R: An Implementation of the EcoTroph Ecosystem Modelling Approach

# An Implementation of the EcoTroph Ecosystem Modelling Approach

## Documentation for package ‘EcoTroph’ version 1.6.1

- DESCRIPTION file.

## Help Pages

a13.eq | function used within the multiplier effort analysis
a13.eq.ac | function used within the multiplier effort analysis
check.table | convert.list2tab enables to convert the list object returned by the create.ETdiagnosis function into a list of data.frames. These data.frames contain calculated variables by TL class and combinations of effort multipliers.
convert.list2tab | Check Ecopath table function
create.ETdiagnosis | ET-Transpose provides a picture of an ecosystem under a given fishing mortality. ET-Diagnosis is a routine simulating how this baseline ecosystem would be impacted by increasing or decreasing fishing effort. Fishing effort can be modified per fleet and/or trophic group. Ecosystem-wide effects of altering fishing effort include potential changes in biomass, accessible biomass, production, kinetics and catch trophic spectra, as well as impacts on the mean trophic level of the catch and biomass. Additionally, ET-Diagnosis constitutes a useful exploratory tool for ecosystem-based management. It simulates how reducing or increasing fishing effort and/or preferentially targeting different trophic levels could improve yield at the ecosystem scale. Lastly, ET-Diagnosis allows to view how different assumptions on ecosystem functioning (biomass input control, top-down effect) affect both trophic level specific and ecosystem-wide properties in relation to fishing.
create.ETmain | This function enables the creation of the ET-Main table (summarizing the principal results/variables in function of the TL classes) and other intermediate tables of the ET-Transpose routine. It provides a picture of an ecosystem under a given fishing mortality.
create.smooth | Create Smooth Function
CTSA.catch.input | Catch input for CTSA
E0.1 | E0.1
ecopath_guinee | EcoTroph example dataset: Guinean data
Emsy | E_MSY
E_MSY_0.1 | E_MSY_0.1 computes two indices of exploitation: Emsy or Fmsy (maximum sustainable yield), and E0.1 or F0.1 ("start" of full exploitation) per TL class.
mf.diagnosis | Effort multiplier diagnosis
plot.ETdiagnosis | This function enables the creation of the principle graphics resulting from the create.ETdiagnosis function. The function returns the principal plots of the global ET-Diagnosis routine: the graphics of the biomass, accessible biomass...rates for the different effort multipliers, the Biomass Trophic Spectra (BTS) for the different effort multipliers, the B/Bref(mE=1) and Y/Yref graphs for the main TL classes and the Catch Trophic Spectra (CTS) (global and per fleet).
plot.ETmain | This function enables the display of the principle plots resulting from the create.ETmain function: Biomass Trophic Spectra, Accessible Biomass Trophic Spectra, Catch by fleet Trophic spectra, Total Catch Trophic Spectra and other summary plots.
plot.smooth | plot.smooth is used to plot the Smooth function. This function enables the user to see the TL distributions around their mean trophic levels.
plot.Transpose | This function returns the two principal plots of the Transpose function : a plot by group and the associated Trophic Spectra (CTS, BTS...).
plot_ETdiagnosis_isopleth | This function enables to plot the mixed impacts of changes in fishing effort for two fleets (or groups of fleets).
read.ecopath.model | Input data import function (from an xml file)
regPB | function used to compute pB for the higest trophic levels
regPB.ac | function used to compute pB for the higest trophic levels and accessible biomass
saturation | Sigma Saturation Function
Transpose | Transpose enables the conversion of data pertaining to specific taxa or functionnal groups into data by trophic class. Data can represent catches, biomasses or production in order to produce continuous distributions of those variables over trophic levels.