Package: StrathE2E2 3.3.1

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. (2021) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package for modelling the dynamics of marine food webs and fisheries. Methods in Ecology and Evolution 12, 280-287.

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

StrathE2E2_3.3.1.tar.gz
StrathE2E2_3.3.1.zip(r-4.7-x86_64)StrathE2E2_3.3.1.zip(r-4.7-arm64)StrathE2E2_3.3.1.zip(r-4.6-x86_64)StrathE2E2_3.3.1.zip(r-4.6-arm64)StrathE2E2_3.3.1.zip(r-4.5-x86_64)
StrathE2E2_3.3.1.tgz(r-4.6-x86_64)StrathE2E2_3.3.1.tgz(r-4.6-arm64)StrathE2E2_3.3.1.tgz(r-4.5-x86_64)StrathE2E2_3.3.1.tgz(r-4.5-arm64)
StrathE2E2_3.3.1.tar.gz(r-4.7-arm64)StrathE2E2_3.3.1.tar.gz(r-4.7-x86_64)StrathE2E2_3.3.1.tar.gz(r-4.6-arm64)StrathE2E2_3.3.1.tar.gz(r-4.6-x86_64)
StrathE2E2_3.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
StrathE2E2/json (API)

# Install 'StrathE2E2' in R:

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

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

On CRAN:

4.40 score 50 scripts 249 downloads 31 exports 3 dependencies

Last updated from:16a4684f3c. Checks:13 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	220
linux-devel-x86_64	ERROR	211
source / vignettes	OK	291
linux-release-arm64	ERROR	179
linux-release-x86_64	ERROR	207
macos-release-arm64	ERROR	182
macos-release-x86_64	ERROR	465
macos-oldrel-arm64	ERROR	151
macos-oldrel-x86_64	ERROR	407
windows-devel-arm64	ERROR	399
windows-devel-x86_64	ERROR	269
windows-release-arm64	ERROR	418
windows-release-x86_64	ERROR	273
windows-oldrel-x86_64	ERROR	226
wasm-release	OK	110

Exports:e2e_calculate_hrscale e2e_compare_obs e2e_compare_runs_bar e2e_compare_runs_box e2e_copy e2e_extract_hr e2e_extract_start e2e_get_parmdoc e2e_get_senscrit e2e_ls e2e_merge_sens_mc e2e_optimize_act e2e_optimize_eco e2e_optimize_hr e2e_plot_biomass e2e_plot_catch e2e_plot_eco e2e_plot_edrivers e2e_plot_fdrivers e2e_plot_migration e2e_plot_opt_diagnostics e2e_plot_sens_mc e2e_plot_trophic e2e_plot_ts e2e_plot_ycurve e2e_process_sens_mc e2e_read e2e_run e2e_run_mc e2e_run_sens e2e_run_ycurve

Dependencies:deSolve MASS NetIndices

CheatSheet

Rendered fromStrathE2E2_CheatSheet.Rnwusingutils::Sweave

Last update: 2020-06-11
Started: 2020-06-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 workspace	e2e_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 Package	StrathE2E2