Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.1.2 dated 2023-03-14 and 2.2.2 dated 2023-03-15
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Davis Vaughan [aut, cre],
data.table team [cph] and
their contribution to R's order),
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between vctrs versions 0.5.2 dated 2023-01-23 and 0.6.0 dated 2023-03-15
vctrs-0.5.2/vctrs/R/compat-friendly-type.R |only vctrs-0.5.2/vctrs/R/compat-lifecycle.R |only vctrs-0.5.2/vctrs/R/compat-linked-version.R |only vctrs-0.5.2/vctrs/R/compat-obj-type.R |only vctrs-0.5.2/vctrs/R/compat-purrr.R |only vctrs-0.5.2/vctrs/R/compat-types.check.R |only vctrs-0.5.2/vctrs/man/vec_identify_runs.Rd |only vctrs-0.5.2/vctrs/src/rlang-rcc.cpp |only vctrs-0.6.0/vctrs/DESCRIPTION | 33 vctrs-0.6.0/vctrs/LICENSE | 2 vctrs-0.6.0/vctrs/MD5 | 286 ++-- vctrs-0.6.0/vctrs/NAMESPACE | 13 vctrs-0.6.0/vctrs/NEWS.md | 48 vctrs-0.6.0/vctrs/R/assert.R | 212 ++- vctrs-0.6.0/vctrs/R/compare.R | 6 vctrs-0.6.0/vctrs/R/conditions.R | 83 - vctrs-0.6.0/vctrs/R/equal.R | 2 vctrs-0.6.0/vctrs/R/group.R | 7 vctrs-0.6.0/vctrs/R/import-standalone-linked-version.R |only vctrs-0.6.0/vctrs/R/import-standalone-obj-type.R |only vctrs-0.6.0/vctrs/R/import-standalone-purrr.R |only vctrs-0.6.0/vctrs/R/import-standalone-types-check.R |only vctrs-0.6.0/vctrs/R/match.R | 305 +++-- vctrs-0.6.0/vctrs/R/partial-factor.R | 13 vctrs-0.6.0/vctrs/R/proxy.R | 2 vctrs-0.6.0/vctrs/R/rep.R | 2 vctrs-0.6.0/vctrs/R/runs.R | 50 vctrs-0.6.0/vctrs/R/size.R | 2 vctrs-0.6.0/vctrs/R/slice-chop.R | 81 + vctrs-0.6.0/vctrs/R/slice.R | 11 vctrs-0.6.0/vctrs/R/subscript-loc.R | 2 vctrs-0.6.0/vctrs/R/subscript.R | 8 vctrs-0.6.0/vctrs/R/type-list-of.R | 2 vctrs-0.6.0/vctrs/R/type-misc.R | 77 + vctrs-0.6.0/vctrs/R/type-rcrd.R | 2 vctrs-0.6.0/vctrs/R/type-vctr.R | 6 vctrs-0.6.0/vctrs/R/vctrs-deprecated.R | 93 + vctrs-0.6.0/vctrs/R/vctrs-package.R | 6 vctrs-0.6.0/vctrs/README.md | 10 vctrs-0.6.0/vctrs/inst/doc/s3-vector.R | 52 vctrs-0.6.0/vctrs/inst/doc/s3-vector.Rmd | 488 +++++--- vctrs-0.6.0/vctrs/inst/doc/s3-vector.html | 203 +-- vctrs-0.6.0/vctrs/inst/doc/stability.R | 6 vctrs-0.6.0/vctrs/inst/doc/stability.Rmd | 6 vctrs-0.6.0/vctrs/inst/doc/stability.html | 44 vctrs-0.6.0/vctrs/inst/doc/type-size.html | 4 vctrs-0.6.0/vctrs/inst/include/vctrs.c | 10 vctrs-0.6.0/vctrs/inst/include/vctrs.h | 8 vctrs-0.6.0/vctrs/man/faq-error-scalar-type.Rd | 4 vctrs-0.6.0/vctrs/man/faq/developer/howto-faq-fix-scalar-type-error.Rmd | 4 vctrs-0.6.0/vctrs/man/figures/logo.png |binary vctrs-0.6.0/vctrs/man/howto-faq-fix-scalar-type-error.Rd | 6 vctrs-0.6.0/vctrs/man/new_vctr.Rd | 2 vctrs-0.6.0/vctrs/man/obj_is_list.Rd |only vctrs-0.6.0/vctrs/man/partial_factor.Rd | 13 vctrs-0.6.0/vctrs/man/runs.Rd |only vctrs-0.6.0/vctrs/man/vctrs-package.Rd | 8 vctrs-0.6.0/vctrs/man/vec_assert.Rd | 81 - vctrs-0.6.0/vctrs/man/vec_chop.Rd | 55 vctrs-0.6.0/vctrs/man/vec_is_list.Rd | 56 vctrs-0.6.0/vctrs/man/vec_locate_matches.Rd | 101 + vctrs-0.6.0/vctrs/man/vec_size.Rd | 2 vctrs-0.6.0/vctrs/man/vec_slice.Rd | 11 vctrs-0.6.0/vctrs/man/vec_unchop.Rd | 8 vctrs-0.6.0/vctrs/man/vector-checks.Rd |only vctrs-0.6.0/vctrs/man/vector_recycling_rules.Rd | 2 vctrs-0.6.0/vctrs/src/assert.c | 48 vctrs-0.6.0/vctrs/src/assert.h | 9 vctrs-0.6.0/vctrs/src/bind.c | 2 vctrs-0.6.0/vctrs/src/c-unchop.c | 8 vctrs-0.6.0/vctrs/src/c.c | 2 vctrs-0.6.0/vctrs/src/callables.c | 2 vctrs-0.6.0/vctrs/src/cast.c | 4 vctrs-0.6.0/vctrs/src/decl/match-decl.h | 33 vctrs-0.6.0/vctrs/src/decl/rep-decl.h | 5 vctrs-0.6.0/vctrs/src/decl/runs-decl.h | 48 vctrs-0.6.0/vctrs/src/decl/slice-chop-decl.h |only vctrs-0.6.0/vctrs/src/decl/type-info-decl.h | 6 vctrs-0.6.0/vctrs/src/empty.c | 2 vctrs-0.6.0/vctrs/src/expand.c | 2 vctrs-0.6.0/vctrs/src/fields.c | 2 vctrs-0.6.0/vctrs/src/globals.c | 1 vctrs-0.6.0/vctrs/src/globals.h | 1 vctrs-0.6.0/vctrs/src/init.c | 51 vctrs-0.6.0/vctrs/src/match.c | 442 ++++++- vctrs-0.6.0/vctrs/src/names.c | 2 vctrs-0.6.0/vctrs/src/order-collate.c | 2 vctrs-0.6.0/vctrs/src/ptype.c | 6 vctrs-0.6.0/vctrs/src/rep.c | 81 - vctrs-0.6.0/vctrs/src/rlang/attrib.c | 3 vctrs-0.6.0/vctrs/src/rlang/c-utils.h | 20 vctrs-0.6.0/vctrs/src/rlang/decl/env-decl.h | 2 vctrs-0.6.0/vctrs/src/rlang/env.c | 9 vctrs-0.6.0/vctrs/src/rlang/env.h | 9 vctrs-0.6.0/vctrs/src/rlang/globals.c | 3 vctrs-0.6.0/vctrs/src/rlang/globals.h | 3 vctrs-0.6.0/vctrs/src/rlang/node.c | 11 vctrs-0.6.0/vctrs/src/rlang/rlang.c | 6 vctrs-0.6.0/vctrs/src/rlang/rlang.hpp | 3 vctrs-0.6.0/vctrs/src/rlang/vec-lgl.c | 110 + vctrs-0.6.0/vctrs/src/rlang/vec.h | 2 vctrs-0.6.0/vctrs/src/runs.c | 364 +++--- vctrs-0.6.0/vctrs/src/runs.h | 3 vctrs-0.6.0/vctrs/src/size-common.c | 4 vctrs-0.6.0/vctrs/src/size.c | 4 vctrs-0.6.0/vctrs/src/slice-assign.c | 4 vctrs-0.6.0/vctrs/src/slice-chop.c | 597 ++++++---- vctrs-0.6.0/vctrs/src/slice-chop.h | 4 vctrs-0.6.0/vctrs/src/slice.c | 8 vctrs-0.6.0/vctrs/src/split.c | 2 vctrs-0.6.0/vctrs/src/subscript.c | 2 vctrs-0.6.0/vctrs/src/type-info.c | 39 vctrs-0.6.0/vctrs/src/type-info.h | 4 vctrs-0.6.0/vctrs/src/utils.c | 35 vctrs-0.6.0/vctrs/src/utils.h | 14 vctrs-0.6.0/vctrs/src/vctrs.h | 1 vctrs-0.6.0/vctrs/src/vec-bool.h |only vctrs-0.6.0/vctrs/src/version.c | 2 vctrs-0.6.0/vctrs/tests/testthat/_snaps/assert.md | 112 + vctrs-0.6.0/vctrs/tests/testthat/_snaps/c.md | 6 vctrs-0.6.0/vctrs/tests/testthat/_snaps/cast.md | 11 vctrs-0.6.0/vctrs/tests/testthat/_snaps/compare.md | 23 vctrs-0.6.0/vctrs/tests/testthat/_snaps/conditions.md | 2 vctrs-0.6.0/vctrs/tests/testthat/_snaps/equal.md |only vctrs-0.6.0/vctrs/tests/testthat/_snaps/error-call.md | 51 vctrs-0.6.0/vctrs/tests/testthat/_snaps/expand.md | 2 vctrs-0.6.0/vctrs/tests/testthat/_snaps/lifecycle-deprecated.md | 16 vctrs-0.6.0/vctrs/tests/testthat/_snaps/match.md | 443 ++++++- vctrs-0.6.0/vctrs/tests/testthat/_snaps/rep.md | 8 vctrs-0.6.0/vctrs/tests/testthat/_snaps/runs.md | 44 vctrs-0.6.0/vctrs/tests/testthat/_snaps/size.md | 10 vctrs-0.6.0/vctrs/tests/testthat/_snaps/slice-chop.md | 132 ++ vctrs-0.6.0/vctrs/tests/testthat/_snaps/slice.md | 2 vctrs-0.6.0/vctrs/tests/testthat/_snaps/type-misc.md | 8 vctrs-0.6.0/vctrs/tests/testthat/helper-rational.R | 8 vctrs-0.6.0/vctrs/tests/testthat/helper-vctrs.R | 2 vctrs-0.6.0/vctrs/tests/testthat/test-assert.R | 195 ++- vctrs-0.6.0/vctrs/tests/testthat/test-cast.R | 6 vctrs-0.6.0/vctrs/tests/testthat/test-compare.R | 10 vctrs-0.6.0/vctrs/tests/testthat/test-equal.R | 12 vctrs-0.6.0/vctrs/tests/testthat/test-error-call.R | 33 vctrs-0.6.0/vctrs/tests/testthat/test-lifecycle-deprecated.R | 20 vctrs-0.6.0/vctrs/tests/testthat/test-match.R | 385 +++++- vctrs-0.6.0/vctrs/tests/testthat/test-proxy-restore.R | 2 vctrs-0.6.0/vctrs/tests/testthat/test-rep.R | 6 vctrs-0.6.0/vctrs/tests/testthat/test-runs.R | 115 + vctrs-0.6.0/vctrs/tests/testthat/test-slice-chop.R | 177 ++ vctrs-0.6.0/vctrs/tests/testthat/test-slice.R | 2 vctrs-0.6.0/vctrs/tests/testthat/test-type-integer64.R | 6 vctrs-0.6.0/vctrs/tests/testthat/test-type-list-of.R | 2 vctrs-0.6.0/vctrs/tests/testthat/test-type-misc.R | 134 ++ vctrs-0.6.0/vctrs/vignettes/s3-vector.Rmd | 488 +++++--- vctrs-0.6.0/vctrs/vignettes/stability.Rmd | 6 153 files changed, 4968 insertions(+), 2076 deletions(-)
Title: Inference Tools in Time Series Based on Record Statistics
Description: Statistical tools based on the probabilistic properties of the
record occurrence in a sequence of independent and identically distributed
continuous random variables. In particular, tools to prepare a time series
as well as distribution-free trend and change-point tests and graphical
tools to study the record occurrence. Details about the implemented tools
can be found in Castillo-Mateo et al. (2023) <doi:10.18637/jss.v106.i05>.
