dot-cell_counts: Obtain cell counts

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

Obtain cell counts

Description

This function creates expected cell counts (and probabilities) for a specific test pattern based on the diagnostic characteristics of the reference test(s) and experimental test.

Usage

.cell_counts(
  SnR,
  SpR,
  Prev,
  SnE,
  SpE,
  sus.perc,
  N_mat,
  nstates,
  suspect2staterows,
  X,
  Xpos,
  Xsus,
  Xneg,
  ncells,
  ntests
)

Arguments

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.
SnE	Sensitivity of the experimental test kit.
SpE	Specificity of the experimental test kit.
sus.perc	vector A vector containing 2 elements, c(\delta, \gamma) for the experimental test kit. A vector of zeros for a 2-state experimental kit. \delta and \gamma are values between 0 and 1 (inclusive) corresponding to the proportion of the remaining probability (i.e. 1 - \pi or 1 - \theta) that is suspect (\psi or \phi). \delta = \frac{\psi}{(1-\pi)} and \gamma = \frac{\phi}{(1-\theta)}.
N_mat	matrix Needs to be filled out
nstates	vector A vector with length one greater 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

vector A vector of expected counts corresponding to the properties of the reference and experimental tests. The expected counts are obtained based on a conditional independence assumption of all test methods.

Author(s)

DiagTestKit-package

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