Data from "Lithological substrates influence tropical dry forest structure, diversity, and composition, but not its dynamics"

Datasets and script of the manuscript “Lithological substrates influence tropical dry forest structure, diversity, and composition, but not its dynamics” authored by R. Muñoz*, M. Enríquez, F. Bongers, R.D. López-Mendoza, C. Miguel-Talonia & J.A. Meave*, published in Frontiers in Forests and Global Change (2023).

* Correspondence: R. Muñoz (rod.munozaviles@gmail.com) & J.A. Meave (jorge.meave@ciencias.unam.mx)

The original publication can be found in https://doi.org/10.3389/ffgc.2023.1082207

TERMS OF USE FOR THE CURRENT DATASETS AND SCRIPTS

All data and scripts associated with the current publication are intended ONLY for the reproduction and validation of the analyses conducted in the manuscript cited above. Use of this data for other purposes (for example, other publications or meta-analyses) is strictly forbidden without prior consent from the corresponding authors (R. Muñoz and/or J.A. Meave, contact details above).

FOLDER STRUCTURE

The ZIP folder is structured in the following manner:

– Munoz et al 2023 Frontiers.zip

          – READ ME.txt

          – Script Munoz et al 2023 Frontiers.R

          – Data source

                    – Dataset Munoz et al 2023 Frontiers stand data.csv

                    – Dataset Munoz et al 2023 Frontiers species matrix.csv

                    – Dataset Munoz et al 2023 Frontiers ONI.csv

                    – Dataset Munoz et al 2023 Frontiers ENSO events.csv

DESCRIPTION OF SCRIPT

The script provided in the root of the ZIP folder (Script Munoz et al 2023 Frontiers.R) allows to reproduce the analyses, figures and tables supporting the original publication in Frontiers. When executed in full, the script generates a new folder named “Figures” where all figures are stored in their raw, unedited version. The figures for publication were later edited in Adobe Illustrator to enhance their visual appearance.

DESCRIPTION OF DATASETS

Four datasets are provided in this ZIP file (“Data source” folder):

1. Dataset Munoz et al 2023 Frontiers stand data.csv (Stand data)

2. Dataset Munoz et al 2023 Frontiers species matrix.csv (Species matrix)

3. Dataset Munoz et al 2023 Frontiers ONI.csv (ONI)

4. Dataset Munoz et al 2023 Frontiers ENSO events.csv (ENSO events)

STAND DATA contains information about the seven forest attributes included in the study, per substrate and year. It contains the following variables:

1. Year: Year of measurement
2. Plot: Plot code
3. Set: Can only be “MatCan” (Mature Canopy)
4. Subset: Either “Lim” (limestone) or “Phy" (phyllite)
5. Dynamics: Whether there is a previous measurement allowing the estimation of dynamic rates (e.g., net change; FALSE/TRUE) 
6. Basal: Basal area expressed in m2/ha
7. DeltaBasal: Annual net change in basal area
8. R.basal: Annual change in basal area due to recruitment
9. G.basal: Annual change in basal area due to growth
10. M.basal: Annual change in basal area due to mortality
11. AGB: Aboveground biomass expressed in Mg/ha, estimated from the allometric equation of Chave et al. 2014 (including DBH, height and WD)
12. DeltaAGB: Annual net change in AGB
13. R.agb: Annual change in AGB due to recruitment
14. G.agb: Annual change in AGB due to growth
15. M.agb: Annual change in AGB due to mortality
16. Dens: Tree density expressed in individuals/ha
17. DeltaDens: Annual net change in tree density
18. R.dens: Annual change in tree density due to recruitment
19. G.dens: Annual change in tree density due to “growth”. Here, “growth” is a term introduced to account for small differences in tree densities between years due to changes in the extrapolation factor of a tree. Due to the nested sampling design of the vegetation survey, sometimes trees change their extrapolation factor as they grow larger. Thus, is a tree changes extrapolation factor, those differences (that are neither recruitment or mortality) are added up here.
20. M.dens: Annual change in tree density due to mortality
21. Species: Species richness expressed in spp/plot. Redundant with “q0” column.
22. DeltaSpecies: Annual net change in species richness
23. R.species: Annual change in species richness due to recruitment
24. M.species: Annual change in species richness due to mortality
25. Height: Average plot canopy height expressed in m
26. q0: Hill number of order 0 expressed in species effective number (species richness)
27. q1: Hill number of order 1 expressed in species effective number (typical species)
28. q2: Hill number of order 2 expressed in species effective number (dominant species)

SPECIES MATRIX contains an abundance matrix per species, plot and year. It contains the following variables:

1. PlotYear: This column actually does not have a name to it in the file, but is the first column in the dataset, It contains the three-character identifier for the plot and the four numbers of the year of measurement. For instance, “BER2008” would represent the observations made for the plot BER in 2008.
2. treat: This indicates whether the plot is located on limestone (1) or phyllite (2) substrate
3. sp001-sp127: indicates the abundance (in number of individuals per plot) of a given species. Species numbers were assigned randomly, thus they do not match the order of the table provided in Supplementary Material 3 of the publication in Frontiers.

ONI contains the Oceanic El Niño Index values per month and year. It is a “year by month” contingency matrix, where years are presented in the rows name, and months are presented in the columns name. ONI values are given in Celsius degrees, and they represent the 3-month rolling average of the temperature anomaly in the Nino3.4 region. The data source and details of this dataset can be found at the NOAA webpage (https://origin.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/ONI_v5.php).

ENSO EVENTS contains the occurrence of events of El Niño (warm and dry episodes) and La Niña (cold and wet episodes). It contains the following variables:

1. Year: Year
2. Month: Month
3. ONI: Oceanic El Niño Index (see ONI dataset description above)
4. Year.cont: Time as a continuous variable (instead of having years and months separately, for plotting)
5. Nino: El Niño (warm and dry) episode occurrence (“1” indicates occurrence)
6. Nina: La Niña (cold and wet) episode occurrence (“1” indicates occurrence)