Author: Jorge Castillo-Mateo [aut, cre, cph]
,
Ana C. Cebrian [ths] ,
Jesus Asin [ths]
Maintainer: Jorge Castillo-Mateo <jorgecastillomateo@gmail.com>
Diff between RecordTest versions 2.1.1 dated 2022-11-06 and 2.1.2 dated 2023-03-15
DESCRIPTION | 13 - MD5 | 24 +- R/N.plot.R | 3 R/RecordTest.R | 8 README.md | 33 ++- inst/CITATION | 34 ++- inst/NEWS.Rd | 8 inst/doc/RecordTest.html | 6 man/N.plot.Rd | 3 man/N.test.Rd | 302 ++++++++++++++++---------------- man/RecordTest-package.Rd | 422 +++++++++++++++++++++++----------------------- man/change.point.Rd | 274 ++++++++++++++--------------- man/foster.test.Rd | 340 ++++++++++++++++++------------------- 13 files changed, 759 insertions(+), 711 deletions(-)
Title: Split, Combine and Compress PDF Files
Description: Content-preserving transformations transformations of PDF files such
as split, combine, and compress. This package interfaces directly to the 'qpdf'
C++ API and does not require any command line utilities. Note that 'qpdf' does
not read actual content from PDF files: to extract text and data you need the
'pdftools' package.
Author: Jeroen Ooms [aut, cre] ,
Ben Raymond [ctb],
Jay Berkenbilt [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between qpdf versions 1.3.0 dated 2022-10-07 and 1.3.1 dated 2023-03-15
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS | 4 ++++ src/Makevars | 1 - src/include/qpdf/PointerHolder.hh | 7 +++++++ 5 files changed, 21 insertions(+), 11 deletions(-)
Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a
combination of narrative, figures, videos, exercises, and quizzes to
create self-paced tutorials for learning about R and R packages.
Author: Garrick Aden-Buie [aut, cre] ,
Barret Schloerke [aut] ,
JJ Allaire [aut, ccp],
Alexander Rossell Hayes [aut] ,
Nischal Shrestha [ctb] ,
Angela Li [ctb] ,
Posit, PBC [cph, fnd],
Ajax.org B.V. [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Payne [ctb, cph] [...truncated...]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between learnr versions 0.11.2 dated 2022-11-08 and 0.11.3 dated 2023-03-15
DESCRIPTION | 31 +- MD5 | 32 +-- NEWS.md | 10 R/exercise.R | 22 +- R/knitr-hooks.R | 9 inst/doc/multilang.R | 6 inst/doc/multilang.Rmd | 10 inst/doc/multilang.html | 180 ++++++++--------- inst/lib/tutorial/tutorial.js | 2 inst/lib/tutorial/tutorial.js.map | 4 man/learnr-package.Rd | 12 - man/tutorial.Rd | 2 tests/testthat/test-exercise.R | 62 ++--- tests/testthat/test-knitr-hooks.R | 14 + tests/testthat/tutorials/exercise-option-is-symbol.Rmd |only tests/testthat/tutorials/hint-copy/hint-copy.html |only tests/testthat/tutorials/hint-div/hint-div.html |only tests/testthat/tutorials/hint-next/hint-next.html |only vignettes/multilang.Rmd | 10 19 files changed, 220 insertions(+), 186 deletions(-)
Title: Analysis and Visualization Tools for Genetic Barcode Data
Description: Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).
Author: Lars Thielecke <lars.thielecke@tu-dresden.de>
Maintainer: Lars Thielecke <lars.thielecke@tu-dresden.de>
Diff between genBaRcode versions 1.2.5 dated 2022-05-27 and 1.2.6 dated 2023-03-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/genBaRcode_GUI_Vignette.pdf |binary inst/doc/genBaRcode_Vignette.pdf |binary 4 files changed, 6 insertions(+), 6 deletions(-)
Title: Differential Gene Correlation Analysis
Description: Performs differential correlation analysis on input
matrices, with multiple conditions specified by a design matrix. Contains
functions to filter, process, save, visualize, and interpret differential
correlations of identifier-pairs across the entire identifier space, or with
respect to a particular set of identifiers (e.g., one). Also contains several
functions to perform differential correlation analysis on clusters (i.e., modules)
or genes. Finally, it contains functions to generate empirical p-values for the
hypothesis tests and adjust them for multiple comparisons. Although the package
was built with gene expression data in mind, it is applicable to other types of
genomics data as well, in addition to being potentially applicable to data from
other fields entirely. It is described more fully in the manuscript
introducing it, freely available at <doi:10.1186/s12918-016-0349-1>.
Author: Bin Zhang [aut],
Andrew McKenzie [aut, cre]
Maintainer: Andrew McKenzie <amckenz@gmail.com>
Diff between DGCA versions 1.0.2 dated 2019-12-09 and 1.0.3 dated 2023-03-15
DESCRIPTION | 6 MD5 | 36 ++-- R/dcTopPairs.R | 2 R/ddMEGENA.R | 2 R/ddcorAll.R | 2 R/ddcorGO.R | 2 R/dgca_package.R | 2 R/filterGenes.R | 2 R/getCors.R | 2 R/moduleGO.R | 2 R/pairwiseDCor.R | 2 R/plotCors.R | 2 R/plotGOOnegroup.R | 2 R/plotVals.R | 2 R/topDCGenes.R | 2 README.md | 3 build/vignette.rds |binary inst/doc/DGCA_basic.R | 10 - inst/doc/DGCA_basic.html | 340 ++++++++++++++++++++++++++++++----------------- 19 files changed, 262 insertions(+), 159 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 either 'Java Database Connectivity' ('JDBC') or other DB I drivers to connect to databases.
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 6.0.0 dated 2023-01-30 and 6.1.0 dated 2023-03-15
DESCRIPTION | 12 +- MD5 | 47 ++++---- NEWS.md | 22 ++++ R/Andromeda.R | 18 --- R/Connect.R | 47 +++++++- R/DBI.R | 3 R/DbiDateFunctions.R | 2 R/HelperFunctions.R | 4 R/InsertTable.R | 48 +++----- R/RStudio.R | 2 R/Sql.R | 19 +-- inst/csv/jarChecksum.txt | 2 inst/doc/Connecting.pdf |binary inst/doc/DbiAndDbplyr.pdf |binary inst/doc/Querying.pdf |binary inst/java/DatabaseConnector.jar |binary java/org/ohdsi/databaseConnector/BatchedInsert.java | 40 ++++++- java/org/ohdsi/databaseConnector/BatchedQuery.java | 108 ++++++++++++-------- tests/testthat/dbplyrTestFunction.R | 7 - tests/testthat/test-dataHash.R | 27 +++++ tests/testthat/test-dbplyr.R | 36 ++++++ tests/testthat/test-duckdb.R |only tests/testthat/test-fetchResults.R | 40 +------ tests/testthat/test-getTableNames.R | 15 ++ tests/testthat/test-insertTable.R | 36 ++++++ 25 files changed, 359 insertions(+), 176 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Brace Expansions
Description: Performs brace expansions on strings. Made popular by Unix shells, brace expansion allows users to concisely generate certain character vectors by taking a single string and (recursively) expanding the comma-separated lists and double-period-separated integer and character sequences enclosed within braces in that string. The double-period-separated numeric integer expansion also supports padding the resulting numbers with zeros.
Author: Trevor L Davis [aut, cre] ,
Jon Schlinkert [aut]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between bracer versions 1.2.1 dated 2021-05-19 and 1.2.2 dated 2023-03-15
DESCRIPTION | 25 +++++++++++-------------- MD5 | 10 +++++++--- NEWS.md | 10 ++++++++++ README.md | 25 ++++++++++++++----------- build |only inst/doc |only vignettes |only 7 files changed, 42 insertions(+), 28 deletions(-)
Title: Almost Linear-Time k-Medoids Clustering
Description: Interface to a high-performance implementation of k-medoids clustering described in Tiwari, Zhang, Mayclin, Thrun, Piech and Shomorony (2020) "BanditPAM: Almost Linear Time k-medoids Clustering via Multi-Armed Bandits" <https://proceedings.neurips.cc/paper/2020/file/73b817090081cef1bca77232f4532c5d-Paper.pdf>.
