Package index • Rpath

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

Auxiliary Tools

Additional tools

MTI(): Quantify mixed trophic impacts

import.eiixml(): Reads in EwE exported XML file and parses into data frames

create.rpath.from.eiixml(): Creates an Rpath object from an EwE exported model (EIIXML format)