Packages

Fishy Packages

How to Install Packages

The following are instructions to install packages from within various ways to interact with R – within RStudio, the R GUI for Windows, or the R GUI for Macintosh OS.

General Packages

More Focused Packages

  • actel – Standardised analysis of acoustic telemetry data from fish moving through receiver arrays.
  • ALKr – age-length keys [As of 16-Jan-19 this package has been archived on CRAN]
  • AnglerCreelSurveySimulation – simulate creel survey data
  • AquaticLifeHistory – fisheries life history analyses (e.g., length-at-age modelling using a multi-model approach, estimating age-at-maturity and length-at-maturity) using contemporary approaches as simple R functions.
  • BayesGrowth – combines length-at-age modelling for fisheries with MCMC implemented using Stan.
  • Bioenergetics 4.0 – a shiny app for bioenergetics modeling
  • Bioenergetics at ISEMP – bioenergetics modeling as part of the Integrated Status and Monitoring Program
  • CatDyn – population parameters from catch dynamics data
  • cuttlefish.model – Perform LPUE standardization and stock assessment of the English Channel cuttlefish stock using a two-stage biomass model
  • EGRET – An R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season
  • fecR – Calculates fishing effort following the DG MARE Ad-Hoc Workshops on Transversal Variables in Zagreb (2015) and Nicosia (2016)
  • FESta: Fishing effort standardization
  • FSAWs – construct and validate standard weight (Ws) equations
  • fishMod – fits models to catch and effort data
  • fishmove – predict fish movement parameters
  • fishualize: Color palettes based on fish species
  • hafroAssmt – fisheries stock assessment at Hafro, the Marine Research Institute in Iceland
  • kobe – methods for summarising results from stock assessments and Management Strategy Evaluations in the Kobe format
  • LBSPR: Length-Based Spawning Potential Ratio – Simulate expected equilibrium length composition, YPR, and SPR using the LBSPR model. Fit the LBSPR model to length data to estimate selectivity, relative fishing mortality, and spawning potential ratio for data-limited fisheries.
  • LeMaRns – Set-up, run, and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006), focused on the marine environment. Introductory publication is here.
  • mapplots – *Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data
  • marindicators: Functions to calculate indicators for four marine ecosystem attributes (Biodiversity, Ecosystem Structure and Functioning, Ecosystem Stability and Resistance to Perturbations, Resource Potential) and one marine ecosystem pressure (Fishing Pressure) from fishery independent trawl survey data and commercial landings data.
  • mixdist – fit mixture distributions — e.g., possibly separating age-classes from a length frequency
  • mizer – multispecies, trait based and community size spectrum ecological models, focused on the marine environment See Introduction to mizer
  • MQMF: Companion for “Using R for Modelling and Quantitative Methods in Fisheries” book
  • ObsCovgTools – Estimates minimum fisheries observer coverage required to achieve a specific objective. Related Shiny app is here.
  • oceanmap – Plotting toolbox for 2D oceanographic data
  • optistock – Functions that aid calculating the optimum time to stock hatchery-reared fish into a body of water given the growth, mortality, and cost of raising a particular number of individuals to a certain length.
  • PBSmapping – two-dimensional plotting features similar to those commonly available in a Geographic Information System
  • PBSmodelling – facilitates the design, testing, and operation of computer models; focused on tools that make it easy to construct and edit a customized graphical user interface
  • RchivalTag – functions to generate, access and analyze standard data products from archival tagging data
  • rct3 – Predict fish year-class strength by calibration regression analysis of multiple recruitment index series.
  • r4ss – analyze and plot the output from Stock Synthesis version 3, a fisheries stock assessment model written in ADMB
  • RFishBC – helps fisheries scientists collect growth data from calcified structures and back-calculate estimated lengths at previous ages
  • rfishdraw – Automatic generation of fish drawings based on JavaScript library.
  • scape – import and plot results from statistical catch-at-age models; generally used to connect with ADMB.
  • select – a flexible and user-extendable framework for size-selectivity via the SELECT model
  • shapeR – study otolith shape variation among fish populations
  • simecol – implementation of dynamic simulation models
  • skewtools – estimation of growth models parameters using the robust ECME method via heteroscedastic nonlinear regression growth model with scale mixture of skew-normal distributions
  • ss3sim – framework for fisheries stock assessment simulation testing with Stock Synthesis 3
  • smartR: Spatial management and assessment of demersal resources for trawl fisheries
  • stacomiR – Graphical outputs and treatment for a database of fish pass monitoring
  • swfscDAS: Southwest Fisheries Science Center shipboard DAS data processing
  • swfscMisc – Collection of conversion, analytical, geodesic, mapping, and plotting functions used by the Southwest Fisheries Science Center
  • toxEval – functions to analyze, visualize, and organize measured concentration data as it relates to toxicity forecasting or other user-selected chemical-biological interaction benchmark data such as water quality criteria
  • tRophicPosition – Bayesian estimation of trophic position from consumer stable isotope ratios
  • VAST – estimate spatial variation in density using spatially referenced data, with the goal of habitat associations (correlations among species and with habitat) and estimating total abundance for a target species in one or more years
  • vmsbase – vessel monitoring system and logbook data management and analysis
  • X2R with FishGraph – import the structured output from a given numerical model written in a compiled language (e.g., ADMB, fortran) into R for postprocessing (graphing, further analysis)
  • ypr – yield-per-recruit analysis

Packages for Capture-Recapture Analyses

General or Traditional

Spatially Explicit

Other

Packages of Data

  • FSAdata: Data for FSA – Collection of many fisheries-related data sets
  • fishdata – Four datasets (fish size and per-day growth history) of migratory fish, from 2015-2016, in the Wellington region of New Zealand
  • fishkirkko2015 – Length and weight measurements of fish species at Kirkkojarvi Lake, Finland
  • fishbc: Raw and curated data on the codes, classification, and conservation status of freshwater fishes in British Columbia

Packages to Access Online Databases

  • DATRAS – read and manipulate trawl survey data from the DATRAS database
  • fishtree: interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes
  • LTERdata – functions for retrieving NTL LTER data
  • ramlegacy – Download, import, convert, and cache the RAM Legacy Stock Assessment Database
  • rfishbase – a programmatic interface to fishbase.org
  • rfisheries – a programmatic interface to OpenFisheries.org

Packages for Limnological Data

  • GLMr – the General Lake Model in R
  • glmtools – Tools for interacting with the General Lake Model in R
  • LakeMetabolizer – collection of lake metabolism functions
  • rLakeAnalyzer – standardized methods for calculating common important derived physical features of lakes
  • waterData – Imports U.S. Geological Survey (USGS) daily hydrologic data from USGS web services, plots the data, addresses some common data problems, and calculates and plots anomalies

Collections of Code that are Not Yet a Package

Packages Not Actively Maintained