xtractomatic R package for accessing environmental data
xtractomatic is an R package developed to subset and extract satellite and other oceanographic related data from a remote server. The program can extract data for a moving point in time along a user-supplied set of longitude, latitude and time points; in a 3D bounding box; or within a polygon (through time). The
xtractomatic functions were originally developed for the marine biology tagging community, to match up environmental data available from satellites (sea-surface temperature, sea-surface chlorophyll, sea-surface height, sea-surface salinity, vector winds) to track data from various tagged animals or shiptracks (
xtracto). The package has since been extended to include the routines that extract data a 3D bounding box (
xtracto_3D) or within a polygon (
xtractomatic package accesses data that are served through the ERDDAP (Environmental Research Division Data Access Program) server at the NOAA/SWFSC Environmental Research Division in Santa Cruz, California. The ERDDAP server can also be directly accessed at http://coastwatch.pfeg.noaa.gov/erddap. ERDDAP is a simple to use yet powerful web data service developed by Bob Simons.
There are three main data extraction functions in the
xtracto <- function(xpos, ypos, tpos, dtype, xlen, ylen, verbose=FALSE)
xtracto_3D <- function(xpos, ypos, tpos, dtype, verbose=FALSE)
xtractogon <- function(xpos, ypos, tpos, dtype, verbose=FALSE)
There also are two information functions in the
searchData <- function(searchList=list(list("varname","chl")))
getInfo <- function(dtype)
xtractomatic uses the
sp packages , and these packages (and the packages imported by these packages) must be installed first or
xtractomatic will fail to install.
install.packages("httr", dependencies = TRUE) install.packages("ncdf4") install.packages("sp")
xtractomatic package is available from CRAN and can be installed by:
or the development version is available from Github and can be installed from Github,
The vignette provides a lot of examples of using
xtractomatic, and it is not built by default by
To install and build the Vignette, do:
install.packages("devtools") devtools::install_github("rmendels/xtractomatic", build_vignettes = TRUE)
The Vignette examples require the following packages and will not build if they are not installed:
Note however, that the Vignette generates graphics by doing a large number of downloads using
xtractomatic, and the build may fail if the server is busy or your internet line is slow.
If you can not get the Vignette to build, a pdf version can be downloaded from http://coastwatch.pfeg.noaa.gov/xtracto or email me at firstname.lastname@example.org.
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