Table 1.
The apparent prevalence estimates for each species in the study based on the individual and cumulative test results from the T. brucei s.l. specific PCR, T. brucei s.l. ITS-PCR.
Table 2.
Test cross tabulation by species (T1 = T. brucei s.l. specific PCR; T2 = T. brucei s.l. ITS-PCR).
Figure 1.
Probability density plots for each test parameter estimate for the T. brucei s.l. specific PCR (sensitivity = Se[1]; specificity = Sp[1]), T. brucei s.l. ITS-PCR (sensitivity = Se[2]; specificity = Sp[2]) and the adjusted prevalence estimates from the Hui-Walter model assuming conditional independence for cattle (p[1]), goats (p[2]), pigs (p[3]) and sheep (p[4]). The x axes give the parameter estimate and the y axis the relative likelihood of it taking that value.
Figure 2.
MCMC history plots for each parameter of the Hui-Walter model for parameter estimates and true prevalence estimates for the T. brucei s.l. specific PCR (sensitivity = Se[1]; specificity = Sp[1]), T. brucei s.l. ITS-PCR (sensitivity = Se[2]; specificity = Sp[2]), cattle (p[1]), goats (p[2]), pigs (p[3]) and sheep (p[4]). The plots record every 10th sample from 500,000 iterations and the x axis is the sequence of iterations and the y axis the parameter value from that iteration.
Table 3.
Parameter estimates (and Bayesian 95% credibility intervals, BCI) for the T. brucei s.l. specific PCR (Se1 and Sp1), T. brucei s.l. ITS-PCR (Se2 and Sp2) and adjusted T. brucei s.l. prevalence estimates for cattle (pcattle), goats (pgoats), pigs (ppigs) and sheep (psheep) from the Hui-Walter model assuming conditional independence.
Figure 3.
The positive (PPV) and negative predictive value (NPV) of the T. brucei s.l. specific PCR and the ITS PCR over a range of prevalence of T. brucei s.l. PPV is the positive predictive value of the test at a given prevalence i.e. how likely the animal is to have the pathogen given that it has a positive test result. NPV is the negative predictive value of the test at a given prevalence i.e. how likely is an animal not to have the pathogen given that it had a negative test result.
Table 4.
Estimated predictive values of the two tests in the four sub-populations (Test 1 = T. brucei s.l. specific PCR; test 2 = T. brucei s.l. ITS-PCR).
Figure 4.
Approximate sample sizes for a simple random survey to estimate infection prevalence using the two tests. The samples sizes are calcualted to estimate prevalence with a 95% confidence interval for an absolute precision of +/− 5%.