Various curve constructors for alluvia and flows are consolidated into
positions_to_flow(), which are now exported to the user as well as used internally by
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".
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.
Corrections 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,
majors, are better documented.
a field of
vaccinations (the within-survey fraction of respondents, which can be computed from the other fields) has been removed, and the
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:
FALSEif 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 = NULLand
alluvium = NULLhave 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.
For consistency with the behavior of
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.
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
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
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 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.
knot.pos parameter of
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
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
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.
stat_stratum()are deprecated in favor of
max.y(which better adhere to ggplot2 conventions) and extended to the other
stat_stratum()is deprecated in favor of
infer.label, which is extended to the other
stat_*()layers and sets
alluviumin those cases rather than to
stat_alluvium()is deprecated in favor of
cement.alluvia, and the underlying procedure is debugged.
stat_alluvium()now prefers character string options to logical values, described in the lode ordering vignette:
"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.
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
stat_*() internals have been simplified and standardized, in particular the manner in which lodes are ordered within strata.
The lode guidance functions have been renamed as follows and their original names retained as aliases:
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):
stat_*()s (replaced with
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.
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.
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.
An earlier solution to the z-ordering problem sufficed for matched layers (
*_flow()) but failed for the combination of
geom_flow(). This is been corrected in the code for
GeomFlow$draw_panel(), though a more elegant and general solution is preferred.
A vignette illustrating two methods for labeling small strata, using other ggplot2 extensions, is included.
weightaesthetic for the three
stat_*()functions is replaced by the
yaesthetic, so that
scale_y_continuous()will correctly transform the vertical scales of the layers. An example is provided in the documentation for
yaesthetic must be present in order for scales to be correctly transformed. The
weightparameter is still available but deprecated.
stat_alluvium()is replaced with
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.
to_*()are renamed to
to_*_form()for consistency. Their old names are deprecated.
is_alluvial()is deprecated and will be removed in a future version.
logicalis deprecated. In a future version, the functions
is_*_form()will only return logical values.
silent = TRUEnow silences all messages.
FALSEif any weights are negative, with a message to this effect.
diffuseparameters, using up-to-date rlang and tidyselect functionality.
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
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.
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.
to_*()functions are combined; see
is_alluvial_alluvianow prints a message rather than a warning when some combinations of strata are not linked by any alluvia.
to_lodes()now has a
diffuseparameter to join any original variables to the reformatted data by the
idvariable (alluvium). This makes it possible to assign original variables to aesthetics after reformatting, as illustrated in a new example.
to_alluvia()now has a
distillparameter to control the inclusion of any original variables that vary within values of
idinto the reformatted data, based on a distilling function that returns a single value from a vector.
to_lodes()now has a logical
discernparameter 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.
StatAlluvium$compute_panel()has been fixed.
ggalluvial() shortcut function, which included a formula interface, deprecated in version 0.4.0, is removed.