This version brings rotated rectangles as a new shape to eulerr, as well as the ability to customize the optimizer used to fit the diagram. eulerr is also parallelized now, and because the fitting pipeline now runs the full fit in several branches (in parallel), this should bring significant speedups for larger diagrams.
eea3542)330e42b)n_threads option for parallelizing fits (845a54f)transform option to fitter (f4b99c1),
closes #963ff50c6)9b05074)This is a major milestone for eulerr. The 8.0.0 release introduces a complete rewrite of the underlying C++ codebase, now relying instead on the Rust library Eunoia, which is a library I have developed. Here are some of the highlights this brings:
nlm() method. The CMA-ES fallback replaces the previous use
of the GenSA package, and is invoked whenever the LM
method reaches a minimum that’s above a level of error (configurable by
the user).2^n - 1-sized vector anywhere.decc985)44c9a1a)308167a)annotations argument for annotating intersections
(19d2d87),
closes #70+, / and
| (d974c08),
closes #46gap and separate labels by gap and tether (17802a2)template to quantities in
plot() (59ddd71),
closes #994ed75b4),
closes #69 and
#4b6ce232),
closes #13loss_aggregator (03e7dea)max_sets in control for capping max
sets (621a898),
closes #85by_groups to plot() for
panel-specifics (f2d5533),
closes #125decc985)ceb3138)530fb11)6400fae)symbol_size to configure
legend symbol (1491a49),
closes #60rotate parameter (706735c),
closes #12top and
left for labeling strips (c1a87fb),
closes #123021ceb4)3b7a32e),
closes #111caf1c76),
closes #83venn_eulerr (244a657),
closes #78quantities$format for number formatting (b01e69b),
closes #756e297a5),
closes #76bg option for plot.euler() (bf70290),
closes #74quantities (4c7d091),
fixes #112plot.euler() +
labels (cea5e43),
closes #118a58fce5),
closes #1094880f5e),
closes #116air.toml in Rbuildignore to fix R
CMD check warning.arma::is_finite() in C++
code.loss and
loss_aggregator. There is a new vignette that showcases
this new feature.adjust_labels in
plot.euler() has been deprecated and removed to fix
sanitizer warnings.inst/CITATIONPI to M_PI to support
STRICT_R_HEADERS in C++ code (#82, thanks
euler() with
adjust_labels = TRUE) no longer repels text labels away
from the edges of the shapes in the diagram.stringsAsFactors = TRUE inside all relevant
functions in euler() to avoid errors in upcoming R
version.venn() exceeds 5 (##65)euler() and venn() (##64, @privefl)data.frame inputs to
euler() when categorical variables are character vectors
and not factors.plot.euler(), percentages can be added to the plot
in addition to or instead of counts by providing a list to
the quantities argument with an item type that
can take any combination of counts and
percent. This change also comes with a redesign of the grid
graphics implementation for labels.eulerr_options() gains a new argument
padding which controls the amount of padding between labels
and quantities. (##48)plot.euler() now uses code from the
ggrepel package to prevent labels from overlapping or
escaping the plot area if adjust_labels is set to
TRUE.cex for quantity labels has changed from
1.0 to 0.9.data slot in the
object created by calling to plot.euler() (##57)venn() is a new function that produces Venn diagrams
for up to 5 sets. The interface is almost identical to
euler() except that a single integer can also be provided.
A new vignette, Venn diagrams with eulerr, exemplifies its
use.plot.euler() when a list
of Euler diagrams is given has been improved. Setting
fontsize or cex now results in appropriately
sized strips as one would expect.eulergram() objects from plot.euler() now
have a proper grob name for the canvas grob, so that extracting
information from them is easier.euler() now correctly
says “ellipses” and not “coefficients”.data.frame or matrix inputs now work
properly when values are numerical. (##42)error_plot() is a new function that offers diagnostic
plots of fits from euler(), letting the user visualize the
error in the resulting Euler diagram.euler() once again uses the residual sums of squares,
rather than the stress metric, as optimization objective, which means
that output is always scaled appropriately to input (##28).plot.euler() now uses the polylabelr
package to position labels for the overlaps of the ellipses, which has
improved performance in plotting complicated diagrams considerably and
reduced the amount of code in this package greatly.euler.data.frame() method (and by proxy the
euler.matrix() method) can now take matrices with factors
in addition to the previously supported logical and integer (binary)
input. The function will dummy code the variables for the user.plot.euler() have
been made defunct.plants, to exemplify the list method
for euler().fruits, to exemplify the data.frame
method for euler().euler.data.frame() gains an argument sep,
which is a character vector used to separate dummy-coded factors if
there are factors or characters in the input.organisms, to exemplify the matrix
method for euler().pain, to exemplify the table method
for euler().euler.table() gains an argument,
factor_names, for specifying whether the factor names
should be included when generating dummy-coded variables in case the
input is a data.frame with character or factor vectors or if the input
is a table with more than two columns or rows.euler.list() now passes its ellipsis argument along
properly. (##33, thanks,
plot.euler() now returns a gTree object.
