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

Michael H. Prager Mike.Prager at noaa.gov
Thu Nov 20 14:13:52 CET 2008

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 
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

* 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 that requires licensing by the 
* Note 3. AD Model Builder, formerly a commercial product, is now an 
open-source free-software project. See http://admb-project.org/.

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