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 NameDescription

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 2List 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 4Model 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 5Model 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.RR scripts used for processing data and computing diversity indices.

Analysis_RegressionTests.RR 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.txtFasta alignment file of the Mitochondrial Cytochrome b gene sequences used to construct a time-calibrated phylogenetic tree for the field data.

Data_PhylogeneticTree_FieldData.txtTime-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."