################################################################################
## Files for Reproducibility of 

Ogle, D.H. and I.J. Winfield.  2009.  Ruffe weight-length relationships with
  a proposed standard weight equation.  North American Journal of Fisheries
  Management.  29:XXX-XXX.

All files, except where noted below, should be kept in this same directory.
  Note that this directory must have a sub-directory called "figs".


################################################################################
## File #1 -- Files_Explanation.txt
   
This file.  Describes all files required to reproduce the results in the
  Ogle and Winfield (2009) paper.
  

################################################################################
## File #2 -- RuffeWr_v2.mdb

A Microsoft Access file that contains all of the data, both used and excluded in,
  the analysis.  This file contains three primary related tables of interest:
  
    data:         all of the raw length-weight and associated data
    LocationInfo: information specific to the location of the data
    SourceInfo:   information specific to the source of the data

The data are ultimately read into R in the RuffeWr_Cleaning.RNW file from the
  query saved in SourceData_All.

################################################################################
##  RuffeWrCleaning_v10.rnw (--> .tex --> .pdf)

A Sweave file (and resulting tex and pdf files) used to construct an initial
  cleaning of the data.  The processse in this file follow the cleaning
  methods outlined in the manuscript.
  
This file relies on the following R packages (and all their dependencies)

  FSA v0.1-1 (available in this directory -- see below)
  NCStats v0.1-1 (available in this directory -- see below)
  RODBC v1.2-5
  xtable v1.5-4 
  
The working directory in R must be set to where you save this file and the 
  MS Access file described above.  The directory can be set with setwd(), e.g.,
  
     setwd("c://folderfoo1//folderfoo2//")
     
  where folderfoo1 and folderfoo2 are replaced with appropriate directories on
  your system.
  
Once the directory is set this file can be Sweaved in R with

     Sweave('RuffeWrCleaning_v10',stylepath=TRUE,syntax="SweaveSyntaxNoweb")

The actual commands used can be extracted with

     Stangle('RuffeWrCleaning_v10')


################################################################################
## File #4 -- rwr.txt

A tab-delimited text file that is produced when RuffeWrCleaning_v10.rnw is
  Sweaved.  This text file is included in the distributed directory but will be
  recreated when the cleaning file is Sweaved.  This file is the input file to
  RuffeWrAnalysis_v7.rnw and OgleWinfield2009repro.rnw.  Thus, if you make
  changes to the cleaning procedure then a new rwr.txt fill will be produced.
  Therefore, it is recommended that you modify the cleaning procedure to
  produce a file with a different name.
  
These are the raw data after cleaning.  Many users may want to just start with
  these data.


################################################################################
## File #5 -- RuffeWrAnalysis_v7.rnw (--> .tex --> .pdf)

A Sweave file (and resulting tex and pdf files) used to construct the analyses
  reported in the paper and additional analyses either not reported or used in
  responses to reviewers comments.  The very end of the document contains R
  code that is not evaluated as part of the Sweaving but can be used to
  construct the graphics submitted for the manuscript.  Graphics produced
  earlier in this file are NOT the graphics submitted.
  
This file relies on the following R packages (and all their dependencies)

  FSA v0.1-1 (available in this directory -- see below)
  NCStats v0.1-1 (available in this directory -- see below)
  car v1.2-12
  gdata v2.4.2
  quantreg v2.8.0
  xtable v1.5-4 

This file also requires the rwr.txt tab-delimited text file that is the result
  of the cleaning conducted in the RuffeWrCleaning_v10.rnw file as an input.
  
The working directory in R will have to be set before Sweaving this file as
  described above for the cleaning file.  Once the directory is set this file
  can be Sweaved in R with

     Sweave('RuffeWrAnalysis_v7',stylepath=TRUE,syntax="SweaveSyntaxNoweb")

The actual commands used can be extracted with

     Stangle('RuffeWrAnalysis_v7')
     

################################################################################
## File #6 -- RuffeWr_Maps.rnw (--> .tex --> .pdf)

A Sweave file that is used to produce the map depicting sampling locations.  It
  produces Fig3_SamplesMap.PDF.  This file does NOT HAVE to be Sweaved as the
  figure already exists in the figs folder.

