Code for manipulating and analyzing lichen data from the FIA.
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Data
OLD_scripts
cluster_scripts
download_data
format_data
.gitattributes
.gitignore
README.md
analysis.R
fia_lichen_analysis_functions.R
load_data.R
make_data_tables_for_analysis.R
make_richness_maps.R

README.md

FIA-Lichens

Code for manipulating and analyzing lichen data from the FIA.


Directories:

Data Derived data tables for conducting final analyses.

OLD_scripts: Scripts used in prior versions of the project, including SEMs and analysis of soil attributes.

cluster_scripts: Scipts that were run on the computing cluster, including model dredging, sems, calculation of regional species richness

download_data: Scripts for downloading data from FIA and CNALH websites and conducting quality control (e.g. taxonomic revisions).

format_data: Scripts for calculating environmental covariates and richness estimates and combing FIA data sets. Includes: forest structure attributes, regional species richness, local richness, solar insolation, tree species composition, and climate variables.


Scripts:

analysis.R: Contains variance partitioning and model averagaing analysis reported in Coyle & Hurlbert "Environmental optimality, not heterogeneity, drives regional and local species richness in lichen epiphytes"

fia_lichen_analysis_function.R: Contains functions used in analyses.

load_data.R: Loads data needed to conduct analyses into an R workspace.

make_data_tables_for_analysis.R: Combines lichen data and environmental data into tables for analysis (see Data directory).

make_richness_maps.R: Plots local and regional macrolichen species richness as maps.