tidybayes-deprecated {tidybayes} | R Documentation |
Deprecated functions, arguments, and column names in tidybayes
Description
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 (see Deprecated Functions and Deprecated Arguments and Column Names below) or due to the deprecation of horizontal shortcut geoms and stats in tidybayes 2.1 (see Deprecated Horizontal Shortcut Geoms and Stats).
Deprecated Functions
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.
Functions deprecated in tidybayes 3.0:
-
fitted_draws
andadd_fitted_draws
are deprecated because their names were confusing: it was unclear to many users if these functions returned draws from the posterior predictive, the mean of the posterior predictive, or the linear predictor (and depending on model type it might have been either of the latter). Useepred_draws()
/add_epred_draws()
if you want the expectation of the posterior predictive and uselinpred_draws()
/add_linpred_draws()
if you want the linear predictor.
Functions deprecated in tidybayes 1.0:
-
spread_samples
,extract_samples
, andtidy_samples
are deprecated names forspread_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 forgather_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 forunspread_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 forungather_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 forfitted_draws
/add_fitted_draws
, reflecting a package-wide move to using draws instead of samples for describing multiple realizations from a distribution. (though see the note above about the deprecation offitted_draws
in favor ofepred_draws()
andlinpred_draws()
). -
predicted_samples
/add_predicted_samples
are deprecated names forpredicted_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
andgather_emmeans_samples
are deprecated aliases forgather_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 neweremmeans
package. It also reflects a package-wide move to using draws instead of samples for describing multiple realizations from a distribution. -
as_sample_tibble
andas_sample_data_frame
are deprecated aliases fortidy_draws()
. The original intent ofas_sample_tibble
was to be used primarily internally (hence its less user-friendly name); however, increasingly I have come across use cases oftidy_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.stat_eye()
offers a horizontal eye plot geom that can be used instead ofggeye
. See the sections below for additional deprecated functions, including horizontal geoms, stats, and point_intervals
Deprecated Eye Geom Spellings
geom_eye
, geom_eyeh
, and geom_halfeyeh
are deprecated spellings of stat_eye()
and
stat_halfeye()
from before name standardization of stats and geoms. Use those functions instead.
Deprecated Horizontal Shortcut Geoms and Stats
Due to the introduction of automatic orientation detection in tidybayes 2.1,
shortcut geoms and stats (which end in h
) are no longer necessary, and are
deprecated. In most cases, these can simply be replaced with the same
geom without the h
suffix and they will remain horizontal; e.g.
stat_halfeyeh(...)
can simply be replaced with stat_halfeye(...)
.
If automatic orientation detection fails, override it with the orientation
parameter; e.g. stat_halfeye(orientation = "horizontal")
.
These deprecated stats and geoms include:
-
stat_eyeh
/stat_dist_eyeh
-
stat_halfeyeh
/stat_dist_halfeyeh
-
geom_slabh
/stat_slabh
/stat_dist_slabh
-
geom_intervalh
/stat_intervalh
/stat_dist_intervalh
-
geom_pointintervalh
/stat_pointintervalh
/stat_dist_pointintervalh
-
stat_gradientintervalh
/stat_dist_gradientintervalh
-
stat_cdfintervalh
/stat_dist_cdfintervalh
-
stat_ccdfintervalh
/stat_dist_ccdfintervalh
-
geom_dotsh
/stat_dotsh
/stat_dist_dotsh
-
geom_dotsintervalh
/stat_intervalh
/stat_dist_intervalh
-
stat_histintervalh
Deprecated Horizontal Point/Interval Functions
These functions ending in h
(e.g., point_intervalh
, median_qih
)
used to be needed for use with ggstance::stat_summaryh
, but are
no longer necessary because ggplot2::stat_summary()
supports
automatic orientation detection, so they have been deprecated.
They behave identically to the corresponding function without the h
,
except that when passed a vector, they return a data frame with
x
/xmin
/xmax
instead of y
/ymin
/ymax
.
-
point_intervalh
-
mean_qih
/median_qih
/mode_qih
-
mean_hdih
/median_hdih
/mode_hdih
-
mean_hdcih
/median_hdcih
/mode_hdcih
Deprecated Arguments and Column Names
Arguments deprecated in tidybayes 3.0 are:
The
n
argument is now calledndraws
inpredicted_draws()
,linpred_draws()
, etc. This prevents some bugs due to partial matching of argument names wheren
might be mistaken fornewdata
.The
value
argument inlinpred_draws()
is now spelledlinpred
and defaults to".linpred"
in the same way that thepredicted_draws()
andepred_draws()
functions work.The
scale
argument inlinpred_draws()
is no longer allowed (usetransform
instead) as this naming scheme only made sense whenlinpred_draws()
was an alias forfitted_draws()
, which it no longer is (see note above about the deprecation offitted_draws()
).
Versions of tidybayes before version 1.0 used a different naming scheme for several arguments and output columns.
Arguments and column names deprecated in tidybayes 1.0 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).
Author(s)
Matthew Kay