This file relies on the following R packages (and all their dependencies)

  FSA v0.1-1 (available in this directory -- see below)
  NCStats v0.1-1 (available in this directory -- see below)
  RODBC v1.2-5
  mapproj v1.1-7.2
  sp v0.9-29
  rgdal v0.6-5 

This file also relies on several data files

  world_countries.rda
  glgis_gl_shore_noaa_70k.dbf
  glgis_gl_shore_noaa_70k.prj
  glgis_gl_shore_noaa_70k.shp
  glgis_gl_shore_noaa_70k.shx

The working directory in R will have to be set before Sweaving this file as
  described above for the cleaning file.  Once the directory is set this file
  can be Sweaved in R with

     Sweave('RuffeWrMap_v5',stylepath=TRUE,syntax="SweaveSyntaxNoweb")

The actual commands used can be extracted with

     Stangle('RuffeWrMap_v5')


################################################################################
## File #7 -- OgleWinfield2009repro.rnw (--> .tex --> .pdf)

A Sweave file that is used to produce a document that has the same content as
  the published article in NAJFM.  The produced PDF document is, however, only
  a close facsimile to that produced by NAJFM (as they require MSWord upon
  submission and do their own typesetting).

This file relies on the following R packages (and all their dependencies)

  FSA v0.1-1 (available in this directory -- see below)
  NCStats v0.1-1 (available in this directory -- see below)
  car v1.2-12
  gdata v2.4.2
  MASS v7.2-45
  quantreg v2.8.0
  xtable v1.5-4 

In addition to the LaTeX packages required in the general preamble (see below)
  this file also requires access to the captof package, the afs bibliographic
  style file (see below), and the OgleWinfield2009.bib bibliographic database
  (see below) for proper typesetting with LaTeX.
  
This file also requires the rwr.txt tab-delimited text file that is the result
  of the cleaning conducted in the RuffeWrCleaning_v10.rnw file as an input.
  
The working directory in R will have to be set before Sweaving this file as
  described above for the cleaning file.  Once the directory is set this file
  can be Sweaved in R with

     Sweave('OgleWinfield2009repro',stylepath=TRUE,syntax="SweaveSyntaxNoweb")

The actual commands used can be extracted with

     Stangle('OgleWinfield2009repro')


################################################################################
## File #8 -- GnrlPreamble.tex

A LaTeX file containing specific packages, option choices, and code definitions 
  used to LaTeXify the .tex files resulting from Sweaving the .rnw files
  described above.  This preamble requires several packages listed at the very
  beginning of the file.
  

################################################################################
## File #9 -- afs.bst

This bibliographic style file was created by me to mimic as close as possible
  the bibliographic requirements of AFS journals.  This bst is NOT, unfortunately,
  distributed by AFS.
  
This file MUST BE COPIED to the directory where your LaTeX compiler expects to
  find bst files.  This should be fairly close to where your natbib is installed.
  This bst file will NOT BE LOCATED by your LaTeX complier if you do not copy
  it to a different directory.
  

################################################################################
## File #10 -- OgleWinfield2009.bib

This file is a bibliographic database for all citations used in the document.
  This file should be located by the LaTeX compiler in this directory.


################################################################################
## Folder #1 -- figs

A folder to contain the figures created by Sweaving the various rnw files.  This
  folder is required.

  
################################################################################
## Folder #2 -- Local Packages

A folder that contains ... 

  FSA_0.1-1.zip --> A Windows binary ZIP file of the FSA package.  On Windows
    this can be installed from "a local directory."  Newer versions are available
    at www.rforge.net
  NCStats_0.1-1.zip --> A Windows binary ZIP file of the FSA package.  On Windows
    this can be installed from "a local directory."  Newer versions are available
    at www.rforge.net


################################################################################
## Folder #3 -- WebAnims

A folder that contains an R source file and the results of that file in three
  other folders.  Each of these folders contains an html page that shows
  animations of various aspects of the Wr analysis.  Each of these aspects is
  described in the animation file.  These files are a supplement to the 
  actual manuscript.


################################################################################
## Folder #4 -- Reviews

A folder with files that contain most of the reviewers comments and all of our
  responses to those comments.  Of course, the comments refer to previous 
  versions of the manuscript.