Package: Rpath 1.2.0

Kerim Aydin

Rpath: R implementation of Ecopath with Ecosim

This package implements the core mass balance equations made popular by Ecopath with Ecosim. There are two parts to the package, the static snapshot of energy flow through the system using rpath and dynamic simulations run using the rsim family of functions.

Authors:Kerim Aydin [aut, cre], Sean Lucey [aut], Andy Beet [aut], Bia Dias [aut], Sarah Gaichas [aut], Max Grezlik [aut], Ron Klasky [aut], Sarah Weisberg [aut], Andy Whitehouse [aut]

Rpath_1.2.0.tar.gz
Rpath_1.2.0.zip(r-4.7-x86_64)Rpath_1.2.0.zip(r-4.7-arm64)Rpath_1.2.0.zip(r-4.6-x86_64)Rpath_1.1.0.zip(r-4.6-arm64)Rpath_1.2.0.zip(r-4.5-x86_64)
Rpath_1.2.0.tgz(r-4.6-x86_64)Rpath_1.2.0.tgz(r-4.6-arm64)Rpath_1.2.0.tgz(r-4.5-x86_64)Rpath_1.2.0.tgz(r-4.5-arm64)
Rpath_1.2.0.tar.gz(r-4.7-arm64)Rpath_1.2.0.tar.gz(r-4.7-x86_64)Rpath_1.2.0.tar.gz(r-4.6-arm64)Rpath_1.2.0.tar.gz(r-4.6-x86_64)
Rpath_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rpath/json (API)

# Install 'Rpath' in R:
install.packages('Rpath', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/noaa-edab/rpath/issues

Pkgdown/docs site:https://noaa-edab.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

7.47 score 43 stars 150 scripts 66 exports 39 dependencies

Last updated from:97871f34e6. Checks:12 WARNING, 2 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING192
linux-devel-x86_64WARNING455
source / vignettesOK517
linux-release-arm64WARNING195
linux-release-x86_64WARNING146
macos-release-arm64WARNING187
macos-release-x86_64WARNING330
macos-oldrel-arm64WARNING144
macos-oldrel-x86_64WARNING421
windows-devel-arm64WARNING285
windows-devel-x86_64WARNING147
windows-release-arm64FAIL211
windows-release-x86_64WARNING163
windows-oldrel-x86_64WARNING178
wasm-releaseOK246

Exports:adjust.fishingadjust.forcingadjust.scenariocheck.rpath.paramscreate.rpath.from.eiixmlcreate.rpath.paramsextract.nodefitcatch.to.forcecatchfrate.tableget.pp.linkget.rsim.fishingget.rsim.forcingget.rsim.paramsget.rsim.stanzasget.rsim.start_stateggwebplotimport.eiixmlMTIread.fitting.biomassread.fitting.catchread.rpath.paramsrpathrpath.consumersrpath.detritalrpath.gearsrpath.groupsrpath.livingrpath.mixotrophsrpath.producersrpath.stanzasrsim.derivrsim.dietrsim.fishingrsim.fit.applyrsim.fit.list.bio.bysurveyrsim.fit.list.bio.seriesrsim.fit.list.catch.seriesrsim.fit.objrsim.fit.obj.speciesrsim.fit.remove.bio.timeseriesrsim.fit.runrsim.fit.set.bio.wtrsim.fit.set.catch.wtrsim.fit.set.qrsim.fit.tablersim.fit.updatersim.forcingrsim.mortrsim.paramsrsim.plotrsim.plot.fitrsim.plot.fitspeciesrsim.predprey.tablersim.runrsim.scenariorsim.sensersim.stanzasrsim.statersim.stepset.rsim.scenestanzaplotsummarize.for.webplotwebplotwrite.Rpathwrite.rpath.paramswrite.Rsim

Dependencies:clicpp11data.tabledplyrfarvergenericsggplot2ggrepelgluegtablehmsisobandjanitorlabelinglifecyclelubridatemagrittrMASSpillarpkgconfigpurrrR6RColorBrewerRcpprlangS7scalessnakecasestringistringrtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithrxml2

Convert EwE to Rpath
Model parameters | Differences between Rpath and EwE balances
Rendered fromConvert_EwE_to_Rpath.Rmdusingknitr::rmarkdown

Last update: 2025-09-05
Started: 2025-09-05

Set up a food web model
Setting up a food web model | Parameter file generation | Model parameters | Stanza Parameters | Diet Parameters | Pedigree parameters
Rendered fromModelSetup.Rmdusingknitr::rmarkdown

Last update: 2025-09-05
Started: 2024-05-31

Create a static food web model in Rpath
Running Rpath
Rendered fromRunRpath.Rmdusingknitr::rmarkdown

Last update: 2025-06-18
Started: 2024-05-31

Generating an Rsim ensemble with Ecosense
Ecosense | Setting up Ecosense | Generating an ensemble of Ecosim parameter sets | Run the kept systems with a perturbation
Rendered fromecosense.Rmdusingknitr::rmarkdown

Last update: 2025-06-18
Started: 2024-05-31

Rpath: an open source food web model
Installation | References
Rendered fromRpath.Rmdusingknitr::rmarkdown

Last update: 2025-06-18
Started: 2019-06-15

Run a dynamic food web simulation in Rsim
Rendered fromRunRsim.Rmdusingknitr::rmarkdown

