dot-minimize_cell: minimize cell

In ABS-dev/DiagTestKit: Functions used in evaluating sensitivity and specificity at CVB Statistics

minimize cell

Description

A function used for optimizing the values of sensitivity and specificity (and \delta and \gamma for a 3-state kit). The objective function minimizes the sum of the squared deviations (expected - observed cell counts).

Usage

.minimize_cell(
  parm,
  SnR,
  SpR,
  Prev,
  xdat,
  N_mat,
  nstates,
  suspect2staterows,
  X,
  Xpos,
  Xsus,
  Xneg,
  ncells,
  ntests
)

Arguments

parm	vector A vector of starting values to be used for the optimization that is passed to .minimize_cell. For a 2-state experimental test, this is a vector of length 2 with entries (\pi, \theta) For a 3-state experimental test, this is a vector of length 4 with entries (\pi, \delta, \theta, \gamma). See also estimateSnSp.
SnR	data.frame Each column corresponds to one reference test. Row 1 contains the sensitivity for the reference test(s). Row 2 contains the probability of a suspect result as a fraction of the non-correct test result. This is a value between 0 and 1 (inclusive). Namely, P(T? | D+) = \psi = \delta * (1 - \pi) where \delta is the second row for a given column (reference test). \delta = \frac{\psi}{(1 - \pi)}. Use a zero for a 2-state test (i.e. no suspect region).
SpR	data.frame Each column corresponds to one reference test. Row 1 contains the specificity for each reference test. Row 2 contains the probability of a suspect result as a fraction of the non-correct test result. This is a value between 0 and 1 (inclusive). Namely, P(T? | D-) = \phi = \gamma * (1 - \theta) where \gamma is the second row for a given column (reference test). \gamma = \frac{\phi}{(1 - \theta)}. Use a zero for a 2-state test (i.e. no suspect region).
Prev	vector A named vector containing the prevalence for each population sampled.
xdat	vector A vector of the observed cell counts.
N_mat	matrix Needs to be filled out
nstates	vector A vector with length one more than the number of reference tests. The first element is the number of states of the experimental test and the remaining entries are the number of states of each reference test (using the same ordering as SnR and SpR).
suspect2staterows	Needs to be filled out.
X	Needs to be filled out.
Xpos	Needs to be filled out.
Xsus	Needs to be filled out.
Xneg	Needs to be filled out.
ncells	Needs to be filled out.
ntests	Needs to be filled out.

Value

The sum of the squared deviations between the expected and observed cell counts.

Author(s)

DiagTestKit-package

ABS-dev/DiagTestKit documentation built on Sept. 23, 2024, 9:37 a.m.