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Rpath

Functions for creating a mass balance food web

create.rpath.params()
Creates a shell for the Rpath.params object
check.rpath.params()
Check Rpath parameter files
read.rpath.params()
Read Rpath parameters from .csv files
rpath()
Ecopath module of Rpath
rpath.stanzas()
Calculate biomass and consumption for multistanza groups
rpath.consumers()
List of Rpath consumer groups
rpath.detrital()
List of Rpath detrital groups
rpath.gears()
List of Rpath gears groups
rpath.groups()
Rpath functional group names
rpath.living()
List of Rpath living groups
rpath.mixotrophs()
List of Rpath mixotroph groups
rpath.producers()
List of Rpath producer groups

Rsim

Functions for creating dynamic simulations of the mass balance model

rsim.scenario()
Specify a dynamic simulation scenario
rsim.run()
Run a dynamic simulation
rsim.step()
Function to add a time step to an Rsim run
rsim.params()
Initial set up for Rsim dynamic simulation
rsim.fishing()
Initialize fishing matrix for Rsim scenario
rsim.forcing()
Initialize forcing matrix for Rsim scenario
rsim.deriv()
Calculate the derivatives for a time step
rsim.diet()
Output consumption of each prey by an individual predator group from Rsim run
rsim.mort()
Output biomass removed by each predator for an individual prey group from Rsim run
rsim.stanzas()
Initialize list of age structured group (stanza) parameters for dynamic simulation
rsim.state()
Initialize starting state matrix for Rsim scenario
rsim.sense()
Ecosense function for Rpath
get.rsim.fishing()
Retrieve fishing forcing parameters from an Rsim scenario
get.rsim.forcing()
Retrieve forcing parameters from an Rsim scenario
get.rsim.params()
Retrieve parameters from an Rsim scenario
get.rsim.stanzas()
Retrieve stanza parameters from an Rsim scenario
get.rsim.start_state()
Retrieve starting state values from an Rsim scenario
set.rsim.scene()
Set Rsim.scenario parameters

Models

Example ecosysem models

Ecosense.EBS
Eastern Bering Sea 1990s Ecopath model
Ecosense.ECS
Eastern Chukchi Sea Ecopath model
Ecosense.GOA
Gulf of Alaska (west/central) 1990s Ecopath model
AB.params
AB.params
REco.params
REco.params

Adjustment Tools

Functions for adjusting Rsim scenarios

adjust.scenario()
Adjust Rsim.scenario parameters
adjust.fishing()
Adjust Fishing Mortality
adjust.forcing()
Adjust Forcing Parameters

Visualization Tools

Functions for visualizing rpath and rsim outputs

webplot()
Plot routine for Ecopath food web
ggwebplot()
ggplot routine for Rpath food web
rsim.plot()
Plot routine for Rsim runs
stanzaplot()
Plot routine for Ecopath multistanzas
summarize.for.webplot()
Prepare food web model to plot

Output Tools

Functions for writing and exporting outputs from Rpath

write.rpath.params()
Write Rpath parameters to .csv files
write.Rpath()
Write function for Rpath food web object
write.Rsim()
Write function for Rsim run
frate.table()
Fishing Mortality Table
extract.node()
Extract node/group data from an Rsim run
Rpath-package
Rpath: A package implementing mass balance algorithms designed to work with fisheries data sources.

Auxiliary Tools

Additional tools

MTI()
Quantify mixed trophic impacts