.1/tidyterra/build/partial.rdb |binary tidyterra-0.2.1/tidyterra/build/vignette.rds |binary tidyterra-0.2.1/tidyterra/data/cross_blended_hypsometric_tints_db.rda |binary tidyterra-0.2.1/tidyterra/data/hypsometric_tints_db.rda |binary tidyterra-0.2.1/tidyterra/data/volcano2.rda |binary tidyterra-0.2.1/tidyterra/inst/WORDLIST | 1 tidyterra-0.2.1/tidyterra/inst/doc/tidyterra.Rmd | 145 ++ tidyterra-0.2.1/tidyterra/inst/doc/tidyterra.html | 70 - tidyterra-0.2.1/tidyterra/man/as_tibble.Rd | 2 tidyterra-0.2.1/tidyterra/man/tidyterra-package.Rd | 1 tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spat_contour.R | 68 - tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spat_contour_fill.R | 68 - tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spatraster_1lyr.R | 48 tidyterra-0.2.1/tidyterra/tests/testthat/test-geom_spatraster_rgb.R | 64 - tidyterra-0.2.1/tidyterra/vignettes/full_spatvector-1.png |only tidyterra-0.2.1/tidyterra/vignettes/hypso-1.png |only tidyterra-0.2.1/tidyterra/vignettes/rgb-1.png |only tidyterra-0.2.1/tidyterra/vignettes/rgb-2.png |only tidyterra-0.2.1/tidyterra/vignettes/terra_sf-1.png |only tidyterra-0.2.1/tidyterra/vignettes/terra_sf-2.png |only tidyterra-0.2.1/tidyterra/vignettes/terraplots-1.png |only tidyterra-0.2.1/tidyterra/vignettes/terraplots-2.png |only tidyterra-0.2.1/tidyterra/vignettes/terraplots-3.png |only tidyterra-0.2.1/tidyterra/vignettes/tidyterra.Rmd | 145 ++ tidyterra-0.2.1/tidyterra/vignettes/unnamed-chunk-3-1.png |only tidyterra-0.2.1/tidyterra/vignettes/unnamed-chunk-8-1.png |only 36 files changed, 1052 insertions(+), 730 deletions(-)
Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode',
'Rscript' (Shells Including Windows Command-Line / / Unix
Terminal), and 'source'
Description: Determine the full path of the executing script. Works when
running a line or selection from a script in 'RStudio', 'Rgui', and
'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio',
and 'testthat::source_file', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>
Diff between this.path versions 1.0.0 dated 2022-09-21 and 1.0.1 dated 2022-09-23
DESCRIPTION | 6 - MD5 | 8 - build/partial.rdb |binary src/basename2.c | 308 +++++++++++++++++++++++++++++++++++++++++++++++++----- src/pathjoin.c | 4 5 files changed, 292 insertions(+), 34 deletions(-)
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant
versions of 'install.packages' and `require` for CRAN packages, packages
no longer on CRAN (i.e., archived), specific versions of packages,
and GitHub packages. This approach is developed to create reproducible
workflows that are flexible and fast enough to use while in development stages,
while able to build snapshots once a stable package collection is found.
As with other functions in a reproducible workflow, this package
emphasizes functions that return the same result whether it is
the first or subsequent times running the function, with subsequent times being
sufficiently fast that they can be run every time without undue waiting burden on
the user or developer.
Author: Eliot J B McIntire [aut, cre] ,
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.0.13 dated 2021-05-31 and 0.1.2 dated 2022-09-23
Require-0.0.13/Require/R/pkgDepAlt.R |only Require-0.0.13/Require/man/messageDF.Rd |only Require-0.0.13/Require/tests/testit/test-extract.R |only Require-0.0.13/Require/tests/testit/test-helpers.R |only Require-0.0.13/Require/tests/testit/test-other.R |only Require-0.0.13/Require/tests/testit/test-packagesLong.R |only Require-0.0.13/Require/tests/testit/test-pkgDep.R |only Require-0.1.2/Require/DESCRIPTION | 33 Require-0.1.2/Require/MD5 | 107 Require-0.1.2/Require/NAMESPACE | 139 Require-0.1.2/Require/NEWS.md | 299 - Require-0.1.2/Require/R/CRAN.R | 102 Require-0.1.2/Require/R/Require-helpers.R | 3953 +++++++++------- Require-0.1.2/Require/R/Require-package.R | 6 Require-0.1.2/Require/R/Require.R | 1106 ++-- Require-0.1.2/Require/R/RequireOptions.R | 199 Require-0.1.2/Require/R/extract.R | 210 Require-0.1.2/Require/R/helpers.R | 618 +- Require-0.1.2/Require/R/pkgDep.R | 1771 +++---- Require-0.1.2/Require/R/pkgSnapshot.R | 222 Require-0.1.2/Require/R/setLibPaths.R | 396 - Require-0.1.2/Require/R/setup.R | 438 + Require-0.1.2/Require/R/zzz.R | 83 Require-0.1.2/Require/README.md | 419 - Require-0.1.2/Require/inst/WORDLIST | 50 Require-0.1.2/Require/inst/cache-README |only Require-0.1.2/Require/inst/dotR |only Require-0.1.2/Require/inst/dotccache |only Require-0.1.2/Require/inst/examples/example_checkPath.R | 45 Require-0.1.2/Require/man/DESCRIPTION-helpers.Rd | 89 Require-0.1.2/Require/man/GitHubTools.Rd | 100 Require-0.1.2/Require/man/Require-internals.Rd | 197 Require-0.1.2/Require/man/Require.Rd | 579 +- Require-0.1.2/Require/man/RequireCacheDir.Rd |only Require-0.1.2/Require/man/RequireOptions.Rd | 163 Require-0.1.2/Require/man/checkPath.Rd | 131 Require-0.1.2/Require/man/chooseCRANmirror2.Rd | 30 Require-0.1.2/Require/man/detachAll.Rd | 75 Require-0.1.2/Require/man/extractPkgName.Rd | 70 Require-0.1.2/Require/man/getOptionRPackageCache.Rd |only Require-0.1.2/Require/man/installGithubPackage.Rd |only Require-0.1.2/Require/man/invertList.Rd | 44 Require-0.1.2/Require/man/linkOrCopy.Rd |only Require-0.1.2/Require/man/messageVerbose.Rd |only Require-0.1.2/Require/man/modifyList2.Rd | 54 Require-0.1.2/Require/man/normPath.Rd | 118 Require-0.1.2/Require/man/paddedFloatToChar.Rd |only Require-0.1.2/Require/man/pkgDep.Rd | 411 - Require-0.1.2/Require/man/pkgDepIfDepRemoved.Rd | 69 Require-0.1.2/Require/man/pkgSnapshot.Rd | 216 Require-0.1.2/Require/man/rCurrentVersion.Rd |only Require-0.1.2/Require/man/rversions.Rd |only Require-0.1.2/Require/man/setLibPaths.Rd | 161 Require-0.1.2/Require/man/setLinuxBinaryRepo.Rd |only Require-0.1.2/Require/man/setup.Rd | 117 Require-0.1.2/Require/man/tempdir2.Rd | 46 Require-0.1.2/Require/man/tempfile2.Rd | 56 Require-0.1.2/Require/man/trimVersionNumber.Rd | 40 Require-0.1.2/Require/man/useLinuxSourceCache.Rd |only Require-0.1.2/Require/tests/test-all.R | 7 Require-0.1.2/Require/tests/testit/test-0pkgSnapshot.R | 240 Require-0.1.2/Require/tests/testit/test-1packages.R | 400 - Require-0.1.2/Require/tests/testit/test-2extract.R |only Require-0.1.2/Require/tests/testit/test-3helpers.R |only Require-0.1.2/Require/tests/testit/test-4other.R |only Require-0.1.2/Require/tests/testit/test-5packagesLong.R |only Require-0.1.2/Require/tests/testit/test-6pkgDep.R |only 67 files changed, 7579 insertions(+), 6030 deletions(-)
Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning
platform that offers parallelized implementations of many supervised and
unsupervised machine learning algorithms such as Generalized Linear
Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests,
Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes,
Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection,
Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre],
Navdeep Gill [aut],
Spencer Aiello [aut],
Anqi Fu [aut],
Arno Candel [aut],
Cliff Click [aut],
Tom Kraljevic [aut],
Tomas Nykodym [aut],
Patrick Aboyoun [aut],
Michal Kurka [aut],
Michal Malohlava [aut],
Ludi Rehak [ctb],
Eric [...truncated...]
