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This patch fixes a bug involivng the {dplyr} functions
first() and last() that was shifted but not
fixed in 0.12.4. Rather than being imported during build, they are
accessed internally and thus imported during use. See issues #107 https://github.com/corybrunson/ggalluvial/issues/107 and
#108 https://github.com/corybrunson/ggalluvial/issues/108 on
GitHub for details.
linewidth
aesthetic (breaking change)An upcoming release of ggplot2 controls stroke width using
the new linewidth aesthetic rather than size.
This release adapts to this change internally by updating row and column
layers as recommended here: https://www.tidyverse.org/blog/2022/08/ggplot2-3-4-0-size-to-linewidth/
Various curve constructors for alluvia and flows are consolidated
into data_to_alluvium() and
positions_to_flow(), which are now exported to the user as
well as used internally by GeomAlluvium$draw_group and
GeomFlow$draw_panel, respectively.
Rather than throw an error when y values are
NA, the stat layers now follow ggplot2
convention, using remove_missing() at the setup step with
the na.rm parameter passed to each layer.
To address #78 and for clarity, the legacy default
colour = 0 of three Geom*()s is changed to
colour = "transparent".
\dontrun markers have been replace by
\donttest, per the advice here: https://stackoverflow.com/a/68936484/4556798. More have
been added in order to reduce the time required to run.
The primary vignette now uses the HairEyeColor data set,
rather than over-using Titanic, to illustrate the parallel
sets plot.
The Shiny vignette includes an embedded app using IFrame.
The deprecated .dots argument of
dplyr::group_by() has been replaced with
dplyr::across(), preventing a warning.
A new vignette by Quentin D. Read shows how to build interactive Shiny apps with tooltips sensitive to the locations of graphical elements. This is especially important for the spline boundaries of flows and alluvia.
vaccinations dataCorrections have been made to erroneous legacy code, found in one
example and two vignettes, to reorder the factor levels of the
"response" field in the data set vaccinations.
The documentation is updated accordingly.
Also, an explanation of the (misleading) column names of this data set has been added to the main vignette.
This patch addresses a bug introduced in v0.12.0 that had
is_lodes_form() return an error when a data frame contains
duplicate id-axis pairings, which may be appropriate for producing
faceted plots. The new site parameter can be passed one or
more grouping variables for this purpose, and internally it is passed
"PANEL" to prevent this error from being thrown.
This patch corrects a bug introduced in v0.12.0 that dropped missing
values used internally by StatFlow$compute_panel() to keep
track of flowless lodes. The problem was illustrated in issue #64.
Both installed data sets, vaccinations and
majors, are better documented.
The a field of vaccinations (the
within-survey fraction of respondents, which can be computed from the
other fields) has been removed, and the start_date and
end_date fields (Dates, obtained from the ALP
website) have been added.
The following changes broke no examples or tests but could change behavior in rare cases:
is_lodes_form() now returns FALSE if any
axis-alluvium pairs are duplicated, and throws the previous warning as a
message. This should be more helpful than the previous behavior of
suppressing the warning and leaving tidyr::gather() to
throw an error referring to rows of the already-transformed internal
data.stratum = NULL and
alluvium = NULL have been added to the stats. This prevents
the “unknown aesthetics” warnings that print when these aesthetics are
passed to layers rather than to the plot initialization.lode.orderingFor consistency with the behavior of aes.bind,
stat_alluvium() now invokes lode.ordering
together with lode.guidance: If the vectors of
lode.ordering include duplicates, i.e. they do not
completely determine an order, then the remaining deposits are used to
refine the order. Previously, lode.ordering was assumed to
consist of permutation vectors, so the two parameters were mutually
exclusive.
Additionally, for consistency with other influences on the lode
order, the vectors of lode.ordering are reversed if
reverse = TRUE (the default). This will change some
plots but will not produce new errors.
The lode.ordering parameter of
stat_alluvium() has been deprecated. Instead, the new
order aesthetic gives priority to its argument over the
differentiation aesthetics in arranging the lodes within each stratum,
without producing graphical artifacts. This aesthetic can also be used
in stat_flow().
Alluvia within “deposits” are now consistently ordered in positive
and negative strata, rather than according to absolute.
This avoids the “twisting” of flows between strata of different signs.
Whereas the orderings of the deposits matter to the stacked-histogram
reading of the plot, the orderings of the alluvia should simply maximize
its elegance and readability. This will change some plots but
will not produce new errors.
