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2 (de) vizualizări7 paginiBayesian theory for psychologists

Jul 17, 2019

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Bayesian theory for psychologists

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Bayesian theory for psychologists

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All psychologists have learned Bayes’ Theorem. But what was it about again? Wasn’t that

one of those complicated formulae? Oh well, that is far from practice. But beware, the

Bayes’ rule has everything to do with practice. By ignoring the rule, serious mistakes can

be made. We will explain this with an example and show how easy to use the rule is.

Probabilities?

Suppose you work in community mental healthcare and a patient was referred by the general

practitioner (GP) because of an increased score on a depression questionnaire. In this general

practice, 11% of the patients have a depression (the prevalence). If a patient has a depression, the

chance that the patient scores positively on this depression questionnaire is 83% (sensitivity). A

patient who does not have a depression, has an 80% chance of a negative score on the list

(specificity) and a 20% chance of a positive score (chance of a false positive result). What is the

chance that the referred patient has a depression? (give an answer before you continue reading).

All psychologists have learned at university how to answer this question. You must indeed take into

account the sensitivity and specificity of a psychological test, but what should you do with that

prevalence of 11%? Filling in Bayes' rule, as learned; but wasn’t that a complicated formula? Well,

if this patient has a high score on a depression questionnaire, the chance of a depression is fairly

high, isn’t it? You do not have to calculate that, and certainly not using such a formula that has

nothing to do with practice. Bayes’ rule, however, has everything to do with practice. By ignoring

the rule, serious mistakes will be made. Probably this indeed happens regularly and there may be a

lot of overdiagnosis and overtreatment. We will explain this using the above example, both by

applying Bayes’ formula, but also in two simpler ways.

Bayes' theorem helps determine the probability of an individual's disorder, given the prevalence of

that disorder in the population of that individual, given the outcome of a test and the psychometric

characteristics of that test. The population to which the individual belongs is essential in Bayes'

theorem, but it is often overlooked. If a disorder is rare in a population (the prevalence of that

disorder is low), the probability of the disorder will be higher with a positive test than before the

test was taken, but still very low. This means that the same test result in different populations

gives a different probability of the disorder. This is intuitively very difficult to understand, even if

you are familiar with the rule. Consider, for example, testing for a tropical disorder in the tropics or

1

in the Netherlands. In the Netherlands, the probability that a positive test result is due to

coincidence is much higher because the prevalence is much lower. It helps to understand this by

making the calculation every time a test result has to be interpreted. Below we show that Bayes’

formula might be difficult, but that the calculation is actually childishly simple.

Difficult formula?

In our example, the probability that a patient the GP sees has a depression is 11%. This is the

prevalence (prev) in the consultation-hour population. This is also called the base rate, the basic

probability or pre-test probability; the probability before being tested. Do not drop out now, it will

really become easy. The left part of figure 1 first shows this probability of depression and below

that, it shows the probability that a patient who actually has a depression, has a positive score on a

depression questionnaire (sensitivity, 83%) and the probability that a patient who does not have

depression, scores negatively on that list (specificity, 80%). These probabilities are based on

research by Cameron and colleagues who tested three depression questionnaires in GP practices1.

From this study, we use the most favourable values for the sensitivity (Se) and specificity (Sp) of

the Brief Depression Inventory II (BDI-II)2.

Figure 1. The probability of depression with a positive depression test: Bayes' formula

Next to the diagram in Figure 1 on the left, Bayes’ formula is on the right. The P stands for

'probability' or chance. The vertical line means 'under the condition that' or 'given'. So P(D+|T+)

means the probability (P) that the patient has a depression (D+) given (|) a positive test result

(T+) on a depression questionnaire. We want to know that probability and we can use Bayes’

formula for this:

P(T+|D+) is the probability that a patient with a positive test has depression, so the

sensitivity, here 0.83.

P(D+) is the probability that a patient in this population has a depression, the prevalence,

here 0.11.