Maintainer: Erin LeDell <erin@h2o.ai>
Diff between h2o versions 3.36.1.2 dated 2022-05-27 and 3.38.0.1 dated 2022-09-23
h2o-3.36.1.2/h2o/man/with_no_h2o_progress.Rd |only h2o-3.38.0.1/h2o/DESCRIPTION | 27 h2o-3.38.0.1/h2o/MD5 | 103 +-- h2o-3.38.0.1/h2o/NAMESPACE | 9 h2o-3.38.0.1/h2o/R/communication.R | 41 + h2o-3.38.0.1/h2o/R/deeplearning.R | 2 h2o-3.38.0.1/h2o/R/explain.R | 376 +++++++++--- h2o-3.38.0.1/h2o/R/export.R | 10 h2o-3.38.0.1/h2o/R/extendedisolationforest.R | 2 h2o-3.38.0.1/h2o/R/frame.R | 12 h2o-3.38.0.1/h2o/R/gbm.R | 29 h2o-3.38.0.1/h2o/R/glm.R | 86 ++ h2o-3.38.0.1/h2o/R/import.R | 2 h2o-3.38.0.1/h2o/R/infogram.R | 1 h2o-3.38.0.1/h2o/R/isolationforest.R | 2 h2o-3.38.0.1/h2o/R/isotonicregression.R |only h2o-3.38.0.1/h2o/R/models.R | 131 +++- h2o-3.38.0.1/h2o/R/modelselection.R | 54 + h2o-3.38.0.1/h2o/R/naivebayes.R | 2 h2o-3.38.0.1/h2o/R/randomforest.R | 15 h2o-3.38.0.1/h2o/R/rulefit.R | 38 + h2o-3.38.0.1/h2o/R/segment.R | 2 h2o-3.38.0.1/h2o/R/stackedensemble.R | 2 h2o-3.38.0.1/h2o/R/upliftrandomforest.R | 2 h2o-3.38.0.1/h2o/R/xgboost.R | 13 h2o-3.38.0.1/h2o/inst/branch.txt | 2 h2o-3.38.0.1/h2o/inst/buildnum.txt | 2 h2o-3.38.0.1/h2o/man/case_insensitive_match_arg.Rd |only h2o-3.38.0.1/h2o/man/dot-has_model_coefficients.Rd |only h2o-3.38.0.1/h2o/man/dot-process_models_or_automl.Rd | 5 h2o-3.38.0.1/h2o/man/h2o-package.Rd | 6 h2o-3.38.0.1/h2o/man/h2o.anomaly.Rd | 2 h2o-3.38.0.1/h2o/man/h2o.as_date.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.confusionMatrix.Rd | 4 h2o-3.38.0.1/h2o/man/h2o.day.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.dayOfWeek.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.exportFile.Rd | 7 h2o-3.38.0.1/h2o/man/h2o.gbm.Rd | 17 h2o-3.38.0.1/h2o/man/h2o.get_predictors_added_per_step.Rd |only h2o-3.38.0.1/h2o/man/h2o.get_predictors_removed_per_step.Rd |only h2o-3.38.0.1/h2o/man/h2o.get_variable_inflation_factors.Rd |only h2o-3.38.0.1/h2o/man/h2o.glm.Rd | 46 + h2o-3.38.0.1/h2o/man/h2o.hour.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.isotonicregression.Rd |only h2o-3.38.0.1/h2o/man/h2o.make_leaderboard.Rd |only h2o-3.38.0.1/h2o/man/h2o.modelSelection.Rd | 20 h2o-3.38.0.1/h2o/man/h2o.month.Rd | 10 h2o-3.38.0.1/h2o/man/h2o.no_progress.Rd | 11 h2o-3.38.0.1/h2o/man/h2o.pareto_front.Rd |only h2o-3.38.0.1/h2o/man/h2o.r2.Rd | 2 h2o-3.38.0.1/h2o/man/h2o.randomForest.Rd | 9 h2o-3.38.0.1/h2o/man/h2o.rule_importance.Rd |only h2o-3.38.0.1/h2o/man/h2o.rulefit.Rd | 6 h2o-3.38.0.1/h2o/man/h2o.show_progress.Rd | 11 h2o-3.38.0.1/h2o/man/h2o.upload_model.Rd | 12 h2o-3.38.0.1/h2o/man/h2o.xgboost.Rd | 9 h2o-3.38.0.1/h2o/man/is.factor.Rd | 11 h2o-3.38.0.1/h2o/man/plot-methods.Rd |only h2o-3.38.0.1/h2o/man/show-H2OParetoFront-method.Rd |only 59 files changed, 973 insertions(+), 220 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', and 'SQLite'). Also includes support for
fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] ,
PostgreSQL Global Development Group [cph] ,
Oracle Inc. [cph] ,
Amazon Inc. [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 5.0.4 dated 2022-06-28 and 5.1.0 dated 2022-09-23
DatabaseConnector-5.0.4/DatabaseConnector/build/DatabaseConnector.pdf |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbAppendTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbClearResult-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbColumnInfo-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbCreateTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbDisconnect-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbExecute-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbExistsTable-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbFetch-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetRowCount-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetRowsAffected-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbGetStatement-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbHasCompleted-DatabaseConnectorResult-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbIsValid-DatabaseConnectorDbiConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbIsValid-DatabaseConnectorJdbcConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbListFields-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbListTables-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbQuoteIdentifier-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbQuoteString-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbReadTable-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbRemoveTable-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/dbWriteTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only DatabaseConnector-5.0.4/DatabaseConnector/man/show-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-5.1.0/DatabaseConnector/DESCRIPTION | 14 DatabaseConnector-5.1.0/DatabaseConnector/MD5 | 95 +--- DatabaseConnector-5.1.0/DatabaseConnector/NAMESPACE | 1 DatabaseConnector-5.1.0/DatabaseConnector/NEWS.md | 23 + DatabaseConnector-5.1.0/DatabaseConnector/R/Andromeda.R | 77 ++- DatabaseConnector-5.1.0/DatabaseConnector/R/BulkLoad.R | 8 DatabaseConnector-5.1.0/DatabaseConnector/R/Connect.R | 100 +++- DatabaseConnector-5.1.0/DatabaseConnector/R/CtasHack.R | 17 DatabaseConnector-5.1.0/DatabaseConnector/R/DBI.R | 207 ++++------ DatabaseConnector-5.1.0/DatabaseConnector/R/DatabaseConnector.R | 2 DatabaseConnector-5.1.0/DatabaseConnector/R/Drivers.R | 27 - DatabaseConnector-5.1.0/DatabaseConnector/R/InsertTable.R | 62 +- DatabaseConnector-5.1.0/DatabaseConnector/R/ListTables.R | 8 DatabaseConnector-5.1.0/DatabaseConnector/R/RStudio.R | 20 DatabaseConnector-5.1.0/DatabaseConnector/R/Sql.R | 26 - DatabaseConnector-5.1.0/DatabaseConnector/build/vignette.rds |binary DatabaseConnector-5.1.0/DatabaseConnector/inst/COPYRIGHTS | 9 DatabaseConnector-5.1.0/DatabaseConnector/inst/doc/Connecting.pdf |binary DatabaseConnector-5.1.0/DatabaseConnector/inst/doc/Querying.pdf |binary DatabaseConnector-5.1.0/DatabaseConnector/inst/java/DatabaseConnector.jar |binary DatabaseConnector-5.1.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedInsert.java | 18 DatabaseConnector-5.1.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedQuery.java | 7 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnector-package.Rd | 2 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorConnection-class.Rd | 107 +++++ DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorDbiConnection-class.Rd | 7 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorJdbcConnection-class.Rd | 7 DatabaseConnector-5.1.0/DatabaseConnector/man/DatabaseConnectorResult-class.Rd | 22 + DatabaseConnector-5.1.0/DatabaseConnector/man/connect.Rd | 12 DatabaseConnector-5.1.0/DatabaseConnector/man/createConnectionDetails.Rd | 12 DatabaseConnector-5.1.0/DatabaseConnector/man/dbms.Rd |only DatabaseConnector-5.1.0/DatabaseConnector/man/downloadJdbcDrivers.Rd | 6 DatabaseConnector-5.1.0/DatabaseConnector/man/jdbcDrivers.Rd | 2 DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/setup.R | 1 DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/test-connection.R | 108 ++++- DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/test-fetchResults.R | 161 ++++--- DatabaseConnector-5.1.0/DatabaseConnector/tests/testthat/test-sqlite.R |only 63 files changed, 754 insertions(+), 414 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also
contains a number of lower level 'CLI' elements: rules, boxes, trees,
and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI
colors and text styles as well.
