flash_fit {flashier} | R Documentation |
Extract a flash_fit object
Description
flash_fit
objects are the "internal" objects used by flash
functions to fit an EBMF model. Whereas flash
objects
(the end results of the fitting process) include user-friendly fields and
methods, flash_fit
objects were not designed for public
consumption and can be unwieldy. Nonetheless, some advanced
flash
functionality requires the wielding of
flash_fit
objects. In particular, initialization, convergence,
and "verbose" display functions all take one or more flash_fit
objects as input (see parameter init_fn
in function
flash_greedy
; parameter fn
in
flash_set_conv_crit
;
and parameter fns
in flash_set_verbose
).
For users who would like to write custom functions, the accessor functions
and methods enumerated below may prove useful. See
flash_set_verbose
for an example.
Usage
flash_fit(flash)
flash_fit_get_pm(f, n)
flash_fit_get_p2m(f, n)
flash_fit_get_est_tau(f)
flash_fit_get_fixed_tau(f)
flash_fit_get_tau(f)
flash_fit_get_elbo(f)
flash_fit_get_KL(f, n)
flash_fit_get_g(f, n)
Arguments
flash |
A |
f |
A |
n |
Set |
Details
The following S3 methods are available for flash_fit
objects at all
times except while optimizing new factor/loadings pairs as part of a
"greedy" fit:
fitted.flash_fit
Returns the "fitted values"
E(LF') = E(L) E(F)'
.residuals.flash_fit
Returns the expected residuals
Y - E(LF') = Y - E(L) E(F)'
.ldf.flash_fit
Returns an
LDF
decomposition, with columns ofL
andF
scaled as specified by the user.
Value
See function descriptions below.
Functions
-
flash_fit_get_pm()
: The posterior means for the loadings matrixL
(when parametern
is equal to1
) or factor matrixF
(whenn = 2
). While optimizing new factor/loadings pairs as part of a "greedy" fit, only the posterior means for the new loadings\ell_{\cdot k}
or factorf_{\cdot k}
will be returned. -
flash_fit_get_p2m()
: The posterior second moments for the loadings matrixL
(when parametern
is equal to1
) or factor matrixF
(whenn = 2
). While optimizing new factor/loadings pairs, only the posterior second moments for the new loadings\ell_{\cdot k}
or factorf_{\cdot k}
will be returned. -
flash_fit_get_est_tau()
: Equal to1 / \sigma^2
, where\sigma^2
is the estimated portion of the residual variance (total, by row, or by column, depending on the variance type). -
flash_fit_get_fixed_tau()
: Equal to1 / s^2
, wheres^2
is the fixed portion of the residual variance (total, by row, or by column). -
flash_fit_get_tau()
: The overall precision1 / (\sigma^2 + s^2)
. -
flash_fit_get_elbo()
: The variational lower bound (ELBO). -
flash_fit_get_KL()
: A vector containing the KL-divergence portions of the ELBO, with one value for each factor (whenn = 2
) or set of loadings (whenn = 1
). While optimizing new factor/loadings pairs, only the KL-divergence for the new factor or loadings will be returned. -
flash_fit_get_g()
: A list containing estimated priors on loadings\hat{g}_\ell
(whenn = 1
) or factors\hat{g}_f
(whenn = 2
). While optimizing new factor/loadings pairs, only the estimated prior on the new factor or loadings will be returned.