Added a new function simulate_spec(), which allows for
the flexible simulation of naturalistic spectra (inc. reflectance,
irradiance, radiance, absorbance). See ?simulate_spec for
examples and information, and the handbook for further discussion.
plot.rspec() now accepts a logical labels
argument (and labels.cex), to control whether text labels
identifying each spectrum should be added to the outer plot margins.
This was previously only available, and was required, for ‘stacked’ plot
types, but is now optional for both ‘overlay’ (the default) and
‘stacked’ spectral plots.
the wlmin and wlmax arguments in
summary.rspec() are being deprecated in favour of a single
lim argument, for consistency across functions.
MINOR FEATURES AND BUG FIXES
summary.rspec() has been rewritten for efficiency, and
now only calculates the required variables when subset is
used. As a result, the function is also slightly slower (0.5 x) when
calculating the full set of variables, but much faster (10 x) when
calculating a subset.
Removed the start-up message.
Removed the previously-deprecated margins argument from
various colourspace plots.
Replace rgl.triangles with triangles3d()
internally to avoid a deprecation issue.
Fixed a bug in the categorical colourspace, so it now returns
sensible category values when x and/or y is
equal to 0.
pavo 2.8.0
MINOR FEATURES AND BUG
FIXES
Updated documentation to fix broken HTML5 equation rendering
Line width in the legend of aggplot() (as specified by
lwd) is now consistent with line width on the plot
(#235)
procspec(spec, opt = "smooth") now works correctly with
uninterpolated spectra. Previously, it was causing a shift of the
spectra towards long-wavelengths (#234).
coldist() now returns Euclidean distances when given
data from the ciexyz model.
as.rspec() now preserves numeric column names when
converting from a tibble.
pavo 2.7.1
MINOR FEATURES AND BUG
FIXES
Minor release to avoid breaking changes to tests.
pavo 2.7.0
NEW FEATURES AND
SIGNIFICANT CHANGES
It is now possible to filter images according to the AcuityView 2.0
algorithm (Caves et al. 2018) in order to to model the visual acuity of
animals, prior to analysis. The functionality is implemented in
procimg(), with details and examples available in the
function’s help documentation and the vignette.
Added the argument raw to bootcoldist().
When TRUE, the full raw list of bootstrapped
colour-distances are returned (equal in length to the number of
replicates specified by boot.n), rather than the summary
statistics which are returned by default.
Added the visual phenotype of the Vinegar fly Drosophila
melanogaster (Sharkey et al. 2020). See ?vismodel() or
?sensdata() for instructions on selecting it.
coldist() now uses the package farver when
calculating CIE2000 colour distances between points in the CIELab and
CIELch spaces.
MINOR FEATURES AND BUG
FIXES
Fixed a bug where procimg() would fail when using resize/rotate
followed by further options, on single images.
Fixed a bug in plot.colspace(gamut = TRUE) (as well as
triplot(), tcsplot(),
tetraplot()) where it would incorrectly display
"Max gamut cannot be plotted." and fail to plot the max
gamut each time.
Fixed a recent bug whereby the D65 illuminant was expressed in units
of radiant flux, by default. It has instead been converted to photon
flux (umol.s-1.m-2).
Added an informative error message when raw quantum catch estimates
are < 1, and an attempt is made to calculate colour distances in the
receptor-noise model using noise = 'quantum'. Taking the
root of negative values following log-transformation, as required when
noise = 'quantum', would previously produce an
uninformative error, which has been rectified.
The margins argument has been deprecated for cie, coc,
hexagon, segment, projplot, di-, tri-, and tetra-chromatic plots. It was
causing problems when later adding points to plots, and margin-handling
is best left to the user anyway. The default plots may therefore look
slightly different, but the margins can be adjusted to taste using the
standard par(mar = c()) pathway.
Fixed a bug where bootcoldist() would not run until
supplied with receptor-noise model arguments (n, weber, weber.ref), even
when not running the receptor-noise model.
Fixed a bug where bootcoldist() would sometimes fail
when given data from colourspace models containing lots of negative
coordinate values. This was particularly common for the hexagon
model.
