dhw: an R package for calculating various SST metrics (Maximum Monthly Mean Climatology, SST Anomalies, Coral Bleaching HotSpots, Degree Heating Weeks)
The dhw package calculates SST metrics from raw SST datasets by following the methods of the National Oceanic and Atmospheric Administration’s (NOAA) Coral Reef Watch (CRW) Coral Bleaching Heat Stress Product Suite Version 3.1 (see Skirving et al. 2020 for product description and methods).
The package is organised into three layers: a deterministic NOAA calculation core, optional data-access utilities, and downstream analysis/visualisation. Core tests use compact offline reference fixtures; complete regional NOAA validation inputs are downloaded reproducibly into an external cache instead of being bundled with the installed package.
The NOAA Coral Reef Watch (CRW) daily global 5km satellite coral bleaching Degree Heating Week (DHW) product shows accumulated heat stress during the most recent 12-week period, and ranges from 0 to 20 °C-weeks. DHW is directly related to the timing and intensity of coral bleaching and is the most common metric in assessing coral bleaching events (see here for further details).
The v3.1 climatology is derived from daily CoralTemp SST for 1985–2012. Daily SST is first averaged within each year-month; each calendar month’s 28 annual means are regressed against year; and the regression is evaluated at 1988.286. This package applies that method to support internally consistent anomaly and heat-stress products.
The dhw package provides functions to recreate the CRW metrics using SST products such as OISST. Rebuilding the NOAA v3.1 climatology requires the complete 1985–2012 baseline; alternatively, an aligned official 12-layer climatology can be supplied directly.
The package uses terra for raster processing. Selective products and direct-to-disk outputs should be used for large regional datasets; full global histories still require careful storage and memory planning.
Also included are functions for visualising SST metrics and reliably downloading common datasets (e.g. CRW and OISST) from the NOAA NCEI THREDDS server.
Please file any issues and comments and suggestions to george.roff@csiro.au.
the current development version of dhw can be installed from github:
#install.packages("remotes")
devtools::install_github("https://github.com/marine-ecologist/dhw", force=TRUE)References
Skirving et al (2020) Remote Sensing 12(3856) doi:10.3390/rs12233856