[R-pkgs] Update of X2R (with FishGraph) at CRAN, 20 Nov 2008

From: Michael H. Prager <Mike.Prager_at_noaa.gov>
Date: Thu, 20 Nov 2008 08:13:52 -0500


X2R is a bundle of three software libraries for passing complicated data structures from Fortran, C/C++, or AD Model Builder to R. An update has been sent to CRAN and should be available from mirrors shortly. From the menu at the left of the CRAN home page, look under Software / Other.

We also have updated FishGraph, a compatible set of R functions for examining output from fish population models.

Changes in this Update

The update adds minor bug fixes only. In For2R, nested lists are now handled correctly. In FishGraph, correct axis units are now used in the CLD.plots (catch, landings, discards) routine.

More detail, for those interested:

X2R is 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.

The compatible software 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. The required 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 from routine fish stock assessments. The FishGraph functions can be modified or supplemented to reflect the needs of the analysis at hand.

X2R is supplied as files X2R.zip and X2R.tar.gz, which are equivalent. Version and release date are found in file "VersionInfo.txt" in the root of each archive. The new version is dated November 19, 2008.

FishGraph (same CRAN directory) is supplied as a Windows installer. We will gladly collaborate with anyone interested in adapting FishGraph to other operating systems.

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. The authors will endeavor to fix bugs promptly and to add requested features. Send bug reports, suggestions, and extensions to

Michael H. Prager - mike.prager_at_noaa.gov Southeast Fisheries Science Center
National Marine Fisheries Service, NOAA
101 Pivers Island Road
Beaufort, North Carolina 28516 USA


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