Objectives
mapme.biodiversity facilitates statistical data analysis for protected areas around the globe. It supports a high number of biodiversity related datasets and associated indicators that can be utilized to monitor and evaluate the effectiveness of protection efforts. Several indicators are available at regular intervals for almost two decades (2000 to 2020). This allows users to analyse spatial and temporal dynamics of their biodiversity portfolios. The package abstracts repetitive tasks, such as temporal and spatial selection of resources. This allows a seamless approach to quantitative data analysis even for very large (potentially global) portfolios where users are enabled to focus on the aims of their analysis. The package has been tested on Microsoft Azure’s cloud infrastructure as well as on local machines. The internal framework was designed to allow an easy process to provide extensions in the form of custom resources and indicators, unlocking the potential for a future growth in supported datasets. We thus highly appreciate Pull-Requests contributing new resources/indicators. For geographic data analysis, the package uses sf for operation of vector data and terra for raster data.
mapme.biodiversity package
mapme.biodiversity provides a standardized interface to download and analyse a great variety of biodiversity related spatial datasets allowing users to focus on the aims of their analysis. The sometimes cumbersome process of handling different spatial data formats and the spatial and temporal selection is handled internally. Many organizations provide value-added datasets related to biodiversity. These organizations often use different technology stacks to distribute their data. mapme.biodiversity contains simple routines to communicate with these different backends to provide a seamless access to the data. Once the desired resources have been made available locally, users can decide which indicators they want to calculate and fine-control of these routines is provided.
Functionalities
Currently, the package offers several functionalities, which should ideally be used in a consecutive order to realize a seamless analysis workflow:
- construct a portfolio based on an sf object
- get resources for the spatio-temporal extent of the portfolio
- calculate indicators based on the available resources for each asset in the portfolio
- write the results to disk as a GeoPackage and use it with other Geo-Spatial software, or
- conduct your statistical analysis in R
Inputs, Outputs
an sf object containing only geometries of type
'POLYGON'with arbitrary metadataraster and vector resources matching the spatio-temporal extent of the portfolio will be downloaded and made available locally. These are necessary inputs for the subsequent calculation of indicators, but the raw resource also can be used, e.g. for custom visualizations or analysis. Importantly, the same resource directory can be used for different portfolios or analysis runs, because the matching resources are figured out during run time. Thus, there is no need to store multiple copies of the input resources.
the results of the indicator calculation will be added to the portfolio object as nested list columns. This approach makes it feasible to support a variety of indicators with differently shaped outputs (e.g. time variant vs. invariant indicators). When the analysis is done in R, this does not pose serious limitations, because the desired indicator can easily be unnested via
tidyr::unnest(). However, if the data was to be shared to use it in other geospatial software (e.g. QGIS), a routine to write a portfolio object as a GeoPackage to disk is provided. Each indicator will be written to an independent table and a unique identifier allows joining the attributes with the geometries later.
Limitations
a potential limiting factor for now is the processing of single very large polygons. While the terra package provides a memory-save framework to process large raster extents, RAM overflows could occur when several large polygons are processed in parallel. We advise to process very large polygons sequentially.
we took a great effort to evaluate efficient processing routines for each indicator. If you submit a new indicator using a more efficient routine than currently implemented in the package, please contact the maintainers via e-mail, issue or pull-request and we will happily discuss the options how to integrate your routine into the wider framework
We are planning to add new features and to extend the functionality of mapme.biodiversity to address these limitations best possible.