The alluvial stats now compute four variables for use with
after_stat(): numeric variables n,
count, and prop; and character variables
lode (when the alluvium aesthetic is
specified) and flow (when using the flow stat). The
numerical variables can be weighted using the weight
aesthetic, which is dropped during computation (so that it does not
confuse the geoms), while lode is distilled according to a
new distill parameter. This use of weight may
cause confusion with its use by the is_*_form() functions
until they are upgraded in the next version.
These new variables complement the already-computed but heretofore
undocumented variables stratum and deposit.
stratum obviates the need for the infer.label
parameter, which is deprecated. Its alias, label.strata, is
now defunct. (The variable alluvium is often computed, but
it is manipulated to be used by the geom layers and should not be passed
to an aesthetic.) deposit takes contiguous integer values
forward along the axes and upward along the (signed) strata at each
axis.
The knot.pos parameter of geom_alluvium()
and geom_flow() is now interpreted as a proportion of the
total length of each flow, i.e. of the gap between adjacent strata
(not axes). This means that values will vary with axis
positions and stratum widths. Setting the new knot.prop
parameter to FALSE prevents this by interpreting
knot.pos as a constant value in the x
direction.
These flows are rendered using grid::xsplineGrob() with
four control points each: the endpoints and the two knots. To complement
them, several other curves are now available: linear (equivalent to
knot.pos = 0), cubic, quintic, sinusoidal, arctangent, and
sigmoid, summoned by the new curve_type parameter (which
defaults to the x-spline). (The asymptotic functions, arctangent and
sigmoid, are compressed according to the new curve_range
parameter.) The new curves are rendered piecewise linearly, with
resolution controlled by the new segments parameter
(similar to ggplot2::stat_ellipse()).
The stratum and lode ordering parameters now default to
NULL, in which case they are reassigned to global options
internally. This simplifies their documentation. The new curve
parameters curve_type, curve_range, and
segments can also be set as options and are documented in
the same way.
In response to ggplot2 v3.2.0, which removes the plyr dependency, the dependency has been removed from ggalluvial as well.
The function self_adjoin() is debugged for use with a
continuous-valued x variable. An example, taking
x to be the date of each vaccination survey in
vaccinations, is documented with
stat_stratum().
This patch fixes a bug with including negative observations in
alluvia-form data due to outdated code that prohibited negative
y values. This was discovered while drafting two examples
of this usage, which are included in the documentation.
min.height and max.height parameters
of stat_stratum() are deprecated in favor of
min.y and max.y (which better adhere to
ggplot2 conventions) and extended to the other
stat_*() layers.label.strata parameter of
stat_stratum() is deprecated in favor of
infer.label, which is extended to the other
stat_*() layers and sets label to
alluvium in those cases rather than to
stratum.aggregate.y parameter of
stat_alluvium() is deprecated in favor of
cement.alluvia, and the underlying procedure is
debugged.aes.bind parameter of stat_flow() and
stat_alluvium() now prefers character string options to
logical values, described in the lode ordering vignette:
"none", "flows", and "alluvia".
The default "none" produces different behavior than the
previous default FALSE, in that under this setting the
aesthetic variables are not at all prioritized.weight and
aggregate.wts are discontinued.Negative values can now be meaningfully passed to y,
producing behavior that mimics that of geom_bar(). The new
logical parameter absolute controls whether negative
strata, and lodes within them, are ordered vertically in the same way as
positive strata and lodes (FALSE) or in the opposite way
(TRUE). Additionally, the negate.strata
parameter can be used to negate the observations associated with
specific strata, in order to situate them below rather than above the
x axis.
The new lode guidance function lode_zagzig() mimics the
behavior of lode_zigzag() except in initially “zagging”
toward the farther end rather than “zigging” toward the closer end.
stat_*() internals have been simplified and
standardized, in particular the manner in which lodes are ordered within
strata.
Tests have been added for the statistical transformations. Visual regression tests using vdiffr have been added for the geoms.
The lode guidance functions have been renamed as follows and their original names retained as aliases:
| original | renamed |
|---|---|
| rightward | forward |
| leftward | backward |
| rightleft | frontback |
| leftright | backfront |
Additionally, lode.ordering now accepts a single integer
vector of length the number of cases (alluvia), and will use the vector
to sort the lodes within strata at each axis.
Finally, a new vignette showcases this and related functionality using a small example.
The following parameters, deprecated in previous versions, are now defunct (with informative messages):
weight in the stat_*()s (replaced with
y)aggregate.wts in stat_alluvium() (replaced
with aggregate.y)logical in the is_*_form()sThe width and knot.pos parameters sometimes
required by Geom*$setup_data() are now set to the same
defaults as in the geom_*()s when called from a stat.
Previously-implemented warnings have been removed.
The lode.guidance argument of
stat_alluvial() now accepts functions as input, making the
use of custom functions easier as demonstrated in an example.
