[R] Development versions of xtractomatic and rerddapXtracto

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Sat Dec 23 00:35:23 CET 2017

If you are a user of the R package "xtractomatic",  I have a new development version available,  as well as a test version of the package "rerddapXtracto".  The  biggest changes are functions that can take the output of any of the data download functions and quickly map the data.   These functions use the package "plotdap". Also, a lot of the code in the development version of "xtractomatic" has been cleaned up and simplified.   If you have used "xtractomatic" before,  be certain to read the vignette  (https://rmendels.github.io/Usingxtractomatic_Dev.nb.html) as there have been some changes,  most notably in the order that arguments are passed in the function calls, what is optional in the call, and the two new plotting routines.  These changes were  made to support the idea that "data" should be the first argument  in the function calls,  and also to make the xtractomatic functions very close to the calls in  "rerddapXtracto".  This is important because this will likely be the last version of "xtractomatic", with future development being put on "rerddapXtracto".

"rerddapXtracto" has the same functionality as "xtractomatic" but will work with any gridded dataset on any ERDDAP server,  by making use of the R package "rerddap", while "xtractomatic" only works with certain datasets on the ERD ERDDAP server.  The advantage of the "xtractomatic" approach is we chose what we thought were the most useful datasets (out of over 1000 datasets), and information about those datasets are built into the program.  But that means the "xtractomatic" package can not be used to access a large number of datasets.  "rerddapXtracto" is much more general,  but  the user must know the ERDDAP server they want to access, which dataset, and must first obtain information about that dataset by using the function rerddap::info().  "rerddapXtracto" also now has simple mapping of the data using the package "plotdap".  The vignette for "rerddapXtracto" is at  https://rmendels.github.io/UsingrerddapXtracto.nb.html.

I have not submitted these packages to CRAN because at the moment they depend  either on packages or versions of packages that are only on Github,  not CRAN.  While I know there are ways around this when submitting to CRAN,  I feel that this defeats a lot of the purpose of CRAN.  CRAN checks consistency of package with other packages,  with development versions of R,  and also notifies developers when packages they use are changed, and provides an uniform installation of compatible packages.  These packages will be submitted to CRAN when the packages they depend on are available.  

The best information on installation is the vignettes.  The quick start version,  the development version of "xtractomatic" can be installed using:

devtools::install_github("rmendels/xtractomatic",  ref = "development")

and "rerddapXtracto" can be installed using:


Several warnings about the installations:

1.  Both packages use the package "plotdap" for graphics.  This package at the moment is available only on Github,  at:


2. "plotdap" itself depends on a fairly large number of packages,  In some testing,  people sometimes had to get a more recent,  non-CRAN version of other packages to have correct functionality.  If you run into problems let me know. 

3. "rerddapXtracto" depends on the package "rerddap",  but not on the CRAN version.  There was some changes in functionality in the Github version, in particular the handling of caches,  as well as some code changes.  To use "rerddapXtracto" you must install the Github version of "rerddap" available from https://github.com/ropensci/rerddap.

Basically the initial installation of either package may not go cleanly,  if there are problems let me know, it may take several attempts to get all the dependencies correct.  As noted earlier,  this is one of the benefits provided by CRAN,  and why I do not want to put these packages on CRAN until all of their dependencies are there also.



"The contents of this message do not reflect any position of the U.S. Government or NOAA."
Roy Mendelssohn
Supervisory Operations Research Analyst
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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