Package: EcoTroph 1.6.1

EcoTroph: An implementation of the EcoTroph Ecosystem modelling approach

An approach and software for modelling marine and freshwater ecosystems. It is articulated entirely around trophic levels. EcoTroph's key displays are bivariate plots, with trophic levels as the abscissa, and biomass flows or related quantities as ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow of biomass surging up the food web, from lower to higher trophic levels, due to predation and ontogenic processes. Such an approach, wherein species as such disappear, may be viewed as the ultimate stage in the use of the trophic level metric for ecosystem modelling, providing a simplified but potentially useful caricature of ecosystem functioning and impacts of fishing. This version contains catch trophic spectrum analysis (CTSA) function and corrected versions of the mf.diagnosis and create.ETmain functions.

Authors:J. Guitton, M. Colleter, P. Gatti, and D. Gascuel

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EcoTroph/json (API)

# Install 'EcoTroph' in R:
install.packages('EcoTroph', repos = c('https://polehalieutique.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/polehalieutique/ecotroph/issues

Datasets:

On CRAN:

16 exports 0.94 score 1 dependencies 1 mentions 17 scripts 328 downloads

Last updated 1 years agofrom:d59c3e098d. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-winWARNINGSep 06 2024
R-4.5-linuxWARNINGSep 06 2024
R-4.4-winWARNINGSep 06 2024
R-4.4-macWARNINGSep 06 2024
R-4.3-winWARNINGSep 06 2024
R-4.3-macWARNINGSep 06 2024

Exports:check.tableconvert.list2tabcreate.ETdiagnosiscreate.ETmaincreate.smoothCTSA.catch.inputE_MSY_0.1E0.1Emsymf.diagnosisplot_ETdiagnosis_isoplethread.ecopath.modelregPBregPB.acsaturationTranspose

Dependencies:XML

Readme and manuals

Help Manual

Help pageTopics
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.check.table
Check Ecopath table functionconvert.list2tab
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.ETdiagnosis
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.ETmain
Create Smooth Functioncreate.smooth
Catch input for CTSACTSA.catch.input
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.E_MSY_0.1
E0.1E0.1
EcoTroph example dataset: Guinean dataecopath_guinee
E_MSYEmsy
Effort multiplier diagnosismf.diagnosis
This function enables to plot the mixed impacts of changes in fishing effort for two fleets (or groups of fleets).plot_ETdiagnosis_isopleth
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.ETdiagnosis
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.ETmain
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.smooth
This function returns the two principal plots of the Transpose function : a plot by group and the associated Trophic Spectra (CTS, BTS...).plot.Transpose
Input data import function (from an xml file)read.ecopath.model
function used to compute pB for the higest trophic levels @param compteur @param pb.mf @param TL_out @param range.highTLregPB
function used to compute pB for the higest trophic levels and accessible biomass @param compteur @param pb.mf @param TL_out @param range.highTLregPB.ac
Sigma Saturation Functionsaturation
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.Transpose