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minimize cell

dot-minimize_cell.Rd

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

DiagTestKit-package