Author: Balasubramanian Narasimhan [aut, cre],
Mo Tiwari [aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between banditpam versions 1.0 dated 2023-03-14 and 1.0-1 dated 2023-03-15
DESCRIPTION | 9 ++++----- MD5 | 7 ++++--- README.md | 11 +---------- inst/doc/kmediods.html | 2 +- man/banditpam-package.Rd |only 5 files changed, 10 insertions(+), 19 deletions(-)
Title: Normalizing Transformation Functions
Description: Estimate a suite of normalizing transformations, including
a new adaptation of a technique based on ranks which can guarantee
normally distributed transformed data if there are no ties: ordered
quantile normalization (ORQ). ORQ normalization combines a rank-mapping
approach with a shifted logit approximation that allows
the transformation to work on data outside the original domain. It is
also able to handle new data within the original domain via linear
interpolation. The package is built to estimate the best normalizing
transformation for a vector consistently and accurately. It implements
the Box-Cox transformation, the Yeo-Johnson transformation, three types
of Lambert WxF transformations, and the ordered quantile normalization
transformation. It estimates the normalization efficacy of other
commonly used transformations, and it allows users to specify
custom transformations or normalization statistics. Finally, functionality
can be integrated into a machine learning workflow via r [...truncated...]
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between bestNormalize versions 1.8.3 dated 2022-06-13 and 1.9.0 dated 2023-03-15
DESCRIPTION | 12 - MD5 | 45 ++-- NAMESPACE | 7 NEWS.md | 7 R/bestNormalize.R | 14 - R/double_reverse_log.R |only R/no_transform.R | 3 R/step_best_normalize.R | 5 R/step_orderNorm.R | 10 + build/vignette.rds |binary inst/CITATION | 6 inst/doc/bestNormalize.R | 13 - inst/doc/bestNormalize.Rmd | 15 - inst/doc/bestNormalize.html | 295 ++++++++++++++++--------------- inst/doc/customization.html | 36 ++- man/bestNormalize.Rd | 4 man/double_reverse_log.Rd |only man/no_transform.Rd | 4 man/reexports.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/test_bestNormalize.R | 8 tests/testthat/test_bn_custom_normstat.R | 2 tests/testthat/test_custom_fn.R | 7 tests/testthat/test_double_reverse_log.R |only tests/testthat/test_step_fns.R | 7 vignettes/bestNormalize.Rmd | 15 - 26 files changed, 293 insertions(+), 222 deletions(-)
Title: Analysis of Omics Data in Observational Studies
Description: A collection of fast and flexible functions for analyzing
omics data in observational studies. Multiple different approaches for
integrating multiple environmental/genetic factors, omics data, and/or
phenotype data are implemented. This includes functions for performing
omics wide association studies with one or more variables of interest
as the exposure or outcome; a function for performing a meet in the
middle analysis for linking exposures, omics, and outcomes (as
described by Chadeau-Hyam et al., (2010)
<doi:10.3109/1354750X.2010.533285>); and a function for performing a
mixtures analysis across all omics features using quantile-based
g-Computation (as described by Keil et al., (2019)
<doi:10.1289/EHP5838>).
Author: Jesse Goodrich [aut, cre]
Maintainer: Jesse Goodrich <jagoodri@usc.edu>
Diff between epiomics versions 0.0.1 dated 2023-01-09 and 1.0.0 dated 2023-03-15
DESCRIPTION | 45 ++--- MD5 | 28 +-- NAMESPACE | 75 ++++---- NEWS.md | 12 + R/owas.R | 6 R/owas_mixed_effects.R | 31 +-- R/owas_qgcomp.R | 127 ++++++++++----- R/volcano_owas.R | 2 README.md | 260 ++++++++++++++++--------------- man/epiomics-package.Rd | 2 man/owas.Rd | 2 man/owas_qgcomp.Rd | 34 +++- tests/testthat/test-owas.R | 50 ++++- tests/testthat/test-owas_mixed_effects.R | 249 +++++++++++++++++++++++++++-- tests/testthat/test-owas_qgcomp.R | 50 +++++ 15 files changed, 685 insertions(+), 288 deletions(-)
Title: Regularized Linear Modeling with Tidy Data
Description: An extension to the 'R' tidy data environment for automated machine learning. The package allows fitting and cross validation of linear regression and classification algorithms on grouped data.
Author: Johann Pfitzinger [aut, cre]
Maintainer: Johann Pfitzinger <johann.pfitzinger@gmail.com>
Diff between tidyfit versions 0.6.2 dated 2023-02-19 and 0.6.3 dated 2023-03-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/generics.R | 8 ++++---- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework.
The plots, which include loaPlot(), RgoogleMapsPlot() and trianglePlot(), use panelPal(), a function that
extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel
and panel-to-key synchronization/management.
Author: Karl Ropkins [aut, cre]
Maintainer: Karl Ropkins <karl.ropkins@gmail.com>
Diff between loa versions 0.2.47.1 dated 2021-04-12 and 0.2.48.1 dated 2023-03-15
DESCRIPTION | 12 +++++++----- MD5 | 8 ++++---- NEWS | 5 +++++ inst/CITATION | 14 ++++++-------- man/loa-package.Rd | 4 ++-- 5 files changed, 24 insertions(+), 19 deletions(-)
Title: Use Browser Cookies with 'shiny'
Description: Browser cookies are name-value pairs that are saved in a
user's browser by a website. Cookies allow websites to persist
information about the user and their use of the website. Here we
provide tools for working with cookies in 'shiny' apps, in part by
wrapping the 'js-cookie' JavaScript library
<https://github.com/js-cookie/js-cookie>.
Author: Jon Harmon [aut, cre, cph] ,
Klaus Hartl [cph] ,
Fagner Brack [cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between cookies versions 0.2.1 dated 2023-01-10 and 0.2.2 dated 2023-03-15
DESCRIPTION | 39 ++-- MD5 | 30 +-- NEWS.md | 5 R/aaa.R | 66 +++---- R/server.R | 110 ++++++++++- R/ui_wrapper.R | 4 README.md | 4 inst/js/cookie_input.js | 38 +++- man/dot-is_http_only.Rd |only man/dot-root_session.Rd |only man/dot-shared-parameters.Rd | 3 man/get_cookie.Rd | 4 man/remove_cookie.Rd | 4 man/set_cookie.Rd | 4 tests/testthat/_snaps/ui_wrapper.md | 338 ++++++++++++++++++------------------ tests/testthat/test-onload.R | 222 +++++++++++------------ tests/testthat/test-server.R | 85 ++++++++- 17 files changed, 583 insertions(+), 373 deletions(-)
More information about BayesianPlatformDesignTimeTrend at CRAN
Permanent link
Title: File-System Toolbox for RAVE Project
Description: Includes multiple cross-platform read/write interfaces for
'RAVE' project. 'RAVE' stands for "R analysis and visualization of human
intracranial electroencephalography data". The whole project aims at
providing powerful free-source package that analyze brain recordings from
patients with electrodes placed on the cortical surface or inserted into
the brain. 'raveio' as part of this project provides tools to read/write
neurophysiology data from/to 'RAVE' file structure, as well as several
popular formats including 'EDF(+)', 'Matlab', 'BIDS-iEEG', and 'HDF5',
etc. Documentation and examples about 'RAVE' project are provided at
<https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("raveio")' for
details.
Author: Zhengjia Wang [aut, cre, cph],
Beauchamp lab [cph, fnd]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between raveio versions 0.0.9 dated 2022-10-14 and 0.1.0 dated 2023-03-15
raveio-0.0.9/raveio/man/configure_knitr.Rd |only raveio-0.1.0/raveio/DESCRIPTION | 15 raveio-0.1.0/raveio/MD5 | 114 +++--- raveio-0.1.0/raveio/NAMESPACE | 21 + raveio-0.1.0/raveio/NEWS.md | 23 + raveio-0.1.0/raveio/R/backward-compatibility.R | 2 raveio-0.1.0/raveio/R/class-BlackrockFile.R | 7 raveio-0.1.0/raveio/R/class-electrode-abstract.R | 6 raveio-0.1.0/raveio/R/class-epoch.R | 2 raveio-0.1.0/raveio/R/class-pipeline_tools.R | 105 ++++- raveio-0.1.0/raveio/R/class-preprocess.R | 2 raveio-0.1.0/raveio/R/class-subject.R | 190 +++++++++- raveio-0.1.0/raveio/R/cmd-3dAlineate.R | 5 raveio-0.1.0/raveio/R/cmd-aaa.R | 49 ++ raveio-0.1.0/raveio/R/cmd-ants-registration.R |only raveio-0.1.0/raveio/R/cmd-dcm2niix.R | 167 ++++++-- raveio-0.1.0/raveio/R/cmd-flirt.R | 31 + raveio-0.1.0/raveio/R/cmd-niftyreg.R |only raveio-0.1.0/raveio/R/cmd-recon-all.R | 24 - raveio-0.1.0/raveio/R/fst.R | 58 +++ raveio-0.1.0/raveio/R/hdf5r.R | 19 + raveio-0.1.0/raveio/R/module-create.R | 2 raveio-0.1.0/raveio/R/nifti.R |only raveio-0.1.0/raveio/R/pipeline-docs.R | 38 ++ raveio-0.1.0/raveio/R/pipeline-knitr.R | 186 ++++++++- raveio-0.1.0/raveio/R/pipeline-run.R | 29 + raveio-0.1.0/raveio/R/pipeline-serializer.R |only raveio-0.1.0/raveio/R/pipeline-tools.R | 186 ++++++++- raveio-0.1.0/raveio/R/py-nipy-coreg.R |only raveio-0.1.0/raveio/R/rave-export-repository.R |only raveio-0.1.0/raveio/R/rave-import.R | 4 raveio-0.1.0/raveio/R/rave-meta.R | 84 ++-- raveio-0.1.0/raveio/R/rave-raw.R | 10 raveio-0.1.0/raveio/R/rave-reference.R | 44 -- raveio-0.1.0/raveio/R/rave-snippets.R |only raveio-0.1.0/raveio/R/rave-wavelet.R | 2 raveio-0.1.0/raveio/R/threeBrain-instance.R | 62 ++- raveio-0.1.0/raveio/R/validate-subject.R | 14 raveio-0.1.0/raveio/R/zzz.R | 22 + raveio-0.1.0/raveio/README.md | 2 raveio-0.1.0/raveio/build/partial.rdb |binary raveio-0.1.0/raveio/inst/CITATION | 68 +-- raveio-0.1.0/raveio/inst/WORDLIST | 5 raveio-0.1.0/raveio/inst/python-scripts |only raveio-0.1.0/raveio/inst/rave-pipelines/template-rmd-bare/main.Rmd | 25 - raveio-0.1.0/raveio/inst/rave-pipelines/template-rmd/main.Rmd | 25 - raveio-0.1.0/raveio/inst/shell-templates/fsl-flirt-coregistration.sh | 84 ++++ raveio-0.1.0/raveio/inst/shell-templates/rave-ants-coregistration.R |only raveio-0.1.0/raveio/inst/shell-templates/rave-ants-mri-to-template.R |only raveio-0.1.0/raveio/inst/shell-templates/rave-nifty-coregistration.R |only raveio-0.1.0/raveio/inst/shell-templates/rave-nipy-coregistration.R |only raveio-0.1.0/raveio/inst/shell-templates/recon-all-t1.sh | 71 +++ raveio-0.1.0/raveio/inst/shell-templates/transform-mat.txt |only raveio-0.1.0/raveio/man/LazyH5.Rd | 22 + raveio-0.1.0/raveio/man/PipelineTools.Rd | 24 + raveio-0.1.0/raveio/man/RAVESubject.Rd | 33 + raveio-0.1.0/raveio/man/ants_coreg.Rd |only raveio-0.1.0/raveio/man/as_rave_subject.Rd | 4 raveio-0.1.0/raveio/man/cmd-external.Rd | 13 raveio-0.1.0/raveio/man/convert-fst.Rd |only raveio-0.1.0/raveio/man/mgh_to_nii.Rd |only raveio-0.1.0/raveio/man/niftyreg_coreg.Rd |only raveio-0.1.0/raveio/man/pipeline-knitr-markdown.Rd |only raveio-0.1.0/raveio/man/pipeline_settings_get_set.Rd | 8 raveio-0.1.0/raveio/man/py_nipy_coreg.Rd |only raveio-0.1.0/raveio/man/rave-pipeline.Rd | 9 raveio-0.1.0/raveio/man/rave-snippet.Rd |only raveio-0.1.0/raveio/man/rave_brain.Rd | 6 raveio-0.1.0/raveio/man/rave_export.Rd |only 69 files changed, 1528 insertions(+), 394 deletions(-)
Title: Common Fragmentation and Connectivity Indices for Riverscapes
Description: Indices for assessing riverscape fragmentation, including the Dendritic Connectivity Index, the Population Connectivity Index, the River Fragmentation Index, the Probability of Connectivity, and the Integral Index of connectivity. For a review, see Jumani et al. (2020) <doi:10.1088/1748-9326/abcb37> and Baldan et al. (2022) <doi:10.1016/j.envsoft.2022.105470> Functions to calculate temporal indices improvement when fragmentation due to barriers is reduced are also included.
