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geom_linerange() instead of geom_errorbarh()
as default in stat_wb_hbar().autotitle() to better support
collections of spectra and multiple spectra in long form.autoplot.calibration_spct() (bug introduced in version
0.3.12).cps_spct objects
with multiple columns of cps data (bug introduced in
version 0.3.12).autoplot()
methods revealed by stricter checks.autoplot.response_spct() change default argument
norm = "max" to norm = "update" for
consistency with the other autoplot() methods and to avoid
“surprising” users.axis.symbols with
default given by R option ggspectra.axis.symbols.pc.out with default given by R
option ggspectra.pc.out.autoplot() methods so that the default
argument for the pc.out can be set with R option
ggspectra.pc.out.autoplot() methods for objects of class
generic_spct and derived so that summaries requested by
arguments passed to parameter plot.data are computed for
multiple spectra in long form like they are for collections of
spectra.idfactor handling in autoplot()
methods for objects of class generic_spct and derived.autoplot() methods a plotmath expression for the
wavelength axis label, including lambda as symbol, for consistency with
the labels of the y-axis.autoplot() methods to that the default argument
for range can be set with R option
ggspectra.wlrange.autoplot() look, e.g.,
limit number of digits in labels and improve some annotations in the
case of multiple spectra.ylim in autoplot()
methods works correctly with any values passed as argument. Plots with
non-default ylim values may change (for the better) and
occasionally a plot made with defaults may look the same but not be
identical.autoplot.source_spct() introduced in version
0.3.10: bad handling of single waveband objects as argument to
w.band.PAR() (photosynthetically active radiation)
as a BSWF (biological spectral weighting function). The labeling as PAR
is now restored when plotting spectral photon response using the
autoplot() method.autoplot().autoplot() to use
linetype aesthetic with more than the 13 supported levels.
This changes plots with more than 13 spectra compared to earlier
versions, but in these plots some spectra were missing. New behaviour is
to use semi-transparent solid lines for more than 13 spectra.PAR() (photosynthetically active radiation)
as a BSWF (biological spectral weighting function). The previous
definition of PAR() as a wavelength range returned a value
that should be called “PAR” only when used to compute photon irradiance.
This change does not affect the numerical values of energy irradiances
or other spectral quantities, but now the waveband is labelled
PhR instead of PAR in such cases.sec_axis_energy_eV() and
sec_axis_energy_J() to express wavelength as energy per
photon, and sec_axis_wl() to allow a secondary wavelength
axis with wavelengths expressed using a different scale factor than in
the main axis.scale_x_wavenumber_continuous(),
scale_x_frequency_continuous().
scale_x_energy_eV_continuous() and
scale_x_energy_J_continuous().autoplot() methods adding formal parameter
geom.This update brings many improvements to autoplot()
methods. These include enhanced capabilities for handling of normalized
and scaled spectral data, as well as cosmetic tweaks to labels. It also
tracks changes in packages ‘ggrepel’ (>= 0.9.1), ‘photobiology’
(>= 0.10.10) and ‘ggplot2’ (>= 3.3.3) and deprecation of functions
in ‘tidyr’ (>= 1.0.0). The updated code depends on the revised
normalize() function in ‘photobiology’ (>= 0.10.10) and
on ‘ggrepel’ (>= 0.9.1).
autoplot() methods to support on-the-fly
normalization internally using
photobiology::normalize().autoplot() methods for source_spct,
response_spct, filter_spct,
reflector_spct, source_mspct,
response_mspct, filter_mspct, and
reflector_mspct so that if the data are already normalized,
by default the normalization is updated according to the arguments
passed to unit.out or plot.qty and
range. (Update is possible only for objects normalized with
‘photobiology’ (>= 0.10.7). For objects created with earlier
versions, the old behaviour of plotting spectra as is remains
unchanged.)autoplot() method for object_mspct
to force use of facets when plot.qty = "all" instead of
forcing plotting of transmittance only.autoplot() method for object_mspct
to correctly handle normalization of collections of spectra, one
spectrum at a time, correcting a bug.autoplot() methods to generate shorter
y-axis labels also improving reporting of scaling and
normalization when needed.autoplot() methods to fix bug leading to bad
object name in plot title due to delayed evaluation.autoplot.cps_mspct() and
autoplot.raw_mspct() methods.autoplot() methods for
collections of spectra.autoplot() methods for collections of
spectra adding support for sum, prod,
var, sd, and se as summaries.
