Version 3.3.0 adds a significant extension to the sensitivity analysis function in the package, implements some changes to the equations governing migrations of birds, pinnipeds and cetaceans, and updates the citation details for the package:
The sensitivity analysis extension allows the criterion of for the analysis to be selected from any one of the list of state variable and flux outputs from the model, in addition to the existing default (likelihood of observed data).
Changes to the migration equations necessitate re-parameterisation of the example model of the North Sea, so the release includes new sets of parameter files. The accompanying example data package is also updated along with the documentation.
The citation details are updated to reflect publication of our manuscript in Methods in Ecology and Evolution.
Version 3.2.0 accompanied a review revision our manuscript to Methods in Ecology and Evolution in August 2020:
The variable name for omnivorous zooplankton in the code changed from from 'herb' to 'omni'.
Two instances of return without () in internal.R removed to comply with new cran check requirements.
Version 3.1.0 accompanied a pre-review revision our manuscript to Methods in Ecology and Evolution in July 2020
Version 3.1.0 has the same user-facing functionality as 3.0.0, but is somewhat different in the background. These changes were made to enable the package to pass tests for inclusion in CRAN. Version 3.0.0 was about 15 Mb, whereas 3.1.0 is only 2.6 Mb. The main differences are:
The example data sets which were embedded in the package in 3.0.0 are now provided in a separate supplementary data-package. The data-package is download and installed from our GitLab site when example data are first invoked from a function, and silently present thereafter.
Documentation which was included in the package in 3.0.0 has been removed and hosted on our GitLab website. The only remaining internal vignette is the CheatSheet.
Changes to sub-folder and file names in the model parameter folder to fit within path-length constraints.
Changes to data read/write input/output conventions. Functions in 3.1.0 do not read/write results data from/to disc unless specifically requested by means of function arguments. All except plotting functions always return results data objects to memory. Unless a data path is provided, input/output dafaults to a temporary folder.
A variety of cosmetic changes to functions, but in particular changes to internal.R to accommodate the differences between R3.x and R4.x in the way that strings are read in from csv files.
Version 2.0.0 accompanied submission of a manuscript to Methods in Ecology and Evolution in December 2019 (Heath, Speirs, Thurlbeck, Wilson, StrathE2E2: an R package for modelling the dynamics of marine food webs and fisheries). The editors recommended resubmission after development and inclusion of a comprehensive testing suite.
The release 2.0.0 was used to generate results for the report: Heath & Cook 2020. Risks to North Sea fish stocks and wildlife if post-Brexit fishery negotiations fail to reach agreement on quotas and access to UK waters: EXTENDED TECHNICAL REPORT. University of Strathclyde, March 2020. 136pp. https://doi.org/10.17868/71708
Early versions build out of inter-linked R scripts rather than packaged functions. The most recent of these represents the precursor to the StrathE2E2 package.
NERC Marine Ecosystems Programme (MERP) version - see:
https://www.marine-ecosystems.org.uk/Research_outcomes/Model_Interactive.
This model fully resolved inshore and offshore horizontal
compartments, disaggregated the former 'birds and mammals' functional
group into separate guilds for birds, pinnipeds and cetaceans, and
included a dynamic representation of active migrations by fish and
top predators. Larval stages of benthos were included, and the
representation of seabed sediment geochemistry was greatly
enhanced.
An intermediate version of the model, between the MERP version and StrathE2E1. This included a prototype for the fishing fleet model, a prototype method for representing seabed sediment heterogenity and separate inshore and offshore zone. See: Heath, Wilson & Speirs (2015). Modelling the whole-ecosystem impacts of trawling. A study commissioned by Fisheries Innovation Scotland (FIS) 86pp. https://fiscot.org/wp-content/uploads/2019/06/FIS003.pdf
StrathE2E1 is horizontally homogeneous, with two vertical water column layers overlying a single homogeneous sediment layer, so inshore and offshore zones are not resolved. There is no fishing fleet model, so harvest rates are applied directly as external driving data. Birds, pinnipeds and cetaceans are bundled together as a combined 'bird & mammal' guild.
R code for the North Sea implementation of StrathE2E1 as available from: DOI 10.15129/c050f1e8-81d6-464f-9517-30d61816ff34 https://pureportal.strath.ac.uk/en/datasets/strathe2e-marine-foodweb-model
StrathE2E1 is described in: Heath (2012). Ecosystem limits to food web fluxes and fishery yields in the North Sea simulated with an end-to-end food web model. Progress in Oceanography, 102, 42-66. https://www.sciencedirect.com/science/article/abs/pii/S0079661112000213.
Publications using the StrathE2E1 model:
Heath, Cook, Cameron, Morris & Speirs, D.C. (2014). Cascading ecological effects of eliminating fishery discards. Nature Communications, 5:3893 doi: 10.1038/ncomms4893 https://www.nature.com/articles/ncomms4893
Heath, Speirs, & Steele (2014). Understanding patterns and processes in models of trophic cascades. Ecology Letters, 17, 101-114. https://onlinelibrary.wiley.com/doi/full/10.1111/ele.12200
Morris, Cameron, Heath & Speirs, D. (2014). Global sensitivity analysis of an end-to-end marine ecosystem model of the North Sea: factors affecting the biomass of fish and benthos. Ecological Modelling, 273, 251-263. https://www.sciencedirect.com/science/article/pii/S030438001300567X
Hyder, Rossberg, Allen et al. (2015). Making modelling count - increasing the contribution of shelf-seas community and ecosystem models to policy development and management. Marine Policy, 61, 291-302. https://www.sciencedirect.com/science/article/pii/S0308597X1500216X?via%3Dihub
Spence, Blanchard, Rossberg, Heath et al. (2018). A general framework for combining ecosystem models. Fish and Fisheries, 19, 1031-1042. https://onlinelibrary.wiley.com/doi/full/10.1111/faf.12310