Baserate — the series
-
What a positive test is worth
A test that is 90% sensitive and 95% specific sounds accurate. For a condition affecting one person in a thousand, 98% of its positive results are wrong, and a worse test on a commoner condition beats a better test on a rare one.
-
The base rate was always Bayes
The screening arithmetic everybody finds counter-intuitive is a posterior update with a prior of one in a thousand. Naming it that way turns a famous puzzle into an instance of a rule, and makes the sequential version obvious.
-
The second test that is not a second opinion
Two positives from a 90/95 test on a one-in-a-thousand condition give a 24.49% chance of disease if the tests are independent. At a correlation of 0.1 between their errors it is 10.16%, and at 0.5 it is 3.16% — barely more than the 1.77% one positive was worth.
-
The test is a point somebody chose
A test reported as 90% sensitive and 95% specific is not two properties of a test. It is one property read at a threshold, and the threshold that minimises harm runs from 3.05 standard deviations of the score at a prevalence of one in ten thousand to −0.12 at one in two — 45% of cases detected at one end and 99.9% at the other.
-
The prevalence the test has to estimate
Every predictive value takes a prevalence as given, and the prevalence is usually estimated from the same test's positive rate. At a true prevalence of one in a thousand that rate reads 5.09% — fifty times the truth — and the correction that inverts it is unbiased, 18% more variable, and negative on 48.6% of samples of a thousand.
-
An upper limit is the finding
A survey of a thousand people with a 90%-sensitive, 95%-specific test, estimating a prevalence of one in a thousand, prints a corrected 95% interval that covers the truth 95.17% of the time — and reaches below zero in 97.95% of surveys and lies entirely below zero in 3.35%. Coverage is not the problem. The problem is what the interval can say, and the honest summary of a typical survey is one number: the prevalence is below 1.64%. Bringing that limit down to twice the truth takes 184,521 people at this specificity and 5,083 with a test that never gives a false positive.
-
A threshold that jumps
When a test's scores are equally spread in the healthy and the diseased, the harm-minimising threshold slides smoothly as the prevalence changes. Make the diseased scores twice as spread — the ordinary shape of a group that mixes mild and severe cases — and keep the published 90/95 pair, and the best threshold flags 81.1% of healthy people at a prevalence just under 25.7% and every healthy person just above it. At three times the spread it jumps from 45.7% to everyone at 13.0%. A threshold that jumps cannot be given as a formula; it has to be given with the second-best point beside it.
-
The threshold a validation study can see
When diseased scores are twice as spread as healthy ones, the harm-minimising threshold jumps near a prevalence of 26% from an interior cut to flagging everyone, because the true operating curve keeps climbing in a tail where few diseased people score. A validation study of a hundred diseased and three hundred healthy cannot see that tail: its own curve reaches 100% sensitivity at its lowest diseased score and goes flat. Just past the jump, only 7.7% of such studies recommend flagging everyone, and their recommended thresholds cause 15.4% more harm than the best on average. Fitting a normal curve to each group first sees the tail: 47.4% of studies then recommend flagging everyone and the excess harm falls to 2.5%. More healthy people in the study change nothing; more diseased people do.
-
A test whose tail is not normal
A validation study that fits a normal curve to each group saw the tail where a threshold jumps — when the diseased scores really were normal. Give the same published test a diseased group with no lower tail at all, and the binormal fit invents one: 89.7% of studies recommend flagging everyone, adding 67.08 false alarms' worth of harm per hundred people to a best threshold that costs 5.61. Give it a lump of mild cases instead, and the binormal fit misses the tail that is there and does worse than the study's own curve. A normality test on the hundred diseased scores sees the missing tail every time and the lump 60.4% of the time, and a study that fits the binormal model only when normality is not rejected is never the worst of the four.
-
A threshold reported with its interval
Resample a validation study of a hundred diseased and three hundred healthy people, refit the binormal model each time, and read off the threshold each resample recommends. Far from the prevalence at which the best threshold jumps to flagging everyone, the interval is tight — flagging 12% to 24% of healthy people at a prevalence of 5%. Near the jump, the median study's interval runs from flagging under half of the healthy to flagging everyone, and 91% of intervals cross the jump. The two ends differ by fifteen false alarms' worth of harm per hundred people, and no rule for choosing inside the interval beats the study's own choice at every prevalence.