NEWS
eulerr 7.0.2 (2024-03-28)
Bug Fixes
eulerr 7.0.1 (2024-02-16)
Minor Changes
- Fixed some incorrect documentation of internal functions.
- Corrected an url for eulerAPE.
eulerr 7.0.0 (2022-12-09)
New Features
- It is now possible to set the loss function to be used when trying to
optimize the Euler diagram layout via
loss and loss_aggregator.
There is a new vignette that showcases this new feature.
Minor Changes
- C++14 is now required for the package.
Bug Fixes
- Label repelling via
adjust_labels in plot.euler() has been
deprecated and removed to fix sanitizer warnings.
eulerr 6.1.1 (2021-09-06)
Minor changes
- citation to conference paper added to
inst/CITATION
- error messages for erroneous input have been improved in several places
- switched
PI to M_PI to support STRICT_R_HEADERS in C++ code
(#82, thanks @eddelbuettel)
Bug fixes
- error in documentation for list method has been fixed, thanks @gprezza (##77)
eulerr 6.1.0 (2020-03-09)
Minor changes
- Label repelling (activated by calling
euler() with adjust_labels = TRUE)
no longer repels text labels away from the edges of the shapes in
the diagram.
Bug fixes
- Rectify sanitizer error from clang-ASAN test environment.
eulerr 6.0.2 (2020-03-04)
Bug fixes
- Set
stringsAsFactors = TRUE inside all relevant functions in euler()
to avoid errors in upcoming R version.
- Fix broken link in eulerr under the hood vignette.
eulerr 6.0.1
Minor changes
- Throw an error message when the number of sets in
venn() exceeds 5 (##65)
- Performance improved when large lists are used as input to
euler() and
venn() (##64, @privefl)
Bug fixes
- Correctly handle
data.frame inputs to euler() when categorical
variables are character vectors and not factors.
eulerr 6.0.0 (2019-09-27)
New features
- In
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.- A new vignette featuring a gallery of plots from the package has been
added.
Minor changes
- The default
cex for quantity labels has changed from 1.0 to 0.9.
- Labels for sets that overlap are now merged (partly fixes ##45)
- The fill colors for sets which are completely contained within another set
are now once again composed of a mix of the color of the subset and
the superset.
- Plotting data has been exposed in a
data slot in the object created
by calling to plot.euler() (##57)
Bug fixes
- An error in layout normalization that occurred sometimes
with ellipses has been fixed.
eulerr 5.1.0 (2019-02-04)
New features
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.
Minor changes
- Calculations for the strips in
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.
- Tiny overlaps (where the fraction of the area is less than one
thousandth of the largest overlap) in the final diagram are no longer
plotted.
eulergram() objects from plot.euler() now have a proper grob name
for the canvas grob, so that extracting information from them is easier.
Bug fixes
- Return value documentation for
euler() now correctly says "ellipses"
and not "coefficients".
data.frame or matrix inputs now work properly
when values are numerical. (##42)- Fixed some spelling errors in news and vignettes.
eulerr 5.0.0 (2018-11-05)
New features
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.
Major changes
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.- The c++ internals have been rewritten using more memory-efficient, performant
and expressive code.
Minor changes
- The
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.
- A few performance fixes.
- Additional unit tests.
- Previously deprecated arguments to
plot.euler() have been made defunct.
- Added a data set,
plants, to exemplify the list method for euler().
- Added a data set,
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.- Added a data set,
organisms, to exemplify the matrix method for euler().
- Added a data set,
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.- Parts of the eulerr under the hood vignette has been branched off into
a new vignette regarding visualization.
Bug fixes
- Empty combinations can now be provided and will be plotted (generating
completely blank plots).
euler.list() now passes its ellipsis argument along properly. (##33,
thanks, @banfai)- Several spelling and grammar mistakes were corrected in vignettes and
documentation.
eulerr 4.1.0 (2018-04-20)
Minor changes
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().- Fitting and plotting Euler diagrams with empty sets is now allowed (##23).
Empty sets in the input will be returned as
NA in the resulting
data.frame of ellipses.
- The last-ditch optimizer has been switched back to
GenSA::GenSA() from
RcppDE::DEoptim().
Bug fixes
- The grid parameters available for edges are now correctly specified in
the manual for
plot.euler().
euler.data.frame() now works as expected for tibbles (from the tibble
package) when argument by is used.
eulerr 4.0.0 (2018-02-05)
Major changes
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).- The default color palette has been redesigned from scratch to suit the
new plot method.
- A new function
eulerr_options() have been provided in order to set
default graphical parameters for the diagrams.
Minor changes
- Arguments
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.- Layouts are now partially normalized so that diagrams will look
approximately the same even with different random seeds.
