reitsma-class: Methods for 'reitsma' objects.

In mada: Meta-Analysis of Diagnostic Accuracy

Methods for reitsma objects.

Description

Objects of the class reitsma are output by the function with the same name. Apart from standard methods the functions sroc, mcsroc and ROCellipse provide SROC curves and confidence regions for fits.

Usage

## S3 method for class 'reitsma'
print(x, digits = 4, ...)
## S3 method for class 'reitsma'
summary(object, level = 0.95, sroc.type = "ruttergatsonis", ...)
## S3 method for class 'reitsma'
sroc(fit, fpr = 1:99/100, type = "ruttergatsonis", return_function = FALSE, ...)
## S3 method for class 'reitsma'
mcsroc(fit, fpr = 1:99/100, replications = 10000, lambda = 100, ...)
## S3 method for class 'reitsma'
ROCellipse(x, level = 0.95, add = FALSE, pch = 1, ...)
## S3 method for class 'reitsma'
crosshair(x, level = 0.95, length = 0.1, pch = 1, ...)
## S3 method for class 'reitsma'
plot(x, extrapolate = FALSE, plotsumm = TRUE, level = 0.95, 
     ylim = c(0,1), xlim = c(0,1), pch = 1, sroclty = 1, sroclwd = 1, 
     predict = FALSE, predlty = 3, predlwd = 1, type = "ruttergatsonis", ...)
## S3 method for class 'reitsma'
anova(object, fit2, ...)
## S3 method for class 'anova.reitsma'
print(x, digits = 4, ...)

Arguments

x	a reitsma object.
object	a reitsma object.
fit	a reitsma object.
fit2	a reitsma object.
digits	number of decimal digits to print.
level	numeric, the level for calculations of confidence intervals (summary) or regions (ROCellipse)
sroc.type	character, which SROC curve should be used to calculate the AUC in the summary? Besides the default ruttergatsonis the option naive is available.
return_function	logical. Should a function on ROC space be returned or the values at the points given by fpr?
fpr	numeric, the false positives rates for which to calculate the predicted sensitivities
replications	integer, the number of replications for the Monte-Carlo SROC curve
lambda	numeric, the parameter lambda of the Monte-Carlo run, see details
add	logical, should the confidence region be added to the current plot? If set to FALSE a matrix of points of the ellipse is returned
extrapolate	logical, should the SROC curve be plotted beyond the observed false positive rates?
plotsumm	logical, should the summary pair of sensitivity and false positive rate together with its confidence region be plotted?
length	positve numeric, length of the "whiskers" of the crosshairs.
ylim	numeric of length 2, which section of the sensitivities to plot?
xlim	numeric of length 2, which section of the false positive rates to plot?
pch	integer, symbol for the pair of mean sensitivity and false positive rate
sroclty	integer, line type of the SROC curve
sroclwd	integer, line width of the SROC curve
predict	logical, draw prediction region?
predlty	integer, line type of prediction region
predlwd	integer, line width of prediction region
type	character, type of SROC curve to plot. Can be either the generalization of the Rutter & Gatsonis (2001) SROC curve (see below) or the naive curve implied the bivariate model.
...	arguments to be passed on to other functions

Details

The confidence regions of ROCellipse are first calculated as ellipses on logit-ROC space, so the back-transformed regions that are output are not necessarily ellipses. The Monte-Carlo SROC curves are generated from random samples from the fitted model and a lowess smooth through them is output. Many computational details are to be found in Doebler et al. (2012).

The summary function for reitsma objects also contains the five parameters of the HSROC model by Rutter & Gatsonis (2001) if no regression is performed. These values are calculated by using the formulae from Harbord et al. (2007).

The plot method for reitsma objects will plot the generalization of the Rutter-Gatsonis curve.

If you require positive or negative likelihood ratios, you should use SummaryPts. If you require positive or negative predictive values, see predv_r and predv_d.

Value

sroc returns a matrix ready for plotting. Each row corresponds to one point in ROC space. mcsroc returns a lowess smooth. ROCellipse returns a list, the first element being a matrix of points in ROC space that delimit the confidence region and the second is the point estimate of the pair of sensitivity and false positive rate in ROC space.

Author(s)

Philipp Doebler <[e-mail]>

References

Doebler, P., Holling, H., Boehning, D. (2012) “A Mixed Model Approach to Meta-Analysis of Diagnostic Studies with Binary Test Outcome.” Psychological Methods, to appear

See Also

reitsma, SummaryPts

Examples

# load data
data(Dementia)
# fit model
fit <- reitsma(Dementia)
# calculate a confidence region but do not plot it
cr.Dementia <- ROCellipse(fit)
#calculate a SROC curve
sroc.Dementia <- sroc(fit)
# plot the confidence region in ROC space as a line
plot(cr.Dementia$ROCellipse, type = "l", xlim = c(0,1), ylim = c(0,1))
# add the point estimate of the mean
points(cr.Dementia$fprsens)
# add the SROC curve
lines(sroc.Dementia)

mada documentation built on Sept. 9, 2022, 3:01 p.m.