Amph4pop model for the simulation of foraging, dispersal and population processes of UK amphibians

Amph4pop is a process-based model, written in R, that simulates the foraging, dispersal and population processes of amphibians. It accounts for amount and configuration of habitat resources to predict spatially-explicit relative abundance and foraging rates, for a given input landscape. It can also optionally incorporate road mortality effects for a single breeding population located in the centre of the input landscape. The input landcover information must be in raster format. The model can ingest a base landcover raster as well as edgecover rasters, which represent the locations of small landcover features that occupy only a fraction of a pixel. It requires road classes (assumed to relate to traffic frequency) to be distinguished in the input rasters, if road mortality effects are to be simulated. Model outputs are raster stacks with the same spatial extent and resolution as the input landcover raster.

The amph4pop model was co-developed by the UK Centre for Ecology & Hydrology, the Amphibian and Reptile Groups of the UK, and Froglife. It has been parameterised for one UK amphibian species (common toad; Bufo bufo). These parameter files (amph_guild_params.csv and amph_habitat_params.csv) are included. The model’s predictions have been validated against observations of toad habitat use reported by volunteer Toad Patrols across Great Britain, who are supported by Froglife through their Toads on Roads Project.

Data in amph_guild_params.csv includes typical movement ranges (adult foraging range around the breeding pond in meters), population growth parameters (maximum clutch size, maximum tadpole density, growth parameters in arbitrary units) and survival parameters (fraction of tadpoles surviving to metamorphosis, metamorph survival to breeding age probability, adult female yearly survival probability, mortality probability on UK motorway, mortality probability on UK urban A road, mortality probability on UK rural A road, mortality probability on UK urban minor road, mortality probability on UK rural minor road) for common toad, used in the amph4pop model.

Data in amph_habitat_params consists of scores representing the relative suitability as an aquatic breeding habitat (on a scale from 0-1, where 0 = none and 1 = very high) and the relative availability of foraging resources (on a scale from 0-5, where 0 = none and 5 = very high) for common toad and the 78 landcover classes, used in the amph4pop model. Given scores are the mean values across n contributing experts. The data also include the number of contributing experts, the standard error on the mean score, and the alpha and beta values that describe a beta distribution consistent with the measured mean and variance for each score.

This model is intended to help support understanding of how amphibians might be using landscapes. No decisions should ever be made solely on the basis of this model’s predictions – on-the-ground ecological surveys and integration of local knowledge are always required before any landscape-level or site-level decisions are made, due to real-life amphibian activity levels potentially differing from predicted levels. Users are recommended to get in touch with the model developers to ensure they have the most up-to-date version of the code and to receive support on model use and interpretation.