recover_types: Decorate a model fit or sample with data types recovered from...

In tidybayes: Tidy Data and 'Geoms' for Bayesian Models

Decorate a model fit or sample with data types recovered from the input data

Description

Decorate a Bayesian model fit or a sample from it with types for variable and dimension data types. Meant to be used before calling spread_draws() or gather_draws() so that the values returned by those functions are translated back into useful data types.

Usage

recover_types(model, ...)

Arguments

model	A supported Bayesian model fit. Tidybayes supports a variety of model objects; for a full list of supported models, see tidybayes-models.
...	Lists (or data frames) providing data prototypes used to convert columns returned by spread_draws() and gather_draws() back into useful data types. See Details.

Details

Each argument in ... specifies a list or data.frame. The model is decorated with a list of constructors that can convert a numeric column into the data types in the lists in ....

Then, when spread_draws() or gather_draws() is called on the decorated model, each list entry with the same name as the variable or a dimension in variable_spec is a used as a prototype for that variable or dimension — i.e., its type is taken to be the expected type of that variable or dimension. Those types are used to translate numeric values of variables back into useful values (for example, levels of a factor).

The most common use of recover_types is to automatically translate dimensions of a variable that correspond to levels of a factor in the original data back into levels of that factor. The simplest way to do this is to pass in the data frame from which the original data came.

Supported types of prototypes are factor, ordered, and logical. For example:

• if prototypes$v is a factor, the v column in the returned draws is translated into a factor using factor(v, labels=levels(prototypes$v), ordered=is.ordered(prototypes$v)).

• if prototypes$v is a logical, the v column is translated into a logical using as.logical(v).

Additional data types can be supported by providing a custom implementation of the generic function as_constructor.

Value

A decorated version of model.

Author(s)

Matthew Kay

See Also

spread_draws(), gather_draws(), compose_data().

Examples

## Not run: 

library(dplyr)
library(magrittr)
library(rstan)

# Here's an example dataset with a categorical predictor (`condition`) with several levels:
set.seed(5)
n = 10
n_condition = 5
ABC = tibble(
  condition = factor(rep(c("A","B","C","D","E"), n)),
  response = rnorm(n * 5, c(0,1,2,1,-1), 0.5)
)

# We'll fit the following model to it:
stan_code = "
  data {
    int<lower=1> n;
    int<lower=1> n_condition;
    int<lower=1, upper=n_condition> condition[n];
    real response[n];
  }
  parameters {
    real overall_mean;
    vector[n_condition] condition_zoffset;
    real<lower=0> response_sd;
    real<lower=0> condition_mean_sd;
  }
  transformed parameters {
    vector[n_condition] condition_mean;
    condition_mean = overall_mean + condition_zoffset * condition_mean_sd;
  }
  model {
    response_sd ~ cauchy(0, 1);       // => half-cauchy(0, 1)
    condition_mean_sd ~ cauchy(0, 1); // => half-cauchy(0, 1)
    overall_mean ~ normal(0, 5);

    //=> condition_mean ~ normal(overall_mean, condition_mean_sd)
    condition_zoffset ~ normal(0, 1);

    for (i in 1:n) {
      response[i] ~ normal(condition_mean[condition[i]], response_sd);
    }
  }
"

m = stan(model_code = stan_code, data = compose_data(ABC), control = list(adapt_delta=0.99),
  # 1 chain / few iterations just so example runs quickly
  # do not use in practice
  chains = 1, iter = 500)

# without using recover_types(), the `condition` column returned by spread_draws()
# will be an integer:
m %>%
  spread_draws(condition_mean[condition]) %>%
  median_qi()

# If we apply recover_types() first, subsequent calls to other tidybayes functions will
# automatically back-convert factors so that they are labeled with their original levels
# (assuming the same name is used)
m %<>% recover_types(ABC)

# now the `condition` column with be a factor with levels "A", "B", "C", ...
m %>%
  spread_draws(condition_mean[condition]) %>%
  median_qi()


## End(Not run)

tidybayes documentation built on Aug. 13, 2023, 1:06 a.m.