Improved safety and error handling in adjacent().
pavo 2.6.1
MINOR FEATURES AND BUG
FIXES
Minor fix to a vignette to avoid installation issues.
options() and par() are now always set
locally, including in vignettes and examples, as to prevent spillover of
these changes in the user session
pavo 2.6.0
MINOR FEATURES AND BUG
FIXES
bootcoldist() and adjacent() now use a
random number generator that generates statistically sound values, even
when ran in parallel. The output of these functions is thus expected to
slightly change, even if you set the seed before.
The alphashape3d package has been moved to Suggests,
which means it will not be installed automatically when you install pavo
from CRAN and that you will need to install it yourself if you need it
(for vol(type = "alpha"), vol(type = "alpha")
and voloverlap(type = "alpha"))
pavo 2.5.0
NEW FEATURES AND
SIGNIFICANT CHANGES
Add ability to compute colour volume by using alphashapes instead of
convex hulls. The functions vol(), tcsvol()
and voloverlap() gain a new argument
type = c("convex", "alpha") to decide how you want to
compute the colour volume. Please refer to the vignette
vignette("pavo-5-alphashapes", package = "pavo") for
more information. As a result, the argument order in these 3 function
has changed. Check the documentation to update your scripts accordingly.
The function summary.colspace() also gains an additional
column that returns that colour volume computed with an alpha-shape of
parameter alpha* in the case of tcs objects.
MINOR FEATURES AND BUG
FIXES
getimg() now imports image files with uppercase
extensions (e.g., JPG or PNG), such as those produced by some camera
brands or processing software.
Maximum quantum catches computation (data.maxqcatches
attribute) now works for segment “visual model” as well. As a side
effect, this removes a warning that occurred when users ran
vismodel(..., visual = "segment").
sensmodel() now accepts the argument
sensnames, for specifying the names of the resulting
sensitivity curves on-the-fly.
CIE models now accept data created outside of
vismodel(), by allowing users to specify the illuminant and
viewer sensitivity function used when estimating XYZ values (via
illum and visual arguments in
colspace()).
bootcoldist() is now laxer in its argument checks and
accept objects that are neither vismodel or
colspace objects. This means you can now use this function
on quantum catches dataframe that you obtained outside of pavo, such as
the MICA toolbox.
summary.colspace() now prints a more explicit error
when the by argument value is not a multiple of the number
of rows in the colspace object (i.e., the number of spectra)
Added a continuous measure of hue to the output of the categorical
model of Troje (1993)
teal example dataset columns have been renamed to add
an additional zero in front of single digit numbers, so that column
names now sort in the correct order by default.
Some very small negative values in the built-in visual system data
have been corrected .
as.rspec() is now more lenient for wavelength trimming
when interp = FALSE and now works even if the specified
lims do not correspond to actual wl values from the input
object.
pavo 2.4.0
NEW FEATURES AND
SIGNIFICANT CHANGES
Fixed a bug introduced in version 2.3.0 that gave wrong values for
S1UV and S1V in summary.rspec().
several plot() functions for colspace
(triplot(), tcsplot(),
tetraplot()) gain a new gamut argument to plot
the maximum gamut for a given visual system and illuminant.
summary.colspace() also now returns the maximum colour
volume for a given visual system and illuminant that you can use to
compare to the realised volume by a given dataset. More information in
PR #180.
parallel processing now relies on the future package,
which offers windows and high performance computing (HPC) environments
support. The progress bar is produced by the progressr
package and can be customised as well. As a consequence, the
cores argument in getspec(),
adjacent() and classify() has been
deprecated.