Author: Damiano Baldan [aut, cre] ,
David Cunillera-Montcusi [ctb]
,
Andrea Funk [ctb]
Maintainer: Damiano Baldan <damiano.baldan91@gmail.com>
Diff between riverconn versions 0.3.25 dated 2023-01-16 and 0.3.26 dated 2023-03-15
DESCRIPTION | 6 MD5 | 12 README.md | 3 inst/doc/Tutorial.R | 4 inst/doc/Tutorial.Rmd | 71 +- inst/doc/Tutorial.html | 1577 +++++++++++++++++++++++++++++++------------------ vignettes/Tutorial.Rmd | 71 +- 7 files changed, 1114 insertions(+), 630 deletions(-)
Title: Hardy-Weinberg Equilibrium in Polyploids
Description: Inference concerning equilibrium and random mating in
autopolyploids. Methods are available to test for equilibrium
and random mating at any even ploidy level (>2) in the presence
of double reduction at biallelic loci. For autopolyploid populations
in equilibrium, methods are available to estimate the degree of
double reduction. We also provide functions to calculate genotype
frequencies at equilibrium, or after one or several rounds of
random mating, given rates of double reduction. The main function is
hwefit(). This material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The opinions,
findings, and conclusions or recommendations expressed are those of
the author and do not necessarily reflect the views of the National
Science Foundation. For details of these methods, see
Gerard (2022a) <doi:10.1111/biom.13722> and
Gerard (2022b) <doi:10.1101/2022.08.11.503635>.
Author: David Gerard [aut, cre] ,
NSF DBI 2132247 [fnd]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between hwep versions 2.0.0 dated 2022-08-16 and 2.0.1 dated 2023-03-15
DESCRIPTION | 8 MD5 | 23 - NAMESPACE | 1 NEWS.md | 42 + R/bayes.R | 9 R/stanmodels.R | 52 +- configure |only configure.win |only inst/doc/introduction.html | 124 ++--- man/ddirmult.Rd |only src/Makevars | 4 src/Makevars.win | 4 src/stanExports_gl_alt.h | 768 +++++++++++++++++++++-------------- src/stanExports_gl_null.h | 980 ++++++++++++++++++++++++++------------------- 14 files changed, 1190 insertions(+), 825 deletions(-)
Title: Get Data from the French National Database on Water 'Hub'Eau'
Description: Collection of functions to help retrieving data from
'Hub'Eau' the free and public French National APIs on water
<https://hubeau.eaufrance.fr/>.
Author: David Dorchies [aut, cre] ,
Pascal Irz [ctb],
Sebastien Grall [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>
Diff between hubeau versions 0.3.1 dated 2022-08-16 and 0.4.0 dated 2023-03-15
DESCRIPTION | 29 +++-- MD5 | 65 +++++++----- NAMESPACE | 13 ++ NEWS.md | 111 ++++++++++++-------- R/doApiQuery.R | 100 ++++++++++++++++-- R/get_ecoulement.R | 14 +- R/get_hydrobio.R |only R/get_hydrometrie.R | 43 ++++--- R/get_indicateurs_services.R | 20 +-- R/get_niveaux_nappes.R | 26 ++-- R/get_poisson.R | 9 - R/get_prelevements.R | 30 +---- R/get_qualite_eau_potable.R |only R/get_qualite_nappes.R |only R/get_temperature.R |only R/globals.R |only R/sysdata.rda |binary README.md | 124 +++++++++++++++-------- build |only inst/CITATION |only inst/WORDLIST | 33 +++++- inst/doc |only inst/vignettes |only man/convert_list_to_tibble.Rd | 5 man/doApiQuery.Rd | 16 ++ man/get_ecoulement.Rd | 13 +- man/get_hydrobio.Rd |only man/get_hydrometrie.Rd | 34 +++--- man/get_indicateurs_services.Rd | 19 ++- man/get_niveaux_nappes.Rd | 21 ++- man/get_poisson.Rd | 100 +++++++++--------- man/get_prelevements.Rd | 19 ++- man/get_qualite_eau_potable.Rd |only man/get_qualite_nappes.Rd |only man/get_temperature.Rd |only man/hubeau.Rd | 35 ++++++ tests/testthat/Rplots.pdf |only tests/testthat/test-convert_ellipsis_to_params.R |only tests/testthat/test-doApiQuery.R | 7 + tests/testthat/test-run_all_examples.R |only vignettes |only 41 files changed, 577 insertions(+), 309 deletions(-)
Title: Carlson Elliptic Integrals and Incomplete Elliptic Integrals
Description: Evaluation of the Carlson elliptic integrals and the
incomplete elliptic integrals with complex arguments. The
implementations use Carlson's algorithms <doi:10.1007/BF02198293>.
Applications of elliptic integrals include probability distributions,
geometry, physics, mechanics, electrodynamics, statistical mechanics,
astronomy, geodesy, geodesics on conics, and magnetic field
calculations.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between Carlson versions 1.1.0 dated 2022-06-28 and 2.0.0 dated 2023-03-15
DESCRIPTION | 14 +- MD5 | 64 ++++++------- NAMESPACE | 24 ++-- NEWS.md | 31 +++--- R/RC.R | 40 ++++---- R/RD.R | 70 ++++---------- R/RF.R | 62 ++++-------- R/RG.R | 54 +++++------ R/RJ.R | 85 +++++------------ R/RcppExports.R |only R/aaa.R |only R/elliptic_E.R | 90 +++++++++--------- R/elliptic_F.R | 116 +++++++++++------------ R/elliptic_PI.R | 100 ++++++++++---------- R/elliptic_Z.R | 64 ++++++------- man/Carlson_RC.Rd | 58 +++++------ man/Carlson_RD.Rd | 58 +++++------ man/Carlson_RF.Rd | 58 +++++------ man/Carlson_RG.Rd | 42 ++++---- man/Carlson_RJ.Rd | 58 +++++------ man/elliptic_E.Rd | 54 +++++------ man/elliptic_F.Rd | 54 +++++------ man/elliptic_PI.Rd | 58 +++++------ man/elliptic_Z.Rd | 46 ++++----- src |only tests/testthat.R | 8 - tests/testthat/test-Carlson_RC.R | 34 +++--- tests/testthat/test-Carlson_RG.R | 20 ++-- tests/testthat/test-Carlson_RJ.R | 38 +++---- tests/testthat/test-completeElliptic.R | 74 +++++++-------- tests/testthat/test-elliptic_E.R | 34 +++--- tests/testthat/test-elliptic_F.R | 40 ++++---- tests/testthat/test-elliptic_PI.R | 162 ++++++++++++++++----------------- tests/testthat/test-elliptic_Z.R | 92 +++++++++--------- 34 files changed, 874 insertions(+), 928 deletions(-)
Title: Inference and Prediction of Generic Physiologically-Based
Kinetic Models
Description: Fit and simulate any kind of
physiologically-based kinetic ('PBK') models whatever the number of compartments.
Moreover, it allows to account for any link between pairs of compartments, as
well as any link of each of the compartments with the external medium. Such
generic PBK models have today applications in pharmacology (PBPK models) to
describe drug effects, in toxicology and ecotoxicology (PBTK models) to describe
chemical substance effects. In case of exposure to a parent compound (drug or
chemical) the 'rPBK' package allows to consider metabolites, whatever their number
and their phase (I, II, ...). Last but not least, package 'rPBK' can also be used for
dynamic flux balance analysis (dFBA) to deal with metabolic networks. See also
Charles et al. (2022) <doi:10.1101/2022.04.29.490045>.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Christelle Lopes [aut],
Ophelia Gestin [ctb],
Dominique Lamonica [ctb],
Aurelie Siberchicot [ctb]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
Diff between rPBK versions 0.2.0 dated 2022-09-01 and 0.2.1 dated 2023-03-15
DESCRIPTION | 10 +-- MD5 | 12 +-- README.md | 2 inst/doc/Examples.html | 110 +++++++++++++++++------------------ inst/stan/include/interpolation.stan | 4 - src/stanExports_PBK_AD.h | 14 ++-- src/stanExports_export_interpolate.h | 14 ++-- 7 files changed, 84 insertions(+), 82 deletions(-)
Title: LiDAR Data Voxelisation
Description: Read, manipulate and write voxel spaces. Voxel spaces are
read from text-based output files of the 'AMAPVox' software. 'AMAPVox'
is a LiDAR point cloud voxelisation software that aims at estimating
leaf area through several theoretical/numerical approaches. See more
in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the
technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.
