serocalculator (version 1.3.0)

sim.cs.multi: Simulate multiple data sets

Description

Simulate multiple data sets

Usage

sim.cs.multi(
  nclus = 10,
  lambdas = c(0.05, 0.1, 0.15, 0.2, 0.3),
  num_cores = max(1, parallel::detectCores() - 1),
  rng_seed = 1234,
  renew.params = TRUE,
  add.noise = TRUE,
  verbose = FALSE,
  ...
)

Value

a tibble::tibble()

Arguments

nclus

number of clusters

lambdas

#incidence rate, in events/person*year

num_cores

number of cores to use for parallel computations

rng_seed

starting seed for random number generator, passed to rngtools::RNGseq()

renew.params

whether to generate a new parameter set for each infection

• renew.params = TRUE generates a new parameter set for each infection

• renew.params = FALSE keeps the one selected at birth, but updates baseline y0

add.noise

a logical() indicating whether to add biological and measurement noise

verbose

whether to report verbose information

...

Arguments passed on to sim.cs

lambda

a numeric() scalar indicating the incidence rate (in events per person-years)

n.smpl

number of samples to simulate

age.rng

age range of sampled individuals, in years

age.fx

specify the curve parameters to use by age (does nothing at present?)

antigen_isos

Character vector with one or more antibody names. Values must match curve_params.

n.mc

how many MCMC samples to use:

• when n.mc is in 1:4000 a fixed posterior sample is used

• when n.mc = 0, a random sample is chosen

noise_limits

biologic noise distribution parameters

format

a character() variable, containing either:

• "long" (one measurement per row) or

• "wide" (one serum sample per row)

curve_params

a data.frame() containing MCMC samples of parameters from the Bayesian posterior distribution of a longitudinal decay curve model. The parameter columns must be named:

• antigen_iso: a character() vector indicating antigen-isotype combinations

• iter: an integer() vector indicating MCMC sampling iterations

• y0: baseline antibody level at $t=0$ ($y(t=0)$)

• y1: antibody peak level (ELISA units)

• t1: duration of infection

• alpha: antibody decay rate (1/days for the current longitudinal parameter sets)

• r: shape factor of antibody decay