convertPrevalence: convert prevalences from one age range to another

In malariaAtlas: An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'

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)

malariaAtlas documentation built on Oct. 27, 2023, 9:07 a.m.