Deprecated functions, arguments, and column names and their alternatives are listed below. Many of the deprecations are due to a naming scheme overhaul in tidybayes version 1.0.
Several deprecated versions of functions use slightly different output
formats (e.g., they use names like term and estimate where new
functions use .variable and .value; or they set .iteration even
when iteration information is not available --- new functions always set .draw
but may not set .iteration), so be careful when upgrading to new function names.
See Deprecated Arguments and Column Names, below, for more information.
Deprecated functions are:
spread_samples, extract_samples, and tidy_samples are
deprecated names for spread_draws(). The spread/gather terminology
better distinguishes the resulting data frame format, and draws is more
correct terminology than samples for describing multiple realizations from
a posterior distribution.
gather_samples is a deprecated name for gather_draws(),
reflecting a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
unspread_samples is a deprecated name for unspread_draws(),
reflecting a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
ungather_samples is a deprecated name for ungather_draws(),
reflecting a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
fitted_samples / add_fitted_samples are deprecated names for
fitted_draws() / add_fitted_draws(),
reflecting a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
predicted_samples / add_predicted_samples are deprecated names for
predicted_draws() / add_predicted_draws(),
reflecting a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
gather_lsmeans_samples and gather_emmeans_samples are deprecated aliases
for gather_emmeans_draws(). The new name (estimated marginal means) is more
appropriate for Bayesian models than the old name (least-squares means), and reflects the
naming of the newer emmeans package. It also reflects
a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
as_sample_tibble and as_sample_data_frame are deprecated aliases
for tidy_draws(). The original intent of as_sample_tibble was to be
used primarily internally (hence its less user-friendly name); however, increasingly
I have come across use cases of tidy_draws that warrant a more user-friendly name.
It also reflects a package-wide move to using draws instead of samples for
describing multiple realizations from a distribution.
ggeye is deprecated: for a package whose goal is flexible and customizable
visualization, monolithic functions are inflexible and do not sufficiently capitalize on users'
existing knowledge of ggplot; instead, I think it is more flexible to design geoms and stats
that can used within a complete ggplot workflow. geom_eyeh() offers a horizontal
eye plot geom that can be used instead of ggeye.
Versions of tidybayes before version 1.0 used a different naming scheme for several arguments and output columns.
Deprecated arguments and column names are:
term is now .variable
estimate is now .value
pred is now .prediction
conf.low is now .lower
conf.high is now .upper
.prob is now .width
The .draw column was added, and should be used instead of .chain
and .iteration to uniquely identify draws when you do not care about chains. (.chain and
.iteration are still provided for identifying draws within chains, if desired).
To translate to/from the old naming scheme in output, use to_broom_names()
and from_broom_names().
Many of these names were updated in version 1.0 in order to make terminology more consistent and in order to satisfy these criteria:
Ignore compatibility with broom names on the assumption an adapter function can be created.
Use names that could be compatible with frequentist approaches (hence .width instead of .prob).
Always precede with "." to avoid collisions with variable names in models.
No abbreviations (remembering if something is abbreviated or not can be a pain).
No two-word names (multi-word names can always be standardized on and used in documentation, but I think data frame output should be succinct).
Names should be nouns (I made an exception for lower/upper because they are common).