MPA Zoning analyses (fish)

Zoning analyses (Green vs Blue), Sector/Year combination. Responses:

• HC : group summary table
• SC : group summary table
• A : group summary table
• Total abundance : fish05 (family)
• Large fish abundance : fish05 (family)
• Pomacentridae abundance : fish05 (family)
• Coral trout density : fish05 (species code)
• Trout Biomass : fish05 (species code)
• Secondary Target abundance : fish05 (family)
• Herbivore : fish05 (family) Output: data.frame: cellmeans etc figures: individual sectors

Prior to running please review the following

• parameters/density_table.csv
• parameters/L-W co-eff.csv
• parameters/MPA_paper trophic groups.csv
• parameters/webGroups.csv
• parameters/model.settings.txt

There are two broad purposes for these scripts.

• purpose='Reports' This is to generate a Report on MPA Zoning every two years
• purpose='Web' This is to generate Sector specific outputs for webpages As such, there is a global variable (sector) that indicates which sector to model.

sector can either be the name of an actual sector or 'All' in which case, all sectors will be modelled in a single model

Directory structure

\
|- data
|  |- primary
|  |- processed
|  |- modelled
|- outputs
|  |- figures
|  |- tables
|- R
|  |- helperFunctions.R
|  |- 00_main.R
|- scripts
|  |- dbExport.jar
|- parameters
|  |-