synthos is an R package to generate synthetic data.
The synthos package provides an interface to generate semi-realistic synthetic abundance data. It leverages spatio-temporal dependencies to simulate the underlying deterministic and stochastic processes responsible for fluctuations in ecological community abundance that are recorded through monitoring surveys.
In this first version, synthos generates observations for three habitat-forming benthic communities commonly found on tropical coral reefs - hard coral, soft coral, and macroalgae. Their cover varies in response to disturbances and annual growth that reduce or promote their abundance. Different types of disturbances are generated using deterministic processes representing their spatio-temporal footprints.
The users control the influence of disturbances with a weighting system and the monitoring sampling design. synthos simulates fixed and random monitoring locations as well as point-based or percentage cover data types. More details of each step are provided in the vignettes.
The synthos workflow consists of five main steps:
- Generate the spatial and temporal domains – Define the area of interest, including the shape, extent, and spatial structure of the ecosystem.
- Generate disturbances – Specify and simulate disturbance regimes that drive annual changes in community abundance.
- Generate ecological baselines – Create baseline spatial patterns of ecological communities for the year preceding sampling.
- Generate sampling designs – Define site allocation and hierarchical sampling structures.
- Generate observation data – Choose the type of monitoring data to simulate, such as point-based observations or percentage cover.
The synthos package combines features from the sf and stars packages for spatial data processing; and, R-INLA and gstat for geostatistical models.
Using the package
You can install the latest version of the synthos package:
remotes::install_github("open-AIMS/synthos@julie")
Usage and further information about synthos can be seen on the project page and the vignettes. Help files for the individual functions can be found on the reference page.
Further Information
synthos is provided by the Australian Institute of Marine Science under the GPL-2 License (GPL-2).