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Density Plot Diagnostics

Source: R/plot_jags_densitydx.R
plot_jags_dens.Rd

plot_jags_dens() takes a list output from run_mod() to create density plots for each chain run in the mcmc estimation. Defaults will produce every combination of antigen/antibody, parameters, and stratifications, unless otherwise specified. Antigen/antibody combinations and stratifications will vary by analysis. The antibody dynamic curve includes the following parameters:

  • y0 = baseline antibody concentration

  • y1 = peak antibody concentration

  • t1 = time to peak

  • r = shape parameter

  • alpha = decay rate

Usage

plot_jags_dens(
  data,
  iso = unique(data$curve_params$Iso_type),
  param = unique(data$curve_params$Parameter_sub),
  strat = unique(data$curve_params$Stratification)
)

Arguments

data

A list outputted from run_mod().

iso

Specify character string to produce plots of only a specific antigen/antibody combination, entered with quotes. Default outputs all antigen/antibody combinations.

param

Specify character string to produce plots of only a specific parameter, entered with quotes. Options include:

  • alpha = posterior estimate of decay rate

  • r = posterior estimate of shape parameter

  • t1 = posterior estimate of time to peak

  • y0 = posterior estimate of baseline antibody concentration

  • y1 = posterior estimate of peak antibody concentration

strat

Specify character string to produce plots of specific stratification entered in quotes.

Value

A base::list() of ggplot2::ggplot() objects producing density plots for all the specified input.

Author

Sam Schildhauer

Examples

if (!is.element(runjags::findjags(), c("", NULL))) {
  library(runjags)
  library(ggmcmc)
  library(dplyr)

  data <- serodynamics::nepal_sees_jags_post

plot_jags_dens(
    data = data, #A [serodynamics::run_mod()] [list] output.
    iso = "HlyE_IgA", #A [character] string specifying
    #nantigen/antibody of interest.
    param = "alpha",  #A [character] string specifying parameter of
    # interest.
    strat = "typhi")  #A [character] string specifying
    # stratification of interest.
    }
#> Loading required package: dplyr
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
#> Loading required package: tidyr
#> 
#> Attaching package: ‘tidyr’
#> The following object is masked from ‘package:runjags’:
#> 
#>     extract
#> Loading required package: ggplot2
#> $typhi
#> $typhi$HlyE_IgA

#> 
#>