antibody_model: Overall model function, fast implementation

In adamkucharski/serosolver: Inference Framework for Serological Data

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,
  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,
  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

Value

NumericVector of predicted antibody levels for each entry in biomarker_id_indices

adamkucharski/serosolver documentation built on April 13, 2024, 10:24 a.m.