/xtractomatic

xtractomatic R package for accessing environmental data
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README.md

xtractomatic

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. 

install.packages("httr", dependencies = TRUE)
install.packages("ncdf4") 
install.packages("sp")

The xtractomatic package is available from CRAN and can be installed by:

install.packages("xtractomatic")

or the development version is available from Github and can be installed from Github,

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:

  • ggplot2
  • ggfortify
  • lubridate
  • mapdata
  • RColorBrewer
  • reshape2
  • xts

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 roy.mendelssohn@noaa.gov.

Required legalese

“The United States Department of Commerce (DOC) GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. DOC has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any claims against the Department of Commerce stemming from the use of its GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.”