The support for these summaries depends on
autoplot.generic_spct() which is still experimental and
subject to change.decoration() to track changes in ‘ggrepel’
(>= 0.9.1).decoration() to use
position_nudge() and position_nudge_repel() to
displace labels instead of “off-range” justification.ggplot() methods and by autotitle().autoplot() methods an
explanation of how to modify the default plot annotations and titles
using arguments passed to parameter annotations. Also add
see also links to related help pages.autoplot() methods have changed, in most cases
only cosmetically to shorten them. In a few cases more significant edits
correct problems.stat_wl_strip() performance by simplifying data
before plotting.scale_y_Afr_continuous() for absorptance
spectra.scale_y_mult_continuous() for calibration
spectra.autoplot() methods to generate more compact axis
labels (preliminary).autoplot.source_spct() method to to natively
support facets (partial).stat_wb_box() adding parameter box.height
(default behavior unchanged).stat_wl_strip()
draws fewer rectangles (in most cases these changes are barely
visible).ggplot() method for class
object_spct.stat_spikes(), useful for highlighting spikes.stat_find_wls() using
photobiology::wls_at_target()."wls" and
"wls.labels" in all autoplot() methods.Although this update should not break any code, the plots created will in many cases differ from those created with earlier versions. Changes only affect the text of labels.
"data" member of the
"gg" object. This allows use of methods specific to spectra
in data transformations.set_annotations_default() and
set_w.band_default().autoplot() methods.multiplot() for adding a title to the
composite figure.autoplot() methods. Make autotitle() a
synonim of ggtitle_spct(), which is now deprecated."how.measured" attribute in plot titles, subtitles and
captions.stat_wb_label(), stat_wb_box() and
stat_wl_strip(), solving a bug affecting
autoplot() methods when called with multiple spectra.autoplot() methods as replacements for
plot() methods, which are now deprecated. All documentation
now uses autoplot().autoplot() and the
expected returned value is a ggplot which matches the returned value of
the methods defined here, we have renamed them to
autoplot(). For backwards compatibility plot()
methods remain available, but their use in new code is deprecated.plot() methods for
source_spct and response_spct classes, that
triggered errors in all cases when time.unit was not
"second".scale_y_s.e.irrad_log10() and
scale_y_s.q.irrad_log10().Change the names of some the values calculated by the stats defined in ‘ggspectra’ to avoid confusion with the names of ‘ggplot2’ aesthetics. This is a code breaking change!
Revise to track changes in ‘photobiology’ version 0.9.24 and ‘ggplot2’ 3.0.0, which are now required.
stat_label_peaks() and
stat_label_valleys() now have a new parameter,
label.fill which can be used to set the content of
..x.label.. and ..y.label.. for labels not
labeled as peaks or valleys. The earlier use of "" is
retained as default.stat_find_wls() and stat_find_qtys(),
two new statistics useful for highlighting and labeling features in
spectra.ylim to all plot()
methods.plot() methods to support objects with multiple
spectra in long form.plot() methods to NOT display by default
calculated summaries in annotations when a plot contains multiple
spectra.plot() methods to retrieve and validate the name
of the factor used to identify multiple spectra, using as default the
value stored in the attribute "idfactor" implemented in
‘photobiology’ 0.9.21 and later.autoplot() as an alias of plot() for
spectra and collections of spectra.Revise to track changes in ‘photobiology’ 0.9.20 to avoid spurious messages.
Add ggplot() method specialization for collections
of spectra.
Add plot() method specializations for collections of
spectra.
Track changes in package ‘photobiology’ 0.9.18.
Add plot.calibration_spct().
Add ggplot.calibration_spct().
Improve handling of plot titles.
Add utility function ggtitle_spct().
Update all plot() methods to allow flexible contents
in automatic titles including setting of the time zone and format used
for displaying time.
Track changes in package ‘photobiology’ 0.9.16 and 0.9.17. This among
other improvements makes it easy to plot spectral absorptance. Expand
y scale to expected range in all cases, but do not force these
limits in any case when data exceeds them, except for absorbance for
which the y scale is not expanded past 6 a.u. Add new annotation
"boundaries" to highlight with horizontal line(s) the
expected range of the plotted quantity, highlighting the limit(s)
exceeded if data fall outside the expected/range. Add previously missing
ggplot() method for class object_spct. Revise
vignettes.
