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baker (version 1.0.4)

plot_case_study: visualize the PERCH etiology regression with a continuous covariate

Description

This function is specifically designed for PERCH data, e.g., (NB: dealing with NoA, multiple-pathogen causes, other continuous covariates? also there this function only plots the first slice - so generalization may be useful - give users an option to choose slice s; currently default to the first slice.)

Usage

plot_case_study(
  DIR_NPLCM,
  stratum_bool = stratum_bool,
  bugs.dat = NULL,
  slice = 1,
  RES_NPLCM = NULL,
  do_plot = TRUE,
  do_rug = FALSE,
  return_metric = TRUE
)

Value

A figure of etiology regression curves and some marginal positive rate assessment of model fit; See example for the legends.

Arguments

DIR_NPLCM

File path to the folder containing posterior samples

stratum_bool

integer; for this function, indicates which strata to plot

bugs.dat

The posterior samples (loaded into the environment to save time) -> default is NULL

slice

integer; specifies which slice of bronze-standard data to visualize; Default to 1.

RES_NPLCM

pre-read res_nplcm; default to NULL.

do_plot

TRUE for plotting

do_rug

TRUE for plotting

return_metric

TRUE for showing overall mean etiology, quantiles, s.d., and if truth$Eti is supplied, coverage, bias, truth and integrated mean squared errors (IMSE).