MINOR FEATURES AND BUG
FIXES
fixed a plotting bug introduced in version 2.3.0 where it was
required to run projplot() twice for the background grid to
be displayed.
fixed a bug in summary.colspace() where
NULL was returned instead of
summary.data.frame() for non-tcs colourspaces.
fix partial matching warnings in examples and in
bootcooldist()
the package has a new website at
pavo.colrverse.com
fixed a bug in coldist()that prevented the calculation
of achromatic contrast when using custom quantum catch data
pavo 2.3.0
NEW FEATURES AND
SIGNIFICANT CHANGES
plot.rspec() now adds a linear spectrum alongside the
x-axis to show the hues corresponding to each wavelength (controlled by
the wl.guide boolean argument).
cieplot() (and therefore plot.colspace()
for CIEXYZ model) now adds the background of the CIEXYZ colour space by
default. This can be turned off by switching the ciebg
argument to FALSE.
voloverlap() uses a different algorithm to determine
volume overlaps, which means:
computation is now much more efficient
voloverlap() now works for trispace()
objects as well
accordingly, first two arguments of voloverlap() has
been renamed colsp1 and colsp2 instead of
tcsres1 and tcsres2
slow and possibly inaccurate montecarlo option has been
deprecated
MINOR FEATURES AND BUG
FIXES
errors during argument checks in vismodel() now have
more explicit messages.
all pavo functions (excepted vismodel()
and spec2rgb()) now work with sub-nm precision, for
rspec objects with non-integer wavelengths.
summary.colspace() no longer fails for tcs objects with
only one row.
vismodel() now works for monochromats as well.
procspec(opt = "bin") no longer counts bin edges twice
(once in each consecutive bin). This will cause changes in the bin stops
compared to earlier versions of this function.
coc() and categorical() spaces now return
Weber luminance contrast by default when passed through
coldist(), rather than nothing (as per the original
publications).
coldist() can now take multiple values for
weber, when Weber fractions are known for all receptor
classes
summary.rspec() no longer errors for a single spectrum
when the wavelength range does not contain 450-700nm
pavo 2.2.0
NEW FEATURES AND
SIGNIFICANT CHANGES
added k-medoids clustering as an option in
classify()
coldist() now returns unweighted Euclidean distances
for generic di-, tri-, and tetra-chromatic colspace()
models. Users wishing to estimate noise-weighted distances (i.e. via the
receptor-noise limited model) should continue to use
coldist() directly on vismodel() objects, as
previously.
MINOR FEATURES AND BUG
FIXES
added a message to indicate what distance metric is being calculated
during calls to coldist()
vismodel(), colspace(), and
coldist() now always return lum and
dL columns, for consistency
irrad2flux() and flux2irrad() use slightly
more precise constant values, which may lead to slightly different
results (less than 0.1% difference between this new version and the
previous versions)
getimg() can now import images from URL’s
the cores argument in getimg() is
deprecated, as image import is vectorised
fixed a small bug in classify() when using
refID and kcols for multiple images
the resize argument in procimg() now takes
a percentage, rather than scaling factor
fixed a bug where colspace(space = segment) would
return both a B and (redundant) lum
column
fixed a bug where the rod sensitivity of Canis familiaris
was inaccessible through vismodel()
fixed an issue in getspec() where badly encoded
characters in some spectral files would cause failure
fixed a bug where coldist() would attempt to estimate
receptor-noise weighted distances rather than cie-distances for
cielch model results
pavo 2.1.0
NEW FEATURES AND
POTENTIALLY BREAKING CHANGES
added the argument reclass to procimg(),
which allows users to interactively correct areas within images that
have been misclassified
added the rod sensitivity of Canis familiaris
peakshape() uses a completely different algorithm to
find the FWHM. It now works as expected for spectra with multiple peaks.
See PR #137 for a
detailed overview of the changes.
data used internally by pavo (bgandilum,
transmissiondata, ttvertex,
vissyst) is no longer exposed to users
MINOR FEATURES AND BUG
FIXES
new functions is.vismodel() and
is.colspace() are exported to test whether an object is of
class vismodel or colspace, respectively
fixed a bug where images would sometimes be wrongly detected as
user-classified in as.rimg()
the UV-sensitive cone is now only always named “u”, even for VS
species (such as pfowl and avg.v in
vismodel() and sensdata()). This removes an
unnecessary but harmless warning when colspace() was used
to place quantum catches of such species in the tetrahedral colour
space.
the achro argument in coldist() has been
changed for achromatic to better match the arguments from
vismodel(). Older scripts that use achro
should not be affected and still work as before.
the package imager is no longer a dependency, and is
only loaded if using some features of procimg().
the package mapproj is no longer a dependency, and is
only loaded if using projplot().
added the argument labels.stack to
plot.rspec, which allows the use of custom spectra labels
in stacked plots.
users now receive a warning when interpolating beyond the limits of
the data using as.rspec, and can control the behaviour with
the new argument exceed.limits.
all deprecated functions and arguments have now been fully
removed.
as.rspec() now accepts both numeric and character
vectors to identify the wavelength column using whichwl
(eg. whichwl = "wl").
