Biology Reference
In-Depth Information
-h or --help: show this help message
-x or --xmlfi le <fi lename>: specify the XML parameter fi le
-d or --dumpfi le <fi lename>: put all the population data into the fi lename
or to stdout if <fi lename> is not given
-l or --lifetable <fi lename>: write Leslie lifetable to the fi le fi lename
or to stdout is <fi lename> is not given.
-p or --progressbar : show a progress bar on screen
-v to label all bits of output with date-time and program version
-r or --resultsfi le <fi lename> to send the main results to the fi le fi lename
-s to include a copy of the XML specifi ed parameters in the results fi le
-n or --showNe to have the program report estimates of Ne
(-x) The command line option -x is required since the program cannot run
without input specifying the parameters for the simulation.
(-d) This option causes NEWGARDEN to print all the information about
every individual that occurs in each run of the simulation. It will scroll past
on the computer screen unless you specify the name of a fi le to which the
data should be written.
(-l) This option asks the program to construct a Leslie lifetable mode of the
population based on the values of the input parameters and to print the
Leslie matrix and population growth rate values. This information scrolls
past on the screen unless you specify a fi le to which the information should
be written or redirect all the output of the program to a fi le.
(-p) This option causes the program to show a progress bar displaying the
state of the simulation. Large simulations can take a long time and it is nice to
be reminded occasionally that the program is actually doing something.
(-v) This option causes information about the program version and
execution time to be printed to the main output. It scrolls past on the
computer's screen unless you have specifi ed a main output fi le or redirected
all output to a fi le.
(-r) This option tells the program to print all the main output to a computer
fi le. The fi lename follows “-r” on the command line. This option lets you
capture the main output without redirecting all output to a fi le.
(-s) This option causes the program to print a summary of the input
parameters to the main output (screen, redirected fi le, or that specifi ed
with the -r option).
(-n) This option causes the program to include information about the value
of the effective population size, Ne, in the main output.
So a command generating the maximum possible output and stashing
the various bits in separate fi les would look like the following:
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