- the
rimg2cimg()function has been removed in favour of a customas.cimg()method. jndrot()and by extensionjnd2xyz()have been adjusted for trichromats to only allow rotations in the 2D plane. Until now, 3D rotations were allowed and the result was projected back in 2D but this meant that the output was no longer representing JNDs distances. Becauserotate = TRUEis the default injnd2xyz(), we recommend you re-run anyjnd2xyz()computation on trichromats. From our tests, results stay qualitatively similar but specific values may change.
- default values for some arguments in
explorespec()andsensmodel()are now explicit in the function definition. as.rspec()now works out of the box withtibble, rather than requiring users to pass a standard data.frame.
- dependency on the
viridisLitepackage has been removed in favour of recent base R functions
- Added a new function
simulate_spec(), which allows for the flexible simulation of naturalistic spectra (inc. reflectance, irradiance, radiance, absorbance). See?simulate_specfor examples and information, and the handbook for further discussion. plot.rspec()now accepts a logicallabelsargument (andlabels.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
wlminandwlmaxarguments insummary.rspec()are being deprecated in favour of a singlelimargument, for consistency across functions.
summary.rspec()has been rewritten for efficiency, and now only calculates the required variables whensubsetis 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
marginsargument from various colourspace plots. - Replace
rgl.triangleswithtriangles3d()internally to avoid a deprecation issue. - Fixed a bug in the categorical colourspace, so it now returns sensible category values when
xand/oryis equal to 0.
- Updated documentation to fix broken HTML5 equation rendering
- Line width in the legend of
aggplot()(as specified bylwd) 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 theciexyzmodel.as.rspec()now preserves numeric column names when converting from a tibble.
- Minor release to avoid breaking changes to tests.
- 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
rawtobootcoldist(). WhenTRUE, the full raw list of bootstrapped colour-distances are returned (equal in length to the number of replicates specified byboot.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 packagefarverwhen calculating CIE2000 colour distances between points in the CIELab and CIELch spaces.
- Fixed a bug where procimg() would fail when using resize/rotate followed by further options, on single images.
- vignettes have been moved to https://book.colrverse.com/ and now use a book format
- Fixed a bug in
plot.colspace(gamut = TRUE)(as well astriplot(),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 whennoise = 'quantum', would previously produce an uninformative error, which has been rectified. - The
marginsargument 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 standardpar(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().
- Minor fix to a vignette to avoid installation issues.
options()andpar()are now always set locally, including in vignettes and examples, as to prevent spillover of these changes in the user session
bootcoldist()andadjacent()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 (forvol(type = "alpha"),vol(type = "alpha")andvoloverlap(type = "alpha"))
- Add ability to compute colour volume by using alphashapes instead of convex hulls. The functions
vol(),tcsvol()andvoloverlap()gain a new argumenttype = c("convex", "alpha")to decide how you want to compute the colour volume. Please refer to the vignettevignette("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 functionsummary.colspace()also gains an additional column that returns that colour volume computed with an alpha-shape of parameter alpha* in the case oftcsobjects.
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.maxqcatchesattribute) now works for segment "visual model" as well. As a side effect, this removes a warning that occurred when users ranvismodel(..., visual = "segment"). sensmodel()now accepts the argumentsensnames, 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 (viaillumandvisualarguments incolspace()). bootcoldist()is now laxer in its argument checks and accept objects that are neithervismodelorcolspaceobjects. 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 thebyargument 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)
tealexample 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 wheninterp = FALSEand now works even if the specifiedlimsdo not correspond to actual wl values from the input object.
- 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 newgamutargument 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
futurepackage, which offers windows and high performance computing (HPC) environments support. The progress bar is produced by theprogressrpackage and can be customised as well. As a consequence, thecoresargument ingetspec(),adjacent()andclassify()has been deprecated.