All of the plotting mechanisms are now also found in this function and
plot.eulergram() and print.eulergram()
basically just call grid::grid.draw() on the result of
plot.euler(). This change means that functions such as
gridExtra::grid.arrange() now work as one would intuit on
the objects produced by plot.euler().NA in
the resulting data.frame of ellipses.GenSA::GenSA() from RcppDE::DEoptim().plot.euler().euler.data.frame() now works as expected for tibbles
(from the tibble package) when argument by
is used.plot.euler() has been rewritten completely from
scratch, now using a custom grid-based implementation
rather than lattice. As a result, all
panel.*() functions and label() have been
deprecated as well as arguments fill_alpha,
auto.key, fontface, par.settings,
default.prepanel, default.scales, and
panel. The method for plotting diagrams has also
changed—rather than overlaying shapes on top of each other, the diagram
is now split into separate polygons using the polyclip
package. Instead of relying on semi-transparent fills, the colors of the
fills are now blended in the CIELab color space (##16).eulerr_options() have been provided in
order to set default graphical parameters for the diagrams.counts and outer_strips to
plot.euler() are now defunct.euler() now always returns ellipse-based parameters
with columns h, k, a,
b, and phi, regardless of which shape is used.
This item was previously named “coefficients”, but it now called
“ellipses” instead and a custom coef.euler() method has
been added to make cure that coef() still works.quantities and
labels arguments of plot.euler() now works
correctly (##20).GenSA::GenSA()
to RcppDE::DEoptim().stats::nlm() again.label is now a proper generic with an appropriate
method (label.euler()).counts
argument in one of the vignettes.auto.key = TRUE and
labels were not in alphabetic order. (##15)%\VignetteEngine{knitr::knitr} to
both vignettes. It had mistakenly been left out, which had mangled the
resulting vignettes.shape = "ellipse" in euler(). This
functionality accompanies an overhaul of the innards of the
function.stats::optim(..., method = "L-BFGS-B") to
stats::nlminb().GenSA::GenSA()
when the fit from nlminb() isn’t good enough, by default
for 3 sets and ellipses, but this behavior can be controlled via a new
argument control.diagError and regionError
metrics have been changed from diag_error and
region_error to reflect the original names.label() function has been added to extract
locations for the overlaps for third party plotting (##10).counts argument to plot.euler() and
panel.euler.labels() have been deprecated in favor of the
more appropriate quantities.fill_opacity in plot.euler() that
was deprecated in v2.0.0
has been made defunct.eulerr() has been replaced with euler()
(see update 1.1.0) and made defunct.euler:
euler.list() produces diagrams from a list of sample
spaces.euler.table() produces diagrams from a
table object, as long as there are no dimensions with
values greater than 2.plot.euler() has been rewritten (again) from the ground
up to better match other high-level functions from
lattice. This change is intended to be as smooth as
possible and should not make much of a difference to most
users.polygon_args, mar, and
text_args to plot.euler() have been made
defunct.plot.euler() handles conflicting arguments better.eulerr now use registration.euler() now allows single sets (##9).plot.euler() now use a bold font face by
default in order to distinguish them from the typeface used for
counts.key in plot.euler() has been
deprecated and replaced with auto.key. Notice that using
key does not throw a warning since the argument is used in
lattice::xyplot() (which plot.euler() relies
on).fill_opacity is softly deprecated and has been
replaced with fill_alpha for consistency with other lattice
functions.border argument in plot.euler() works
again (##7).eulerr() and its related methods been deprecated and
are being replaced by euler(), which takes slightly
different input. Notably, the default is now to provide input in the
form of disjoint class combinations, rather than unions. This is partly
to make the function a drop-in replacement for
venneuler::venneuler.plot.euler() has been completely revamped, now
interfacing xyplot() from lattice. As a result, arguments
polygon_args, mar, and text_args
have been deprecated.counts argument to plot.eulerr,
which intersections and complements with counts from the original set
specification (##6).key argument to plot.eulerr that
prints a legend next to the diagram.atan2() from RcppArmadillo.cost and now forces
the function to use sums of squares, which is more or less equivalent to
the cost function from venneuler.plot.euler() now chooses colors
adapted to color vision deficiency (deuteranopia). With increasingly
large numbers of sets, this adaptation is relaxed to make sure that
colors are kept visually distinct.euler() now uses nlm() instead of
optim(method = "Nelder-Mead") for its final
optimization.print.eulerr.cost argument (currently eulerAPE or
venneuler).by argument to eulerr. The result is a list of
Euler diagrams that can be plotted in a grid arrangement via a new plot
method.mar argument to plot.eulerr with a
default that produces symmetric margins.stress statistic
from venneuler.print.eulerr method.