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EcoTroph

EcoTroph (ET) is a modelling approach articulated around the idea that an ecosystem can be represented by its biomass distribution across trophic levels, the biomass trophic spectrum (Gascuel et al., 2005). The ecosystem functioning is viewed as a biomass flow moving from lower to higher trophic levels, due to predation and ontogenetic processes (Gascuel et al. 2009 and 2011). Thus, the ecosystem biomass present at a given trophic level may be estimated from two simple equations, one describing biomass flow, the other their kinetics (which quantifies the velocity of biomass transfers towards top predators).

Such an approach, wherein species as such disappear, may be regarded as the ultimate stage in the use of the trophic level metric for ecosystem modelling. By concentrating on biomass flow as a quasi-physical process, it allows aspects of ecosystem functioning to be explored which are complementary to EwE. It provides users with simple tools to quantify the impacts of fishing at an ecosystem scale and a new way of looking at ecosystems. It thus appears a useful complement to existing ecosystem model such as Ecopath or Osmose.

EcoTroph can be used either in association with an existing Ecopath model or as a stand-alone application, especially in data-poor environments. Furthermore the model can be applied directly through the plug-in developed within the EwE software or the R package available in the Download page. This package constitutes an updated version of the ET model (conform to Gascuel et al., 2011).

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Version

Install

install.packages('EcoTroph')

Monthly Downloads

227

Version

1.6.1

License

GPL

Maintainer

Jerome Guitton

Last Published

April 13th, 2022

Functions in EcoTroph (1.6.1)

plot_ETdiagnosis_isopleth

This function enables to plot the mixed impacts of changes in fishing effort for two fleets (or groups of fleets).
mf.diagnosis

Effort multiplier diagnosis
ecopath_guinee

EcoTroph example dataset: Guinean data
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.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.
saturation

Sigma Saturation Function
create.smooth

Create Smooth Function
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.
E0.1

E0.1
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.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).
read.ecopath.model

Input data import function (from an xml file)
regPB.ac

function used to compute pB for the higest trophic levels and accessible biomass
regPB

function used to compute pB for the higest trophic levels
a13.eq.ac

function used within the multiplier effort analysis
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.
convert.list2tab

Check Ecopath table function
a13.eq

function used within the multiplier effort analysis
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.
CTSA.catch.input

Catch input for CTSA
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.
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.
Emsy

E_MSY