fagan.plot | R Documentation |
These functions create a plot showing the relationship between the prior probability, the LR (combination of sensitivity and specificity), and the posterior probability.
fagan.plot(probs.pre.test, LR, test.result="+")
plotFagan(hscale=1.5, vscale=1.5, wait=FALSE)
plotFagan2(hscale=1.5, vscale=1.5, wait=FALSE)
plotFagan.old()
plotFagan2.old()
probs.pre.test |
The prior probability |
LR |
the likelihood ratio (sensitivity/(1-specificity)) |
test.result |
either '+' or '-' indicating whether you want the probability of the event or of not seeing the event |
hscale |
Horizontal scale, passed to |
vscale |
Vertical scale, passed to |
wait |
Should the R session wait for the window to close |
When Bayes theorem is expressed in terms of log-odds it turns out that
the posterior log-odds are a linear function of the prior log-odds
and the log likelihood ratio. These functions plot an axis on the left
with the prior log-odds, an axis in the middle representing the log
likelihood ratio and an axis on the right representing the posterior
log-odds. A line is then drawn from the prior probability on the left
through the LR in the center and extended to the posterior probability
on the right. The fagan.plot
creates the plot based on input
to the function. The plotFagan
and plotFagan2
functions set up Tk windows with sliders representing the possible
inputs and show how the plot and the posterior probability changes
when you adjust the inputs. The plotFagan
function creates
sliders for the prior probability and the LR, while the
plotFagan2
function replaces the LR slider with 2 sliders for
the sensitivity and specificity.
More detail on the plots and the math behind them can be found at the websites below.
The old functions are run for their side effects and do not return
a meaningful value. If wait
is FALSE then NULL is returned, if
wait
is TRUE, then a list with the current values is returned.
Guazzetti Stefano and Greg Snow 538280@gmail.com
Fagan TJ. Nomogram for Bayes theorem. N Engl J Med 1975;293(5):257-61. https://ebm.bmj.com/content/6/6/164.full
slider
fagan.plot(0.8, 2)
fagan.plot(0.8, 0.95/(1-0.90) )
if(interactive()) {
plotFagan()
plotFagan2()
}
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