2

P(T+|D-) is the probability that a patient with a positive test has no depression, i.e. 1-

specificity (the probability that a patient with a negative test does not have depression),

here 1-0.8 = 0.2

P(D-) is the probability that a patient in this population has no depression, 1-prevalence,

here 1-0.11 = 0.89.

Thus, the probability (P) that the referred patient from the concerning general practice population

has a depression (D+) given (|) a positive test result (T+) on a depression questionnaire,

P(D+|T+), is about a third, 34%. This is also called the after-chance or post-test probability; the

probability after the test has been taken and given the outcome of the test.

It can be easier

When applying Bayes’ formula, you have to do some puzzling and the formula is hard to

remember. However, it is much simpler if the same information is presented in absolute numbers

instead of in probabilities3, as is done in Figure 2.

On the left, the information is in the same flowchart as in figure 1 and on the right in a cross

tabulation, but now in absolute numbers. Using the sensitivity of the test we are able to calculate

how many patients with a depression will have a positive score: 0.83 x 110 = 91.3, rounded to 91.

So 110 - 91 = 19 patients with depression had a negative score on the depression test. The

specificity has been used to calculate how many patients who do not have a depression score

negatively on the test: 0.80 x 890 = 712. So, 890 - 712 = 178 patients who do not have

depression will have a positive score on the depression test. This way, it becomes clear at a glance

3

how many patients have a positive test score (91 + 178) and how many of them actually have a

depression (91). The probability that the patient has a depression given a positive test is therefore:

The probability that the patient does not have a depression given a negative test is:

Although the sensitivity of the BDI in this study by Cameron et al. is 83% and the specificity 80%,

the probability that the patient with a positive test result actually has a depression is much lower,

namely only a third. This is much too low for a treatment indication. A negative test result, on the

other hand, gives a relatively high level of certainty in this population about the absence of

depression, a probability that is higher than the specificity. This test could therefore be used to

exclude depression.

From the above it becomes obvious that it is not recommended simply to rely on the score of a

test. A positive test does not necessarily mean that the disorder is present and a negative test does

not necessarily indicate that it is absent. Neither can we rely on the sensitivity or 'chance of being

caught' and the specificity of an instrument only. Especially when the prevalence is very low, a

positive test result will never give a very high probability of the disorder even when the sensitivity

and specificity of a test are good.

This becomes clear when we use the same depression test, with the same sensitivity and

specificity, but now in the general population, where the prevalence of depression is lower than in

general practice: 5%. Then the probability of depression with a positive test result is less than 20%

(figure 3): 42 / (42 + 190) = 0.18. Suppose that in the situation of figure 3 the specificity is not

80% but 95%. The number of non-depressed patients with a positive score will be 48. The a post-

test probability is much higher now, 42 / (42 + 48) = 0.47, but is still lower than 50%.

4

Figure 3. The probability of depression for a positive depression test in the general population

The figures with the examples show why it is necessary in practice to always keep Bayes’ theorem

in mind. When calculating the sensitivity and specificity of a test in scientific research, it is known

which respondents do and do not have the disorder. In practice, this is unknown, and that is

precisely why the test is administered. The psychologist only sees a positive test result! In the

above example, this is the case with 23% (42 + 190/1000) of the people tested, while only 5%

have a depression. The psychologist does not know which of those 23% do or do not have a

depression. But if the psychologist is aware of Bayes' rule, it is clear that extra diagnostics is

needed in addition to taking a BDI.

Bayes’ theorem, in formula or in one of the other simpler forms, helps to determine the posterior

probability of a disorder, given the test result, the pre-test probability (the prevalence) and the

sensitivity and specificity of the diagnostic instrument. Clinicians often forget to include the pre-test

probability in their interpretation, they only consider the sensitivity of a test and a positive score is

interpreted as the presence of the disorder. How easy but incorrect this conclusion is, shoud be

clear now.

