This repository holds code and data for analyses of a variety of treatments investigating the relationship between Lehmann lovegrass, Eragrostis lehmanniana, and Palmer's agave, Agave palmeri.

The primary questions are:

1. How do various treatments affect agave survival and growth, where: a. agave-survival: survival is measured by whether an individual plant survived the experiment, and b. agave-growth: growth is measured by the number of leaves from three plants in a row
2. How do a subset of treatments affect percent cover of Lehman lovegrass, considering also: a. lovegrass-cover-pa: presence or absence of an agave b. lovegrass-cover-size: size of agave, when present

Bold text above indicates the file-naming strategy used for this project. Scripts and output files use the bolded font as the prefix and descriptor of script / output contents as the suffix. i.e. the script agave-survival-analysis.R runs the analyses for 1a, above, and outputs the results of statistical tests to output/agave-survival-analysis-out.csv. The script agave-survival-boxplot.R creates an accompanying boxplot for 1a and saves the PNG file to output/agave-survival-boxplot.png.

• broom.mixed, formatting of statistical output
• car, Levene test of homoscedasticity
• dplyr, data wrangling
• emmeans, post-hoc, pairwise comparisons
• extrafont, data visualization
  • to avoid errors with ggsave will need to run extrafont::font_import()
• ggplot2, data visualization
• lme4, glmer logistic models
• stringr, formatting of statistical output

• Scripts for running analyses and saving results to files, as well as scripts for creating data visualizations are in the top-level directory. Also in the top-level directory is the data cleaning script (data-preparation.R), which standardized variable names and values. Early development on this work was done in an RMarkdown file, agave-lovegrass-report.Rmd; the file remains, but much of the analyses are deprecated, corresponding to appropriate files in this top-level directory.

• data: raw and tidied data

• functions: custom functions for assistance with data visualization

• output: results of statistical analyses and data visualization files