Functions to Support the ICES Transparent Assessment Framework

Functions to support the ICES Transparent Assessment Framework < https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.

DATRAS Trawl Survey Database Web Services

R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database < https://datras.ices.dk/WebServices/Webservices.aspx>.

String Distance Calculation with Tidy Data Principles

Calculation of string distance following the tidy data principles. Built on top of the 'stringdist' package.

Read and Process 'Pamguard' Binary Data

Functions for easily reading and processing binary data files created by 'Pamguard' (< https://www.pamguard.org/>). All functions for directly reading the binary data files are based on 'MATLAB' code written by Michael Oswald.

Formal Parser and Related Tools for R Markdown Documents

An implementation of a formal grammar and parser for R Markdown documents using the Boost Spirit X3 library. It also includes a collection of high level functions for working with the resulting abstract syntax tree.

Gillespie's Stochastic Simulation Algorithm (SSA)

Provides a simple to use, intuitive, and extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite population continuous-time model. Currently it implements Gillespie's exact stochastic simulation algorithm (Direct method) and several approximate methods (Explicit tau-leap, Binomial tau-leap, and Optimized tau-leap). The package also contains a library of template models that can be run as demo models and can easily be customized and extended. Currently the following models are included, 'Decaying-Dimerization' reaction set, linear chain system, logistic growth model, 'Lotka' predator-prey model, Rosenzweig-MacArthur predator-prey model, 'Kermack-McKendrick' SIR model, and a 'metapopulation' SIRS model. Pineda-Krch et al. (2008) .

Markdown Parser Implemented using the 'MD4C' Library

Provides an R wrapper for the 'MD4C' (Markdown for 'C') library. Functions exist for parsing markdown ('CommonMark' compliant) along with support for other common markdown extensions (e.g. GitHub flavored markdown, 'LaTeX' equation support, etc.). The package also provides a number of higher level functions for exploring and manipulating markdown abstract syntax trees as well as translating and displaying the documents.

Optimization via Subsampling (OPTS)

Subsampling based variable selection for low dimensional generalized linear models. The methods repeatedly subsample the data minimizing an information criterion (AIC/BIC) over a sequence of nested models for each subsample. Marinela Capanu, Mihai Giurcanu, Colin B Begg, Mithat Gonen, Subsampling based variable selection for generalized linear models.

Statistical Inference on Lineup Fairness

Since the early 1970s eyewitness testimony researchers have recognised the importance of estimating properties such as lineup bias (is the lineup biased against the suspect, leading to a rate of choosing higher than one would expect by chance?), and lineup size (how many reasonable choices are in fact available to the witness? A lineup is supposed to consist of a suspect and a number of additional members, or foils, whom a poor-quality witness might mistake for the perpetrator). Lineup measures are descriptive, in the first instance, but since the earliest articles in the literature researchers have recognised the importance of reasoning inferentially about them. This package contains functions to compute various properties of laboratory or police lineups, and is intended for use by researchers in forensic psychology and/or eyewitness testimony research. Among others, the r4lineups package includes functions for calculating lineup proportion, functional size, various estimates of effective size, diagnosticity ratio, homogeneity of the diagnosticity ratio, ROC curves for confidence x accuracy data and the degree of similarity of faces in a lineup.

String Diff, Match, and Patch Utilities

A wrapper for Google's 'diff-match-patch' library. It provides basic tools for computing diffs, finding fuzzy matches, and constructing / applying patches to strings.