Reference images in classify() can now be specified
using either a numeric vector (to identify by image position in a list)
or character vector (to identify by image name).
fixed a bug in aggspec() when wavelength column was
previously removed by the user.
fixed a bug where cocplot() would failed whenever
type graphical parameter was specified.
spec2rgb() has been simplified to rely more on
vismodel(). As a result, output values may be slightly
different but upon testing, we found that differences between the old
and the new version were barely noticeable.
the vignette have been split into three smaller parts, which should
help new users to get started with pavo
numerous under-the-hood changes for stability and speed, with thanks
to three reviewers and an associate editor at MEE.
pavo 2.0.0
NEW FEATURES
image-based workflow for the combined analysis of colour and pattern
geometry
added the visual systems of the (trichromatic) jumping spider
Habronattus pyrrithrix and the (trichromatic) triggerfish
Rhinecanthus aculeatus
getspec() can now read Avantes binary files
(.TRM files)
MINOR FEATURES AND BUG
FIXES
Carotenoid chroma (S9) in summary.rspec() has been
fixed to (R700 - R450)/R700. This gives the same result as before but
with a flipped sign, and better reflects the original formula in the
literature.
cieLAB values have been rescaled, and are expressed in the more
standard range: L [0,100], ab [-128,127]
getspec() has an additional argument
ignore.case set to TRUE by default to ignore
case in file extension matching
fix a bug where getspec() would sometimes fail with
files including numbers in scientific format
add a new option in tetraplot() to add cone names
(u,s,m,l)
pavo 1.4.0
NEW FEATURES
getspec() can now read OceanOptics
.ProcSpec files
added the visual system of Ctenophorus ornatus, the
(trichromatic) ornate dragon lizard
MAJOR CHANGES
getspecf() (and the argument fast = TRUE
in getspec()) have been deprecated
summary.rspec() returned incorrect values for S7. If
you use S7, please re-run your analyses
MINOR FEATURES AND BUG
FIXES
summary.rspec() now properly outputs NA
for monotonically decreasing spectra
fixed warning when subset.rspec() was provided with a
logical vector
fixed harmless warning when summary.colspace() was used
on a tcs object
by argument in merge.rspec() is no longer
ignored
fixed bug in voloverlap() when plot = TRUE
fixed bug in vismodel() when transmission has more than
one column
fixed bug in vismodel() that applied von Kries
correction to achromatic channel
added argument fill=FALSE in
voloverlap()
fixed bug in jndplot() when suppressing the plotting of
arrows
better handling of subset data when using summary.colspace() and
summary.vismodel()
fixed bug in coldist() when
noise = "quantum" and achro = TRUE were
used
fixed bug in jndplot() when arrow = "none"
and achro = TRUE
spec2rgb() now takes into account the 390-400 nm
wavelength range into account when possible
as.rspec() no longer fails with tibbles
bin option of procspec() now works for all values of
bins
non-relative quantum catches from dataframe object were not
correctly scaled in “di”, “tri”, “categorical” and “coc”
colorspaces
fixed a bug in colspace() where it would incorrectly
infer a preference for a general trichromatic space, when a cie model is
more appropriate
fixed a bug so that cie color matching functions can be more easily
be used in a general trichromatic space (i.e. maxwell triangle)
pavo 1.3.1
NEW FUNCTIONS
bootcoldist() uses bootstrap to calculate the
confidence intervals on the mean color distance between samples
MINOR FEATURES AND BUG
FIXES
fixed bug in coldist() when fewer samples than the
number of photoreceptors
fixed bug in getspec() that would cause it to crash
with errors
fixed bug in tetraplot() when saving images
pavo 1.3.0
NEW FUNCTIONS
jnd2xyz() converts distances (in JND, resulting from a coldist()
call) into cartesian coordinates
plot() methods for objects resulting from jnd2xyz()
jndrot() produces rotations of Cartesian coordinates resulting from
jnd2xyz()
