Data and R code for "Landscape-scale diversity of plants, bumblebees and butterflies in mixed farm-forest landscapes of Northern Europe: clear-cuts do not compensate for the negative effects of plantation forest cover"
The data and code in this repository has been generated to empirically assess the contributions of five different habitat types (cereals, leys, semi-natural pastures, mature coniferous forest and clear-cuts) to the local and landscape-scale species richness of plants, bumblebees and butterflies at local scale. We collected the data in the highlands of Jönköpings län, Småland, Sweden, from 87 sites selected across independent gradients of landscape-scale cover of forest, cereal crops, leys and semi-natural pastures, allowing us to assess the effect of the surrounding landscape on local diversity and the validity of the area-based approaches. We use the cSARs to simulate landscape-scale species richness outcomes for different agricultural and forest habitat mixtures. In the associated paper, we assess whether the relative contribution of clear-cuts to biodiversity in forest-farmland mosaics is sufficient to compensate for the expected negative effects of losing marginal farmland to forest habitats. We also assess how important the contribution of leys and/or cereal crops is to landscape-scale richness, as these habitats are have received much less attention than semi-natural grasslands.
Steps to reproduce
The code is in R language and the folder structure within the ZIP-file is optimized for use with RStudio. If you are using RStudio, proceed as follows. Download the zip folder, unzip the subfolders and the files they contain (data,R,figures and output) into a target folder of your choice, keeping that structure intact. Open RStudio. Define the target folder containing the downloaded folders and files as an RStudio project folder. Open that project. Open the R file "overview.R" from the code folder "R" and follow the instructions. If you are using another R interface (not RStudio), you may need to adapt the procedure (e.g. by specifying that the folder containing the downloaded folders and files is the working directory). A list of packages used is