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Extract basic rates from model output

get_rates.Rd

Extract basic rates from model output

Usage

get_rates(
  x,
  time_divisor,
  baseline_t,
  age_divisor,
  scaler,
  treatment_scaler,
  baseline_treatment,
  aggregate_age = FALSE
)

Arguments

x

Input data.frame

time_divisor

Aggregation level. Default = 1 (no aggregation). Setting to 365 would allow annual aggregation, 30 monthly, 7 weekly etc.

baseline_t

A baseline time to add to the time output

age_divisor

Aggregation level. For example setting to 365 will return age units in years

scaler

Scaler for severe cases to deaths. The original fitted scaler for P. falciparum is 0.215. See Griffin et al (2016).

treatment_scaler

The impact of treatment coverage on progression to severe disease and death. A highly uncertain parameter, the analysis by Griffin et al (2016) sampled from a uniform diastribution (0, 1).

baseline_treatment

The proportion of uncomplicated malaria cases that are effectively treated historically.

aggregate_age

Aggregate output over age groups