Data and code from: Increasing fire severity changes the assembly and coupling between plant taxonomic and functional diversity in a dry conifer forest understory
Data files
Oct 02, 2026 version files 172.60 KB
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Beta_Deviation.R
4.56 KB
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bootstrap_beta_2020.R
6.23 KB
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bootstrap_beta_2021.R
6.04 KB
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bootstrap_beta_2022.R
6.04 KB
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bootstrap_beta_2023.R
6.04 KB
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bootstrap_beta_2024.R
6.04 KB
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bootstrap_beta.R
1.71 KB
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Community_longForm_2020.csv
4.16 KB
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Community_longForm_2021.csv
7.94 KB
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Community_longForm_2022.csv
7.83 KB
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Community_longForm_2023.csv
7.69 KB
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Community_longForm_2024.csv
6.94 KB
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CommunityMatrix2020.csv
5.44 KB
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CommunityMatrix2021.csv
9.71 KB
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CommunityMatrix2022.csv
10.21 KB
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CommunityMatrix2023.csv
9.47 KB
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CommunityMatrix2024.csv
8.94 KB
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Coupling.R
4.28 KB
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CoverSep2020.csv
3.45 KB
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CoverSep2021.csv
5.60 KB
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CoverSep2022.csv
6.27 KB
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CoverSep2023.csv
5.60 KB
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CoverSep2024.csv
5.45 KB
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Long-Form_Matrices.R
2 KB
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NMDS.R
6.83 KB
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Null_Beta.R
5.64 KB
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Null_Model.R
6.03 KB
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README.md
1.88 KB
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Species.csv
2.50 KB
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traitMatrix.csv
2.05 KB
Abstract
We collected community composition data in 60 plots across a burn severity gradient (unburned, low severity, high severity) for five years after a mixed severity fire. We also assembled a trait table for our observed species and included three traits: specific leaf area (SLA), leaf dry matter content (LDMC), and height. R scripts included in this repository are used to analyze the effect of fire severity on beta diversity, functional redundancy, and community composition.
Data and code associated with "Increasing fire severity changes the assembly and coupling between plant taxonomic and functional diversity in a dry conifer forest understory"
Included in this repository are:
- Species.csv -- List of species and associated species codes used throughout the trait community matrices
- traitMatrix.csv -- Trait matrix. LDMC = Leaf Dry Matter Content (gg -1), height = height (m), SLA = Specific Leaf Area (mm2 mg -1).
- CoverSep2020.csv - CoverSep2024.csv -- Community matrices with absolute cover
- CommunityMatrix2020.csv - CommunityMatrix2024.csv -- Community matrices with relativized cover
- ** all analyses use relativized cover **
- Long-Form_Matrices.R -- Code for pivoting relativized community matrices into long-form
- Community_longForm_2020.csv - Community_longForm_2024.csv -- Long-form relativized community matrices, formatted for use in the null model
- bootstrap_beta_2020.R - bootstrap_beta_2024.R -- Code that resamples beta diversity values in each year
- bootstrap_beta.R -- Code that combines all bootstrapped beta diversity values across years
- Null_Model.R -- Code that contains null model
- Null_Beta.R -- Code that runs null model to generate null beta diversity values
- Beta_Deviation.R -- Code for calculating and plotting beta deviations using bootstrapped observed beta diversity and null beta diversity
- Coupling.R -- Code for calculating functional redundancy using Rao's quadratic entropy and species richness
- NMDS.R -- Code for NMDS plots and PERMANOVA of community composition
Plot numbers and the burn severity gradient:
- Unburned (U): 1-20
- Low severity (L): 21-40
- High severity (H): 41-60
Empty plots are omitted in the community matrices, but are accounted for in the analyses. Plot numbers and row numbers in community matrices may not necessarily align when plots are empty or missing.