Pooled Prevalence

Simulate sampling for fixed pool size and uncertain test sensitivity and specificity

Design parameters:

Assumed true prevalence

Estimated test sensitivity

Estimated test specificity

Sample size for estimating sensitivity

Sample size for estimating specificity

True test sensitivity

True test specificity

Desired confidence level

0.9 0.95 0.98 0.99

Simulation details:

Number of iterations

1,000 2,000 5,000 10,000

Paste data in the space below. Data columns can be in any order but must include columns labeled "Poolsize" and "Pools". A header row specifying column names must also be included.

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Introduction

This utility simulates sampling and prevalence estimation for alternative pooling strategies for assumed values of prevalence and test sensitivity and specificity and for a specified level of confidence. The program runs multiple iterations of sampling and estimation and calculates the mean prevalence and estimated bias across all iterations. See the User Guide for more details. See demonstration analysis.

This method estimates prevalence using a method that assumes that test sensitivity and specificity are both uncertain and with the level of uncertainty determined by the sample size used to estimate the values. The program also allows for alternative the estimates of the true sensitivity and specificity of the test to be entered, allowing assessment of the potential impact of inaccurate estimates of sensitivity and specificity on the resulting prevalence estimate.

Input values

Required inputs for this program are:

• assumed true prevalence of infection - between 0 and 1;
• estimated test sensitivity and specificity - between 0 and 1;
• sample sizes used for estimating test sensitivity and specificity (for second method only) - a positive integer;
• true test sensitivity and specificity - between 0 and 1;
• the desired level of confidence - between 0 and 1;
• the number of iterations to simulate - a positive integer; and
• the size and number of pools to be tested for each strategy to be simulated. This data should be copied and pasted from a spreadsheet format as described below.

Outputs

Outputs are summarised across all iterations for each strategy entered and presented in a summary table. The main outputs are:

• mean prevalence;
• minimum and maximum prevalence estimates;
• mean bias in the estimated prevalence;
• mean (asymptotic) confidence interval width;
• mean standard error of the estimated prevalence;
• mean squared error of the estimated prevalence (mean variance plus the square of the mean bias);
• relative bias as a proportion of the mean estimated (apparent) prevalence (AP);
• relative bias as a proportion of the specified design (true) prevalence (TP);
• squared mean bias as a proportion of the mean squared error; and
• proportion of "valid" estimates, where the confidence interval for the estimated prevalence contains the true (design) prevalence.

Note

Data for pool sizes and associated numbers of pools tested should be pasted into the data submission area. You can enter any number of scenarios to simulate, with a new row required for each scenario. You must enter at least two columns of data, labeled "PoolSize" and "Pools". Include a header row containing the names.