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regen_compile_data.R: take survey data and geospatial data (e.g. climate, elevation) to extract relevant data summarized by plot and by plotXspecies (the intermediate products--see below)
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regen_compile_data_functions.R: functions used by the script above
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regen_analysis.R: take intermediate data products, compute appropriate summaries and perform analyses
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regen_analysis_functions.R: functions used by the script above
- Access database tables (exported as csv)
- Climatic variables
- DEM
- Solar radiation (March)
- Plot-level dataframe
- includes columns for: climate variables, shrub etc % cover, fire-level data repeated by plot, topographic variables, distance to seed tree,
- Species data by plot dataframe
- includes columns for: plot, species, number and basal area of adults (defined in a previous input script as greater than some diameter), total number of seedlings, number of “young” seedlings (0-2 years old, defined in previous script), number of “old” seedlings (germinated in first two years of fire, defined in previous script; accounts for fires of different ages), and number of “all” seedlings. All seedling count values are seedlings per year (over the years that apply--e.g., "Young seedlings" values are average number of seedlings that germinated per year in the last 3 years prior to plot survey)
- root: principal scripts for data compilation and analysis
- data_intermediate: intermediate data files (see header above)
- code_old_reference: old scripts from previous iterations of analysis that could be useful for reference