Estimation of Pathogen Prevalence in Pooled Samples Using MaximumLikelihood Methods and Open-Source Software

摘要

We provide the computer program code to estimate pathogen prevalence and calculate confidence intervals for estimates based on maximum likelihood methods for the open-source statistical and graphics package R and a commercially licensed statistical package, the Statistical Analysis System (SAS). We correct a previously published SAS program to allow use of newer versions of the SAS software and provide a second SAS program that will work in either version of SAS. All of the programs allow users to calculate prevalence from any number of pooled samples representing different numbers of individuals, and two of these programs allow users to make estimates from data pools that are entirely test- positive or test-negative.