Author: Gregoire Vincent [aut],
Julien Heurtebize [aut],
Philippe Verley [aut, cre]
Maintainer: Philippe Verley <philippe.verley@ird.fr>
Diff between AMAPVox versions 0.12.1 dated 2022-12-05 and 1.0.0 dated 2023-03-15
DESCRIPTION | 10 - MD5 | 46 +++---- NAMESPACE | 10 + NEWS.md | 12 ++ R/AMAPVox.R | 8 - R/Run.R | 155 +++++++++++++++++-------- R/VersionManager.R | 105 ++++++++++++----- inst/doc/Installation.R | 12 +- inst/doc/Installation.Rmd | 13 +- inst/doc/Installation.html | 47 +------ inst/doc/Publications.html | 38 +++--- inst/doc/Voxelization.Rmd | 209 ++++++++++++++++++++++++----------- inst/doc/Voxelization.html | 209 ++++++++++++++++++++++++----------- inst/doc/amapvox-gui.html | 4 man/getRemoteVersions.Rd | 4 man/plantAreaDensity.Rd | 2 man/plantAreaIndex.Rd | 2 man/run.Rd | 47 ++++--- vignettes/Installation.Rmd | 13 +- vignettes/Voxelization.Rmd | 209 ++++++++++++++++++++++++----------- vignettes/rsc/amapvox-1st-screen.png |binary vignettes/rsc/amapvox-bibtex.bib | 14 ++ vignettes/rsc/tab_config-files.png |binary vignettes/rsc/tab_output-files.png |binary 24 files changed, 757 insertions(+), 412 deletions(-)
Title: Tools for Stable Isotope Geochemistry
Description: This toolbox makes working with oxygen,
carbon, and clumped isotope data reproducible and straightforward.
Use it to quickly calculate isotope fractionation factors,
and apply paleothermometry equations.
Author: David Bajnai [aut, cre] ,
Julian Toedter [ctb]
Maintainer: David Bajnai <david.bajnai@uni-goettingen.de>
Diff between isogeochem versions 1.1.0 dated 2022-07-19 and 1.1.1 dated 2023-03-15
DESCRIPTION | 8 +- MD5 | 33 +++++------ NEWS.md | 83 ++++++++++++++++------------ R/d17O.R | 62 ++++++++++++++------- README.md | 26 ++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/devils_hole.R | 2 inst/doc/devils_hole.Rmd | 2 inst/doc/devils_hole.html | 124 ++++++++++++++++++++++--------------------- inst/doc/kim_oneil_1997.R | 2 inst/doc/kim_oneil_1997.Rmd | 2 inst/doc/kim_oneil_1997.html | 124 ++++++++++++++++++++++--------------------- man/d17O_c.Rd | 28 +++++++-- tests/testthat/Rplots.pdf |only tests/testthat/test_d17O.R | 19 ++++-- vignettes/devils_hole.Rmd | 2 vignettes/kim_oneil_1997.Rmd | 2 18 files changed, 294 insertions(+), 225 deletions(-)
Title: High Dimensional Penalized Generalized Linear Mixed Models
(pGLMM)
Description: Fits high dimensional penalized generalized linear
mixed models using
the Monte Carlo Expectation Conditional Minimization (MCECM) algorithm.
The purpose of the package is to perform variable selection on both the fixed and
random effects simultaneously for generalized linear mixed models.
The package supports fitting of Binomial, Gaussian, and Poisson data with canonical links, and
supports penalization using the MCP, SCAD, or LASSO penalties. The MCECM algorithm
is described in Rashid et al. (2020) <doi:10.1080/01621459.2019.1671197>.
The techniques used in the minimization portion of the procedure (the M-step) are
derived from the procedures of the 'ncvreg' package (Breheny and Huang (2011)
<doi:10.1214/10-AOAS388>) and 'grpreg' package (Breheny and Huang (2015)
<doi:10.1007/s11222-013-9424-2>), with
appropriate modifications to account for the estimation and penalization of
the random effects. The 'ncvreg' and 'grpreg' packages also describe the MCP, SCAD,
and LAS [...truncated...]
Author: Hillary Heiling [aut, cre],
Naim Rashid [aut],
Quefeng Li [aut],
Joseph Ibrahim [aut]
Maintainer: Hillary Heiling <hheiling@live.unc.edu>
Diff between glmmPen versions 1.5.2.11 dated 2022-12-13 and 1.5.3.0 dated 2023-03-15
DESCRIPTION | 18 ++- MD5 | 61 ++++++------ NAMESPACE | 3 R/E_step.R | 158 +++++++++++++++++++++++++++++---- R/M_step.R | 2 R/M_step_FA.R | 2 R/control_options.R | 66 +++++++++++++ R/fit_dat.R | 10 +- R/fit_dat_FA.R | 29 ++++-- R/formula_data_edits.R | 2 R/glmmPen.R | 34 ++++++- R/methods.R | 5 - R/select_tune.R | 5 + R/select_tune_FA.R | 5 + R/sim_generation.R | 6 - R/sim_generation_FA.R | 20 +++- R/var_start_init.R | 5 + inst/stan/binomial_logit_model.stan | 2 inst/stan/gaussian_identity_model.stan | 2 inst/stan/poisson_log_model.stan | 2 inst/update.R | 19 ++- man/LambdaSeq.Rd | 12 ++ man/coxphControl.Rd |only man/pglmmObj-class.Rd | 4 man/sim.data.Rd | 5 - src/Makevars | 4 src/Makevars.win | 4 src/coord_descent.cpp | 10 -- src/grp_CD_XZ_FA_step.cpp | 19 +-- src/utility_CD.h | 11 ++ src/utility_FA.cpp | 79 ++++++++++++++++ src/utility_grpCD.cpp | 37 +------ 32 files changed, 485 insertions(+), 156 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available mon [...truncated...]
Author: Michael Hoehle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Sabanes B [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.20.3 dated 2022-11-16 and 1.21.0 dated 2023-03-15
DESCRIPTION | 14 +-- MD5 | 130 +++++++++++++++---------------- NAMESPACE | 3 NEWS.md | 25 +++++ R/algo_cusum.R | 2 R/epidataCS_aggregate.R | 6 - R/epidataCS_animate.R | 6 - R/epidataCS_methods.R | 10 +- R/epidataCS_plot.R | 10 +- R/gpc.poly-methods.R | 23 ----- R/graphs.R | 64 +++++---------- R/hhh4_methods.R | 22 ++--- R/hhh4_plot.R | 32 ++++--- R/hhh4_simulate.R | 8 - R/intersectPolyCircle.R | 5 - R/options.R | 7 - R/spatial_tools.R | 90 ++++++++++++++------- R/sts.R | 17 ++-- R/stsplot_space.R | 8 + R/stsplot_spacetime.R | 14 +-- R/twinstim_intensity.R | 5 - R/untie.R | 6 - R/zzz.R | 33 +++---- build/partial.rdb |binary build/vignette.rds |binary demo/cost.R | 88 ++++---------------- inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.R | 9 +- inst/doc/hhh4_spacetime.Rnw | 26 ++---- inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.Rnw | 11 -- inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.Rnw | 11 -- inst/doc/twinSIR.pdf |binary inst/doc/twinstim.R | 4 inst/doc/twinstim.Rnw | 24 +---- inst/doc/twinstim.pdf |binary man/algo.outbreakP.Rd | 6 - man/discpoly.Rd | 14 +-- man/epidataCS.Rd | 28 ++---- man/ha.Rd | 8 - man/hhh4.Rd | 2 man/imdepi.Rd | 6 - man/inside.gpc.poly.Rd | 2 man/layout.labels.Rd | 5 - man/nbOrder.Rd | 26 +----- man/poly2adjmat.Rd | 3 man/sts-class.Rd | 2 man/sts_animate.Rd | 3 man/stsplot.Rd | 23 +---- man/stsplot_space.Rd | 5 - man/stsplot_spacetime.Rd | 3 man/surveillance.options.Rd | 9 -- man/twinstim_epitest.Rd | 6 - man/twinstim_intensity.Rd | 2 man/twinstim_simEndemicEvents.Rd | 5 - man/unionSpatialPolygons.Rd | 18 +--- tests/testthat/test-hhh4_NegBinGrouped.R | 18 ---- tests/testthat/test-nbOrder.R | 4 vignettes/hhh4_spacetime.Rnw | 26 ++---- vignettes/monitoringCounts.Rnw | 11 -- vignettes/references.bib | 11 ++ vignettes/twinSIR.Rnw | 11 -- vignettes/twinstim.Rnw | 24 +---- 66 files changed, 431 insertions(+), 563 deletions(-)
Title: Partial Least Squares Regression for Beta Regression Models
Description: Provides Partial least squares Regression for (weighted) beta regression models (Bertrand 2013, <http://journal-sfds.fr/article/view/215>) and k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between plsRbeta versions 0.2.9 dated 2022-05-02 and 0.3.0 dated 2023-03-15
DESCRIPTION | 12 - MD5 | 76 +++++------ NAMESPACE | 2 R/PLS_beta_wvc.R | 2 R/TxTum.mod.bootBC1.R | 2 R/TxTum.mod.bootBR6.R | 2 R/bootplsbeta.R | 66 ++++----- R/coefs.plsRbeta.R | 16 +- R/coefs.plsRbeta.raw.R | 15 +- R/coefs.plsRbetanp.R | 9 + R/modpls.boot3.R | 2 R/modpls_sub4.R | 2 R/permcoefs.plsRbeta.R | 16 ++ R/permcoefs.plsRbeta.raw.R | 24 ++- R/permcoefs.plsRbetanp.R | 2 R/plsRbeta.R | 10 - R/plsRbetamodel.default.R | 11 - R/plsRbetamodel.formula.R | 12 + R/tilt.bootplsbeta.R | 30 ++-- README.md | 213 +++++++++++++++---------------- build/vignette.rds |binary inst/CITATION | 18 +- inst/doc/tn_Insights.html | 104 +++++++-------- man/PLS_beta_wvc.Rd | 2 man/TxTum.mod.bootBC1.Rd | 6 man/TxTum.mod.bootBR6.Rd | 6 man/bootplsbeta.Rd | 58 ++++---- man/coefs.plsRbeta.Rd | 11 + man/coefs.plsRbeta.raw.Rd | 11 + man/coefs.plsRbetanp.Rd | 17 ++ man/figures/README-bootboxplots-1.png |binary man/figures/README-bootplotconfint-1.png |binary man/modpls.boot3.Rd | 6 man/modpls_sub4.Rd | 6 man/permcoefs.plsRbeta.Rd | 7 + man/permcoefs.plsRbeta.raw.Rd | 13 + man/permcoefs.plsRbetanp.Rd | 2 man/plsRbeta.Rd | 16 +- man/tilt.bootplsbeta.Rd | 20 +- 39 files changed, 461 insertions(+), 366 deletions(-)
Title: Likelihood Analyses for Common Statistical Tests
Description: A collection of functions that calculate the log likelihood
(support) for a range of statistical tests. Where possible the likelihood
function and likelihood interval for the observed data are displayed. The
evidential approach used here is based on the book "Likelihood" by A.W.F.
