Data and code used in "Multiscale spatial dependency of small mammal diversity patterns and their determinants"
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The raw data and code used to prepare the manuscript 'Multiscale spatial dependency of small mammal diversity patterns and their determinants' by Onditi et al. 2025.
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File Name Description
File Name Description
Data Table 1 "List of sampled sites in the study, with details of locality and environmental predictor variables. The abbreviations include ELEV: elevation, TRI: terrain ruggedness, TAM: annual temperature average, TAS: annual seasonality in temperature, PAM: annual mean precipitation, PAS: annual seasonality in precipitation, AET: total evapotranspiration: NDVI: normalized difference vegetation index, PSR: plant species richness, and HFP: human ecological footprint index."
Data Table 2 List of molecular operational taxonomic units delimited from newly-sampled specimens based on mitochondrial cytochrome b gene time-calibrated phylogeny and used as species in the study detailing the functional traits for estimating functional diversity indices and various taxonomic and conservation status details.
Data Table 3 "List of small mammal species of Kenya assembled from literature used in the study, with details of functional traits used for estimating various functional diversity indices."
Data Table 4 Model quality and goodness of fit indices and Parameter summaries of the generalized linear mixed models used for estimating diversity-environment associations in the new field survey dataset.
Data Table 5 Model quality and goodness of fit indices and Parameter summaries of the generalized linear mixed models used for estimating diversity-environment associations in the nationwide dataset.
Analysis_IndicesDerivations.R R scripts used for processing data and computing diversity indices.
Analysis_RegressionTests.R R scripts used for running multivariate regression tests.
Data_CommunityMatrix_FieldData.txt "List of species observed at new field survey sites, formatted as a matrix indicating the presence of each species at various locations."
Data_CommunityMatrix_NationwideData.txt "Nationwide species occurrence dataset, formatted as a matrix showing the presence or absence of species across different grid locations."
Data_Metadata_FieldData.txt "Environmental variables for new field survey sites, including elevation, temperature variability, precipitation patterns, and vegetation indices."
Data_Metadata_NationwideData.txt "Environmental variables for national survey grids, similar to the field data but on a national scale."
Data_PhylogeneticTree_FieldData_CYTB_Fasta_alignment.txt Fasta alignment file of the Mitochondrial Cytochrome b gene sequences used to construct a time-calibrated phylogenetic tree for the field data.
Data_PhylogeneticTree_FieldData.txt Time-calibrated phylogenetic tree derived from new field survey data to estimate phylogenetic diversity.
Data_PhylogeneticTree_NationwideData.txt "Phylogenetic tree used for estimating diversity indices in the national dataset, sourced from TimeTree."
Data_Traits_FieldData.txt "Describes the functional traits of species collected during new field surveys, used in biodiversity analysis."
Data_Traits_NationwideData.txt "Functional traits data for species in the national dataset, used in biodiversity studies."
