Model Selection and Multimodel Inference Based on (Q)AIC(c)

Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs', 'rjags', and 'jagsUI' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.

Automated C Code Generation for 'deSolve', 'bvpSolve'

Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.

Functions and C++ Header Files for Computation on Manifolds

We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) if you are interested in statistics on manifolds, and Absil et al (2007, ISBN:9780691132983) on computational aspects of optimization on matrix manifolds.

Handle Missing Tensor Data with C++ Integration

To handle higher-order tensor data. See Kolda and Bader (2009) for details on tensor. While existing packages on tensor data extend the base 'array' class to some data classes, this package serves as an alternative resort to handle tensor only as 'array' class. Some functionalities related to missingness are also supported.

A C++11 Interface for R's C Interface

Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.

Check 'C' and 'C++' Files using 'Cppcheck'

Allow to run 'Cppcheck' (< https://cppcheck.sourceforge.io/>) on 'C' and 'C++' files with a 'R' command or a 'RStudio' addin. The report appears in the 'RStudio' viewer pane as a formatted 'HTML' file. It is also possible to get this report with a 'shiny' application. 'Cppcheck' can spot many error types and it can also give some recommendations on the code.

Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs

Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.

'MsgPack' C++ Header Files and Interface Functions for R

'MsgPack' header files are provided for use by R packages, along with the ability to access, create and alter 'MsgPack' objects directly from R. 'MsgPack' is an efficient binary serialization format. It lets you exchange data among multiple languages like 'JSON' but it is faster and smaller. Small integers are encoded into a single byte, and typical short strings require only one extra byte in addition to the strings themselves. This package provides headers from the 'msgpack-c' implementation for C and C++(11) for use by R, particularly 'Rcpp'. The included 'msgpack-c' headers are licensed under the Boost Software License (Version 1.0); the code added by this package as well the R integration are licensed under the GPL (>= 2). See the files 'COPYRIGHTS' and 'AUTHORS' for a full list of copyright holders and contributors to 'msgpack-c'.

System for Building and Debugging C/C++ Dynamic Libraries

A build system based on 'GNU make' that creates and maintains (simply) make files in an R session and provides GUI debugging support through 'Microsoft Visual Code'.

'2bit' 'C' Library

A trimmed down copy of the "kent-core source tree" turned into a 'C' library for manipulation of '.2bit' files. See < https://genome.ucsc.edu/FAQ/FAQformat.html#format7> for a quick overview of the '2bit' format. The "kent-core source tree" can be found here: < https://github.com/ucscGenomeBrowser/kent-core/>. Only the '.c' and '.h' files from the source tree that are related to manipulation of '.2bit' files were kept. Note that the package is primarily useful to developers of other R packages who wish to use the '2bit' 'C' library in their own 'C'/'C++' code.