coldist2mat() converts coldist() result from a pairwise data.frame
to a distance matrix
sensdata() function for retrieving and/or visualising pavo’s
in-build spectral data
MAJOR CHANGES
tetraplot() and cieplot() have been completely rewritten to allow
finer viewing control
tetraplot() allows forced perspective using size to denote
distance
voloverlap() and vol() have also been changed to work with the new
tetraplot() options
getspec() has been rewritten to be faster, more general, and allow
parallel processing
subset functions now allow more than one argument to be used, and
allow further attributes to be passed onto grep (e.g. invert =
TRUE)
MINOR FEATURES AND BUG
FIXES
fixed bug in coldist() on log-transformation when object was neither
of class vismodel nor colspace
fixed bug in dL calculation when input is a colspace object
fixed bug in vismodel() when a data frame, matrix or rspec object
was passed as the background
fixed bug in colspace() models when using non-standard receptor
names or ordering
fixed bug in hexagon() model when calculating location & metrics
for achromatic stimuli
fixed location of red vertex in tetraplot()
fixed bug in the argument names for expanding text labels in
colspace plots
removed na.rm argument from aggspec() that was causing a bug when
the error function did not have that argument. User should pass it as an
argument to the function if necessary.
changed default to achro=FALSE in coldist()
replaced the modelled receptor sensitivities of the honeybee
Apis mellifera with the empirical sensitivities from Peitsch et
al (1992)
the built-in ‘green’ background spectrum is no longer
normalized
removed wavelength limitations in the calculation of H3 from
summary.rspec
all visual systems (except CIE) have been normalized to have an
integral of 1
pavo 1.2.0
MAJOR CHANGES
added the CIELch model accessed via colspace(space = ‘cielch’)
added the sensdata() function for retrieving and/or visualising
pavo’s in-build spectral data
MINOR FEATURES AND BUG
FIXES
vignettes have been amalgamated & the single, main vignette is
now up-to-date
added more informative labels for the segment analysis plot
pavo 1.1.0
NEW FUNCTIONS
segspace() replaces the deprecated segclass(), and is accessed via
the colspace() argument space = ‘segment’. The results of segspace() are
also now compatible with coldist() for the estimation of Euclidean
colour-distances.
segplot() is a plot for Endler’s (1990) segment analysis, and is
accessed — along with all other 2d plots — via plot.colspace()
MINOR FEATURES AND BUG
FIXES
the use of relative quantum catches is now optional in the
categorical colorspace (though still produces a warning), for greater
flexibility
updated several functions to work when rspec object has only one
spectrum
fixed bug in voloverlap where interactive plots would result in
error
fixed incorrect labels in the maxwell triangle plot
fixed a bug in as.rspec() in which lim was not applied when
interpolate = FALSE
fixed bug in aggplot() which resulted in error when using lty, lwd
arguments
warning if ocular media is being used in both vismodel() and
sensmodel()
added an ‘all’ option to the achromatic argument in vismodel()
added the ability to calculate dL for cielab models in
coldist()
added some more informative messages and warnings
pavo 1.0
See vignette for detailed description of changes.
MAJOR CHANGES
coldist() arguments have been changed. Now the empirically estimated
value for the Weber fraction must be entered, instead of the
noise-to-signal ratio. The noise-to-signal ratio is then calculated
based on the empirically estimated Weber fraction for the reference cone
type, and applied to the remaining cone types. This should avoid
confusion between empirically estimated values for the Weber fraction
and the noise-to-signal ratio, which are currently prevalent in the
literature.
coldist() now has an additional argument, weber.achro, so that the
value for the Weber fraction to be used to calculate achromatic contrast
can be input independently of the cone ratios.
tcs() is deprecated, replaced by colspace().
