Pooled Prevalence Calculator – Demonstration analyses

Simulate sampling for fixed pool size and assumed perfect test

This program simulates sampling and prevalence estimation for a specified (design) prevalence value and level of confidence. The program runs multiple iterations of sampling, pooling and testing from an infinite population with the specified prevalence, estimates true prevalence assuming a prefect test (using Method 2) for each iteration and calculates the mean prevalence and estimated bias across all iterations. It assumes fixed pool sizes and a test with 100% sensitivity and specificity. Values for the true sensitivity and specificity that are different to the assumed values of 100% can also be entered if desired, to check the importance of the assumption of a perfect test

For this analysis, six alternative pooling strategies were evaluated for the estimation of prevalence in a population with an assumed true prevalence of 0.14 (14%). Pool sizes and numbers of pools were previously estimated to provide 95% confidence of estimating a true prevalence of 0.14 with a precision of 0.055 (see sample size examples). This is equivalent to the observed prevalence and precision when 162 samples from little red flying foxes in Queensland were tested individually, with 22 positive results (H. Field, pers com). The true sensitivity and specificity of the test were both assumed to be 1 (100%), equal to the assumed values for prevalence estimation. Input values, pooling strategies and results are summarised in the tables below:

Input

Value

Method

Fixed pool size and known Se & Sp

Assumed Prevalence

0.14

Assumed Sensitivity

1

Assumed Specificity

1

True Sensitivity

1

True Specificity

1

Confidence

0.95

No. of strategies

6

No. of iterations

1000

Strategy

Pool size

Number of pools

1

2

83

2

3

60

3

4

49

4

5

42

5

10

33

6

20

46

Strategy

Mean prevalence

Minimum prevalence

Maximum prevalence

Mean bias

Mean CI width

Mean Std. Error

Mean Sq. Error

Bias/AP

Bias/TP

Bias/MSE

Proportion Valid

1

0.14101

0.06862

0.23165

0.00101

0.11593

0.02794

0.00079

0.00719

0.00724

0.0013

0.968

2

0.14017

0.06528

0.22434

0.00017

0.1161

0.02787

0.00079

0.00124

0.00124

4e-05

0.96

3

0.14037

0.06782

0.25617

0.00037

0.11666

0.02789

0.00079

0.0026

0.00261

0.00017

0.967

4

0.14123

0.06508

0.23506

0.00123

0.11878

0.02826

0.00081

0.00872

0.0088

0.00187

0.965

5

0.14534

0.06983

1

0.00534

0.12772

0.02923

0.00092

0.03671

0.03811

0.03097

0.972

6

0.23773

0.08374

1

0.09773

0.22332

0.02911

0.01046

0.41109

0.69804

0.91322

0.974

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