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Find the maximum likelihood estimate of the incidence rate parameter

Source: R/est.incidence.R
est.incidence.Rd

This function models seroincidence using maximum likelihood estimation; that is, it finds the value of the seroincidence parameter which maximizes the likelihood (i.e., joint probability) of the data.

Usage

est.incidence(
  pop_data,
  curve_params,
  noise_params,
  antigen_isos = pop_data$antigen_iso %>% unique(),
  lambda_start = 0.1,
  stepmin = 1e-08,
  stepmax = 3,
  verbose = FALSE,
  build_graph = FALSE,
  print_graph = build_graph & verbose,
  ...
)

Arguments

pop_data

a data.frame with cross-sectional serology data per antibody and age, and additional columns

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

noise_params

a data.frame() (or tibble::tibble()) containing the following variables, specifying noise parameters for each antigen isotype:

  • antigen_iso: antigen isotype whose noise parameters are being specified on each row

  • nu: biological noise

  • eps: measurement noise

  • y.low: lower limit of detection for the current antigen isotype

  • y.high: upper limit of detection for the current antigen isotype

antigen_isos

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

lambda_start

starting guess for incidence rate, in years/event.

stepmin

A positive scalar providing the minimum allowable relative step length.

stepmax

a positive scalar which gives the maximum allowable scaled step length. stepmax is used to prevent steps which would cause the optimization function to overflow, to prevent the algorithm from leaving the area of interest in parameter space, or to detect divergence in the algorithm. stepmax would be chosen small enough to prevent the first two of these occurrences, but should be larger than any anticipated reasonable step.

verbose

logical: if TRUE, print verbose log information to console

build_graph

whether to graph the log-likelihood function across a range of incidence rates (lambda values)

print_graph

whether to display the log-likelihood curve graph in the course of running est.incidence()

...

Arguments passed on to stats::nlm

typsize

an estimate of the size of each parameter at the minimum.

fscale

an estimate of the size of f at the minimum.

ndigit

the number of significant digits in the function f.

gradtol

a positive scalar giving the tolerance at which the scaled gradient is considered close enough to zero to terminate the algorithm. The scaled gradient is a measure of the relative change in f in each direction p[i] divided by the relative change in p[i].

iterlim

a positive integer specifying the maximum number of iterations to be performed before the program is terminated.

check.analyticals

a logical scalar specifying whether the analytic gradients and Hessians, if they are supplied, should be checked against numerical derivatives at the initial parameter values. This can help detect incorrectly formulated gradients or Hessians.

Value

a "seroincidence" object, which is a stats::nlm() fit object with extra meta-data attributes lambda_start, antigen_isos, and ll_graph

Examples


library(dplyr)

xs_data <- load_pop_data("https://osf.io/download//n6cp3/")

curves <- load_curve_params("https://osf.io/download/rtw5k/") %>%
  filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG")) %>%
  slice(1:100, .by = antigen_iso) # Reduce dataset for the purposes of this example

noise <- load_noise_params("https://osf.io/download//hqy4v/")

est1 <- est.incidence(
  pop_data = xs_data %>% filter(Country == "Pakistan"),
  curve_params = curves,
  noise_params = noise %>% filter(Country == "Pakistan"),
  antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
  iterlim = 5 # limit iterations for the purpose of this example
)

summary(est1)
#> # A tibble: 1 × 10
#>   est.start incidence.rate      SE CI.lwr CI.upr coverage log.lik iterations
#>       <dbl>          <dbl>   <dbl>  <dbl>  <dbl>    <dbl>   <dbl>      <int>
#> 1       0.1          0.142 0.00725  0.128  0.156     0.95  -2378.          4
#> # ℹ 2 more variables: antigen.isos <chr>, nlm.convergence.code <ord>