[R-pkgs] Update of X2R (with FishGraph) sent to CRAN, 30 Jan 2008
X2R is a bundle of three software libraries allowing the user to pass
structured data easily from Fortran, C/C++, or AD Model Builder to R.
An update to X2R has been sent to CRAN and should be available at
mirrors shortly. We also have uploaded FishGraph, a set of R functions
to generate graphics from fish population models. From the menu at the
left of the CRAN home page, look under Software / Other.
Changes in this Update
- Minor bug fixes and improvements have been made throughout, both in
the software and users' guides.
- ADMB2R is compatible with gcc as well as with the Borland compiler.
- FishGraph is available from CRAN.
- ADMB2R includes a detailed example compatible with FishGraph. This
should minimize the learning curve for those getting started with ADMB2R
X2R is supplied as files X2R.zip and X2R.tar.gz, which are equivalent.
The version and release date can be identified from the contents of file
"VersionInfo.txt" in the root of each archive. The new version bears
date January 19, 2008.
FishGraph is supplied separately as a Windows installer in the same
directory. If we hear from anyone interested in using it under other
operating system(s), we can collaborate on making it work.
* * *
More detail for the interested:
X2R is composed of three independent but related software libraries:
C2R, ADMB2R, and For2R (together, X2R). Each contains output routines to
simplify transfer of complicated data structures from models written in
a compiled language to R (note 1). Through calls to X2R routines, the
user's data is written as a structured ASCII file. That file can be read
by R with a single dget() function call to create an R data object of
type list. The list may contain components such as vectors, data frames,
matrices, and other lists.
These are NOT R packages; rather they are subroutine libraries to be
used with programmers' own modeling codes. Limited testing indicates
compatibility with S-PLUS, as well (note 2).
Languages supported are Fortran 95 (with For2R), C and C++ (with C2R)
and AD Model Builder (with ADMB2R) (note 3). Source code and detailed
users' manuals are supplied.
ADMB2R has been tested with ADMB versions 6.03 and 7.71 and recent
versions of the gcc and Borland C++ compilers.
FishGraph is a set of R functions providing exploratory and presentation
graphics of fishery catch-at-age or catch-at-length models. By taking
its data from an R list assumed to have a certain structure (diagram
provided), FishGraph determines which graphs should be generated and for
how many data series, years, etc. The data structure may be generated
with X2R or within R itself and may contain any amount of additional
data. Most FishGraph routines have options to control titles, colors,
and reference lines. The combination of X2R and FishGraph allows
automating graphics production from routine fish stock assessments. The
FishGraph functions can be modified or supplemented to reflect the needs
of the analysis at hand.
This work has been tested and is regularly used by the authors. However,
any software may contain bugs, and these works are classified by NOAA as
"Experimental Products." THIS SOFTWARE IS SUPPLIED WITH NO WARRANTY OF
ANY KIND. Nonetheless, the authors will endeavor to fix bugs promptly
and to add requested features. Send bug reports, suggestions, and
extensions to either author.
Michael H. Prager - [hidden email] Southeast Fisheries Science Center
National Marine Fisheries Service, NOAA
101 Pivers Island Road
Beaufort, North Carolina 28516 USA
Jennifer L. Martin - [hidden email] Northeast Fisheries Science Center
National Marine Fisheries Service, NOAA
166 Water Street
Woods Hole, Massachusetts 02543 USA
* Note 1. Use of product names (commercial or otherwise) does not imply
endorsement or recommendation by any U.S. government agency, nor by the
authors in their government capacities.
* Note 2. S-PLUS is a commercial product, released by Insightful
* Note 3. AD Model Builder is a commercial product, released by Otter