cvjv-restoration-modelling

Code for evaluating areas in California's Central Valley for potential restoration

Organization

code folder

definitions.R

includes directories and some model metadata (e.g., landcover files and names; model objects)

functions

• executable files that actually do the processing, organized in general order of use
• 00_shared_functions.R -- contains shared utility functions that are used in many of the other functions and scripts; must be sourced
• 01_overlay_water_landcover.R --
• 02_water_moving_window.R --
• 03_predict_birds.R --
• 04_extract_predictions.R -- zonal stats for mean within cell and in 5km landscape

scripts

executable files that actually do the processing, organized in order of calling

data folder

data file with some of the required data for predictions, including constant eBird layer

includes model objects

Required model covariates not included in project folder (too large for Github):

in V:\Project\wetland\FWSPartners\code\cvjv-restoration-modelling\data\other_covariates

• monthly average water data
• monthly tmax
• roads raster

in V:\Project\wetland\FWSPartners\analysis\grid

• grid raster unique_ids_masked.tif

Notes on processing

Multi-core processing currently implemented using the future package. Convenient but with the major downside of messages and other conditions not being loggable in any way due to a limitation in R with capturing stderr().

Each function returns a list of processed files which is then used as an input in the next function. Functions have no external dependencies beyond 00_shared_functions.R (which must be sourced) and required packages (terra, dplyr, gbm, dismo).

Todos:

• finish summary code
• add additional months beyond April
• explore logging options