Track changes in package ‘photobiology’ 0.9.14. Add continuous scales with defaults suitable for spectral data, with support for automatic axis labels both as R-expressions and as LaTeX mark-up. Add utility functions for SI scale prefixes. Add utility functions for x-axis-labels and secondary x-axis. Add utility functions for y-axis-labels. Update User Guide (add examples of graphical comparison of multiple lists of wavebands).
Improve handling of annotations parameter in plot()
methods. Add functions ggcolorchart() and
black_or_white(). Add statistics stat_wb_box()
and stat_wb_column() with "rect" as default
geom and stat_wb_hbar() with "errorbarh" as
default geom. Change default geom from "rect" to
"text" in all the summary stats for spectra. Update stats
with “text” as default geom to use an additional variable
BW.color computed by black_or_white() as
default mapping for color. As default geoms and color mapping have
changed, this update can break existing code. Changes to
plot() methods are backwards compatible but default color
of some text labels is changed from "white" to
"black" to improve readability, and fewer peaks and valleys
are highlighted by default. In addition more ticks marks are used on the
wavelength axis. Fix minor bugs in handling of color mapping. Update
documentation.
Import ‘ggplot2’ in whole as only the most basic use of
plot() methods would not require user access to ‘ggplot2’.
Add stat_label_peaks() and
stat_label_valleys() which are designed to fully take
advantage of geom_text_repel() and
geom_label_repel() as revised in package ‘ggrepel’ (>=
0.6.3). Change behaviour of plot() methods so that
“illegal” values such as negative spectral irradiances or transmittances
are plotted by default. Fix several minor bugs affecting
plot() methods with certain non-default sets of
annotations. Improve documentation and vignettes.
Add code to maintain same stacking order under ‘ggplot2’ 1.1.0,
2.0.0, 2.1.0, and 2.1.9000 in plot.object_spct().
Add support for na.rm to all plot() methods
setting default to TRUE, and avoid triggering spurious
warnings from internal code. Make default for parameter
label.qty in plot methods dependent on whether data are
expressed in absolute units or have been rescaled or
normalized. Move from the ‘User Guide’ the sections on
plot() methods creating a new vignette titled ‘Plot
Methods’.
Add support for plot.qty = "absorptance" to
plot.filter_spct(). Add support for plot.qty
to plot.object_spct() with possible values:
"all" or NULL (previous behaviour, and current
default), "transmittance", "absorbance",
"absorptance", and "reflectance". The new
options plot only one quantity at a time as a line instead of the
default area plot.
Add stat_wb_label(), stat_wb_e_irrad(),
stat_wb_q_irrad(), stat_wb_e_sirrad(), and
stat_wb_q_irrad(). Revise plot.raw_spct() to
handle multiple "counts" columns. Revise
plot.cps_spct() to handle multiple "cps"
columns. Add text.size parameter to all plot()
methods. Can be used to control the size of the font used for text
decorations related to wavebands, peaks and valleys. Increase slightly
the default font size for plot decorations, and decrease the number of
peaks and valleys labelled by the plot()
methods. Fix existing bug revealed by dplyr update. Fix bug in
decoration() affecting plot.object_spct(). Fix
other minor bugs.
(First CRAN release)
Clean documentation and code for CRAN submission. Add examples of plotting of waveband objects as these were removed from the vignette of package ‘photobiologyWavebands’.
Fix bug in documentation.
Improve documentation.
Remove wb_guide(). Remove wb_wb_summary().
Add stat_wb_mean(), stat_wb_total(),
stat_wb_contribution(), stat_wb_relative().
Add stat_wb_irrad(), stat_wb_sirrad()
Implement 100% of the old functionality of the plot()
methods, but without using any annotations. In other words, now all
calculations work as expected with grouping and panels. Some aesthetics
may require tweaking in the case of grouping.
Tested with packages ‘ggrepel’ and ‘cowplot’.
Add text explaining examples to User Guide.
Rename several stats and functions with more descriptive names.
stat_color_guide() ->
stat_wl_strip()
stat_average() -> stat_wl_summary()
stat_waveband() -> stat_wb_summary()
color_guide() -> wl_guide()
waveband_guide() -> wb_guide()
Add multiplot() function (unchanged from package
photobiologygg). Improve stat_waveband(). Add
color_guide(), waveband_guide().
Add ggplot() methods for spectra, which use default
mappings if mapping not explicitly supplied as argument to call.
Make plot() methods almost fully functional.
"contribution" and "participation" summary
values not yet implemented. Neither summaries for BSWFs. If requested
these summaries will show as NaN (not a number) in the
plots.
First preview version. Still with incomplete functionality.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.