autotitle() affecting only collections of spectra where all
spectra have the same value for the when.measured attribute and this attribute
is used in title annotations.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 labelling 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 synonym 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 labelled 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 labelling 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.