Last update: 2025-06-18
Started: 2024-05-31

UnitTests
Unit Tests | Details | Regenerating Baseline Files | List of Tests | AB and RK4 Sim Run Tests: | AB and RK4 Sim Run Tests with Jitter on ForcedBiomass: | AB and RK4 Sim Run Tests with Jitter on ForcedMigrate: | AB and RK4 Sim Run Tests with Stepped Noise on ForcedBiomass: | AB and RK4 Sim Run Tests with Stepped Noise on ForcedMigrate: | AB and RK4 Sim Run Tests with Jitter on ForcedEffort: | AB and RK4 Sim Run Tests with Jitter on ForcedFRate: | AB and RK4 Sim Run Tests with Jitter on ForcedCatch: | AB and RK4 Sim Run Tests with Stepped Noise on ForcedEffort: | AB and RK4 Sim Run Tests with Stepped Noise on ForcedFRate: | AB and RK4 Sim Run Tests with Stepped Noise on ForcedCatch: | Figures | Example plots:
Rendered fromUnitTests.Rmdusingknitr::rmarkdown

Last update: 2025-06-18
Started: 2024-05-31

Readme and manuals

Help Manual

Help pageTopics
AB.paramsAB.params
Adjust Fishing Mortalityadjust.fishing
Adjust Forcing Parametersadjust.forcing
Adjust Rsim.scenario parametersadjust.scenario
Check Rpath parameter filescheck.rpath.params
Creates an Rpath object from an EwE exported model (EIIXML format)create.rpath.from.eiixml
Creates a shell for the Rpath.params objectcreate.rpath.params
Eastern Bering Sea 1990s Ecopath modelEcosense.EBS
Eastern Chukchi Sea Ecopath modelEcosense.ECS
Gulf of Alaska (west/central) 1990s Ecopath modelEcosense.GOA
Extract node/group data from an Rsim runextract.node
Convert Fitting Catch to Forced Catch in Rsim Scenariofitcatch.to.forcecatch
Fishing Mortality Tablefrate.table
Get Predator-Prey Link Indexget.pp.link
Retrieve fishing forcing parameters from an Rsim scenarioget.rsim.fishing
Retrieve forcing parameters from an Rsim scenarioget.rsim.forcing
Retrieve parameters from an Rsim scenarioget.rsim.params
Retrieve stanza parameters from an Rsim scenarioget.rsim.stanzas
Retrieve starting state values from an Rsim scenarioget.rsim.start_state
ggplot routine for Rpath food webggwebplot
Reads in EwE exported XML file and parses into data framesimport.eiixml
Quantify mixed trophic impactsMTI
Read and Process Biomass Fitting Dataread.fitting.biomass
Read and Process Catch Fitting Dataread.fitting.catch
Read Rpath parameters from .csv filesread.rpath.params
REco.paramsREco.params
Ecopath module of Rpathrpath
List of Rpath consumer groupsrpath.consumers
List of Rpath detrital groupsrpath.detrital
List of Rpath gears groupsrpath.gears
Rpath functional group namesrpath.groups
List of Rpath living groupsrpath.living
List of Rpath mixotroph groupsrpath.mixotrophs
List of Rpath producer groupsrpath.producers
Calculate biomass and consumption for multistanza groupsrpath.stanzas
Calculate the derivatives for a time steprsim.deriv
Output consumption of each prey by an individual predator group from Rsim runrsim.diet
Initialize fishing matrix for Rsim scenariorsim.fishing
Apply Fitted Parameters to Rpath Simulation Scene Helper function that maps a vector of optimized parameter modifications back into the `Rpath` simulation parameters object (`scene.params`). Since this returns a scenario params object instead of a full scenario, it is primarily intended for internal use.rsim.fit.apply
List Biomass Timeseries Groups by Survey Sourcersim.fit.list.bio.bysurvey
List Biomass Timeseries Groups and Sourcesrsim.fit.list.bio.series
List Catch Timeseries Groupsrsim.fit.list.catch.series
Calculate Objective Function for Rsim Model Fitrsim.fit.obj
Extract Objective Function Fits by Speciesrsim.fit.obj.species
Remove Biomass Timeseries from Fitting Datarsim.fit.remove.bio.timeseries
Run Fitted Rpath Simulation and Evaluate Objective Functionrsim.fit.run
Set Biomass Fitting Data Weightsrsim.fit.set.bio.wt
Set Catch Fitting Data Weightsrsim.fit.set.catch.wt
Set Catchability (q) for Biomass Fitting Datarsim.fit.set.q
Extract Summary Table of Model Fitsrsim.fit.table
Update Rpath Scene with Fitted Parametersrsim.fit.update
Initialize forcing matrix for Rsim scenariorsim.forcing
Output biomass removed by each predator for an individual prey group from Rsim runrsim.mort
Initial set up for Rsim dynamic simulationrsim.params
Plot routine for Rsim runsrsim.plot
Plot Biomass and Catch Fitting Resultsrsim.plot.fit
Plot Full Biomass and Catch Fits for a Single Species Generates a multi-panel figure displaying the simulation fits for a single species across all available biomass observation sources, alongside its catch fitting data.rsim.plot.fitspecies
Extract Predator-Prey Interaction Tablersim.predprey.table
Run a dynamic simulationrsim.run
Specify a dynamic simulation scenariorsim.scenario
Ecosense function for Rpathrsim.sense
Initialize list of age structured group (stanza) parameters for dynamic simulationrsim.stanzas
Initialize starting state matrix for Rsim scenariorsim.state
Function to add a time step to an Rsim runrsim.step
Set Rsim.scenario parametersset.rsim.scene
Plot routine for Ecopath multistanzasstanzaplot
Plot routine for Ecopath food webwebplot
Write function for Rpath food web objectwrite.Rpath
Write Rpath parameters to .csv fileswrite.rpath.params
Write function for Rsim runwrite.Rsim