Code base for a reproducible maxnet modeling methodology written in R.

If you are interest in using this material for your own analysis, three folders are significant

• datePrep : Functions that are called by run_linear.R for individual species model runs.
• dataPrep/dataBaseTransform folder: a series of scripts that covert data from various sources into a common schema. The input datasets for these scripts are not provded in this repo. The final dataset used in the analysis for the paper is available on the Harvard Dataverse.

• alternative : a script called by run_linear.R for species with not enough valid occurrence data to run the Maxnet modeling process.
• maxnet : scripts called by run_linear.R that conduct a variable section, model fitting, model project, and a series of model evaluations.

The gap analysis methodology can be applied to existing species distribution models. We recommend utilizing the GapAnalysis R package if you are applying these assessment methodology for your own work.

• Combinded: a script called by run_linear.R for generate final conservation metric
• exsitu: scripts called by run_linear.R forgenerating the three exsitu conservation metrics
• insitu: scripts called by run_linear.R for generating the three insitu conservation metrics
• redlist: a script called by run_linear.R for evaluting the EOO and AOO red list conservation metrics. Utilizes the function provided by redlisr package

Primary script for declaring all input variables and output locations