Using NEWGARDEN - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 66

java -Xmx256M -cp newgarden.jar Model -x SimData.xml -d datadump.txt
-l lifetable.txt -r output.txt -s -v -n
The order in which NEWGARDEN's command line options are given
is unimportant but it is necessary to include output fi lenames immediately
after the option asking for the output. In practice, one usually stores such a
complicated command line in a script fi le (“.bat” fi le) that can be executed
from a command prompt. Using Windows, the fi le Run.bat (distributed
with the NEWGARDEN program materials) accomplishes this and can be
edited to modify the options selected. The Run.bat fi le should be included
in the same directory as the NEWGARDEN program.
Generating, Modifying, and Testing Input Data Files
Examples of input data fi les are provided in appendices and with the
NEWGARDEN program materials. One way to open input data fi les (these
are fi lename.xml fi les) is by right-clicking on the fi lename, choosing the
“open with” option, and opening with the Wordpad program or any text
editor that refrains from formatting or reformatting the text. As a habit,
you may want to immediately save the fi le under a new fi lename so that
you can work with this new fi le and leave the old fi le (which you know
will work) intact. Always save modifi ed input fi les as plain text fi les using
a name that ends with the “.xml” suffi x. Also provided in appendices with
the program are loci arrays and founder arrays that can be copied into a
new input fi le when you want to compare, for example, 40 founders placed
in a dense square with 100 founders positioned in two lines and separated
from one another by at least 3 grid points. Thus, in this case, you can keep
all the particulars of comparative runs the same, just deleting and inserting
different founder arrays. Obviously, we cannot include all permutations of
such arrays, but provide only a few as examples and for program testing.
You will probably want to save new arrays that you construct, building up
your own more extensive fi le of variants.
General characteristics of the different input parameters and, in most
cases, brief examples of the exact form of the input, have been outlined in
Chapter 4 (Input). More details on specifi c input parameters and input style
may be found in chapters where the effects of altering individual parameters
in comparative trials are discussed (e.g., Chapter 9 on spatial arrangement
of founders, or Chapter 12 on offspring and pollen dispersal).
Using an Output File
Analyzed input data saved into an output fi le have the following general
details.