Parameters min.height and max.height are
introduced to stat_stratum() to allow users to omit strata
outside a given height range. This is probably most relevant for stratum
labeling, as illustrated in the updated vignette.
session_info()Because the only functional (e.g. out README.md)
occurrence of devtools is to call
session_info() at the ends of the vignettes, this
suggestion and usage are switched to sessioninfo.
Documentation is slightly reformatted due to switching roxygen syntax to markdown.
The internal z-ordering function z_order_aes failed to
recognize contiguous segments of alluvia, thereby assigning later
segments missing values of 'group' and preventing them from
being rendered. This has been corrected.
geom_alluvium() patchAn occurrence of weight in geom_alluvium()
was not updated for v0.8.0 and caused geom_alluvium() to
throw an error in some cases. This has been corrected.
geom_flow() patchAn earlier solution to the z-ordering problem sufficed for matched
layers (*_alluvium() and *_flow()) but failed
for the combination of stat_alluvium() with
geom_flow(). This is been corrected in the code for
GeomFlow$draw_panel(), though a more elegant and general
solution is preferred.
The deprecated parameters axis_width (all geom layers)
and ribbon_bend (geom_alluvium() and
geom_flow()) are removed and an explanatory note added to
the layers’ documentation.
A vignette illustrating two methods for labeling small strata, using other ggplot2 extensions, is included.
self_adjoin() exportThe internal function self_adjoin(), invoked by
geom_flow(), is revised, exported, documented, and
exemplified.
weight aesthetic for the three
stat_*() functions is replaced by the y
aesthetic, so that scale_y_continuous() will correctly
transform the vertical scales of the layers. An example is provided in
the documentation for stat_alluvium(). The
y aesthetic must be present in order for scales to be
correctly transformed. The weight parameter is still
available but deprecated.weight to
y, the aggregate.wts parameter to
stat_alluvium() is replaced with aggregate.y;
aggregate.wts is deprecated.stat_*() functions.These changes make the functions that test for and convert between alluvial formats behave more like popular functions in the tidyverse. Some of the changes introduce backward incompatibilities, but most result in deprecation warnings.
is_alluvial_*() and to_*()
are renamed to is_*_form() and to_*_form() for
consistency. Their old names are deprecated.is_alluvial() is deprecated and will be removed in a
future version.logical is deprecated. In a future
version, the functions is_*_form() will only return logical
values.silent = TRUE now silences all
messages.is_*_form() now return FALSE
if any weights are negative, with a message to this effect.key, value, id,
weight, and diffuse parameters, using
up-to-date rlang and tidyselect
functionality.axes parameter in is_alluvia_form()
and to_lodes_form() now accepts dplyr::vars()
objects, as in dplyr::select_at(). Alternatively, variables
can be fed to these functions as in dplyr::select(), to be
collected by rlang::quos(...) and used as axis variables.
If axes is not NULL, then such additional
arguments are ignored.to_*_form() now merge their internal
reshapen data frames with the distilled or diffused variables in a
consistent order, placing the distilled or diffused variables to the
left.Depends on R v3.3.0 (patch
number zero) instead of v3.3.1. I’ve been unable to install
this version locally, so there is a slight chance of incompatibility
that i’ll be watchful for going forward.Suggests rather than Imports.is_alluvial_*() and
to_*() functions are combined; see
help("alluvial-data").is_alluvial_alluvia now prints a message rather than a
warning when some combinations of strata are not linked by any
alluvia.to_lodes() now has a diffuse parameter to
join any original variables to the reformatted data by the
id variable (alluvium). This makes it possible to assign
original variables to aesthetics after reformatting, as illustrated in a
new example.to_alluvia() now has a distill parameter
to control the inclusion of any original variables that vary within
values of id into the reformatted data, based on a
distilling function that returns a single value from a vector.to_lodes() now has a logical discern
parameter that uses make.unique() to make stratum values
that appear at different axes distinct. The stat_*()
functions can pass the same parameter internally and print a warning if
the data is already in lodes form.GeomFlow$draw_panel() now begins by restricting to
complete.cases(), corresponding to flows with both starting
and terminating axes. (This is not done in
StatFlow$compute_panel(), which would have the effect of
excluding missing aesthetic values from legends.)GeomAlluvium$setup_data() now throws a warning if some
color or differentiation aesthetics vary within alluvia.lode.ordering
argument by StatAlluvium$compute_panel() has been
fixed.The ggalluvial() shortcut function, which included a
formula interface, deprecated in version 0.4.0, is removed.
I only started maintaining NEWS.md with version
0.5.0.
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