Bayes in practice

What does it mean in practice when one is aware of Bayes’ theorem? It means that when

interpreting a test result, the setting in which the test was taken must always be considered. The

assessment of the probability of a disorder always starts with the determination or estimation of

the prevalence in the population or setting in which the test was performed.

You may wonder how you can know what the prevalence is or where to find it. That is exactly the

right question. The prevalence of the most common mental illnesses at general population level can

be found in the national Nemesis study4,5, the publication of which can be downloaded free of

5

charge. Most psychologists, however, do not work at general population level, so the prevalences

in general practice or in mental health care are more relevant.

Most numbers on prevalence in general practice are based on registrations by the GP. We know,

however, that this prevalence on the basis of registrations is generally an underestimation. The

prevalence as mentioned in the general practice guidelines6 is, for example, lower than the

prevalence at population level. Because almost everyone in the Netherlands has a GP, the

prevalence in the general practice population should be comparable to the prevalence at population

level. However, patients with depression visit their GP more often than patients without depression.

The prevalence is higher among the patients who come to the consultation hour. A rough guideline

is to double the prevalence found at general population level7.

The prevalence of a mental illness in the setting in which you work is best determined on the basis

of registrations in your own organization. Suppose that about a third of the patients who are

referred to your organization have a depression. If you enter that prevalence in the flowchart as in

figure 2 and keep the same sensitivity and specificity, the probability of depression of a random

patient who scores positively on the BDI is increased to two thirds.

Conclusion

Ignoring Bayes’ theorem leads to overdiagnosis mainly of disorders that do not occur so often (with

a low pre-test probability). This can be clearly understood by looking at the flowcharts. Because

the 'no disorder' part becomes very large - even with very good specificity - the post-test

probability will remain low. This can have major consequences for the treatment policy and thus

the course of the symptoms of a patient. We therefore strongly recommend remembering Bayes'

principle, namely that given a positive test result the probability of a disorder depends on the

population and setting in which is tested. If you have forgotten Bayes’ formula, do not panic. The

calculation with the absolute numbers is easy to do. The steps are summarized in the box.

Calculating using a group of 100 or 1000 patients is very illuminating and provides quick insight

into the probability of a disorder given a score on a specific test.

1. Determine the population to which the person tested belongs and the setting in which the test

was taken

2. Find the prevalence of the disorder that is being tested in that population and setting

3. Find the sensitivity and specificity of the test in the manual of the test

4. Enter the values in a flowchart or crosstabulation as in figure 2

5. Calculate the probability of the presence of the disorder given a positive test result, or the

probability of absence of the disorder given a negative test result.

6

References

1

Cameron, I.M, Cardy, A., Crawford, J.R. et al. (2011). Measuring depression severity in general practice:

discriminatory performance of the PHQ-9,HADS-D, and BDI-II. British Journal of General Practice, July, 419-426,

DOI:10.3399/bjgp11X583209

2

Beck, A.T., Steer, R.A., Ball, R., et al. (1996). Comparison of Beck Depression Inventories-IA and -II in

psychiatric outpatients. J Pers Asses 67(3): 588–597.

3

Gigerenzer, G. (2011) What are natural frequencies? Doctors need to find better ways to communicate risk to

patients. British Medical Journal 343:d6386.

4

De Graaf, R. et al. (2012). Prevalentie van psychische aandoeningen en trends van 1996 tot 2009; resultaten

van NEMESIS-2. Tijdschrift voor Psychiatrie, 54; 27-38.

5

http://www.tijdschriftvoorpsychiatrie.nl/issues/449/articles/9311

6

https://www.nhg.org/standaarden/volledig/nhg-standaard-depressie-tweede-herziening#idm10758112

7

Űstün, T.B., Sartorius, N. (eds). Mental illness in general health care. An international study. Chichester, John

Wiley & Sons Ltd, 1995.

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