exploreHypers: Explore various hyperparameter estimates

In openEBGM: EBGM Disproportionality Scores for Adverse Event Data Mining

Explore various hyperparameter estimates

Description

exploreHypers finds hyperparameter estimates using a variety of starting points to examine the consistency of the optimization procedure.

Usage

exploreHypers(
  data,
  theta_init,
  squashed = TRUE,
  zeroes = FALSE,
  N_star = 1,
  method = c("nlminb", "nlm", "bfgs"),
  param_limit = 100,
  max_pts = 20000,
  std_errors = FALSE
)

Arguments

data	A data frame from processRaw containing columns named N, E, and (if squashed) weight.
theta_init	A data frame of initial hyperparameter guesses with columns ordered as: \alpha_1, \beta_1, \alpha_2, \beta_2, P.
squashed	A scalar logical (TRUE or FALSE) indicating whether or not data squashing was used.
zeroes	A scalar logical specifying if zero counts are included.
N_star	A positive scalar whole number value for the minimum count size to be used for hyperparameter estimation. If zeroes are used, set N_star to NULL.
method	A scalar string indicating which optimization procedure is to be used. Choices are "nlminb", "nlm", or "bfgs".
param_limit	A scalar numeric value for the largest acceptable value for the \alpha and \beta estimates. Used to help protect against unreasonable/erroneous estimates.
max_pts	A scalar whole number for the largest number of data points allowed. Used to help prevent extremely long run times.
std_errors	A scalar logical indicating if standard errors should be returned for the hyperparameter estimates.

Details

The method argument determines which optimization procedure is used. All the options use functions from the stats package:

• "nlminb": nlminb

• "nlm": nlm

• "bfgs": optim (method = "BFGS")

Since this function runs multiple optimization procedures, it is best to start with 5 or less initial starting points (rows in theta_init). If the function runs in a reasonable amount of time, this number can be increased.

This function should not be used with very large data sets unless data squashing is used first since each optimization call will take a long time.

It is recommended to use N_star = 1 when practical. Data squashing (see squashData) can be used to reduce the number of data points.

The converge column in the resulting data frame was determined by examining the convergence code of the chosen optimization method. In some instances, the code is somewhat ambiguous. The determination of converge was intended to be conservative (leaning towards FALSE when questionable). See the documentation for the chosen method for details about code.

Standard errors, if requested, are calculated using the observed Fisher information matrix as discussed in DuMouchel (1999).

Value

A list including the data frame estimates of hyperparameter estimates corresponding to the initial guesses from theta_init (plus convergence results):

• code: The convergence code returned by the chosen optimization function (see nlminb, nlm, and optim for details).

• converge: A logical indicating whether or not convergence was reached. See "Details" section for more information.

• in_bounds: A logical indicating whether or not the estimates were within the bounds of the parameter space (upper bound for \alpha_1, \beta_1, \alpha_2, and \beta_2 was determined by the param_limit argument).

• minimum: The negative log-likelihood value corresponding to the estimated optimal value of the hyperparameter.

Also returns the data frame std_errs if standard errors are requested.

Warning

Make sure to properly specify the squashed, zeroes, and N_star arguments for your data set, since these will determine the appropriate likelihood function. Also, this function will not filter out data points. For instance, if you use N_star = 2 you must filter out the ones and zeroes (if present) from data prior to using this function.

References

DuMouchel W (1999). "Bayesian Data Mining in Large Frequency Tables, With an Application to the FDA Spontaneous Reporting System." The American Statistician, 53(3), 177-190.

See Also

nlminb, nlm, and optim for optimization details

squashData for data preparation

Other hyperparameter estimation functions: autoHyper(), hyperEM()

Examples

data.table::setDTthreads(2)  #only needed for CRAN checks
#Start with 2 or more guesses
theta_init <- data.frame(
  alpha1 = c(0.5, 1),
  beta1  = c(0.5, 1),
  alpha2 = c(2,   3),
  beta2  = c(2,   3),
  p      = c(0.1, 0.2)
)
data(caers)
proc <- processRaw(caers)
squashed <- squashData(proc, bin_size = 300, keep_pts = 10)
squashed <- squashData(squashed, count = 2, bin_size = 13, keep_pts = 10)
suppressWarnings(
  exploreHypers(squashed, theta_init = theta_init)
)

openEBGM documentation built on Sept. 15, 2023, 1:08 a.m.