Author: Gabor Csardi [aut, cre],
Hadley Wickham [ctb],
Kirill Mueller [ctb],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cli versions 3.4.0 dated 2022-09-08 and 3.4.1 dated 2022-09-23
cli-3.4.0/cli/R/rstudio-detect.R |only cli-3.4.1/cli/DESCRIPTION | 6 - cli-3.4.1/cli/MD5 | 99 ++++++++++-------- cli-3.4.1/cli/NEWS.md | 7 + cli-3.4.1/cli/R/aaa-utils.R | 10 + cli-3.4.1/cli/R/aab-rstudio-detect.R |only cli-3.4.1/cli/R/ansi-hyperlink.R | 2 cli-3.4.1/cli/R/ansi-palette.R | 4 cli-3.4.1/cli/R/ansi.R | 25 +++- cli-3.4.1/cli/R/ansiex.R | 36 ++++-- cli-3.4.1/cli/R/app.R | 7 + cli-3.4.1/cli/R/cli-errors.R |only cli-3.4.1/cli/R/cli.R | 99 ++++++++++++------ cli-3.4.1/cli/R/cliapp-docs.R | 2 cli-3.4.1/cli/R/cliapp.R | 4 cli-3.4.1/cli/R/defer.R | 6 - cli-3.4.1/cli/R/diff.R | 14 +- cli-3.4.1/cli/R/errors.R |only cli-3.4.1/cli/R/format-conditions.R | 10 + cli-3.4.1/cli/R/inline.R | 71 ++++++++---- cli-3.4.1/cli/R/onload.R | 2 cli-3.4.1/cli/R/rlang.R | 8 - cli-3.4.1/cli/R/themes.R | 3 cli-3.4.1/cli/R/tty.R | 9 + cli-3.4.1/cli/R/utf8.R | 28 +++-- cli-3.4.1/cli/R/width.R | 42 +++++-- cli-3.4.1/cli/man/format_inline.Rd | 5 cli-3.4.1/cli/man/links.Rd | 2 cli-3.4.1/cli/src/cli.h | 2 cli-3.4.1/cli/tests/testthat/_snaps/ansi-hyperlink.md |only cli-3.4.1/cli/tests/testthat/_snaps/ansi-make.md |only cli-3.4.1/cli/tests/testthat/_snaps/ansiex.md | 46 ++++++++ cli-3.4.1/cli/tests/testthat/_snaps/app.md |only cli-3.4.1/cli/tests/testthat/_snaps/console-width.md |only cli-3.4.1/cli/tests/testthat/_snaps/defer.md |only cli-3.4.1/cli/tests/testthat/_snaps/diff.md | 10 + cli-3.4.1/cli/tests/testthat/_snaps/inline-2.md | 24 ++++ cli-3.4.1/cli/tests/testthat/_snaps/lists.md | 9 + cli-3.4.1/cli/tests/testthat/_snaps/new-r |only cli-3.4.1/cli/tests/testthat/_snaps/old-r |only cli-3.4.1/cli/tests/testthat/_snaps/progress-along.md | 4 cli-3.4.1/cli/tests/testthat/_snaps/rlang-errors.md | 80 -------------- cli-3.4.1/cli/tests/testthat/_snaps/utf8.md |only cli-3.4.1/cli/tests/testthat/helper.R | 8 + cli-3.4.1/cli/tests/testthat/test-ansi-hyperlink.R | 7 + cli-3.4.1/cli/tests/testthat/test-ansi-make.R | 7 + cli-3.4.1/cli/tests/testthat/test-ansiex.R | 30 +++-- cli-3.4.1/cli/tests/testthat/test-app.R |only cli-3.4.1/cli/tests/testthat/test-console-width.R |only cli-3.4.1/cli/tests/testthat/test-defer.R |only cli-3.4.1/cli/tests/testthat/test-diff.R | 15 +- cli-3.4.1/cli/tests/testthat/test-format-conditions.R | 10 + cli-3.4.1/cli/tests/testthat/test-inline-2.R | 20 +++ cli-3.4.1/cli/tests/testthat/test-lists.R | 3 cli-3.4.1/cli/tests/testthat/test-progress-along.R | 5 cli-3.4.1/cli/tests/testthat/test-rlang-errors.R | 29 ----- cli-3.4.1/cli/tests/testthat/test-utf8.R | 6 + cli-3.4.1/cli/tests/testthat/test-utils.R | 2 58 files changed, 517 insertions(+), 301 deletions(-)
Title: Variational Inference for Hierarchical Generalized Linear Models
Description: Estimates hierarchical models using mean-field variational Bayes.
At present, it can estimate logistic, linear, and negative binomial models.
It can accommodate models with an arbitrary number of random effects and
requires no integration to estimate. It also provides the ability to improve
the quality of the approximation using marginal augmentation.
Goplerud (2022) <doi:10.1214/21-BA1266> provides details on the variational
algorithms.
