get.cortad.crw: Extraction of CRW and CoRTAD time series data

In brisneve/THE: Thermal History Exploration

Description

These functions extract time series of sea surface temperature (SST) and related thermal stress metrics from NOAA Coral Reef Watch (CRW) and/or Coral Reef Temperature Anomaly Database (CoRTAD). See references for the further details of these databases.

Usage

get.crw(url,destfile = NULL)

get.cortad(sst,ssta,tsa,lon, lat, method = "bilinear", buffer = 5000, destfile = NULL)

get.cortad.crw(url,sst,ssta,tsa, method = "bilinear", buffer = 5000,destfile = NULL)

Arguments

url	URL of the file to download from CRW database
sst	destination of .nc file for the SST data from CoRDAT
ssta	destination of .nc file for the SSTA data from CoRDAT
tsa	destination of .nc file for the TSA anomaly data from CoRDAT
lon	longitude (in decimal degrees)
lat	latitude (in decimal degrees)
method	See the argument method in extract function
buffer	See the argument buffer in extract function; default is set to 5000
destfile	a destination file to save the file, default (NULL)

Value

This function returns to a data frame with following variables:

date	time of observation (class: date; format: YYYY-MM-DD)
SST	90th percentile of Sea Surface Temperature in degree C (class: numeric)
min_SST	Minimum Sea Surface Temperature in degree C (class: numeric)
max_SST	Maximum Sea Surface Temperature in degree C (class: numeric)
SSTA	Sea Surface Temperature Anomaly in degree C (class: numeric)
TSA	Thermal Stress Anomaly in degee C (class: numeric)
DHW	Degree Heating Weeks in degree C - weeks (class: numeric)
source	databases, e.g. Coral Reef Watch and Coral Reef Temperature Anomaly Database (class: character)

References

NOAA CRW. Coral Reef Watch Satellite Monitoring and Modeled Outlooks. https://coralreefwatch.noaa.gov/satellite/index.php

NOAA CRW. Regional Virtual Stations Product Description. https://coralreefwatch.noaa.gov/vs/map.php

Liu, G., A.E. Strong, W.J. Skirving and L.F. Arzayus (2006). Overview of NOAA Coral Reef Watch Program's Near-Real-Time Satellite Global Coral Bleaching Monitoring Activities. Proceedings of the 10th International Coral Reef Symposium, Okinawa: 1783-1793.

National Center for Atmospheric Research Staff (Eds). Last modified 20 Aug 2013. "The Climate Data Guide: CoRTAD: Coral Reef Temperature Anomaly Database (SST)." Retrieved from https://climatedataguide.ucar.edu/climate-data/cortad-coral-reef-temperature-anomaly-database-sst.

Link to CoRTAD database: ftp://ftp.nodc.noaa.gov/pub/data.nodc/cortad/Version5/

Examples

# GET TIME SERIES DATA FROM CRW

url <- "https://coralreefwatch.noaa.gov/vs/data/bahrain.txt"

## download file without saving
coralwatch <- get.crw(url)

## download and save file
coralwatch <- get.crw(url, destfile = "crw.csv")

head(coralwatch)

# GET TIME SERIES DATA FROM CoRTAD

## .nc files (BIG files!) can be downloaded from ftp://ftp.nodc.noaa.gov/pub/data.nodc/cortad/Version5/
sst <- "cortadv5_WeeklySST.nc"
ssta <- "cortadv5_SSTA.nc"
tsa <- "cortadv5_TSA.nc"
lon <-  50.725
lat <- 26.125

## load file w/out saving
cortad <- get.cortad(sst,ssta,tsa, lon,lat, method = "bilinear", buffer = 5000)

## load and save file
cortad <- get.cortad(sst,ssta,tsa, lon,lat, method = "bilinear", buffer = 5000, destfile = "cortad.csv")

head(cordat)


# GET AND MERGE TIME SERIES DATA FROM CRW and CoRTAD

## load file w/out saving
df <- get.cortad.crw(url, sst, ssta, tsa, method = "bilinear", buffer = 5000)

## load and save file
df <- get.cortad.crw(url, sst, ssta, tsa, method = "bilinear", buffer = 5000, destfile = "./Data/combined.csv")

head(df)

brisneve/THE documentation built on May 21, 2019, 11:09 a.m.