R: Plot three-panel figures for nested partially-latent model...

plot_panels {baker}

R Documentation

Plot three-panel figures for nested partially-latent model results

Description

plot_panels() visualizes the model outputs for communicating how the data inform final latent disease status (etiology). It works for singleton or combo etiologies.

Usage

plot_panels(
  DIR_NPLCM,
  slices = "all",
  bg_color = list(BrS = "lavenderblush", SS = "mistyrose", pie = "antiquewhite"),
  select_latent = NULL,
  exact = TRUE,
  SS_upperlimit = 1,
  eti_upperlimit = 1,
  silent = TRUE,
  ref_eti0 = NULL,
  is_plot = TRUE
)

Arguments

`DIR_NPLCM`	File path to the folder containing posterior samples
`slices`	DEFAULT is "all" - to plot all measurements; Otherwise, one can specify a list: `list(MBS=c(1,3),MSS=1)` means to plot the 1st and 3rd slice of BrS measurements and 1st of SS measurement.
`bg_color`	A list with names "BrS", "SS", "pie" to specify background colors. The current default is `list(BrS = "lavenderblush", SS = "mistyrose", pie="antiquewhite")`. If no background is intended, specify as NULL or for a particular measurement, e.g., `BrS = NULL`.
`select_latent`	a vector of character strings representing latent status. It is used for just plotting a subset of latent status. For example, you can specify `select_latent = "HINF"` to plot all latent status information relevant to `"HINF"`.
`exact`	Default is `TRUE` to use `select_latent` as exact names of causes. If you want to specify a name and plot all single or combo causes with that name, specify it to be `FALSE`.
`SS_upperlimit`	The upper limit of horizontal bar for the silver-standard subpanel (the middle panel). The default value is .25.
`eti_upperlimit`	The upper limit of horizontal bar for the etiology posterior subpanel (the rightmost panel). The default value is .4
`silent`	Default is TRUE to not print any warning messages; FALSE otherwise.
`ref_eti0`	reference quantiles and means; a list: pEti_ref_q, pEti_ref_mean_ord
`is_plot`	default to `TRUE` for plotting only; set to `FALSE` if to get summary.

Details

Missing data for BrS or SS are dropped when calculating observed measurement positive rates

Value