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

  • ALKrage-length keys
  • AnglerCreelSurveySimulationsimulate creel survey data
  • Bioenergetics 4.0a shiny app for bioenergetics modeling
  • Bioenergetics at ISEMPbioenergetics modeling as part of the Integrated Status and Monitoring Program
  • CatDynpopulation parameters from catch dynamics data
  • cuttlefish.modelPerform LPUE standardization and stock assessment of the English Channel cuttlefish stock using a two-stage biomass model
  • fecRCalculates fishing effort following the DG MARE Ad-Hoc Workshops on Transversal Variables in Zagreb (2015) and Nicosia (2016)
  • FSAWsconstruct and validate standard weight (Ws) equations
  • fishModfits models to catch and effort data
  • fishmovepredict fish movement parameters
  • hafroAssmtfisheries stock assessment at Hafro, the Marine Research Institute in Iceland
  • kobemethods for summarising results from stock assessments and Management Strategy Evaluations in the Kobe format
  • LBSPR: Length-Based Spawning Potential RatioSimulate 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.
  • mapplotsCreate simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data
  • mixdistfit mixture distributions — e.g., possibly separating age-classes from a length frequency
  • mizermultispecies, trait based and community size spectrum ecological models, focused on the marine environment See Introduction to mizer
  • oceanmapPlotting toolbox for 2D oceanographic data
  • PBSmappingtwo-dimensional plotting features similar to those commonly available in a Geographic Information System
  • PBSmodellingfacilitates the design, testing, and operation of computer models; focused on tools that make it easy to construct and edit a customized graphical user interface
  • RchivalTagfunctions to generate, access and analyze standard data products from archival tagging data
  • r4ssanalyze and plot the output from Stock Synthesis version 3, a fisheries stock assessment model written in ADMB
  • RFishBChelps fisheries scientists collect growth data from calcified structures and back-calculate estimated lengths at previous ages
  • scapeimport and plot results from statistical catch-at-age models; generally used to connect with ADMB.
  • selecta flexible and user-extendable framework for size-selectivity via the SELECT model
  • shapeRstudy otolith shape variation among fish populations
  • simecolimplementation of dynamic simulation models
  • skewtoolsestimation of growth models parameters using the robust ECME method via heteroscedastic nonlinear regression growth model with scale mixture of skew-normal distributions
  • ss3simframework for fisheries stock assessment simulation testing with Stock Synthesis 3
  • stacomiRGraphical outputs and treatment for a database of fish pass monitoring
  • swfscMiscCollection of conversion, analytical, geodesic, mapping, and plotting functions used by the Southwest Fisheries Science Center
  • tRophicPositionBayesian estimation of trophic position from consumer stable isotope ratios
  • VMSBasevessel monitoring system and logbook data management and analysis
  • X2R with FishGraphimport the structured output from a given numerical model written in a compiled language (e.g., ADMB, fortran) into R for postprocessing (graphing, further analysis)
  • ypryield-per-recruit analysis

Packages for Capture-Recapture Analyses

General or Traditional

Spatially Explicit


Packages of Data

  • FSAdata: Data for FSACollection of many fisheries-related data sets
  • fishkirkko2015Length and weight measurements of fish species at Kirkkojarvi Lake, Finland
  • fishdataFour datasets (fish size and per-day growth history) of migratory fish, from 2015-2016, in the Wellington region of New Zealand

Packages to Access Online Databases

Packages for Limnological Data

  • GLMrthe General Lake Model in R
  • glmtoolsTools for interacting with the General Lake Model in R
  • LakeMetabolizercollection of lake metabolism functions
  • rLakeAnalyzerstandardized methods for calculating common important derived physical features of lakes
  • waterDataImports 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