Posterior Predictive Checks for mvgam models

Perform unconditional posterior predictive checks with the help of the bayesplot package.

Usage

# S3 method for class 'mvgam'
pp_check(
  object,
  type,
  ndraws = NULL,
  prefix = c("ppc", "ppd"),
  group = NULL,
  x = NULL,
  newdata = NULL,
  ...
)

Arguments

object: An object of class mvgam.
type: Type of the ppc plot as given by a character string. See PPC for an overview of currently supported types. You may also use an invalid type (e.g. type = "xyz") to get a list of supported types in the resulting error message.
ndraws: Positive integer indicating how many posterior draws should be used. If NULL all draws are used. If not specified, the number of posterior draws is chosen automatically. Ignored if draw_ids is not NULL.
prefix: The prefix of the bayesplot function to be applied. Either `"ppc"` (posterior predictive check; the default) or `"ppd"` (posterior predictive distribution), the latter being the same as the former except that the observed data is not shown for `"ppd"`.
group: Optional name of a factor variable in the model by which to stratify the ppc plot. This argument is required for ppc *_grouped types and ignored otherwise.
x: Optional name of a variable in the model. Only used for ppc types having an x argument and ignored otherwise.
newdata: Optional dataframe or list of test data containing the variables included in the linear predictor of formula. If not supplied, predictions are generated for the original observations used for the model fit.
...: Further arguments passed to predict.mvgam as well as to the PPC function specified in type.

Value

A ggplot object that can be further customized using the ggplot2 package.

Details

Unlike the conditional posterior checks provided by ppc, This function computes unconditional posterior predictive checks (i.e. it generates predictions for fake data without considering the true observations associated with those fake data). For a detailed explanation of each of the ppc functions, see the PPC documentation of the bayesplot package.

Author

Nicholas J Clark

Examples

# \donttest{
simdat <- sim_mvgam(seasonality = 'hierarchical')
mod <- mvgam(y ~ series +
              s(season, bs = 'cc', k = 6) +
              s(season, series, bs = 'fs', k = 4),
            data = simdat$data_train,
            chains = 2,
            silent = 2)
#> Warning: model has repeated 1-d smooths of same variable.
#> Warning: model has repeated 1-d smooths of same variable.
#> Warning: model has repeated 1-d smooths of same variable.
#> In file included from stan/lib/stan_math/stan/math/prim/prob/von_mises_lccdf.hpp:5,
#>                  from stan/lib/stan_math/stan/math/prim/prob/von_mises_ccdf_log.hpp:4,
#>                  from stan/lib/stan_math/stan/math/prim/prob.hpp:359,
#>                  from stan/lib/stan_math/stan/math/prim.hpp:16,
#>                  from stan/lib/stan_math/stan/math/rev.hpp:16,
#>                  from stan/lib/stan_math/stan/math.hpp:19,
#>                  from stan/src/stan/model/model_header.hpp:4,
#>                  from C:/Users/uqnclar2/AppData/Local/Temp/RtmpotLup8/model-9e8cfe450a0.hpp:2:
#> stan/lib/stan_math/stan/math/prim/prob/von_mises_cdf.hpp: In function 'stan::return_type_t<T_x, T_sigma, T_l> stan::math::von_mises_cdf(const T_x&, const T_mu&, const T_k&)':
#> stan/lib/stan_math/stan/math/prim/prob/von_mises_cdf.hpp:194: note: '-Wmisleading-indentation' is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers
#>   194 |       if (cdf_n < 0.0)
#>       | 
#> stan/lib/stan_math/stan/math/prim/prob/von_mises_cdf.hpp:194: note: adding '-flarge-source-files' will allow for more column-tracking support, at the expense of compilation time and memory

# Use pp_check(mod, type = "xyz") for a list of available plot types

# Default is a density overlay for all observations
pp_check(mod)
#> Using 10 posterior draws for ppc type 'dens_overlay' by default.


# Rootograms particularly useful for count data
pp_check(mod, type = "rootogram")
#> Using all posterior draws for ppc type 'rootogram' by default.


# Grouping plots by series is useful
pp_check(mod, type = "bars_grouped",
        group = "series", ndraws = 50)

pp_check(mod, type = "ecdf_overlay_grouped",
        group = "series", ndraws = 50)

pp_check(mod, type = "stat_freqpoly_grouped",
        group = "series", ndraws = 50)
#> Note: in most cases the default test statistic 'mean' is too weak to detect anything of interest.
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Custom functions accepted
prop_zero <- function(x) mean(x == 0)
pp_check(mod, type = "stat", stat = "prop_zero")
#> Using all posterior draws for ppc type 'stat' by default.
#> Error in get(as.character(FUN), mode = "function", envir = envir): object 'prop_zero' of mode 'function' was not found
pp_check(mod, type = "stat_grouped",
        stat = "prop_zero",
        group = "series")
#> Using all posterior draws for ppc type 'stat_grouped' by default.
#> Error in get(as.character(FUN), mode = "function", envir = envir): object 'prop_zero' of mode 'function' was not found

# Some functions accept covariates to set the x-axes
pp_check(mod, x = "season",
        type = "ribbon_grouped",
        prob = 0.5,
        prob_outer = 0.8,
        group = "series")
#> Using all posterior draws for ppc type 'ribbon_grouped' by default.


# Many plots can be made without the observed data
pp_check(mod, prefix = "ppd")
#> Using 10 posterior draws for ppc type 'dens_overlay' by default.

# }

Posterior Predictive Checks for `mvgam` models