Edwards (1992, ISBN-13 : 978-0801844430), "Statistical Evidence" by R.
Royall (1997, ISBN-13 : 978-0412044113), S.N. Goodman & R. Royall
(2011) <doi:10.2105/AJPH.78.12.1568>, "Understanding
Psychology as a Science" by Z. Dienes (2008, ISBN-13 : 978-0230542310),
S. Glover & P. Dixon <https://link.springer.com/article/10.3758/BF03196706>
and others. This package accompanies "Evidence-Based Statistics" by
P. Cahusac (2020, ISBN-13 : 978-1119549802).
Author: Peter Cahusac [aut, cre]
Maintainer: Peter Cahusac <peteqsac@gmail.com>
Diff between likelihoodR versions 1.0.9 dated 2023-01-21 and 1.1.0 dated 2023-03-15
DESCRIPTION | 6 +-- MD5 | 42 +++++++++++++------------- R/L_1way_ANOVA.R | 4 +- R/L_1way_RM_ANOVA.R | 4 +- R/L_1way_cat.R | 50 ++++++++++++++++++++++--------- R/L_2S_ttest.R | 47 ++++++++++++++++++++++++----- R/L_2way_Factorial_ANOVA.R | 8 ++--- R/L_2way_cat.R | 4 +- R/L_OR.R | 39 ++++++++++++++---------- R/L_RR.R | 71 ++++++++++++++++++++++++++++++++------------- R/L_corr.R | 50 +++++++++++++++++++++++++------ R/L_efficacy.R | 34 +++++++++++++++------ R/L_logistic_regress.R | 6 +-- R/L_regress.R | 4 +- R/L_ttest.R | 49 +++++++++++++++++++++++++------ man/L_1way_cat.Rd | 12 +++++-- man/L_2S_ttest.Rd | 12 ++++++- man/L_OR.Rd | 12 +++++-- man/L_RR.Rd | 15 ++++++--- man/L_corr.Rd | 12 ++++++- man/L_efficacy.Rd | 10 +++++- man/L_ttest.Rd | 12 ++++++- 22 files changed, 358 insertions(+), 145 deletions(-)
Title: Interfacing with Popular Polity, Institutional, and
Constitutional Datasets
Description: An open-source toolkit developed by ISciences, LLC and the DANTE
Project that is intended for learning, accessing, pre-processing, and
visualizing popular political, institutional, and constitutional datasets.
‘demcon' aims to reduce barriers to entry in political science research by
automating common acquisition and pre-processing procedures. This package
particularly focuses on the V-Dem dataset (<https://www.v-dem.net/vdemds.html>),
and provides adaptations of methods presented in Fjelde, H., Knutsen, C. H.
& Nygård, H. M. 2021, <doi:10.1093/isq/sqaa076>.
Author: Joshua Brinks [aut, cre]
Maintainer: Joshua Brinks <jbrinks@isciences.com>
Diff between demcon versions 0.3.0 dated 2022-09-01 and 0.4.0 dated 2023-03-15
DESCRIPTION | 13 MD5 | 49 NEWS.md | 5 R/cshp_mult.R | 2 R/data.R | 5 R/get_cce.R | 3 R/get_polity5.R | 8 R/get_vdem.R | 4 R/plot.cce.R | 4 README.md | 86 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ccode-considerations.html | 137 inst/doc/clean-vdem.html | 838 ++-- inst/doc/constitution-datasets.html | 144 inst/doc/constraint-indices.html | 156 inst/doc/dem-datasets.html | 218 - man/demcon-package.Rd | 50 man/figures/README-unnamed-chunk-6-1.png |only man/get_polity5.Rd | 2 man/iaepv2_adj.Rd | 229 - tests/testthat/_snaps/plot_cshp_mult/blakans-secession-plot.svg | 1724 ++++++++-- tests/testthat/_snaps/plot_cshp_mult/yemens-secession-plot.svg | 952 ++++- tests/testthat/test-get_vdem.R | 2 tests/testthat/test-prep_vdem.R | 7 vignettes/civil-liberties.bib | 1227 +++---- 26 files changed, 4001 insertions(+), 1864 deletions(-)
Title: Models, Datasets and Transformations for Images
Description: Provides access to datasets, models and preprocessing
facilities for deep learning with images. Integrates seamlessly
with the 'torch' package and it's 'API' borrows heavily from
'PyTorch' vision package.
Author: Daniel Falbel [aut, cre],
Christophe Regouby [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchvision versions 0.4.1 dated 2022-01-28 and 0.5.0 dated 2023-03-15
DESCRIPTION | 16 - MD5 | 42 ++-- NAMESPACE | 7 NEWS.md | 36 ++- R/models-alexnet.R | 2 R/models-inception.R |only R/models-mobilenetv2.R | 4 R/tiny-imagenet-dataset.R | 3 R/transforms-defaults.R | 2 R/transforms-tensor.R | 4 R/vision_utils.R | 297 +++++++++++++++++++++++++++++++ man/draw_bounding_boxes.Rd |only man/draw_keypoints.Rd |only man/draw_segmentation_masks.Rd |only man/image_folder_dataset.Rd | 6 man/model_inception_v3.Rd |only man/model_resnet.Rd | 20 +- man/model_vgg.Rd | 18 - man/tensor_image_browse.Rd |only man/tensor_image_display.Rd |only tests/testthat/helper-torchvision.R | 5 tests/testthat/test-models-inception.R |only tests/testthat/test-models-mobilenetv2.R | 15 + tests/testthat/test-models-resnet.R | 44 ++++ tests/testthat/test-transforms.R | 41 ++++ tests/testthat/test-vision-utils.R | 75 +++++++ 26 files changed, 567 insertions(+), 70 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Uses by default the 's2'
package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] ,
Roger Bivand [ctb] ,
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] ,
Kirill Mueller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-10 dated 2023-03-12 and 1.0-11 dated 2023-03-15
DESCRIPTION | 6 +- MD5 | 36 +++++++-------- NAMESPACE | 8 +++ NEWS.md | 12 +++++ R/break_antimeridian.R | 4 - R/crs.R | 9 --- R/geom-transformers.R | 69 +++++++++++++++++++++++++++++ R/make_grid.R | 19 +++++++- inst/doc/sf1.html | 100 +++++++++++++++++++++---------------------- inst/doc/sf2.html | 6 +- inst/doc/sf4.html | 2 inst/doc/sf7.html | 10 ++-- man/geos_unary.Rd | 33 ++++++++++++++ man/st_break_antimeridian.Rd | 4 - man/st_make_grid.Rd | 2 src/gdal.cpp | 10 +++- src/geos.cpp | 24 +++++++++- tests/spatstat.Rout.save | 4 - tests/units.Rout.save | 4 - 19 files changed, 262 insertions(+), 100 deletions(-)
Title: Prediction Intervals for Synthetic Control Methods with Multiple
Treated Units and Staggered Adoption
Description: Implementation of prediction and inference procedures for Synthetic Control methods using least square, lasso, ridge, or simplex-type constraints. Uncertainty is quantified with prediction intervals as developed in Cattaneo, Feng, and Titiunik (2021) <https://mdcattaneo.github.io/papers/Cattaneo-Feng-Titiunik_2021_JASA.pdf>.
Author: Matias Cattaneo [aut],
Yingjie Feng [aut],
Filippo Palomba [aut, cre],
Rocio Titiunik [aut]
Maintainer: Filippo Palomba <fpalomba@princeton.edu>
Diff between scpi versions 2.1.0 dated 2022-12-25 and 2.2.1 dated 2023-03-15
DESCRIPTION | 8 MD5 | 32 +-- R/scdata.R | 55 ++--- R/scdataMulti.R | 131 ++++++++----- R/scest.R | 4 R/scpi-package.R | 4 R/scpi.R | 47 ++--- R/scplot.R | 4 R/scplotMulti.R | 6 R/supporting_functions.R | 441 +++++++++++++++++++++++------------------------ man/scdata.Rd | 7 man/scdataMulti.Rd | 18 + man/scest.Rd | 4 man/scpi-package.Rd | 4 man/scpi.Rd | 4 man/scplot.Rd | 4 man/scplotMulti.Rd | 4 17 files changed, 399 insertions(+), 378 deletions(-)
Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2023) <doi:10.18637/jss.v106.i03>).
Author: Quentin Grimonprez [aut, cre],
Samuel Blanck [ctb],
Alain Celisse [ths],
Guillemette Marot [ths],
Yi Yang [ctb],
Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between MLGL versions 0.6.7 dated 2022-05-25 and 1.0.0 dated 2023-03-15
DESCRIPTION | 12 ++++++------ MD5 | 27 ++++++++++++++------------- NEWS | 3 +++ R/HMT.R | 3 +-- R/MLGL-package.R | 5 +++-- R/print.R | 18 ++++++------------ inst |only man/HMT.Rd | 6 +----- man/MLGL-package.Rd | 5 +++-- man/print.HMT.Rd | 6 +----- man/print.MLGL.Rd | 6 +----- man/print.fullProcess.Rd | 6 +----- man/summary.HMT.Rd | 6 +----- man/summary.MLGL.Rd | 6 +----- man/summary.fullProcess.Rd | 6 +----- 15 files changed, 43 insertions(+), 72 deletions(-)
Title: Gaussian Processes for Estimating Causal Exposure Response
Curves
Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint <arXiv:2105.03454>.
