Package index • saltmarsh

Processing sequence

The primary sequence of preparing data, building models, and making maps. These functions normally spawn batch jobs on Unity via slurmcollie (except for screen which is intrinsically interactive), though you can run locally with local = TRUE.

gather(): Gather and prepare GIS data from data sources

screen(): Visually screen orthoimages via a web app

derive(): Create derived variables

sample(): Sample orthoimages for field-collected data

fit(): Build statistical models of vegetation cover

map(): Produce geoTIFF maps of predicted vegetation cover from fitted models

mosaic(): Combines multiple maps, filling in missing data

Reporting and management functions

These functions report data and model status.

fitinfo(): Display information on model fits

fitset(): Set model scores and comments

fitpurge(): Purge selected fits from fits database

mapinfo(): Display information on maps

mappurge(): Purge selected maps from maps database

assess(): Assess a model fit from validation data

flights_report(): Produce reports on orthoimages for all sites

sample_freq(): Create a frequency table of number of cells by subclass from field data

importance(): Produce a summary of variable importance across multiple fits

Utility functions

Uncommonly-used utility functions.

init(): Initialize marshmap with user parameters

build_flights_db(): Build or update the flights database

find_orthos(): Find orthophotos for a site

slurmcollie functions

These functions are part of the slurmcollie package, used to manage batch jobs on the Unity cluster.

info(): Give info on batch jobs (from slurmcollie)

showlog(): Prints the contents log file for a batch job (from slurmcollie)

kill(): Kill launched Slurm jobs (from slurmcollie)

purge(): Purge selected jobs from the jobs database (from slurmcollie)