dc.hydrography: Download and Cache a Hydrographic Dataset

In dankelley/dc: Download and Cache Data

Description

dc.hydrography() downloads hydrographic datasets from the CCHDO archive, (or mirrors that use the exact same URL structure, apart from the server name) based on a specified "expocode" that specifies the expedition or cruise. This is convenient, because expocodes are how cruises are referred to in the literature. See “Limitiations” for a comments on the brittleness of dc.hydrography().

Usage

dc.hydrography(
  expocode,
  type = "bottle",
  format = "exchange",
  server,
  destdir = ".",
  destfile,
  force = FALSE,
  dryrun = FALSE,
  debug = getOption("dcDebug", 0)
)

Arguments

expocode	String indicating the cruise (or 'expedition') code.
type	String indicating data type, either "bottle" (the default) or "ctd".
format	String indicating data format, either "exchange" (the default) or "whp_netcdf".
server	character value giving the base name of the server, used in the construction of URL queries. Since servers tend to change over time, this is a good argument to check, when debugging code that once worked but now fails.
destdir	character value indicating the directory in which to store downloaded files. The default value of "." means to store the downloaded file in the present working directory. Set destdir=NULL if destfile is a filename with full path information. File clutter is reduced by creating a top-level directory called data, with subdirectories for various file types; see “Examples”.
destfile	character value indicating the name of the file. If not supplied, then the file name is constructed from the other parameters of the function call, so that subsequent calls with the same parameters will yield the same result; this is useful for caching.
force	A logical value that indicates whether to force the download, even if the pathname constructed from destdir and destfile already exists.
dryrun	A logical value that indicates whether to return the constructed web query, without attempting to download the file. This can be helpful in designing responses to changing URLs.
debug	an integer specifying whether debugging information is to be printed during processing. The printing is done by a call to dcDebug(). Setting debug=0 turns off this form of debugging, while higher values yield more information. If one dc function calls another, it passes the value of debug but decreased by 1, which means that the value of debug controls not just the breadth of debugging, but also the depth.

Value

String indicating the full pathname to the downloaded file.

Limitations

Unfortunately, cchdo.ucsd.edu does not provide data organized into URLs that can be inferred from the expocode alone, and so the procedure used here is to scan the HTML for a summary URL that can be inferred, and then to discover links from the HTML text. This is brittle to changes in the formatting used by CCHDO, which means that changes may need to be made to dc.hydrography() whenever CCHDO changes their website. Another consequence is that a web connection is required even if the desired file has already been downloaded.

Author(s)

Dan Kelley (2017-11-25)

References

1. https://cchdo.ucsd.edu

See Also

The work is done with dc().

Other functions that download ocean-related data: dc.coastline(), dc.g1sst(), dc.met(), dc.topo(), dc.woa()

Examples

library(dc)
## Not run: 
library(oce)
## 1. Bottle stations for a Southern Ocean cruise
bottle <- dc.hydrography("09AR20041223", destdir="~/data/hydrography")
plot(read.section(bottle), which="map")
##
## 2. CTD data from same cruise, subsetted to
##    a section between Antarctica and Australia
ctd <- dc.hydrography("09AR20041223", type="ctd", destdir="~/data/hydrography")
secCTD <- read.section(directory=ctd)
transectCTD <- subset(secCTD, 100 < longitude & longitude < 120)
plot(transectCTD)

## End(Not run)

dankelley/dc documentation built on June 3, 2020, 8:25 a.m.