thresTH2 {ThresholdROC} | R Documentation |
Population-based threshold calculation (two-state setting)
Description
This function estimates the theoretical optimum threshold for the specific distribution parameters, decision costs and disease prevalence in a two-state setting.
Usage
thresTH2(dist1, dist2, par1.1, par1.2, par2.1, par2.2, rho,
costs = matrix(c(0, 0, 1, (1 - rho)/rho), 2, 2, byrow = TRUE),
R=NULL, q1 = 0.05, q2 = 0.95, tol = 10^(-8))
Arguments
dist1 |
distribution to be assumed for the healthy population. See Details. |
dist2 |
distribution to be assumed for the diseased population. See Details. |
par1.1 |
first parameter of the distribution chosen for the healthy population. |
par1.2 |
second parameter of the distribution chosen for the healthy population. |
par2.1 |
first parameter of the distribution chosen for the diseased population. |
par2.2 |
second parameter of the distribution chosen for the diseased population. |
rho |
disease prevalence. |
costs |
cost matrix. Costs should be entered as a 2x2 matrix, where the first row corresponds to the true positive and true negative costs and the second row to the false positive and false negative costs. Default cost values are a combination of costs that yields R=1, which is equivalent to the Youden index method (for details about this concept, see References). It must be set to |
R |
if the cost matrix |
q1 |
probability of the left distribution in order to determine a low quantile. Default, 0.05. |
q2 |
probability of the right distribution in order to determine a high quantile. Default, 0.95. |
tol |
tolerance to be used in function |
Details
Parameters dist1
and dist2
can be chosen between the following 2-parameter distributions: "beta"
, "cauchy"
, "chisq"
(chi-squared), "gamma"
, "lnorm"
(lognormal), "logis"
(logistic), "norm"
(normal) and "weibull"
.
Value
An object of class thresTH2
, which is a list with five components:
thres |
threshold estimate. |
prev |
disease prevalence provided by the user. |
costs |
cost matrix provided by the user. |
R |
R term, the product of the non-disease odds and the cost ratio (for further details about this concept, see References). |
method |
method used in the estimation. For an object of class |
Note
It is assumed that dist1
is the distribution with lower values. If not, dist1
and dist2
(and the corresponding parameters) are exchanged.
References
Skaltsa K, Jover L, Carrasco JL. (2010). Estimation of the diagnostic threshold accounting for decision costs and sampling uncertainty. Biometrical Journal 52(5):676-697.
Examples
# example 1
dist1 <- "norm"
dist2 <- "norm"
par1.1 <- 0
par1.2 <- 1
par2.1 <- 2
par2.2 <- 1
rho <- 0.1
thresTH2(dist1, dist2, par1.1, par1.2, par2.1, par2.2, rho)
# example 2
dist1 <- "norm"
dist2 <- "lnorm"
par1.1 <- 0
par1.2 <- 1
par2.1 <- 1
par2.2 <- 0.5
rho <- 0.3
thresTH2(dist1, dist2, par1.1, par1.2, par2.1, par2.2, rho)