Readme.txt

To obtain the latest version of R go to http://www.r-project.org/

The R programs presented here were specially written to visualize the results of Qrule simulations and are provided for the readers interest, use and improvement.  Although an attempt has been made to make each program as general and reliable as possible, it may be necessary to modify these programs to analyze other simulations with Qrule.  Helpful comments are contained within these codes for program use.

The contents of R4Qcode.tar.gz are:

    Fig2.Qcfd.R -- this program calls the function within 'Qcfdfun.R' to plot the cumulative frequency distributions generated by Qrule and contained within the output file 'patch_cfd.dat.'  After plotting, the cumulative frequency distributions are "expanded" for statistical testing.

    Fig3.Wisk.R -- this program reads in the comma-delimited file 'stats.csv' and produces box and whisker plots of selected indices. 

    Fig4.splom.R -- this program uses the lattice package in R to generate correlation plots of simulation results contained within 'stats.csv."

    Zview.R -- this is an optional program for plotting maps from Qrule using the spatstat library.  However, large maps (like the ones contained in MDmaps.tar.gz) and should be rescaled before plotting with Zview.R.  The color table in this program is problematic.  Zview.R calls 'mapview.R' for execution.  The user should place this program in an appropriate directory and alter the 'source' statement to reference the appropriate location.

InOut.tar.gz -- this file contains all of the script files for running Qrule and the output files that were subsequently generated.

script files for running Qrule on the Maryland Piedmont maps and the RwC model
    MDpied01.scr -- for Qrule input running the 2001 map, 'lcc01.map'
    MDpied92.scr -- for Qrule input running the 1992 map, 'lcc92.map'
script files for the RwC model
    pied.01.mask.scr -- extracts mask from 'lcc01.map' and runs 10 iterations of the RwC model
    pied.92.mask.scr -- extracts mask from 'lcc92.map' and runs 10 interations ofthe Rwc model
data files appropriately labelled for the analysis of maps and the RwC simulations
    assmat*.dat -- the association matrices with format
        1st row: map number label
        2nd row: rows, columns, land-cover classes, chi-square value, df
        3rd row: class labels
        4th-nth row: association values for each class
        
    patch_cfd*.dat -- the cumulative frequency data sets with format for each row
        map number, cover type, size class, cfd, edges, radius, fractal index
        
    stats*.csv -- the statistical summaries with format
        1st row is 'header' providing labels for variables
        following rows for each map and cover type are the Qrule variables
        
log files
    rulerun*.log -- the log files documenting simulations
        
MDmaps.tar.gz
  WARNING -- these are large files with the analysis using the RwC likely to take 10-12 days to complete.
  Contents
    lcc01.map -- space delimited map file with 4365 rows and 5550 columns and 9 cover types
    lcc92.map -- space delimited map file with 4365 rows and 5550 columns and 9 cover types