Manipulations of Triangular Meshes Based on the 'VCGLIB' API

Operations on triangular meshes based on 'VCGLIB'. This package integrates nicely with the R-package 'rgl' to render the meshes processed by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI < https://vcg.isti.cnr.it/>, like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk < https://github.com/cnr-isti-vclab/vcglib> and patched to work with options determined by the configure script as well as to work with the header files included by 'RcppEigen'.

An Inclusive, Unifying API for Progress Updates

A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will also work with parallel processing via the 'future' framework, e.g. future.apply::future_lapply(), furrr::future_map(), and 'foreach' with 'doFuture'. The package is compatible with Shiny applications.

Import and Handling for Plain and Formatted Text Files

Functions for importing and handling text files and formatted text files with additional meta-data, such including '.csv', '.tab', '.json', '.xml', '.html', '.pdf', '.doc', '.docx', '.rtf', '.xls', '.xlsx', and others.

Read and Write '.ini' Files

Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.

Solving Linear Inverse Models

Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) subject to equality constraints Ex=f and/or inequality constraints Gx>=h, (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.

Creates Log Files

Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.

Byte Pair Encoding Text Tokenization

Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library < https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) < https://aclanthology.org/P16-1162/>.

Extract Genotypes from a PLINK .bed File

A matrix-like data structure that allows for efficient, convenient, and scalable subsetting of binary genotype/phenotype files generated by PLINK (< https://www.cog-genomics.org/plink2>), the whole genome association analysis toolset, without loading the entire file into memory.

Tools for Using Fonts

Tools to using fonts other than the standard PostScript fonts. This package makes it easy to use system TrueType fonts and with PDF or PostScript output files, and with bitmap output files in Windows. extrafont can also be used with fonts packaged specifically to be used with, such as the fontcm package, which has Computer Modern PostScript fonts with math symbols.

Functional Data Analysis

These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from < https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.