graph.loglik {serocalculator}

Graph log-likelihood of data

Description

Graph log-likelihood of data

Usage

graph.loglik(
  pop_data,
  curve_params,
  noise_params,
  antigen_isos,
  x = 10^seq(-3, 0, by = 0.1),
  highlight_points = NULL,
  highlight_point_names = "highlight_points",
  log_x = FALSE,
  previous_plot = NULL,
  curve_label = paste(antigen_isos, collapse = " + "),
  ...
)

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 listing one or more antigen isotypes. Values must match pop_data.

x

sequence of lambda values to graph

highlight_points

a possible highlighted value

highlight_point_names

labels for highlighted points

log_x

should the x-axis be on a logarithmic scale (TRUE) or linear scale (FALSE, default)?

previous_plot

if not NULL, the current data is added to the existing graph

curve_label

if not NULL, add a label for the curve

...

Arguments passed on to log_likelihood

verbose

logical: if TRUE, print verbose log information to console

Value

a ggplot2::ggplot()

Examples

library(dplyr)
library(tibble)

# Load cross-sectional data
xs_data <- load_pop_data("https://osf.io/download//n6cp3/") %>%
  clean_pop_data()

# Load curve parameters and subset for the purposes of this example
dmcmc <- load_curve_params("https://osf.io/download/rtw5k/") %>%
  filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG")) %>%
  slice(1:100, .by = antigen_iso)

# Load noise parameters
cond <- tibble(
  antigen_iso = c("HlyE_IgG", "HlyE_IgA"),
  nu = c(0.5, 0.5),                          # Biologic noise (nu)
  eps = c(0, 0),                             # M noise (eps)
  y.low = c(1, 1),                           # Low cutoff (llod)
  y.high = c(5e6, 5e6))                      # High cutoff (y.high)

# Graph the log likelihood
lik_HlyE_IgA <- graph.loglik(
  pop_data = xs_data,
  curve_params = dmcmc,
  noise_params = cond,
  antigen_isos = "HlyE_IgA",
  log_x = TRUE
)

lik_HlyE_IgA