jade_path: Fit JADE at a sequence of gamma values without knowing much...
In jean997/jadeTF:

Description Usage Arguments Value

This function requires having previously fit the data at gamma=0. JADE will be fit at a serries of gamma values The function tries to fit JADE at a series of gamma values so that fits occur at evenly spaced values of l1.total.

jade_path(n.fits, out.file, fit0 = NULL, temp.file = NULL, max.it = 10000,
  log.gamma.min = -3, log.gamma.max = 20, start.step = 0.03,
  tol = 0.001, max.fits = 10 * n.fits, buffer = 0.001,
  restart.file = NULL, verbose = TRUE, adjust.rho.alpha = TRUE)

`n.fits`	Desired number of fits along the path. Actual results may vary.
`out.file`	Name of a file to save the results to.
`fit0`	Either a jade object or a file containing a jade object produced by fitting with `gamma=0`
`temp.file`	Name a temp file. If missing will use a default based on `out.file`. This file will be deleted at the end.
`max.it`	Maximum number of jade iterations.
`max.fits`	Maximum number of fits.
`restart.file`	Provide if restarting from a temporary file.
`log.gamma.minlog.gamma.max`	Smallest and largest values of `gamma` that are allowed.
`hard.stop`	Stop at `log.gamma.stop` regardless of if the path is done or not.

The output of this function is both returned and saved to a file. Partial results are saved to a temporary file along the way. The path objects is a list with several components:

gammas: A list of length n of gamma values at which JADE was fit. The first element is always zero.
JADE_fits: A list of n JADE objects in the same order as gammas.
l1.total: Vector of length n giving the total L1 distance between pairs of profiles at each value of gamma
sep.total: Vector of length n giving the total number of separated sites between all pairs of profiles
sep: List of lists of matrices giving the pairwise separation between profiles. sep[[i]][[j-i]] is a p \times n matrix which describes the separation between profiles for group i and group j.
tol: The tolerance at which the seaparation in sep.total and sep were calculated