Author: Naeem Khoshnevis [aut, cre] ,
Boyu Ren [aut] ,
Tanujit Dey [ctb] ,
Danielle Braun [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Diff between GPCERF versions 0.2.0 dated 2023-01-22 and 0.2.1 dated 2023-03-15
GPCERF-0.2.0/GPCERF/R/calc_ac.R |only GPCERF-0.2.0/GPCERF/R/train_GPS.R |only GPCERF-0.2.0/GPCERF/inst/doc/Full-Gaussian-Processes.R |only GPCERF-0.2.0/GPCERF/inst/doc/Full-Gaussian-Processes.Rmd |only GPCERF-0.2.0/GPCERF/inst/doc/Full-Gaussian-Processes.html |only GPCERF-0.2.0/GPCERF/man/calc_ac.Rd |only GPCERF-0.2.0/GPCERF/man/train_gps.Rd |only GPCERF-0.2.0/GPCERF/tests/testthat/test-calc_ac.R |only GPCERF-0.2.0/GPCERF/vignettes/Full-Gaussian-Processes.Rmd |only GPCERF-0.2.1/GPCERF/DESCRIPTION | 9 GPCERF-0.2.1/GPCERF/MD5 | 165 +++++----- GPCERF-0.2.1/GPCERF/NAMESPACE | 2 GPCERF-0.2.1/GPCERF/NEWS.md | 14 GPCERF-0.2.1/GPCERF/R/compute_deriv_nn.R | 120 +++---- GPCERF-0.2.1/GPCERF/R/compute_deriv_weights_gp.R | 48 +- GPCERF-0.2.1/GPCERF/R/compute_inverse.R | 8 GPCERF-0.2.1/GPCERF/R/compute_m_sigma.R | 112 ++++-- GPCERF-0.2.1/GPCERF/R/compute_posterior_m_nn.R | 58 +-- GPCERF-0.2.1/GPCERF/R/compute_posterior_sd_nn.R | 38 +- GPCERF-0.2.1/GPCERF/R/compute_rl_deriv_gp.R | 39 +- GPCERF-0.2.1/GPCERF/R/compute_rl_deriv_nn.R | 43 +- GPCERF-0.2.1/GPCERF/R/compute_sd_gp.R | 30 + GPCERF-0.2.1/GPCERF/R/compute_w_corr.R | 145 +++++--- GPCERF-0.2.1/GPCERF/R/compute_weight_gp.R | 63 ++- GPCERF-0.2.1/GPCERF/R/estimate_cerf_gp.R | 119 +++++-- GPCERF-0.2.1/GPCERF/R/estimate_cerf_nngp.R | 116 ++++--- GPCERF-0.2.1/GPCERF/R/estimate_gps.R |only GPCERF-0.2.1/GPCERF/R/estimate_mean_sd_nn.R | 63 +-- GPCERF-0.2.1/GPCERF/R/estimate_noise_gp.R | 7 GPCERF-0.2.1/GPCERF/R/estimate_noise_nn.R | 8 GPCERF-0.2.1/GPCERF/R/find_optimal_nn.R | 75 ++-- GPCERF-0.2.1/GPCERF/R/generate_synthetic_data.R | 24 - GPCERF-0.2.1/GPCERF/R/plot.R | 135 ++++++-- GPCERF-0.2.1/GPCERF/R/print.R | 77 +--- GPCERF-0.2.1/GPCERF/R/utils.R | 2 GPCERF-0.2.1/GPCERF/R/zzz.R | 19 - GPCERF-0.2.1/GPCERF/README.md | 157 ++++++++- GPCERF-0.2.1/GPCERF/build/vignette.rds |binary GPCERF-0.2.1/GPCERF/inst/CITATION |only GPCERF-0.2.1/GPCERF/inst/doc/GPCERF.R | 71 ++-- GPCERF-0.2.1/GPCERF/inst/doc/GPCERF.Rmd | 76 ++-- GPCERF-0.2.1/GPCERF/inst/doc/GPCERF.html | 157 ++++++--- GPCERF-0.2.1/GPCERF/inst/doc/Nearest-neighbor-Gaussian-Processes.R | 78 ++-- GPCERF-0.2.1/GPCERF/inst/doc/Nearest-neighbor-Gaussian-Processes.Rmd | 85 +++-- GPCERF-0.2.1/GPCERF/inst/doc/Nearest-neighbor-Gaussian-Processes.html | 163 +++++---- GPCERF-0.2.1/GPCERF/inst/doc/Standard-Gaussian-Processes.R |only GPCERF-0.2.1/GPCERF/inst/doc/Standard-Gaussian-Processes.Rmd |only GPCERF-0.2.1/GPCERF/inst/doc/Standard-Gaussian-Processes.html |only GPCERF-0.2.1/GPCERF/man/compute_deriv_nn.Rd | 33 +- GPCERF-0.2.1/GPCERF/man/compute_deriv_weights_gp.Rd | 17 - GPCERF-0.2.1/GPCERF/man/compute_m_sigma.Rd | 23 - GPCERF-0.2.1/GPCERF/man/compute_posterior_m_nn.Rd | 12 GPCERF-0.2.1/GPCERF/man/compute_posterior_sd_nn.Rd | 11 GPCERF-0.2.1/GPCERF/man/compute_rl_deriv_gp.Rd | 28 - GPCERF-0.2.1/GPCERF/man/compute_rl_deriv_nn.Rd | 35 -- GPCERF-0.2.1/GPCERF/man/compute_sd_gp.Rd | 21 - GPCERF-0.2.1/GPCERF/man/compute_w_corr.Rd | 39 +- GPCERF-0.2.1/GPCERF/man/compute_weight_gp.Rd | 19 - GPCERF-0.2.1/GPCERF/man/estimate_cerf_gp.Rd | 28 - GPCERF-0.2.1/GPCERF/man/estimate_cerf_nngp.Rd | 33 -- GPCERF-0.2.1/GPCERF/man/estimate_gps.Rd |only GPCERF-0.2.1/GPCERF/man/estimate_mean_sd_nn.Rd | 22 - GPCERF-0.2.1/GPCERF/man/estimate_noise_gp.Rd | 7 GPCERF-0.2.1/GPCERF/man/figures/png/readme_gp.png |only GPCERF-0.2.1/GPCERF/man/figures/png/readme_nngp.png |only GPCERF-0.2.1/GPCERF/man/find_optimal_nn.Rd | 22 - GPCERF-0.2.1/GPCERF/man/generate_synthetic_data.Rd | 2 GPCERF-0.2.1/GPCERF/man/plot.cerf_gp.Rd | 3 GPCERF-0.2.1/GPCERF/man/plot.cerf_nngp.Rd | 3 GPCERF-0.2.1/GPCERF/src/Makevars | 2 GPCERF-0.2.1/GPCERF/src/Makevars.win | 2 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_deriv_nn.R | 15 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_deriv_weights_gp.R | 12 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_inverse.R | 8 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_m_sigma.R | 14 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_posterior_m_nn.R | 63 +++ GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_posterior_sd_nn.R | 26 - GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_rl_deriv_gp.R | 10 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_rl_deriv_nn.R | 11 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_sd_gp.R | 14 GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_w_corr.R | 30 - GPCERF-0.2.1/GPCERF/tests/testthat/test-compute_weight_gp.R | 21 - GPCERF-0.2.1/GPCERF/tests/testthat/test-estimate_cerf_gp.R | 88 +++-- GPCERF-0.2.1/GPCERF/tests/testthat/test-estimate_cerf_nngp.R | 83 +++-- GPCERF-0.2.1/GPCERF/tests/testthat/test-estimate_gps.R |only GPCERF-0.2.1/GPCERF/tests/testthat/test-estimate_mean_sd_nn.R | 16 GPCERF-0.2.1/GPCERF/tests/testthat/test-estimate_noise_gp.R | 18 - GPCERF-0.2.1/GPCERF/tests/testthat/test-estimate_noise_nn.R | 21 - GPCERF-0.2.1/GPCERF/tests/testthat/test-find_optimal_nn.R | 18 - GPCERF-0.2.1/GPCERF/tests/testthat/test-generate_synthetic_data.R | 22 - GPCERF-0.2.1/GPCERF/vignettes/GPCERF.Rmd | 76 ++-- GPCERF-0.2.1/GPCERF/vignettes/Nearest-neighbor-Gaussian-Processes.Rmd | 85 +++-- GPCERF-0.2.1/GPCERF/vignettes/Standard-Gaussian-Processes.Rmd |only 93 files changed, 2004 insertions(+), 1335 deletions(-)
Title: Render Sequence Plots using 'ggplot2'
Description: A set of wrapper functions that mainly re-produces most of the
sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base
R to produce the plots this library draws on 'ggplot2'.
The plots are produced on the basis of a sequence object defined
with TraMineR::seqdef(). The package automates the reshaping and plotting
of sequence data. Resulting plots are of class 'ggplot', i.e. components
can be added and tweaked using '+' and regular 'ggplot2' functions.
Author: Marcel Raab [aut, cre]
Maintainer: Marcel Raab <marcel.raab@gmail.com>
Diff between ggseqplot versions 0.8.1 dated 2022-10-11 and 0.8.2 dated 2023-03-15
ggseqplot-0.8.1/ggseqplot/R/zzz.R |only ggseqplot-0.8.2/ggseqplot/DESCRIPTION | 12 - ggseqplot-0.8.2/ggseqplot/MD5 | 39 ++-- ggseqplot-0.8.2/ggseqplot/NAMESPACE | 1 ggseqplot-0.8.2/ggseqplot/NEWS.md | 5 ggseqplot-0.8.2/ggseqplot/R/ggseqdplot.R | 12 - ggseqplot-0.8.2/ggseqplot/R/ggseqeplot.R | 9 - ggseqplot-0.8.2/ggseqplot/R/ggseqiplot.R | 14 + ggseqplot-0.8.2/ggseqplot/R/ggseqmsplot.R | 12 + ggseqplot-0.8.2/ggseqplot/R/ggseqmtplot.R | 6 ggseqplot-0.8.2/ggseqplot/R/ggseqrfplot.R | 18 +- ggseqplot-0.8.2/ggseqplot/R/ggseqrplot.R | 18 -- ggseqplot-0.8.2/ggseqplot/R/ggseqtrplot.R | 1 ggseqplot-0.8.2/ggseqplot/build/partial.rdb |binary ggseqplot-0.8.2/ggseqplot/build/vignette.rds |binary ggseqplot-0.8.2/ggseqplot/inst/CITATION | 9 - ggseqplot-0.8.2/ggseqplot/inst/doc/ggseqplot.html | 173 ++++++++++------------ ggseqplot-0.8.2/ggseqplot/man/ggseqmsplot.Rd | 1 ggseqplot-0.8.2/ggseqplot/man/ggseqmtplot.Rd | 1 ggseqplot-0.8.2/ggseqplot/man/ggseqrfplot.Rd | 8 - ggseqplot-0.8.2/ggseqplot/man/ggseqrplot.Rd | 17 -- 21 files changed, 178 insertions(+), 178 deletions(-)
Title: Analysis of Convergent Evolution
Description: Quantifies and assesses the significance of convergent evolution using multiple methods and measures as described in Stayton (2015) <DOI: 10.1111/evo.12729> and Grossnickle et al. 2023. Also displays results in various ways.