Bug fixes
- Providing custom labels to
quantities and labels arguments of
plot.euler() now works correctly (##20).
eulerr 3.1.0 (2018-01-02)
Major changes
- The last-ditch optimizer switched from
GenSA::GenSA() to
RcppDE::DEoptim().
- The optimizer used in all the remaining cases, including all circular
diagrams and initial layouts, was switched back to
stats::nlm() again.
- In final optimization, we now use stress instead of residual sums
of squares as a target for our optimizer.
Minor changes
label is now a proper generic with an appropriate method (label.euler()).- The eulerr under the hood vignette has received a substantial update.
Bug fixes
- Fixed warnings resulting from the deprecated
counts argument in one
of the vignettes.
- Fixed memcheck errors in the final optimizer.
- Corrected erroneous labeling when
auto.key = TRUE and labels were
not in alphabetic order. (##15)
eulerr 3.0.1 (2017-11-15)
Bug fixes
- Added the missing %\VignetteEngine{knitr::knitr} to both vignettes. It had
mistakenly been left out, which had mangled the resulting vignettes.
eulerr 3.0.0 (2017-11-15)
Major changes
- Ellipses are now supported by setting the new argument
shape = "ellipse"
in euler(). This functionality accompanies an overhaul of the
innards of the function.
- Initial optimization function and gradient have been ported to C++.
- The initial optimizer has been switched from
stats::optim(..., method = "L-BFGS-B") to stats::nlminb().
- The final optimizer now falls back to
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.
- A packing algorithm has been introduced to arrange disjoint clusters of
ellipses/circles.
- The label placement algorithm has been rewritten to handle ellipses and
been ported to C++. It now uses numerical optimization, which should
provide slightly more accurate locations.
- The initial optimizer now uses an analytical Hessian in addition to
gradient.
Minor changes
- The initial optimizer now restarts up to 10 times and picks the best
fit (unless it is perfect somewhere along the way).
- The default palette has been changed to a fixed palette, still adapted
to color deficiency, but with some manual adjustments to, among other things,
avoid unnecessary use of color.
- The names of the
diagError and regionError metrics have been changed from
diag_error and region_error to reflect the original names.
- The coordinates for the centers are now called h and k instead of
x and y, respectively.
- A new
label() function has been added to extract locations for the overlaps
for third party plotting (##10).
- The
counts argument to plot.euler() and panel.euler.labels() have
been deprecated in favor of the more appropriate quantities.
- Argument
fill_opacity in plot.euler() that was deprecated in
v2.0.0 has been made
defunct.
eulerr 2.0.0 (2017-06-20)
Major changes
eulerr() has been replaced with euler() (see update 1.1.0) and made
defunct.- There are two new methods for
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.- Arguments
polygon_args, mar, and text_args to plot.euler() have been
made defunct.
Minor changes
plot.euler() handles conflicting arguments better.- c++ routines in
eulerr now use registration.
euler() now allows single sets (##9).- Labels in
plot.euler() now use a bold font face by default in order to
distinguish them from the typeface used for counts.
- Argument
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).
- Argument
fill_opacity is softly deprecated and has been replaced with
fill_alpha for consistency with other lattice functions.
Bug fixes
border argument in plot.euler() works again (##7).
eulerr 1.1.0 (2017-02-05)
Major changes
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.
Minor changes
- Added a
counts argument to plot.eulerr, which intersections and
complements with counts from the original set specification (##6).
- Added a
key argument to plot.eulerr that prints a legend next to the
diagram.
- Switched to
atan2() from RcppArmadillo.
- Added version requirement for RcppArmadillo.
- Dropped dependency on MASS for computing label placement, replacing it
with a faster, geometric algorithm.
- Dropped the cost function argument
cost and now forces the function to
use sums of squares, which is more or less equivalent to the cost function
from venneuler.
- Color palettes in
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.
Bug fixes
- The previous algorithm incorrectly computed loss from unions of sets. It now
computes loss from disjoint class combinations.
- Added missing row breaks in
print.eulerr.
eulerr 1.0.0 (2016-12-10)
New features
- Final optimization routines have been completely rewritten in C++ using Rcpp
and RcppArmadillo.
- Switched to the cost function from EulerAPE for the default optimization
target but added the possibility to choose cost function via a
cost argument
(currently eulerAPE or venneuler).
- Added the option to produce conditional eulerr plots via a
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.
- Improved label placement by using a two-dimensional kernel density estimation
instead of means to calculate label centers.
Bug fixes and minor improvements
- Cleaned up typos and grammar errors in the Introduction to eulerr vignette.
- Added
mar argument to plot.eulerr with a default that produces
symmetric margins.
- Corrected the implementation of the
stress statistic from venneuler.
- Switched to Vogel sampling to generate points to choose label positions from.
- Minor clean up and performance fixes all around.
- Added a
print.eulerr method.
- Updated vignette to cover new features and changes.
eulerr 0.1.0 (2016-10-16)