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@pitt.edu>
Diff between vglmer versions 1.0.1 dated 2022-09-17 and 1.0.2 dated 2022-09-23
DESCRIPTION | 6 - MD5 | 24 ++-- NAMESPACE | 1 NEWS.md | 5 R/aux_functions.R | 19 ++- R/predict_functions.R | 9 + R/print_functions.R | 13 ++ R/spline_functions.R | 29 +++-- R/vglmer_regression.R | 67 +++++++---- man/v_s.Rd | 14 ++ man/vglmer-class.Rd | 6 + tests/testthat/test-predict.R | 20 +-- tests/testthat/test-splines.R | 240 ++++++++++++++++++++++++++++++++++++++---- 13 files changed, 370 insertions(+), 83 deletions(-)
Title: R Utilities for GFF Files
Description: R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Author: Juan Antonio Garcia-Martin [cre, aut]
,
Juan Carlos Oliveros [aut, ctb]
,
Rafael Torres-Perez [aut, ctb]
Maintainer: Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>
Diff between Rgff versions 0.1.4 dated 2022-09-19 and 0.1.5 dated 2022-09-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/Rgff.R | 4 +++- inst/doc/Using_Rgff.html | 10 +++++----- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test
and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between fbst versions 1.7 dated 2022-03-08 and 1.9 dated 2022-09-23
DESCRIPTION | 11 MD5 | 40 +- NAMESPACE | 5 R/fbst.R | 359 ++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/fbet.R | 11 inst/doc/fbet.Rmd | 19 inst/doc/fbet.html | 873 +++++++++++++++++++++------------------------ inst/doc/fbst.R | 12 inst/doc/fbst.Rmd | 15 inst/doc/fbst.html | 729 ++++++++++++++++--------------------- inst/doc/twodimfbst.R |only inst/doc/twodimfbst.Rmd |only inst/doc/twodimfbst.html |only man/bdm.Rd |only man/fbst.Rd | 26 - man/plot.fbet.Rd | 12 man/plot.fbst.Rd | 8 vignettes/fbet.Rmd | 19 vignettes/fbst.Rmd | 15 vignettes/normalModel.stan |only vignettes/twodimfbst.Rmd |only vignettes/twodimfbst_files |only 24 files changed, 1092 insertions(+), 1062 deletions(-)
Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix
estimation, particularly useful in high-dimensional settings. This
method relies upon the theory of loss-based estimator selection to
identify the optimal estimator of the covariance matrix from among a
prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph]
,
Nima Hejazi [aut] ,
Brian Collica [aut] ,
Jamarcus Liu [ctb],
Mark van der Laan [ctb, ths] ,
Sandrine Dudoit [ctb, ths]
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between cvCovEst versions 1.1.0 dated 2022-05-04 and 1.1.1 dated 2022-09-23
DESCRIPTION | 6 MD5 | 10 NEWS.md | 5 R/summary_functions.R | 6 build/partial.rdb |binary inst/doc/using_cvCovEst.html | 731 +++++++++++++++++++++++++++++++++---------- 6 files changed, 585 insertions(+), 173 deletions(-)
Title: Network-Based Communities and Kernel Machine Methods
Description: Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).
Author: Alexandria Jensen [aut, cre] ,
Peter DeWitt [ctb] ,
Debashis Ghosh [ths]
Maintainer: Alexandria Jensen <alexandria.jensen@cuanschutz.edu>
Diff between CommKern versions 1.0.0 dated 2022-09-20 and 1.0.1 dated 2022-09-23
CommKern-1.0.0/CommKern/data/simasd_covars.RData |only CommKern-1.0.1/CommKern/DESCRIPTION | 6 ++--- CommKern-1.0.1/CommKern/MD5 | 25 ++++++++++------------ CommKern-1.0.1/CommKern/NEWS.md | 7 ++++++ CommKern-1.0.1/CommKern/R/community_plot.R | 4 +-- CommKern-1.0.1/CommKern/R/hier_mult_spin.R | 15 +++++++------ CommKern-1.0.1/CommKern/README.md | 5 ++++ CommKern-1.0.1/CommKern/inst/doc/CommKern.R | 2 - CommKern-1.0.1/CommKern/inst/doc/CommKern.Rmd | 4 +-- CommKern-1.0.1/CommKern/inst/doc/CommKern.html | 16 ++++++-------- CommKern-1.0.1/CommKern/man/community_plot.Rd | 4 +-- CommKern-1.0.1/CommKern/man/hms.Rd | 11 +++++---- CommKern-1.0.1/CommKern/tests/test-matrix_to_df.R | 8 ++++++- CommKern-1.0.1/CommKern/vignettes/CommKern.Rmd | 4 +-- 14 files changed, 64 insertions(+), 47 deletions(-)
Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter.
Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between autostsm versions 3.0.2 dated 2022-09-02 and 3.0.3 dated 2022-09-23
autostsm-3.0.2/autostsm/R/RcppExports.R |only autostsm-3.0.2/autostsm/man/Rginv.Rd |only autostsm-3.0.2/autostsm/man/gen_inv.Rd |only autostsm-3.0.2/autostsm/man/kalman_filter.Rd |only autostsm-3.0.2/autostsm/src |only autostsm-3.0.3/autostsm/DESCRIPTION | 15 - autostsm-3.0.3/autostsm/MD5 | 34 +--- autostsm-3.0.3/autostsm/NAMESPACE | 3 autostsm-3.0.3/autostsm/NEWS.md | 7 autostsm-3.0.3/autostsm/R/stsm_detect_anomalies.R | 6 autostsm-3.0.3/autostsm/R/stsm_detect_breaks.R | 6 autostsm-3.0.3/autostsm/R/stsm_estimate.R | 14 - autostsm-3.0.3/autostsm/R/stsm_forecast.R | 11 - autostsm-3.0.3/autostsm/inst/doc/autostsm_vignette.Rmd | 17 -- autostsm-3.0.3/autostsm/inst/doc/autostsm_vignette.html | 57 ++++-- autostsm-3.0.3/autostsm/man/DGS5.Rd | 38 ++-- autostsm-3.0.3/autostsm/man/stsm_detect_anomalies.Rd | 108 ++++++------- autostsm-3.0.3/autostsm/man/stsm_detect_breaks.Rd | 132 ++++++++-------- autostsm-3.0.3/autostsm/vignettes/autostsm_vignette.Rmd | 17 -- 19 files changed, 226 insertions(+), 239 deletions(-)
Title: Process Control and Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyze data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 2.3.0 dated 2020-07-10 and 2.4.0 dated 2022-09-23
strvalidator-2.3.0/strvalidator/R/tableBalance.r |only strvalidator-2.3.0/strvalidator/R/tableBalance_gui.r |only strvalidator-2.3.0/strvalidator/R/tableCapillary.r |only strvalidator-2.3.0/strvalidator/R/tableCapillary_gui.r |only strvalidator-2.3.0/strvalidator/R/tablePrecision.r |only strvalidator-2.3.0/strvalidator/R/tablePrecision_gui.r |only strvalidator-2.3.0/strvalidator/R/tableStutter.r |only strvalidator-2.3.0/strvalidator/R/tableStutter_gui.r |only strvalidator-2.3.0/strvalidator/man/tableBalance.Rd |only strvalidator-2.3.0/strvalidator/man/tableBalance_gui.Rd |only strvalidator-2.3.0/strvalidator/man/tableCapillary.Rd |only strvalidator-2.3.0/strvalidator/man/tableCapillary_gui.Rd |only strvalidator-2.3.0/strvalidator/man/tablePrecision.Rd |only strvalidator-2.3.0/strvalidator/man/tablePrecision_gui.Rd |only strvalidator-2.3.0/strvalidator/man/tableStutter.Rd |only strvalidator-2.3.0/strvalidator/man/tableStutter_gui.Rd |only strvalidator-2.4.0/strvalidator/DESCRIPTION | 17 strvalidator-2.4.0/strvalidator/MD5 | 213 ++--- strvalidator-2.4.0/strvalidator/NAMESPACE | 30 strvalidator-2.4.0/strvalidator/NEWS | 50 + strvalidator-2.4.0/strvalidator/R/addData.r | 2 strvalidator-2.4.0/strvalidator/R/addData_gui.r | 89 +- strvalidator-2.4.0/strvalidator/R/addDye_gui.r | 58 - strvalidator-2.4.0/strvalidator/R/addMarker_gui.r | 62 - strvalidator-2.4.0/strvalidator/R/addSize_gui.r | 66 - strvalidator-2.4.0/strvalidator/R/calculateAT.r | 7 strvalidator-2.4.0/strvalidator/R/calculateAT6.r | 3 strvalidator-2.4.0/strvalidator/R/calculateAT6_gui.r | 164 ++-- strvalidator-2.4.0/strvalidator/R/calculateAT_gui.r | 135 +-- strvalidator-2.4.0/strvalidator/R/calculateAllT_gui.r | 60 - strvalidator-2.4.0/strvalidator/R/calculateAllele_gui.r | 138 +-- strvalidator-2.4.0/strvalidator/R/calculateCapillary_gui.r | 110 +- strvalidator-2.4.0/strvalidator/R/calculateConcordance_gui.r | 63 - strvalidator-2.4.0/strvalidator/R/calculateCopies_gui.r | 51 - strvalidator-2.4.0/strvalidator/R/calculateDropout.r | 5 strvalidator-2.4.0/strvalidator/R/calculateDropout_gui.r | 115 +-- strvalidator-2.4.0/strvalidator/R/calculateHb_gui.r | 74 - strvalidator-2.4.0/strvalidator/R/calculateHeight.r | 49 - strvalidator-2.4.0/strvalidator/R/calculateHeight_gui.r | 111 +- strvalidator-2.4.0/strvalidator/R/calculateLb.r | 3 strvalidator-2.4.0/strvalidator/R/calculateLb_gui.r | 124 +-- strvalidator-2.4.0/strvalidator/R/calculateMixture.r | 3 strvalidator-2.4.0/strvalidator/R/calculateMixture_gui.r | 135 +-- strvalidator-2.4.0/strvalidator/R/calculateOL_gui.r | 29 strvalidator-2.4.0/strvalidator/R/calculateOverlap_gui.r | 33 strvalidator-2.4.0/strvalidator/R/calculatePeaks_gui.r | 58 - strvalidator-2.4.0/strvalidator/R/calculatePullup_gui.r | 91 +- strvalidator-2.4.0/strvalidator/R/calculateRatio_gui.r | 97 +- strvalidator-2.4.0/strvalidator/R/calculateResultType_gui.r | 77 -- strvalidator-2.4.0/strvalidator/R/calculateSlope.r | 4 strvalidator-2.4.0/strvalidator/R/calculateSlope_gui.r | 100 +- strvalidator-2.4.0/strvalidator/R/calculateSpike_gui.R | 72 - strvalidator-2.4.0/strvalidator/R/calculateStatistics.r | 20 strvalidator-2.4.0/strvalidator/R/calculateStatistics_gui.r | 129 ++- strvalidator-2.4.0/strvalidator/R/calculateStutter.r | 2 strvalidator-2.4.0/strvalidator/R/calculateStutter_gui.r | 125 +-- strvalidator-2.4.0/strvalidator/R/checkSubset_gui.r | 78 +- strvalidator-2.4.0/strvalidator/R/columns.r | 7 strvalidator-2.4.0/strvalidator/R/columns_gui.r | 109 +- strvalidator-2.4.0/strvalidator/R/combine_gui.r | 86 +- strvalidator-2.4.0/strvalidator/R/cropData_gui.r | 68 - strvalidator-2.4.0/strvalidator/R/editData_gui.r | 81 +- strvalidator-2.4.0/strvalidator/R/export.r | 2 strvalidator-2.4.0/strvalidator/R/export_gui.r | 32 strvalidator-2.4.0/strvalidator/R/filterProfile.r | 4 strvalidator-2.4.0/strvalidator/R/filterProfile_gui.r | 158 ++-- strvalidator-2.4.0/strvalidator/R/generateEPG_gui.r | 94 +- strvalidator-2.4.0/strvalidator/R/getStrings.r | 7 strvalidator-2.4.0/strvalidator/R/ggsave_gui.r | 277 ++----- strvalidator-2.4.0/strvalidator/R/guessProfile_gui.r | 60 - strvalidator-2.4.0/strvalidator/R/import_gui.r | 28 strvalidator-2.4.0/strvalidator/R/makeKit_gui.r | 45 - strvalidator-2.4.0/strvalidator/R/modelDropout_gui.r | 93 +- strvalidator-2.4.0/strvalidator/R/plotAT_gui.r | 46 - strvalidator-2.4.0/strvalidator/R/plotBalance_gui.r | 63 - strvalidator-2.4.0/strvalidator/R/plotCapillary_gui.r | 50 - strvalidator-2.4.0/strvalidator/R/plotContamination_gui.r | 51 - strvalidator-2.4.0/strvalidator/R/plotDistribution_gui.r | 146 +-- strvalidator-2.4.0/strvalidator/R/plotDropout_gui.r | 63 - strvalidator-2.4.0/strvalidator/R/plotEPG2.R |only strvalidator-2.4.0/strvalidator/R/plotEPG2_gui.r |only strvalidator-2.4.0/strvalidator/R/plotGroups_gui.r | 133 +-- strvalidator-2.4.0/strvalidator/R/plotKit_gui.r | 31 strvalidator-2.4.0/strvalidator/R/plotPeaks_gui.r | 47 - strvalidator-2.4.0/strvalidator/R/plotPrecision_gui.r | 56 - strvalidator-2.4.0/strvalidator/R/plotPullup_gui.r | 72 - strvalidator-2.4.0/strvalidator/R/plotRatio_gui.r | 48 - strvalidator-2.4.0/strvalidator/R/plotResultType_gui.r | 48 - strvalidator-2.4.0/strvalidator/R/plotSlope_gui.r | 85 -- strvalidator-2.4.0/strvalidator/R/plotStutter_gui.r | 73 - strvalidator-2.4.0/strvalidator/R/readBinsFile.r | 2 strvalidator-2.4.0/strvalidator/R/readPanelsFile.r | 2 strvalidator-2.4.0/strvalidator/R/removeArtefact_gui.r | 107 +- strvalidator-2.4.0/strvalidator/R/removeSpike_gui.r | 102 +- strvalidator-2.4.0/strvalidator/R/sample_tableToList.R |only strvalidator-2.4.0/strvalidator/R/slim_gui.r | 84 -- strvalidator-2.4.0/strvalidator/R/strvalidator.r | 195 +++-- strvalidator-2.4.0/strvalidator/R/trim_gui.r | 62 - strvalidator-2.4.0/strvalidator/build |only strvalidator-2.4.0/strvalidator/inst/extdata/kit.txt | 378 ++++++++++ strvalidator-2.4.0/strvalidator/inst/extdata/languages/en_GB.txt | 329 +++----- strvalidator-2.4.0/strvalidator/inst/extdata/languages/es_ES.txt | 327 +++----- strvalidator-2.4.0/strvalidator/inst/extdata/languages/it_IT.txt | 327 +++----- strvalidator-2.4.0/strvalidator/man/calculateAT.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateAT6.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateDropout.Rd | 4 strvalidator-2.4.0/strvalidator/man/calculateHeight.Rd | 35 strvalidator-2.4.0/strvalidator/man/calculateHeight_gui.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateLb.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateMixture.Rd | 2 strvalidator-2.4.0/strvalidator/man/calculateStatistics.Rd | 3 strvalidator-2.4.0/strvalidator/man/calculateStatistics_gui.Rd | 3 strvalidator-2.4.0/strvalidator/man/modelDropout_gui.Rd | 22 strvalidator-2.4.0/strvalidator/man/plotContamination_gui.Rd | 2 strvalidator-2.4.0/strvalidator/man/plotDropout_gui.Rd | 8 strvalidator-2.4.0/strvalidator/man/plotEPG2.Rd |only strvalidator-2.4.0/strvalidator/man/plotEPG2_gui.Rd |only strvalidator-2.4.0/strvalidator/man/sample_tableToList.Rd |only strvalidator-2.4.0/strvalidator/tests/testthat/test-calculateHeight.r | 159 +++- 119 files changed, 3626 insertions(+), 3550 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 1.2.0 dated 2022-09-10 and 1.2.1 dated 2022-09-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/hBayesDM.R | 2 ++ R/plot.hBayesDM.R | 2 ++ man/hBayesDM-package.Rd | 1 + man/plot.hBayesDM.Rd | 1 + 7 files changed, 20 insertions(+), 10 deletions(-)
Title: Integration for the UM-Bridge Protocol
Description: A convenient wrapper for the UM-Bridge protocol. UM-Bridge is a protocol designed for coupling uncertainty quantification (or statistical / optimization) software to numerical models. A model is represented as a mathematical function with optional support for derivatives via Jacobian actions etc.
