CTSA.catch.input        Catch input for CTSA
E0.1                    E0.1
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.
Emsy                    E_MSY
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.
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
ecopath_guinee          EcoTroph example dataset: Guinean data
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.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.
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
