Biphasic antibody boosting-waning model with cross-reactive strains

Biphasic antibody boosting-waning model with cross-reactivity between strains. This model assumes that for each exposure there is a set of long-term boost, long-term boost waning, short-term boost, and short-term boost waning parameters describing antibody kinetics against the infecting strain (i.e., for exposure_id==biomarker_id). The model loops through each exposure type and reduces the amount of boosting as a function of cross-reactivity, which is determined by a proportion given in the biomarker_map data frame as the value variable.

antibody_model_biphasic_cross_reactivity(
  i,
  t1,
  b,
  immune_histories,
  biomarker_states,
  kinetics_parameters,
  biomarker_map,
  ...
)

Arguments

i

individual

t1

time

b

biomarker

immune_histories

An array of immune histories across all individuals, time steps and exposure IDs

biomarker_states

An array of biomarker states (biomarker quantities) across all individuals, time steps and biomarker IDs

kinetics_parameters

A tibble of parameters needed for the antibody kinetics model for all biomarkers

biomarker_map

A table specifying the relationship between exposure IDs and biomarker IDs

...

Additional arguments

Value

A biomarker quantity is returned

See also

Other antibody_models: antibody_model_biphasic_cpp(), antibody_model_biphasic(), antibody_model_monophasic_cpp(), antibody_model_monophasic_cross_reactivity(), antibody_model_monophasic(), antibody_model_typhoid()

Examples

tmp_pars <- list()
## Set up simple model_pars table for this antibody model
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
model_pars_tmp <- example_model_pars_biphasic %>% reformat_biomarker_map() %>% 
mutate(biomarker_id = exposure_id)
## Simulate one infection with exposure ID 1 at t=1
tmp_pars[[1]] <- draw_parameters_fixed_fx(1,1,1,NULL, NULL, model_pars_tmp)
 
## Set up a simple biomarker map for cross-reactivity
biomarker_map = tidyr::expand_grid(exposure_id=1:2, biomarker_id=1:2) %>% 
mutate(value = if_else(exposure_id==biomarker_id, 1, 0.5))
antibody_model_biphasic_cross_reactivity(1,1,1,example_immune_histories_wide, 
example_biomarker_states_wide, tmp_pars, biomarker_map)
#> [1] 0.75