Author: Linus Seelinger [aut, cre]
Maintainer: Linus Seelinger <mail@linusseelinger.de>
Diff between umbridge versions 0.9 dated 2022-09-12 and 1.0 dated 2022-09-23
DESCRIPTION | 6 +- MD5 | 29 ++++++----- NAMESPACE | 1 R/umbridge.R | 100 +++++++++++++++++++++++++++++++---------- man/apply_hessian.Rd | 3 + man/apply_jacobian.Rd | 3 + man/evaluate.Rd | 4 + man/get_models.Rd |only man/gradient.Rd | 3 + man/model_input_sizes.Rd | 6 ++ man/model_output_sizes.Rd | 6 ++ man/supports_apply_hessian.Rd | 4 + man/supports_apply_jacobian.Rd | 4 + man/supports_evaluate.Rd | 4 + man/supports_gradient.Rd | 4 + tests/testthat/test-umbridge.R | 31 ++++++------ 16 files changed, 147 insertions(+), 61 deletions(-)
Title: 'anndata' for R
Description: A 'reticulate' wrapper for the Python package 'anndata'.
Provides a scalable way of keeping track of data and learned
annotations. Used to read from and write to the h5ad file format.
Author: Philipp Angerer [ccp] ,
Alex Wolf [ccp] ,
Isaac Virshup [ccp] ,
Sergei Rybakov [ccp] ,
Robrecht Cannoodt [aut, cre, cph]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between anndata versions 0.7.5.4 dated 2022-08-23 and 0.7.5.5 dated 2022-09-23
DESCRIPTION | 6 +-- MD5 | 23 +++++++------- NAMESPACE | 2 + NEWS.md | 4 ++ R/class_anndata.R | 56 +++++++++++++++++++++++++++++++----- R/package.R | 2 - README.md | 20 ------------ inst/doc/getting_started.html | 21 +++++++++---- inst/doc/scanpy_demo.html | 13 ++++++-- man/AnnDataHelpers.Rd | 6 +++ tests/testthat/test-anndata.R | 4 +- tests/testthat/test-backed_sparse.R |only tests/testthat/test-base.R | 2 - 13 files changed, 105 insertions(+), 54 deletions(-)
Title: Partition/Decomposition of Breeding Values by Paths of
Information
Description: A software that implements a method for partitioning genetic trends to
quantify the sources of genetic gain in breeding programmes.
The partitioning method is described in Garcia-Cortes et al.
(2008) <doi:10.1017/S175173110800205X>. The package includes the
main function AlphaPart for partitioning breeding values and auxiliary
functions for manipulating data and summarizing, visualizing, and saving
results.
Author: Gregor Gorjanc [aut, cre] ,
Jana Obsteter [aut] ,
Thiago de Paula Oliveira [aut]
Maintainer: Gregor Gorjanc <highlander.research.lab@gmail.com>
Diff between AlphaPart versions 0.9.5 dated 2022-07-07 and 0.9.7 dated 2022-09-23
DESCRIPTION | 13 +++++++------ MD5 | 25 +++++++++++++++---------- R/AlphaPartSubset.R | 4 ++-- R/AlphaPartSum.R | 4 ++-- R/methods.R | 6 +++--- R/write.csv.R | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/alphapart-variance.R |only inst/doc/alphapart-variance.Rmd |only inst/doc/alphapart-variance.html |only inst/doc/alphapart-vignette.Rmd | 4 +++- inst/doc/alphapart-vignette.html | 8 ++++---- inst/extdata |only vignettes/alphapart-variance.Rmd |only vignettes/alphapart-vignette.Rmd | 4 +++- 16 files changed, 43 insertions(+), 33 deletions(-)
Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for
simulating large systems with Gillespie's Stochastic Simulation
Algorithm ('SSA'). This package is the spiritual successor to the
'GillespieSSA' package originally written by Mario Pineda-Krch.
Benefits of this package include major speed improvements (>100x),
easier to understand documentation, and many unit tests that try to
ensure the package works as intended. Cannoodt and Saelens et al. (2020)
<doi:10.1101/2020.02.06.936971>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between GillespieSSA2 versions 0.2.8 dated 2021-05-18 and 0.2.10 dated 2022-09-23
DESCRIPTION | 8 +++--- MD5 | 38 ++++++++++++++--------------- NEWS.md | 8 ++++++ R/zzz.R | 2 - README.md | 25 ++----------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/an_introduction.html | 18 +++++++++---- inst/doc/converting_from_GillespieSSA.html | 22 +++++++++++----- inst/doc/decaying_dimer.html | 20 ++++++++++----- inst/doc/epi_chain.html | 20 ++++++++++----- inst/doc/linear_chain.html | 20 ++++++++++----- inst/doc/logistic_growth.html | 20 ++++++++++----- inst/doc/lotka_predator_prey.html | 20 ++++++++++----- inst/doc/radioactive_decay.html | 20 ++++++++++----- inst/doc/rm_predator_prey.html | 20 ++++++++++----- inst/doc/sir.html | 20 ++++++++++----- src/RcppExports.cpp | 5 +++ src/ssa_simulation.cpp | 16 ++++-------- src/test_helper_funs.cpp | 2 + 20 files changed, 188 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-09 3.2.0
2020-09-10 3.1.2
2020-07-05 3.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-08 2.2.0
2022-03-25 2.1.0
2021-05-10 2.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-08 2.0.2
Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern (effect size) of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Si Gao [aut, cre, dtc] ,
Peter Kochunov [aut, dtc, cph, fnd] ,
Kathryn Hatch [ctb, dtc] ,
Yizhou Ma [ctb, dtc] ,
Fatima Talib [ctb]
Maintainer: Si Gao <sgao@som.umaryland.edu>
Diff between RVIpkg versions 0.3.0 dated 2022-03-10 and 0.3.1 dated 2022-09-23
DESCRIPTION | 50 ++++++----- MD5 | 28 +++--- R/EP.GM.R | 6 - R/EP.Subcortical.R | 6 - R/EP.WM.R | 6 - R/RVI_func.R | 208 ++++++++++++++++++++++++------------------------ R/sysdata.rda |binary build/partial.rdb |binary data/EP.GM.rda |binary data/EP.Subcortical.rda |binary data/EP.WM.rda |binary man/EP.GM.Rd | 6 - man/EP.Subcortical.Rd | 6 - man/EP.WM.Rd | 6 - man/RVI_func.Rd | 9 +- 15 files changed, 175 insertions(+), 156 deletions(-)
