Running structure from the command line

There are a number of program parameters which are set by the user. These are in two files (mainparams and extraparams), which are read every time the program executes. You will need to set all the values in mainparams, while the default values in extraparams are probably ok to begin with. Note that the default model assumes admixture, and does not make use of the user-defined PopData. Each parameter is printed in all-caps in one of these two files, preceded by the word ``#define''. (They are also printed in all-caps throughout this document.) The value is set immediately following the name of the parameter (eg ``#define NUMREPS 1000'' sets the number of MCMC repetitions to 1000). Following each parameter definition, there is a brief comment (marked ``//''), describing the parameter. This includes an indication of what sort of value is expected. These include: ``(str)'', for string (used for the names of the input and output files); ``(int)'', for integer; ``(d)'', for double (i.e., a real number such as 3.14); and ``(B)'', for Boolean (i.e., the parameter takes values TRUE or FALSE by setting this to 1 or 0, respectively). The program is insensitive to the order of the parameters, so you can re-arrange them or add comments, etc. The values of all parameters used for a given run are printed at the end of the output file. Several of the parameters in mainparams can be changed from the command line (see below).