nauf.pmm.stan: Posterior samples of marginal means from Bayesian 'nauf'...
In CDEager/nauf: Regression with NA Values in Unordered Factors

Description Usage Arguments Details Value Methods

When nauf_pmmeans is used with Bayesian regressions, the elements of the resulting nauf.pmm.list have class nauf.pmm.stan.

## S3 method for class 'nauf.pmm.stan'
summary(object, probs = c(0.025, 0.975),
  type = c("link", "response"), ...)

## S3 method for class 'summ.nauf.pmm.stan'
print(x, row.names = FALSE, mcse = FALSE,
  rhat = NULL, ...)

## S3 method for class 'nauf.pmm.stan'
as.array(x, ...)

## S3 method for class 'nauf.pmm.stan'
as.matrix(x, ...)

## S3 method for class 'nauf.pmm.stan'
print(x, ...)

## S3 method for class 'nauf.pmm.stan'
as.data.frame(x, row.names = NULL, optional = FALSE,
  ...)

## S3 method for class 'summ.nauf.pmm.stan'
as.data.frame(x, row.names = NULL,
  optional = FALSE, ...)

`object`	A `nauf.pmm.stan` object.
`probs`	A vector of quantiles to calculate for the estimates. The default is a 95 The median (0.5) is always added regardless of whether it is specified.
`type`	If `"link"` (the default), then the estimates are not transformed prior to summary; if `"response"`, then the inverse link function in the object's `family` element is applied to the `samples` element prior to summary.
`...`	See the `Methods` section.
`x`	Either a `nauf.pmm.stan` object, or the `summ.nauf.pmm.stan` object returned by calling `summary` on a `nauf.pmm.stan` object.
`row.names, optional`	Changes from the defaults are ignored.
`mcse`	A logical indicating whether the Monte Carlo standard errors should be printed (default `FALSE` since the column is always recoverable by dividing the `SD` column by the square root of the `ESS` column).
`rhat`	An optional logical indicating whether or not to print the Gelman-Rubin R-hat statistic. If `rhat = NULL` (the default), then the `Rhat` column of the summary is only printed if any of the statistics are greater that `1.1`. Regardless of the value of the `rhat` argument, a warning is issued if any of the statistics are greater than `1.1`.

The nauf.pmm.stan object is a list with the following elements.

names: A data frame with the levels of each factor (or 'inc_1' for covariates), with one row for each element in the third dimension of samples.
contrasts: The fixed effects model matrix showing the contrasts applied to the regression coefficients (rows correspond to the names element).
samples: An array with three dimensions. The first corresponds to iterations, the second to chains, and the third to parameters (the same structure returned by as.array.stanfit).
family: The regression family.
inv.lbl: The label of the inverse link (e.g. probability, rate, etc.).
misc: A list with additional information based on the type of model.

The returned object depends on the function. See the 'Methods' section.

summary: Returns a data frame with class summ.nauf.pmm.stan, with means, standard deviations, medians, mean absolute differences, the posterior probability that the estimate is greater than zero, quantiles specified in probs, the effective sample size, Monte Carlo standard error, and Gelman-Rubin R-hat statistic. Additional arguments in ... are ignored. Quantiles, effective samples size, and Monte Carlo standard error, and R-hat statistics are computed using monitor.
print: For summ.nauf.pmm.stan objects, the data frame is printed, omitting the Monte Carlo standard error and R-hat statistic based on mcse and rhat. If the inverse link function was used, then a message indicating the response type is also printed. Additional arguments in ... are passed to print.data.frame. For nauf.pmm.stan objects, first summary is called, passing along ..., and then print is called on the resulting summ.nauf.pmm.stan, also passing along ... arguments.
as.data.frame: For summ.nauf.pmm.stan objects, removes the data.frame contained in a summ.nauf.pmm.stan. Additional arguments in ... are ignored. For nauf.pmm.stan objects, first summary is called, passing along ..., and then as.data.frame is called on the resulting summ.nauf.pmm.stan object, ignoring ... arugments.
as.array: Returns the samples element of a nauf.pmm.stan object. Additional arguments in ... are ignored.
as.matrix: Returns the samples element of a namf.pmm.stan object, flattening the array into a matrix such that the rows represent iterations ordered by chain and the columns represent parameters.