Data and R code from Davison et al. "Niche types and community assembly" Ecology Letters

Description of the data collection and workflowThe data collection includes 4 R scripts and 4 data sources (3 .csv files and 1 RData object). In combination, the R scripts and data objects can be used to replicate the analyses and figures in Davison et al. "Niche types and community assembly" Ecology Letters. The R scripts call the data sources (which need to be present in the working directory) and should be run in series: step1->step4. However, because some analytical steps are time consuming, the script includes the possibility to save the output of a step as an RData object that can be loaded at the beginning of the following step. It is also possible to load the RData object 'plottingdata.RData', included in the collection, in order to move directly to the analyses and plotting in step 4 without needing to complete steps 1-3.File contentsR scriptsRscript_calculate_niches_step1: Uses AMF communty data and environmental metadata to estimate niche space for AMF taxa (VT).Rscript_analyse_niche_overlap_step2: estimates niche overlap between pairs of VT.RScript_generate_randomisations_step3: implements a stratified randomisation of the AMF community data.RScript_manuscript_analyses_figures_step4: estimates correlations between niche types/axes and models differences in community-level niche differentiation. Plots correlation heatmaps and boxplots. Data sourcesAMFcomm_shared: normalised AMF community data from Davison et al 2021 https://doi.org/10.1111/nph.17240 for use in niche estimation.AMFcomm_shared_raw: raw AMF community data (read counts) from Davison et al 2021 https://doi.org/10.1111/nph.17240 for use in randomisation.plottingdata.RData: data objects including VT niche differentiation estimates and randomised community data matrices for direct use in analysis and plotting (i.e., RScript_manuscript_analyses_figures_step4).meta_shared: environmental meta data from sampling points for use in defining and estimating niche space among VT; and for stratifying randomisation. Soil and climatic variables are taken from Davison et al. (2021) https://doi.org/10.1111/nph.17240; fungal community composition (fungal MDS1 and fungal MDS2) are taken from Vasar et al. (2022) https://doi.org/10.1111/geb.13487; prokaryotic community composition (prokaryotic MDS1 and prokaryotic MDS2) are taken from Vasar et al. (2022) https://doi.org/10.1111/geb.13487; plant community composition (plant MDS1 and plant MDS2) and read counts (bires) are taken from Vasar et al. (2023) https://doi.org/10.3389/fpls.2023.1106617. Columns Olson_REALM and Olson_BIOME_NAME define biogeographic realms and biomes according to Dinerstein et al. 2017 https://doi.org/10.1093/biosci/bix014.