Functions Related to ICES Advice

A collection of functions that facilitate computational steps related to advice for fisheries management, according to ICES guidelines. These include methods for calculating reference points and model diagnostics.

Simulate from ODE-Based Models

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Easy Dockerfile Creation from R

Build a Dockerfile straight from your R session. 'dockerfiler' allows you to create step by step a Dockerfile, and provide convenient tools to wrap R code inside this Dockerfile.

Modelling Framework for the Estimation of Salmonid Abundance

A set of functions to estimate capture probabilities and densities from multipass pass removal data.

Import Professional Baseball Data from 'Retrosheet'

A collection of tools to import and structure the (currently) single-season event, game-log, roster, and schedule data available from < https://www.retrosheet.org>. In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse. This package does the parsing on those files, returning the requested data in the most practical R structure to use for sabermetric or other analyses.

Interface to the 'sparseLM' Levenberg-Marquardt Library

Provides an R interface to the 'sparseLM' C library for large-scale nonlinear least squares problems with arbitrarily sparse Jacobians. The underlying solver implements a sparse variant of the Levenberg-Marquardt algorithm for minimizing sum-of-squares objective functions, supports user-supplied analytic Jacobians or finite-difference approximation, and is designed to exploit sparsity for improved memory use and performance. This package exposes the solver in R and uses sparse matrix classes and the 'CHOLMOD' sparse Cholesky factorization routines through the 'Matrix' package interface. Methods from the C library are described in Lourakis (2010) .

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>.

High-Performance 'WebGl' Rendering for Package 'leaflet'

Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript library to render large data in the browser using 'WebGl'.

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.

Data Structures, Summaries, and Visualisations for Missing Data

Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. 'naniar' provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of 'ggplot2' and tidy data. The work is fully discussed at Tierney & Cook (2023) .