Package: Rpath 0.9.1

Sean Lucey

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], Sean Lucey [aut, cre], Sarah Gaichas [aut]

Rpath_0.9.1.tar.gz
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Rpath_0.9.1.tar.gz(r-4.5-noble)Rpath_0.9.1.tar.gz(r-4.4-noble)
Rpath_0.9.1.tgz(r-4.4-emscripten)Rpath_0.9.1.tgz(r-4.3-emscripten)
Rpath.pdf |Rpath.html✨
Rpath/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • AB.params - AB.params
  • Ecosense.EBS - Eastern Bering Sea 1990s Ecopath model (53 biological groups and 1 fleet).
  • Ecosense.ECS - Eastern Chukchi Sea Ecopath model (52 biological groups and 1 fleet).
  • Ecosense.GOA - Gulf of Alaska (west/central) 1990s Ecopath model (49 biological groups and 1 fleet).
  • REco.params - REco.params

On CRAN:

43 exports 29 stars 7.37 score 3 dependencies 111 scripts

Last updated 4 months agofrom:3c75a6d86d. Checks:OK: 1 ERROR: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 03 2024
R-4.5-win-x86_64ERROROct 03 2024
R-4.5-linux-x86_64ERROROct 03 2024
R-4.4-win-x86_64ERROROct 03 2024
R-4.4-mac-x86_64ERROROct 03 2024
R-4.4-mac-aarch64ERROROct 03 2024
R-4.3-win-x86_64ERROROct 03 2024
R-4.3-mac-x86_64ERROROct 03 2024
R-4.3-mac-aarch64ERROROct 03 2024

Exports:adjust.fishingadjust.forcingadjust.scenariocheck.rpath.paramscreate.rpath.paramsextract.nodefrate.tableget.rsim.fishingget.rsim.forcingget.rsim.paramsget.rsim.stanzasget.rsim.start_stateMTIread.rpath.paramsrpathrpath.consumersrpath.detritalrpath.gearsrpath.groupsrpath.livingrpath.mixotrophsrpath.producersrpath.stanzasrsim.derivrsim.dietrsim.fishingrsim.forcingrsim.mortrsim.paramsrsim.plotrsim.runrsim.scenariorsim.sensersim.sense.pathrsim.stanzasrsim.statersim.stepset.rsim.scenestanzaplotwebplotwrite.Rpathwrite.rpath.paramswrite.Rsim

Dependencies:data.tableMASSRcpp

Create a static food web model in Rpath

Vignette Author

Rendered fromRunRpath.Rmdusingknitr::rmarkdownon Oct 03 2024.

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

Generating an Rsim ensemble with Ecosense

George A. Whitehouse

Rendered fromecosense.Rmdusingknitr::rmarkdownon Oct 03 2024.

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

Rpath: an open source food web model

Sean M. Lucey

Rendered fromRpath.Rmdusingknitr::rmarkdownon Oct 03 2024.

Last update: 2024-06-05
Started: 2019-06-15

Run a dynamic food web simulation in Rsim

Sean M. Lucey

Rendered fromRunRsim.Rmdusingknitr::rmarkdownon Oct 03 2024.

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

Set up a food web model

Vignette Author

Rendered fromModelSetup.Rmdusingknitr::rmarkdownon Oct 03 2024.

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

Unit Tests

Ron Klasky

Rendered fromUnitTests.Rmdusingknitr::rmarkdownon Oct 03 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Rpath: A package implementing mass balance algorithms designed to work with fisheries data sources.Rpath-package Rpath
AB.paramsAB.params
Adjust Fishing Mortalityadjust.fishing
Adjust Forcing Parametersadjust.forcing
Adjust Rsim.scenario parametersadjust.scenario
Check Rpath parameter filescheck.rpath.params
Creates a shell for the Rpath.params objectcreate.rpath.params
Eastern Bering Sea 1990s Ecopath model (53 biological groups and 1 fleet).Ecosense.EBS
Eastern Chukchi Sea Ecopath model (52 biological groups and 1 fleet).Ecosense.ECS
Gulf of Alaska (west/central) 1990s Ecopath model (49 biological groups and 1 fleet).Ecosense.GOA
Extract node dataextract.node
Fishing Mortality Tablefrate.table
Retrieve Rsim fishing forcing parametersget.rsim.fishing
Retrieve Rsim forcing parametersget.rsim.forcing
Retrieve Rsim scenario parametersget.rsim.params
Retrieve Rsim stanza parametersget.rsim.stanzas
Retrieve Rsim starting state valuesget.rsim.start_state
Mixed Trophic ImpactsMTI
Read Rpath parameters from .csv filesread.rpath.params
REco.paramsREco.params
Ecopath module of Rpathrpath
Rpath functional group namesrpath.consumers rpath.detrital rpath.gears rpath.groups rpath.living rpath.mixotrophs rpath.producers
Calculate biomass and consumption for multistanza groupsrpath.stanzas
Calculate the derivatives for a time steprsim.deriv
Output consumption by a grouprsim.diet
Generate Rsim fishing matrixrsim.fishing
Generate Rsim forcing matrixrsim.forcing
Output mortality on a grouprsim.mort
Initial set up for Rsim module of Rpathrsim.params
Plot routine for Rsim runsrsim.plot
Run Rsimrsim.run
Rsim module of 'Rpath'rsim.scenario
Ecosense function for rpath (rsim.sense)rsim.sense
Ecosense function for rpath (rsim.sense.path)rsim.sense.path
Generate Rsim stanza matrixrsim.stanzas
Generate Rsim state matrixrsim.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 Ecopath objectwrite.Rpath
Write Rpath parameters to .csv fileswrite.rpath.params
Write function for Ecosim objectwrite.Rsim