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.9 dated 2021-10-08 and 1.0.10 dated 2022-09-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/calculate_distance.R | 14 +++++++------- README.md | 34 ++-------------------------------- build/vignette.rds |binary inst/doc/functionality.html | 30 +++++++++++++++++++----------- man/calculate_distance.Rd | 24 ++++++++++++++++++------ tests/testthat/test-h5.R | 2 +- 9 files changed, 63 insertions(+), 69 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Melissa Hallow [aut],
Wenping Wang [aut],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Awad H. Al-Mohy [ctb],
Matt Dowle [ctb],
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Arun Srinivasan [ctb],
Ernst Hair [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.0.7 dated 2022-05-17 and 2.0.8 dated 2022-09-22
rxode2-2.0.7/rxode2/vignettes/rxode2-intro.R |only rxode2-2.0.7/rxode2/vignettes/rxode2-tutorials.R |only rxode2-2.0.8/rxode2/DESCRIPTION | 10 rxode2-2.0.8/rxode2/MD5 | 281 - rxode2-2.0.8/rxode2/NAMESPACE | 31 rxode2-2.0.8/rxode2/NEWS.md | 60 rxode2-2.0.8/rxode2/R/RcppExports.R | 70 rxode2-2.0.8/rxode2/R/asFunction.R |only rxode2-2.0.8/rxode2/R/assert.R | 3 rxode2-2.0.8/rxode2/R/dsl.R | 65 rxode2-2.0.8/rxode2/R/err-foceiBase.R | 224 - rxode2-2.0.8/rxode2/R/err-sim.R | 71 rxode2-2.0.8/rxode2/R/err.R | 196 rxode2-2.0.8/rxode2/R/et.R | 4 rxode2-2.0.8/rxode2/R/fixef.R |only rxode2-2.0.8/rxode2/R/geom-amt.R | 4 rxode2-2.0.8/rxode2/R/llik.R |only rxode2-2.0.8/rxode2/R/mu.R | 57 rxode2-2.0.8/rxode2/R/piping-ini.R | 40 rxode2-2.0.8/rxode2/R/piping-model.R | 30 rxode2-2.0.8/rxode2/R/piping.R | 26 rxode2-2.0.8/rxode2/R/plot.R | 26 rxode2-2.0.8/rxode2/R/reexport.R | 3 rxode2-2.0.8/rxode2/R/rxJacobian.R | 2 rxode2-2.0.8/rxode2/R/rxShiny.R | 10 rxode2-2.0.8/rxode2/R/rxUiGet.R | 53 rxode2-2.0.8/rxode2/R/rxValidate.R | 1 rxode2-2.0.8/rxode2/R/rxode-options.R | 5 rxode2-2.0.8/rxode2/R/rxode2.R | 23 rxode2-2.0.8/rxode2/R/rxode2_md5.R | 2 rxode2-2.0.8/rxode2/R/rxrandom.R | 77 rxode2-2.0.8/rxode2/R/rxsolve.R | 69 rxode2-2.0.8/rxode2/R/symengine.R | 434 +- rxode2-2.0.8/rxode2/R/ui-bind.R | 6 rxode2-2.0.8/rxode2/R/ui.R | 47 rxode2-2.0.8/rxode2/R/utils.R | 5 rxode2-2.0.8/rxode2/build/partial.rdb |binary rxode2-2.0.8/rxode2/build/vignette.rds |binary rxode2-2.0.8/rxode2/data/rxReservedKeywords.rda |binary rxode2-2.0.8/rxode2/inst/doc/rxode2-syntax.Rmd | 4 rxode2-2.0.8/rxode2/inst/doc/rxode2-syntax.html | 24 rxode2-2.0.8/rxode2/inst/include/rxode2.h | 69 rxode2-2.0.8/rxode2/inst/include/rxode2_RcppExports.h | 42 rxode2-2.0.8/rxode2/inst/include/rxode2_control.h | 3 rxode2-2.0.8/rxode2/inst/include/rxode2_model_shared.c | 137 rxode2-2.0.8/rxode2/inst/include/rxode2_model_shared.h | 116 rxode2-2.0.8/rxode2/man/add.dosing.Rd | 2 rxode2-2.0.8/rxode2/man/add.sampling.Rd | 2 rxode2-2.0.8/rxode2/man/dot-handleSingleErrTypeNormOrTFoceiBase.Rd | 15 rxode2-2.0.8/rxode2/man/dot-rxGetPredictionDVTransform.Rd |only rxode2-2.0.8/rxode2/man/dot-rxJacobian.Rd | 2 rxode2-2.0.8/rxode2/man/dot-s3register.Rd | 6 rxode2-2.0.8/rxode2/man/et.Rd | 8 rxode2-2.0.8/rxode2/man/etRbind.Rd | 2 rxode2-2.0.8/rxode2/man/etRep.Rd | 2 rxode2-2.0.8/rxode2/man/etSeq.Rd | 2 rxode2-2.0.8/rxode2/man/ini.Rd | 6 rxode2-2.0.8/rxode2/man/llikBeta.Rd |only rxode2-2.0.8/rxode2/man/llikBinom.Rd |only rxode2-2.0.8/rxode2/man/llikCauchy.Rd |only rxode2-2.0.8/rxode2/man/llikChisq.Rd |only rxode2-2.0.8/rxode2/man/llikExp.Rd |only rxode2-2.0.8/rxode2/man/llikF.Rd |only rxode2-2.0.8/rxode2/man/llikGamma.Rd |only rxode2-2.0.8/rxode2/man/llikGeom.Rd |only rxode2-2.0.8/rxode2/man/llikNbinom.Rd |only rxode2-2.0.8/rxode2/man/llikNbinomMu.Rd |only rxode2-2.0.8/rxode2/man/llikNorm.Rd |only rxode2-2.0.8/rxode2/man/llikPois.Rd |only rxode2-2.0.8/rxode2/man/llikT.Rd |only rxode2-2.0.8/rxode2/man/llikUnif.Rd |only rxode2-2.0.8/rxode2/man/llikWeibull.Rd |only rxode2-2.0.8/rxode2/man/model.Rd | 6 rxode2-2.0.8/rxode2/man/phi.Rd | 2 rxode2-2.0.8/rxode2/man/reexports.Rd | 4 rxode2-2.0.8/rxode2/man/rxAppendModel.Rd | 5 rxode2-2.0.8/rxode2/man/rxCompile.Rd | 6 rxode2-2.0.8/rxode2/man/rxGetDistributionSimulationLines.Rd | 6 rxode2-2.0.8/rxode2/man/rxIndLin_.Rd | 2 rxode2-2.0.8/rxode2/man/rxPreferredDistributionName.Rd | 4 rxode2-2.0.8/rxode2/man/rxSolve.Rd | 23 rxode2-2.0.8/rxode2/man/rxToSE.Rd | 6 rxode2-2.0.8/rxode2/man/rxbeta.Rd | 9 rxode2-2.0.8/rxode2/man/rxbinom.Rd | 5 rxode2-2.0.8/rxode2/man/rxcauchy.Rd | 9 rxode2-2.0.8/rxode2/man/rxchisq.Rd | 5 rxode2-2.0.8/rxode2/man/rxexp.Rd | 5 rxode2-2.0.8/rxode2/man/rxf.Rd | 9 rxode2-2.0.8/rxode2/man/rxgamma.Rd | 13 rxode2-2.0.8/rxode2/man/rxgeom.Rd | 5 rxode2-2.0.8/rxode2/man/rxnbinom.Rd |only rxode2-2.0.8/rxode2/man/rxode2.Rd | 31 rxode2-2.0.8/rxode2/man/rxpois.Rd | 5 rxode2-2.0.8/rxode2/man/rxt.Rd | 5 rxode2-2.0.8/rxode2/man/rxunif.Rd | 9 rxode2-2.0.8/rxode2/man/rxweibull.Rd | 9 rxode2-2.0.8/rxode2/man/stat_amt.Rd | 16 rxode2-2.0.8/rxode2/man/stat_cens.Rd | 14 rxode2-2.0.8/rxode2/src/Makevars.in | 6 rxode2-2.0.8/rxode2/src/RcppExports.cpp | 270 + rxode2-2.0.8/rxode2/src/codegen.c | 504 +- rxode2-2.0.8/rxode2/src/codegen.h | 2 rxode2-2.0.8/rxode2/src/codegen2.h | 194 rxode2-2.0.8/rxode2/src/etTran.cpp | 61 rxode2-2.0.8/rxode2/src/expm.cpp | 2 