Author: William H. Brightly, C. Tristan Stayton
Maintainer: C. Tristan Stayton <tstayton@bucknell.edu>
Diff between convevol versions 1.3 dated 2018-11-04 and 2.0.0 dated 2023-03-15
convevol-1.3/convevol/R/allmaxdist.R |only convevol-1.3/convevol/R/ancestrallineages.R |only convevol-1.3/convevol/R/calcchanges.R |only convevol-1.3/convevol/R/convrat.R |only convevol-1.3/convevol/R/convratsig.R |only convevol-1.3/convevol/R/findanc.R |only convevol-1.3/convevol/R/labelstonumbers.R |only convevol-1.3/convevol/R/maxdist.R |only convevol-1.3/convevol/man/allmaxdist.Rd |only convevol-1.3/convevol/man/ancestrallineages.Rd |only convevol-1.3/convevol/man/calcchanges.Rd |only convevol-1.3/convevol/man/convrat.Rd |only convevol-1.3/convevol/man/convratsig.Rd |only convevol-1.3/convevol/man/findanc.Rd |only convevol-1.3/convevol/man/labelstonumbers.Rd |only convevol-1.3/convevol/man/maxdist.Rd |only convevol-2.0.0/convevol/DESCRIPTION | 19 ++-- convevol-2.0.0/convevol/MD5 | 50 +++++------ convevol-2.0.0/convevol/NAMESPACE | 53 ++++++------ convevol-2.0.0/convevol/R/calcConv.R |only convevol-2.0.0/convevol/R/calcConvCt.r |only convevol-2.0.0/convevol/R/calcCs.R |only convevol-2.0.0/convevol/R/calcCsCt.r |only convevol-2.0.0/convevol/R/convSig.r |only convevol-2.0.0/convevol/R/convSigCt.R |only convevol-2.0.0/convevol/R/convnum.R | 30 +++---- convevol-2.0.0/convevol/R/convnumsig.R | 31 +++---- convevol-2.0.0/convevol/R/multianc.R | 22 ++--- convevol-2.0.0/convevol/R/plotCt.r |only convevol-2.0.0/convevol/R/pullNodeSeq.R |only convevol-2.0.0/convevol/man/calcConv.Rd |only convevol-2.0.0/convevol/man/calcConvCt.Rd |only convevol-2.0.0/convevol/man/calcCs.Rd |only convevol-2.0.0/convevol/man/calcCsCt.Rd |only convevol-2.0.0/convevol/man/convSig.Rd |only convevol-2.0.0/convevol/man/convSigCt.Rd |only convevol-2.0.0/convevol/man/convnum.Rd | 102 ++++++++++++----------- convevol-2.0.0/convevol/man/convnumsig.Rd | 107 +++++++++++++------------ convevol-2.0.0/convevol/man/multianc.Rd | 74 ++++++++--------- convevol-2.0.0/convevol/man/plotCt.Rd |only convevol-2.0.0/convevol/man/plotellipse.Rd | 48 +++++------ convevol-2.0.0/convevol/man/pullNodeSeq.Rd |only 42 files changed, 277 insertions(+), 259 deletions(-)
Title: Plot Jacobson-Truax Reliable Change Indices
Description: The concept of reliable and clinically significant change
(Jacobson & Truax, 1991) helps you answer the following questions for a
sample with two measurements at different points in time (pre & post):
Which proportion of my sample has a (considering the reliability of the
instrument) probably not-just-by-chance difference in pre- vs. post-scores?
Which proportion of my sample does not only change in a statistically
significant way (see question one), but also in a clinically significant way
(e.g. change from a test score regarded "dysfunctional" to a score regarded
"functional")?
This package allows you to very easily create a scatterplot of your sample
in which the x-axis maps to the pre-scores, the y-axis maps to the
post-scores and several graphical elements (lines, colors) allow you to gain
a quick overview about reliable changes in these scores.
An example of this kind of plot is Figure 2 of Jacobson & Truax (1991).
Referenced article:
Jacobson, N. S., & Truax, P. [...truncated...]
Author: Maximilian Hagspiel [aut, cre, cph]
Maintainer: Maximilian Hagspiel <maxhag@mailbox.org>
Diff between rciplot versions 0.1.0 dated 2022-11-18 and 0.1.1 dated 2023-03-15
DESCRIPTION | 6 +- MD5 | 8 +-- NAMESPACE | 1 R/rciplot.R | 146 ++++++++++++++++++++++++++++++++++++++++++++++++++------- man/rciplot.Rd | 21 ++++++++ 5 files changed, 158 insertions(+), 24 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Lightweight parallel code execution, local or distributed across
the network. Designed for simplicity, a 'mirai' evaluates an arbitrary
expression asynchronously, resolving automatically upon completion.
Built on 'nanonext' and 'NNG' (Nanomsg Next Gen), uses scalability protocols
not subject to R connection limits and transports faster than TCP/IP where
applicable.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.7.2 dated 2023-01-17 and 0.8.0 dated 2023-03-15
mirai-0.7.2/mirai/man/eval_mirai.Rd |only mirai-0.7.2/mirai/man/is_error_value.Rd |only mirai-0.7.2/mirai/man/is_mirai_interrupt.Rd |only mirai-0.8.0/mirai/DESCRIPTION | 8 mirai-0.8.0/mirai/MD5 | 32 - mirai-0.8.0/mirai/NAMESPACE | 10 mirai-0.8.0/mirai/NEWS.md | 22 mirai-0.8.0/mirai/R/mirai-package.R | 43 - mirai-0.8.0/mirai/R/mirai.R | 785 +++++++++++++++++++++------- mirai-0.8.0/mirai/README.md | 435 ++++++++++++--- mirai-0.8.0/mirai/man/daemons.Rd | 247 +++++++- mirai-0.8.0/mirai/man/dispatcher.Rd |only mirai-0.8.0/mirai/man/dot-.Rd |only mirai-0.8.0/mirai/man/figures/logo.png |binary mirai-0.8.0/mirai/man/is_mirai.Rd | 3 mirai-0.8.0/mirai/man/is_mirai_error.Rd | 37 + mirai-0.8.0/mirai/man/mirai-package.Rd | 15 mirai-0.8.0/mirai/man/mirai.Rd |only mirai-0.8.0/mirai/man/server.Rd | 68 +- mirai-0.8.0/mirai/tests/tests.R | 63 +- 20 files changed, 1359 insertions(+), 409 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-20 0.5.1
2022-05-11 0.5.0
2022-01-24 0.4.2
2021-10-30 0.4.1
2021-09-11 0.4.0
2021-05-18 0.3.8
2021-04-19 0.3.7
2021-04-09 0.3.6
2021-04-02 0.3.5
2021-03-21 0.3.4
2021-02-01 0.3.3
2021-01-28 0.3.2
2021-01-15 0.3.1
2021-01-12 0.3.0
2020-11-18 0.2.0
2020-10-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-08 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-04 0.9.5-1
2022-08-29 0.9.5
2021-04-06 0.9.4
2021-03-07 0.9.3
2020-12-11 0.9.2
2020-03-13 0.9.1
2020-02-26 0.9.0
More information about shiny.blueprint at CRAN
Permanent link
Title: Create Publication-Ready Regression Tables with Panels
Description: Create an automated regression table that is well-suited for models that are estimated with multiple dependent variables. 'panelsummary' extends 'modelsummary' (Arel-Bundock, V. (2022) <doi:10.18637/jss.v103.i01>) by allowing regression tables to be split into multiple sections with a simple function call. Utilize familiar arguments such as fmt, estimate, statistic, vcov, conf_level, stars, coef_map, coef_omit, coef_rename, gof_map, and gof_omit from 'modelsummary' to clean the table, and additionally, add a row for the mean of the dependent variable without external manipulation.
Author: Michael Topper [aut, cre],
Vincent Arel-Bundock [cph]
Maintainer: Michael Topper <miketopper123@gmail.com>
Diff between panelsummary versions 0.1.0 dated 2022-12-20 and 0.1.1 dated 2023-03-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/panelsummary.R | 2 ++ R/panelsummary_raw.R | 1 + README.md | 12 +++++++----- build/partial.rdb |binary man/panelsummary.Rd | 24 +++++++++++++++++------- man/panelsummary_raw.Rd | 24 +++++++++++++++++------- 9 files changed, 63 insertions(+), 31 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 2.1.17 dated 2023-01-13 and 2.1.19 dated 2023-03-15
growthPheno-2.1.17/growthPheno/man/traitSmooth.Rd |only growthPheno-2.1.19/growthPheno/DESCRIPTION | 8 - growthPheno-2.1.19/growthPheno/MD5 | 22 +-- growthPheno-2.1.19/growthPheno/R/PVA.v3.r | 4 growthPheno-2.1.19/growthPheno/R/traitSmooth.r | 20 ++- growthPheno-2.1.19/growthPheno/build/partial.rdb |binary growthPheno-2.1.19/growthPheno/inst/News.Rd | 8 + growthPheno-2.1.19/growthPheno/inst/doc/Rice.pdf |binary growthPheno-2.1.19/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-2.1.19/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-2.1.19/growthPheno/man/probeSmooths.Rd | 57 +--------- growthPheno-2.1.19/growthPheno/man/traitExtractFeatures.Rd | 7 + growthPheno-2.1.19/growthPheno/man/traitSmooth..Rd |only 13 files changed, 53 insertions(+), 73 deletions(-)