Package: StrathE2E2 3.3.0

StrathE2E2: End-to-End Marine Food Web Model

A dynamic model of the big-picture, whole ecosystem effects of hydrodynamics, temperature, nutrients, and fishing on continental shelf marine food webs. The package is described in: Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R.J. (2020) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package for modelling the dynamics of marine food webs and fisheries. 8pp.

Authors:Michael Heath [aut], Ian Thurlbeck [ctb]

StrathE2E2_3.3.0.tar.gz
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StrathE2E2.pdf |StrathE2E2.html✨
StrathE2E2/json (API)
NEWS

# Install 'StrathE2E2' in R:
install.packages('StrathE2E2', repos = c('https://mrheath.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://gitlab.com/marineresourcemodelling/strathe2e

On CRAN:

31 exports 0.00 score 3 dependencies 15 scripts 153 downloads

Last updated 4 years agofrom:629dc5e7f2. Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 07 2024
R-4.5-win-x86_64ERRORSep 07 2024
R-4.5-linux-x86_64ERRORSep 07 2024
R-4.4-win-x86_64ERRORSep 07 2024
R-4.4-mac-x86_64ERRORSep 07 2024
R-4.4-mac-aarch64ERRORSep 07 2024
R-4.3-win-x86_64ERRORSep 07 2024
R-4.3-mac-x86_64ERRORSep 07 2024
R-4.3-mac-aarch64ERRORSep 07 2024

Exports:e2e_calculate_hrscalee2e_compare_obse2e_compare_runs_bare2e_compare_runs_boxe2e_copye2e_extract_hre2e_extract_starte2e_get_parmdoce2e_get_senscrite2e_lse2e_merge_sens_mce2e_optimize_acte2e_optimize_ecoe2e_optimize_hre2e_plot_biomasse2e_plot_catche2e_plot_ecoe2e_plot_edriverse2e_plot_fdriverse2e_plot_migratione2e_plot_opt_diagnosticse2e_plot_sens_mce2e_plot_trophice2e_plot_tse2e_plot_ycurvee2e_process_sens_mce2e_reade2e_rune2e_run_mce2e_run_sense2e_run_ycurve

Dependencies:deSolveMASSNetIndices

CheatSheet

Rendered fromStrathE2E2_CheatSheet.Rnwusingutils::Sweaveon Sep 07 2024.

Last update: 2020-07-08
Started: 2020-07-08

Readme and manuals

Help Manual

Help pageTopics
Calculate initial values of the scaling parameters for the fishing fleet model which link effort to harvest ratios.e2e_calculate_hrscale
Box and whisker plots comparing annual or monthly observational data with corresponding model outputs.e2e_compare_obs
Create tornado bar-plots of the differences between two model runs.e2e_compare_runs_bar
Box and whisker plots comparing annual or monthly outputs from single or Monte Carlo baseline and scenario model runs.e2e_compare_runs_box
Make a copy of a named model/variant and documentation in a user defined workspacee2e_copy
Extract the values of harvest ratios generated by the fleet model.e2e_extract_hr
Extract the values of all the state variables at the end of a model run and format for use as new initial conditions.e2e_extract_start
Get documentation on the parameters in the model.e2e_get_parmdoc
Get documentation on the model outputs available as the basis for sensitivity analysis.e2e_get_senscrit
List the available models in a designated workspace.e2e_ls
Combine two or more sets of raw output data from parallel sensitivity or Monte Carlo analysis runs performed on separate machines/processors.e2e_merge_sens_mc
Optimize StrathE2E fishing gear activity multipliers to maximumize the likelihood of either observed ecosystem target data or know harvest ratios.e2e_optimize_act
Optimize StrathE2E ecology model parameters to maximise the likelihood of observed ecosystem target data.e2e_optimize_eco
Optimize StrathE2E harvest ratio multipliers to maximum the likelihood of observed ecosystem target data.e2e_optimize_hr
Plot showing the annual annual average biomass densities of each guild in the inshore and offshore zones, optionally with credible intervals.e2e_plot_biomass
Plot the distribution and composition of annual catches across guild, zones and gears in the final year of a model run.e2e_plot_catch
Plot daily data on ecological outputs from the model over the final year of a run, optionally with credible intervals.e2e_plot_eco
Plot climatological year of environmental driving data.e2e_plot_edrivers
Plot shaded-grid-cell diagrams of the distributions of fishing-related drivers across gears, guilds and seabed habitats.e2e_plot_fdrivers
Plot daily data on migration fluxes by actively mobile guilds during the final year of a run, optionally with credible intervals.e2e_plot_migration
Plot diagnostic data on the performance of parameter optimization functions.e2e_plot_opt_diagnostics
Plot diagnostic data from sensitivity and Monte Carlo analyses.e2e_plot_sens_mc
Plot showing the annual mean trophic level index, and the omnivory index of each guild during the final year of a model run, optionally with credible intervals.e2e_plot_trophic
Plot ecology model state variables or fishery catches for the full duration of a model run.e2e_plot_ts
Plot fishery yield curve data for planktivorous or demersal fish.e2e_plot_ycurve
Post-process already-created data from sensitivity or Monte Carlo analysis runs.e2e_process_sens_mc
Read all the configuration, driving and parameter files for a designated model and compile the data into a list object.e2e_read
Run the StrathE2E model with a given configuration.e2e_run
Run a Monte Carlo simulation with StrathE2E and derive centiles of credible values of model outputs.e2e_run_mc
Perform a parameter sensitivity analysis on the StrathE2E model.e2e_run_sens
Run a set of models to generate fishery yield curve data for either planktivorous or demersal fish.e2e_run_ycurve
StrathE2E2 PackageStrathE2E2