run_exp_camostat: estimate parameters for the different models in the study

In ada-w-yan/deltaomicron1: Fit model to Delta and Omicron growth curves with and without Camostat

estimate parameters for the different models in the study

Description

estimate parameters for the different models in the study

Usage

run_exp_camostat(
  save_dir,
  strain,
  PCR = FALSE,
  n_L = 1,
  n_I = 1,
  camostat_only = FALSE,
  different_eclipse = FALSE,
  reparameterise = FALSE,
  k1_endosomal_limit = FALSE,
  mvr = TRUE,
  length_run = 2,
  run_flag = TRUE
)

Arguments

save_dir	string ending in "/": directory to save results in
strain	character vector. names of strains.
PCR	logical. whether to include PCR data (TRUE) or only plaque data (FALSE)
camostat_only	logical. Whether to fit camostat data only (TRUE) or but no drug and camostat data (FALSE)
different_eclipse	logical. if TRUE, fit different eclipse phases for the pathways
k1_endosomal_limit	logical. if TRUE, 0 <= k1_endosomal/k1_tmprss2 <= 1
mvr	logical. If TRUE, use multivariate proposal, if FALSE, use univariate proposal.
length_run	integer. If length == 1, short run (for testing purposes); if length == 2, normal run; if length = 3, extra long run. otherwise, run until convergence
run_flag	logial. if TRUE, run and postprocess; if FALSE, postprocess only
reparameterise:	logical. if FALSE, use beta, p etc, if TRUE, use probability of infection (beta T_0) / c, burst size, delta, c

Value

NULL (results saved to file)

ada-w-yan/deltaomicron1 documentation built on June 24, 2022, 5:41 a.m.