NEW FUNCTIONS
colspace() replaces tcs() and introduces several new
colorspaces
plot() methods for several colspace() outputs, including a static
tetrahedral colorspace
projpoints() allows the plotting of points in a projplot()
figure
vol() draws volume polygons in static tetrahedral plots
axistetra() draws reference x, y and z axis arrows in static
tetrahedral plots
legendtetra() adds legends to static tetrahedral plots
MINOR FEATURES AND BUG
FIXES
summary.colspace() for tcs spaces now returns relative color volume
as well as absolute
tcsvol() and voloverlap() now allow control for line width
procspec() fixed error when attempting to smooth rspec object
without column names
procspec() handles smoothing before fixing negatives to avoid
re-adding negatives when smoothing
procspec(), aggplot() accept additional arguments to summary
functions (e.g., na.rm=TRUE)
peakshape() default wavelength limits (lim) now taken from rspec
object rather than 300-700
peakshape() returns warning if a spectrum contains duplicate
reflectance values
summary.rspec() works with single spectra
aggplot() and aggspec() fixed bug on ordering of levels when they
don’t match the sequence in the rspec object
aggplot() added logical argument “legend” for automatically adding a
legend to the plot
vismodel() returns error if bkg=NULL
getspec() patched to stop returning warnings in Yosemite
getspec() has a faster (~5-10X), but less flexible, algorithm used
when all input files are from the same source.
pavo 0.5-6
BUG FIXES
fixed bug in calculation of dichromat contrast in coldist()
pavo 0.5-5
MINOR FEATURES AND BUG
FIXES
fixed bug in calculation of H3 in summary.rspec()
pavo 0.5-4
MINOR FEATURES AND BUG
FIXES
changed default values for coldist()
pavo 0.5-2
MINOR FEATURES AND BUG
FIXES
fixes to the blue tit visual system, changed vismodel() argument to
“bluetit”
pavo 0.5-1
MINOR FEATURES AND BUG
FIXES
vismodel() accepts matrix, data.frame or rspec objects for the
illuminant, updated warning messages associated with this use
getspec() now removes empty columns (generated by bad
tabulation)
plot.rspec() fix color labelling issue (previously, when user
specified fewer colors than number of spectra, ‘stack’ and ‘overlay’
colored spectra differently)
pavo 0.3
NEW FUNCTIONS
subset() class methods for rspec, vismodel and tcs
summary() method for vismodel, returns attributes used in visual
model
VISUAL MODEL
vismodel() output includes only Qi or fi (as selected by qcatch
argument)
vismodel() von Kries correction is now an optional argument
coldist() subset argument for partial filtering
Updated sensitivity curves
MINOR FEATURES
getspec() works with Avasoft 8 output
aggspec() if no “by” argument is supplied, applies function to all
spectra
BUG FIXES
tcs() accepts receptor names other than usml, issues warning
aggplot() allows control for different line types per spectra
voloverlap() now assigns darkgrey color for overlap if color vector
is of length 1 or 2
pavo 0.1-2
NEW FUNCTIONS
merge.rspec() combines rspec objects in a single object
VISUAL MODEL
Changed vismodel() output: von Kries correction is now an optional
argument, output includes only Qi and fi
vismodel() accepts a scale parameter (multiplies illuminant in order
to make it in flux units)
coldist() includes option for receptor noise calculation
Updated sensitivity curves
MINOR FEATURES
sensmodel() accepts user-defined ocular media transmission
voloverlap() allows greater user control of plotting options
voloverlap() includes Monte Carlo option for overlap
calculation
as.rspec() accepts “whichwl” argument for user-defined wavelength
column selection
as.rspec() includes “interp” argument; updated automatic search for
wavelength column
aggspec() aggregates spectra by multiple vectors (e.g. average
spectra by species and sex using by=list(species,sex) )
peakshape() gives plot titles, allows ask=TRUE and mfrow
BUG FIXES
explorespec() “free” argument fixed
summary.rspec() S5 variable fixed; segments now divided by B1
(brightness-independent measure of saturation)
summary.rspec() checks for positive values when bmaxneg is
calculated, returns NA
tcs() accepts “v” cone class
aggspec() fixed matching of names
procspec() works with rspec objects that include a single
reflectance spectrum