Skip to contents

Changelog

StrathE2E2 4.0.1

  • Version 4.0.1 minor bug fixes to v4.0.0 in particular:

    • the url for the sran repository for installing the examples package in internal.R was still pointing to the old address not maths.strath.ac.uk

    • logical error fixed … regarding recruitment of benthos larvae to settled benthos in the offshore zone when there is an overhang over deep water (recruitment needed to be attenuated by the area-proportion of the overhang).

    • Final year sediment properties plot function modified to accommodate habitats with zero areas.

    • Configuration of spawning and recruitment periods for fish and benthos adaped to enable them to carry over across year-ends.

    • Configuration of fish immigration and emigration periods adaped to enable them to carry over across year-ends.

StrathE2E2 4.0.0

  • Version 4.0.0 major update to enable an overhang from shelf waters out over the deep ocean. Also includes user scenario configurations affecting the biology of taxa in the model.

    • The deep ocean overhang means that the offshore zone is extended out into a region where the lower offshore layer is out of contact with the seabed sediments. Fluxes of material in and out of the base of this layer represent upwelling/downwelling, mixing and sinking of material.

    • The user scenario configuration enables external mortality rates to be applied to any guild (representing a lethal pressure), and a multiplier to be applied to uptake rates (representing a non-letahl pressure). These can be applied separately in the inshore and offshore zones.

    • Some changes to the Monte Carlo function for deriving credible intervals of model outputs - the parameters which are regarded as fixed and not fitted for optimization purposes are now also sampled from uniform priors in the MC scheme.

    • From version 4.0.0 onwards all our code and downloads are hosted on a University of Strathclyde gitlab server rather than on an external site.

StrathE2E2 3.3.1

  • Version 3.3.1 includes update on the citation, and minor typograpical corrections in help text and vignette.

StrathE2E2 3.3.0

CRAN release: 2021-01-22

  • 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.

StrathE2E2 3.2.0

CRAN release: 2020-09-02

  • 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.

StrathE2E2 3.1.0

CRAN release: 2020-07-08

  • 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.

StrathE2E2 3.0.0

  • Version 3.0.0 accompanied the re-submission our manuscript to Methods in Ecology and Evolution in May 2020, and was developed from version 2.0.0. The key differences were inclusion of a comprehensive testing suite based on the R testthat package which provides >92% code coverage. The version also includes a range of additional functions, and an end-to-end tidy-up of the code.

StrathE2E2 2.0.0

  • 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

StrathE2E2 1.0.0

  • Version 1.0.0 was a prototype R package developed in 2018 from a set of inter-linked R scripts (version 0.0.0)

StrathE2E2 0.0.0

  • 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