Estimate true prevalence from individuals samples
Description
Bayesian estimation of true prevalence from apparent prevalence obtained by testing individual samples.
Usage
1 2 3 
Arguments
x 
The apparent number of positive samples 
n 
The sample size 
SE, SP 
The prior distribution for sensitivity (SE) and specificity SP); see 'Details' below for specification of these distributions 
prior 
The parameters of the prior Beta distribution for true
prevalence; defaults to 
nchains 
The number of chains used in the estimation process;

burnin 
The number of discarded model iterations; defaults to 10,000 
update 
The number of withheld model iterations; defaults to 10,000 
verbose 
Logical flag, indicating if JAGS process output should be
printed to the R console; defaults to 
Details
truePrev
calls on JAGS/rjags to
estimate the true prevalence from the apparent prevalence in a Bayesian
framework. The default model, in BUGS language, is given below. To see the
actual fitted model, see the model slot of the
prevobject.
1 2 3 4 5 6 7 8  model {
x ~ dbin(AP, n)
AP < SE * TP + (1  SP) * (1  TP)
# SE ~ userdefined (see below)
# SP ~ userdefined (see below)
TP ~ dbeta(prior[1], prior[2])
}

The test sensitivity (SE
) and specificity (SP
) can be
specified, independently, as one of "fixed"
, "uniform"
,
"beta"
, "pert"
, or "betaexpert"
, with "fixed"
as the default.
Distribution parameters can be specified in a named list()
as follows:
Fixed:
list(dist = "fixed", par)
Uniform:
list(dist = "uniform", min, max)
Beta:
list(dist = "beta", alpha, beta)
BetaPERT:
list(dist = "pert", method, a, m, b, k)
'method'
must be"classic"
or"vose"
;
'a'
denotes the pessimistic (minimum) estimate,'m'
the most likely estimate, and'b'
the optimistic (maximum) estimate;
'k'
denotes the scale parameter.
SeebetaPERT
for more information on BetaPERT parametrization.BetaExpert:
list(dist = "betaexpert", mode, mean, lower, upper, p)
'mode'
denotes the most likely estimate,'mean'
the mean estimate;
'lower'
denotes the lower bound,'upper'
the upper bound;
'p'
denotes the confidence level of the expert.
Onlymode
ormean
should be specified;lower
andupper
can be specified together or alone.
SeebetaExpert
for more information on BetaExpert parametrization.
For Uniform, Beta and BetaPERT distributions, BUGSstyle shorthand notation is also allowed:
Uniform:
~dunif(min, max)
Beta:
~dbeta(alpha, beta)
BetaPERT:
~dpert(min, mode, max)
Value
An object of class prev
.
Note
Markov chain Monte Carlo sampling in truePrev
is performed by
JAGS (Just Another Gibbs Sampler) through the
rjags package. JAGS can be downloaded from
http://sourceforge.net/projects/mcmcjags/.
Author(s)
Brecht Devleesschauwer <brechtdv@gmail.com>
References
Speybroeck N, Devleesschauwer B, Joseph L, Berkvens D (2013) Misclassification errors in prevalence estimation: Bayesian handling with care. Int J Public Health 58:791795
Online Shiny application: http://users.ugent.be/~bdvleess/R/prevalence/shiny/
See Also
coda for various functions that can be applied to the prev@mcmc
object
truePrevMulti
: estimate true prevalence from apparent prevalence obtained by testing individual samples with multiple tests, using a conditional probability scheme
truePrevMulti2
: estimate true prevalence from apparent prevalence obtained by testing individual samples with multiple tests, using a covariance scheme
truePrevPools
: estimate true prevalence from apparent prevalence obtained by testing pooled samples
betaPERT
: calculate the parameters of a BetaPERT distribution
betaExpert
: calculate the parameters of a Beta distribution based on expert opinion
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  ## Taenia solium cysticercosis in Nepal
## 142 positives out of 742 pigs sampled
## Model SE and SP based on literature data
## Sensitivity ranges uniformly between 60% and 100%
## Specificity ranges uniformly between 75% and 100%
#> BUGSstyle:
truePrev(x = 142, n = 742,
SE = ~dunif(0.60, 1.00), SP = ~dunif(0.75, 1.00))
#> liststyle:
SE < list(dist = "uniform", min = 0.60, max = 1.00)
SP < list(dist = "uniform", min = 0.75, max = 1.00)
truePrev(x = 142, n = 742, SE = SE, SP = SP)
## Model SE and SP based on expert opinions
## Sensitivity lies in between 60% and 100%; most likely value is 90%
## Specificity is with 95% confidence larger than 75%; most likely value is 90%
SE < list(dist = "pert", a = 0.60, m = 0.90, b = 1.00)
SP < list(dist = "betaexpert", mode = 0.90, lower = 0.75, p = 0.95)
truePrev(x = 142, n = 742, SE = SE, SP = SP)
## Model SE and SP as fixed values (each 90%)
truePrev(x = 142, n = 742, SE = 0.90, SP = 0.90)
