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 (xtractogon). The 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 xtractomatic package:
-
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 xtractomatic package:
-
searchData <- function(searchList=list(list("varname","chl"))) -
getInfo <- function(dtype)
xtractomatic uses the httr, ncdf4 and sp packages , and these packages (and the packages imported by these packages) must be installed first or xtractomatic will fail to install (the Windows version of ncdf4 is not available through CRAN because of some quirks in CRAN policy, but it can be obtained at http://cirrus.ucsd.edu/~pierce/ncdf/).
install.packages("httr", dependencies = TRUE)
install.packages("ncdf4")
install.packages("sp")
The xtractomatic package at the moment can be installed from Github using the devtools package:
install.packages("devtools")
devtools::install_github("rmendels/xtractomatic")
The vignette provides a lot of examples of using xtractomatic, and it is not built by default by devtools.
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:
ggplot2ggfortifylubridatemapdataRColorBrewerreshape2xts
The package ggfortify is not on CRAN at the moment. To install ggfortify:
devtools::install_github("sinhrks/ggfortify")
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 [email protected].
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