infer

var Command = &command.Command{
	Usage: `infer -i|--input <prefix> [-o|--output <prefix>]
	[--cpu <number>]
	[-p|--particles <number>]
	<project-file>`,
	Short: "infer parameters from simulated data",
	Long: `
Command infer reads the results of a data simulation and performs a maximum
likelihood inference of the parameters used to generate the data.

The argument of the command is the name of a project file that contains the
paleogeographic models (plate motion model, landscape model, and the pixel
priors).

The flag --input, or -i, is required and defines the prefix of the files that
contain the results of the simulation (the tree '<prefix>-trees.tab', the
particles '<prefix>-particles.tab', and the value of lambda
'<prefix>-lambda.tab').

The flag --output, or -o, defines the prefix of the files produced in the
inference. The file '<prefix>-infer-particles.tab' produces the inferred
stochastic mapping for the lambda value estimated with maximum likelihood. The
lambda values are stored in '<prefix>-infer-lambda.tab'. If no prefix is
defined, the command will use the prefix used for the input.

By default, the calculations will use all available CPUs. Use the flag --cpu
to change the number of processors.

By default, 1000 particles will be simulated for the stochastic mapping. The
number of particles can be changed with the flag --particles, or -p.

	`,
	SetFlags: setFlags,
	Run:      run,
}