rxode2-2.0.8/rxode2/src/genModelVars.h | 6 rxode2-2.0.8/rxode2/src/getTime.h | 4 rxode2-2.0.8/rxode2/src/handle_evid.h | 1 rxode2-2.0.8/rxode2/src/init.c | 88 rxode2-2.0.8/rxode2/src/lincmt.c | 1843 ++++---- rxode2-2.0.8/rxode2/src/lincmtB.cpp | 12 rxode2-2.0.8/rxode2/src/llik.h |only rxode2-2.0.8/rxode2/src/llik2.h |only rxode2-2.0.8/rxode2/src/llikBeta.cpp |only rxode2-2.0.8/rxode2/src/llikBinom.cpp |only rxode2-2.0.8/rxode2/src/llikCauchy.cpp |only rxode2-2.0.8/rxode2/src/llikChisq.cpp |only rxode2-2.0.8/rxode2/src/llikExp.cpp |only rxode2-2.0.8/rxode2/src/llikF.cpp |only rxode2-2.0.8/rxode2/src/llikGamma.cpp |only rxode2-2.0.8/rxode2/src/llikGeom.cpp |only rxode2-2.0.8/rxode2/src/llikNbinom.cpp |only rxode2-2.0.8/rxode2/src/llikNbinom2.cpp |only rxode2-2.0.8/rxode2/src/llikNorm.cpp |only rxode2-2.0.8/rxode2/src/llikPois.cpp |only rxode2-2.0.8/rxode2/src/llikT.cpp |only rxode2-2.0.8/rxode2/src/llikUnif.cpp |only rxode2-2.0.8/rxode2/src/llikWeibull.cpp |only rxode2-2.0.8/rxode2/src/ode.h | 4 rxode2-2.0.8/rxode2/src/par_solve.cpp | 6 rxode2-2.0.8/rxode2/src/par_solve.h | 20 rxode2-2.0.8/rxode2/src/parseFuns.h | 22 rxode2-2.0.8/rxode2/src/parseFunsRandom.h | 55 rxode2-2.0.8/rxode2/src/parseStatements.h | 3 rxode2-2.0.8/rxode2/src/parseSyntaxErrors.h | 23 rxode2-2.0.8/rxode2/src/parseVars.h | 1 rxode2-2.0.8/rxode2/src/rxData.cpp | 2118 +++++----- rxode2-2.0.8/rxode2/src/rxData.h | 2 rxode2-2.0.8/rxode2/src/rxThreadData.h |only rxode2-2.0.8/rxode2/src/rxthreefry.cpp | 82 rxode2-2.0.8/rxode2/src/rxthreefry.h | 5 rxode2-2.0.8/rxode2/src/tran.c | 9 rxode2-2.0.8/rxode2/src/tran.h | 5 rxode2-2.0.8/rxode2/tests/testthat/test-dsl.R | 4 rxode2-2.0.8/rxode2/tests/testthat/test-expand-grid.R | 1 rxode2-2.0.8/rxode2/tests/testthat/test-fixef.R |only rxode2-2.0.8/rxode2/tests/testthat/test-fun.R | 35 rxode2-2.0.8/rxode2/tests/testthat/test-lincmt-solve.R | 40 rxode2-2.0.8/rxode2/tests/testthat/test-llik.R |only rxode2-2.0.8/rxode2/tests/testthat/test-parsing.R | 4 rxode2-2.0.8/rxode2/tests/testthat/test-rxSumProd-1.qs |only rxode2-2.0.8/rxode2/tests/testthat/test-rxSumProd.R |only rxode2-2.0.8/rxode2/tests/testthat/test-rxflag.R |only rxode2-2.0.8/rxode2/tests/testthat/test-ui-bad.R | 3 rxode2-2.0.8/rxode2/tests/testthat/test-ui-err.R | 24 rxode2-2.0.8/rxode2/tests/testthat/test-ui-expit.R |only rxode2-2.0.8/rxode2/tests/testthat/test-ui-focei-ord.R |only rxode2-2.0.8/rxode2/tests/testthat/test-ui-good.R | 42 rxode2-2.0.8/rxode2/tests/testthat/test-ui-ini-str.R |only rxode2-2.0.8/rxode2/tests/testthat/test-ui-piping.R | 21 rxode2-2.0.8/rxode2/tests/testthat/test-ui-pred-err.R | 2 rxode2-2.0.8/rxode2/tests/testthat/test-ui-promote.R |only rxode2-2.0.8/rxode2/tests/testthat/test-ui-simulation.R | 315 + rxode2-2.0.8/rxode2/tests/testthat/test-ui.R | 80 rxode2-2.0.8/rxode2/tests/testthat/test-zzzzz.R | 3 rxode2-2.0.8/rxode2/vignettes/rxode2-syntax.Rmd | 4 166 files changed, 5639 insertions(+), 2877 deletions(-)
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 1.1.1 dated 2022-08-12 and 1.1.1.992 dated 2022-09-22
DESCRIPTION | 6 - MD5 | 22 +++--- R/TCGA_id_conversion.R | 11 +-- R/fpkm_count_conversion.r | 42 ++++++++--- README.md | 17 +++- build/vignette.rds |binary inst/doc/GeoTcgaData.R | 6 + inst/doc/GeoTcgaData.Rmd | 27 +++++-- inst/doc/GeoTcgaData.html | 168 +++++++++++++++++++++++++--------------------- man/countToFpkm_matrix.Rd | 9 +- man/countToTpm_matrix.Rd | 9 +- vignettes/GeoTcgaData.Rmd | 27 +++++-- 12 files changed, 217 insertions(+), 127 deletions(-)
Title: Perform Batch Balanced KNN in R
Description: A fast and intuitive batch effect removal tool for single-cell data. BBKNN is originally used in the 'scanpy' python package, and now can be used with 'Seurat' seamlessly.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <liyuchen_1995@outlook.com>
Diff between bbknnR versions 1.0.1 dated 2022-08-23 and 1.0.2 dated 2022-09-22
bbknnR-1.0.1/bbknnR/tests/testthat/test_ridge.R |only bbknnR-1.0.2/bbknnR/DESCRIPTION | 8 ++++---- bbknnR-1.0.2/bbknnR/MD5 | 11 +++++------ bbknnR-1.0.2/bbknnR/NAMESPACE | 2 +- bbknnR-1.0.2/bbknnR/R/ridge_regression.R | 12 ++++++------ bbknnR-1.0.2/bbknnR/README.md | 7 +++++++ bbknnR-1.0.2/bbknnR/inst/doc/bbknnR-tutorial.html | 15 +++++++++++---- 7 files changed, 34 insertions(+), 21 deletions(-)
Title: Isoscape Computation and Inference of Spatial Origins using
Mixed Models
Description: Building isoscapes using mixed models and inferring the geographic
origin of samples based on their isotopic ratios. This package is essentially a
simplified interface to several other packages which implements a new
statistical framework based on mixed models. It uses 'spaMM' for fitting and
predicting isoscapes, and assigning an organism's origin depending on its
isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for
plotting the maps produced with 'raster' using 'lattice'.
Author: Alexandre Courtiol [aut, cre] ,
Francois Rousset [aut] ,
Marie-Sophie Rohwaeder [aut],
Stephanie Kramer-Schadt [aut]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>
Diff between IsoriX versions 0.8.3 dated 2022-09-12 and 0.9.0 dated 2022-09-22
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/calibfit.R | 2 +- R/isofind.R | 16 +++++++++------- inst/NEWS.Rd | 15 ++++++++++++++- man/calibfit.Rd | 2 +- 6 files changed, 35 insertions(+), 19 deletions(-)