'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')

'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (< https://cwb.sourceforge.io>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (< https://www.r-project.org/Licenses/GPL-3>). The 'CWB' relies on 'pcre2' (BSD license, see < https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>) and 'GLib' (LGPL license, see < https://www.gnu.org/licenses/lgpl-3.0.en.html>). See the file LICENSE.note for further information. The package includes modified code of the 'rcqp' package (GPL-2, see < https://cran.r-project.org/package=rcqp>). The original work of the authors of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code is the approach used by 'RcppCWB'.

Database Interface and MariaDB Driver

Implements a DBI-compliant interface to MariaDB (< https://mariadb.org/>) and MySQL (< https://www.mysql.com/>) databases.

Provide the 'x13ashtml' Seasonal Adjustment Binary

The US Census Bureau provides a seasonal adjustment program now called 'X-13ARIMA-SEATS' building on both earlier programs called X-11 and X-12 as well as the SEATS program by the Bank of Spain. The US Census Bureau offers both source and binary versions -- which this package integrates for use by other R packages.

Generic Coordinate System Transformations Using 'PROJ'

A wrapper around the generic coordinate transformation software 'PROJ' that transforms coordinates from one coordinate reference system ('CRS') to another. This includes cartographic projections as well as geodetic transformations. The intention is for this package to be used by user-packages such as 'reproj', and that the older 'PROJ.4' and version 5 pathways be provided by the 'proj4' package.

Interface to 'Phylocom'

Interface to 'Phylocom' (< https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.

Cast '(R)Markdown' Files to 'XML' and Back Again

Parsing '(R)Markdown' files with numerous regular expressions can be fraught with peril, but it does not have to be this way. Converting '(R)Markdown' files to 'XML' using the 'commonmark' package allows in-memory editing via of 'markdown' elements via 'XPath' through the extensible 'R6' class called 'yarn'. These modified 'XML' representations can be written to '(R)Markdown' documents via an 'xslt' stylesheet which implements an extended version of 'GitHub'-flavoured 'markdown' so that you can tinker to your hearts content.

Co-Data Learning for Bayesian Additive Regression Trees

Estimate prior variable weights for Bayesian Additive Regression Trees (BART). These weights correspond to the probabilities of the variables being selected in the splitting rules of the sum-of-trees. Weights are estimated using empirical Bayes and external information on the explanatory variables (co-data). BART models are fitted using the 'dbarts' 'R' package. See Goedhart and others (2023) for details.

Correcting Drift and Carry-over in Continuous Isotopic Measurements

A series of functions that allow an easy and fast correction for drift and carry-over in continuous isotopic measurements. This implementation provides queries allowing users to perform the implemented corrections according to their needs. These functions further enable the processing of large datasets and can provides apt visualizations of the corrections performed.

Fused Partitioned Regression for Clinical and Omics Data

Fit (generalized) linear regression models in each leaf node of a tree. The tree is constructed using clinical variables only. The linear regression models are constructed using (high-dimensional) omics variables only. The leaf-node-specific regression models are estimated using the penalized likelihood including a standard ridge (L2) penalty and a fusion penalty that links the leaf-node-specific regression models to one another. The intercepts of the leaf nodes reflect the effects of the clinical variables and are left unpenalized. The tree, fitted with the clinical variables only, should be constructed outside of the package with the 'rpart' 'R' package. See Goedhart and others (2024) for details on the method.

Programming with Big Data -- Interface to 'ZeroMQ'

'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.