antibody_model: Overall model function, fast implementation
In seroanalytics/serosolver: Inference Framework for Serological Data

antibody_model

R Documentation

Overall model function, fast implementation

Description

Overall model function, fast implementation

Usage

antibody_model(
  theta,
  unique_theta_indices,
  unique_biomarker_groups,
  infection_history_mat,
  infection_history_mat_indices,
  indiv_theta_groups,
  possible_exposure_times,
  possible_exposure_times_indices,
  sample_times,
  type_data_start,
  biomarker_groups,
  sample_data_start,
  antibody_data_start,
  nrows_per_sample,
  biomarker_id_indices,
  start_level_indices,
  starting_antibody_levels,
  births,
  antigenic_map_long,
  antigenic_map_short,
  antigenic_distances,
  timevarying_groups = FALSE,
  boost_before_infection = FALSE
)

Arguments

`theta`	NumericVector, the named vector of model parameters
`infection_history_mat`	IntegerMatrix, the matrix of 1s and 0s showing presence/absence of infection for each possible time for each individual.
`possible_exposure_times`	NumericVector, the time periods that the infection history vector corresponds to
`possible_exposure_times_indices`	IntegerVector, which entry in the melted antigenic map that each possible infection time corresponds to
`sample_times`	NumericVector, the times that each blood sample was taken
`type_data_start`	IntegerVector, one entry for each unique individual. Each entry gives the starting index for each individual of the data frame 'unique(antibody_data[,c("individual","biomarker_group")])'.
`biomarker_groups`	IntegerVector, result of 'unique(antibody_data[,c("individual","biomarker_group")])$biomarker_group'
`sample_data_start`	IntegerVector, one entry for each unique individual and observation type combination. Each entry dictates how many indices through sample_times to iterate per individual and observation type (ie. how many sample times does each individual have?)
`antibody_data_start`	IntegerVector, How many cumulative rows in the antibody data correspond to each unique individual and observation type combination?
`nrows_per_sample`	IntegerVector, one entry per sample taken. Dictates how many entries to iterate through cum_nrows_per_individual_in_data for each sampling time considered
`biomarker_id_indices`	IntegerVector, the indices of all measured biomarkers in the melted antigenic map, with one entry per measured biomarker
`antigenic_map_long`	arma::mat, the collapsed cross reactivity map for long term boosting, after multiplying by cr_long see `create_cross_reactivity_vector`
`antigenic_map_short`	arma::mat, the collapsed cross reactivity map for short term boosting, after multiplying by cr_short, see `create_cross_reactivity_vector`
`antigenic_distances`	NumericVector, the collapsed cross reactivity map giving euclidean antigenic distances, see `create_cross_reactivity_vector`
`boost_before_infection`	bool to indicate if calculated antibody level for that time should be before the infection has occurred, used to calculate antibody-mediated immunity