convertPrevalence {malariaAtlas}

convert prevalences from one age range to another

Description

convert prevalences from one age range to another

Usage

convertPrevalence(
  prevalence,
  age_min_in,
  age_max_in,
  age_min_out = rep(2, length(prevalence)),
  age_max_out = rep(9, length(prevalence)),
  parameters = "Pf_Smith2007",
  sample_weights = NULL
)

Arguments

prevalence

Vector of prevalence values

age_min_in

Vector of minimum ages sampled

age_max_in

Vector maximum ages sampled.

age_min_out

Length 1 numeric or vector of same length as prevalence given the required age range upper bound

age_max_out

Length 1 numeric or vector of same length as prevalence given the required age range lower bound

parameters

Specifies the set of parameters to use in the model. This can either be "Pf_Smith2007" to use the parameters for *Plasmodium falciparum* defined in that paper, "Pv_Gething2012" for the *P. vivax* parameters used in that paper, or a user-specified vector givng the values of parameters 'b', 's', 'c' and 'alpha', in that order. If specified,

sample_weights

Must be a vector of length 85 giving the sample weights for each age category (the proportion of the population in that age category) . If 'NULL', The sample weights used in Smith et al. 2007 are used.

References

Smith, D. L. et al. Standardizing estimates of the Plasmodium falciparum parasite rate. Malaria Journal 6, 131 (2007).

Gething, Peter W., et al. "A long neglected world malaria map: Plasmodium vivax endemicity in 2010." PLoS neglected tropical diseases 6.9 (2012): e1814.

Code written by Nick Golding and Dave Smith

Examples

# Convert from prevalence 2 to 5 to prevalence 2 to 10
pr2_10 <- convertPrevalence(0.1, 2, 5, 2, 10)

# Convert many surveys all to 2 to 10.
pr <- runif(20, 0.1, 0.15)
min_in <- sample(1:5, 20, replace = TRUE)
max_in <- rep(8, 20)
min_out <- rep(2, 20)
max_out <- rep(10, 20)
pr_standardised <- convertPrevalence(pr, min_in, max_in,
                                     min_out, max_out)

plot(pr_standardised, pr)