- 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()whereNULLwas returned instead ofsummary.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
plot.rspec()now adds a linear spectrum alongside the x-axis to show the hues corresponding to each wavelength (controlled by thewl.guideboolean argument).cieplot()(and thereforeplot.colspace()for CIEXYZ model) now adds the background of the CIEXYZ colour space by default. This can be turned off by switching theciebgargument toFALSE.voloverlap()uses a different algorithm to determine volume overlaps, which means:- computation is now much more efficient
voloverlap()now works fortrispace()objects as well- accordingly, first two arguments of
voloverlap()has been renamedcolsp1andcolsp2instead oftcsres1andtcsres2 - slow and possibly inaccurate
montecarlooption has been deprecated
- errors during argument checks in
vismodel()now have more explicit messages. - all
pavofunctions (exceptedvismodel()andspec2rgb()) now work with sub-nm precision, forrspecobjects 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()andcategorical()spaces now return Weber luminance contrast by default when passed throughcoldist(), rather than nothing (as per the original publications).coldist()can now take multiple values forweber, when Weber fractions are known for all receptor classessummary.rspec()no longer errors for a single spectrum when the wavelength range does not contain 450-700nm
- added k-medoids clustering as an option in
classify() coldist()now returns unweighted Euclidean distances for generic di-, tri-, and tetra-chromaticcolspace()models. Users wishing to estimate noise-weighted distances (i.e. via the receptor-noise limited model) should continue to usecoldist()directly onvismodel()objects, as previously.
- added a message to indicate what distance metric is being calculated during calls to
coldist() vismodel(),colspace(), andcoldist()now always returnlumanddLcolumns, for consistencyirrad2flux()andflux2irrad()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
coresargument ingetimg()is deprecated, as image import is vectorised - fixed a small bug in
classify()when usingrefIDandkcolsfor multiple images - the
resizeargument inprocimg()now takes a percentage, rather than scaling factor - fixed a bug where
colspace(space = segment)would return both aBand (redundant)lumcolumn - 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 forcielchmodel results
- added the argument
reclasstoprocimg(), 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
- new functions
is.vismodel()andis.colspace()are exported to test whether an object is of classvismodelorcolspace, 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
pfowlandavg.vinvismodel()andsensdata()). This removes an unnecessary but harmless warning whencolspace()was used to place quantum catches of such species in the tetrahedral colour space. - the
achroargument incoldist()has been changed forachromaticto better match the arguments fromvismodel(). Older scripts that useachroshould not be affected and still work as before. - the package
imageris no longer a dependency, and is only loaded if using some features ofprocimg(). - the package
mapprojis no longer a dependency, and is only loaded if usingprojplot(). - added the argument
labels.stacktoplot.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 argumentexceed.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 usingwhichwl(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 whenevertypegraphical parameter was specified. spec2rgb()has been simplified to rely more onvismodel(). 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.
- 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 (.TRMfiles)
- 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 argumentignore.caseset toTRUEby 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)
getspec()can now read OceanOptics.ProcSpecfiles- added the visual system of Ctenophorus ornatus, the (trichromatic) ornate dragon lizard
getspecf()(and the argumentfast = TRUEingetspec()) have been deprecatedsummary.rspec()returned incorrect values for S7. If you use S7, please re-run your analyses
summary.rspec()now properly outputsNAfor 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 byargument inmerge.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=FALSEinvoloverlap() - 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()whennoise = "quantum"andachro = TRUEwere used - fixed bug in
jndplot()whenarrow = "none"andachro = TRUE spec2rgb()now takes into account the 390-400 nm wavelength range into account when possibleas.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)
bootcoldist()uses bootstrap to calculate the confidence intervals on the mean color distance between samples
- 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
- 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
- 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)
- 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
- added the CIELch model accessed via colspace(space = 'cielch')
- added the sensdata() function for retrieving and/or visualising pavo's in-build spectral data
- vignettes have been amalgamated & the single, main vignette is now up-to-date
- added more informative labels for the segment analysis plot
- 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()
- 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
- See vignette for detailed description of 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().
- 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
- 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.
- fixed bug in calculation of dichromat contrast in coldist()
- fixed bug in calculation of H3 in summary.rspec()
- changed default values for coldist()
- fixes to the blue tit visual system, changed vismodel() argument to "bluetit"
- vismodel() accepts matrix, data.frame or rspec objects for the illuminant, updated warning messages associated with this use
- vismodel() accepts user-defined achromatic receptors
- tcsplot(), tcsvol() & tcspoints(): transparency control passed to user
- getspec() works with OceanView files
- updated citation()
- vismodel() vonkries = TRUE does not return a NULL result
- vismodel() works with a single spectrum object
- tcsplot() allows greater control of tetrahedron appearance
- summary.rspec() allows for user-defined minimum wavelength (for calculation of UV variables)
- irrad2flux() and flux2irrad() to convert illuminant measurements
- vismodel() less cryptic error messages
- as_rspec() fix message pertaining wavelength column
- 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)
- subset() class methods for rspec, vismodel and tcs
- summary() method for vismodel, returns attributes used in 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
- getspec() works with Avasoft 8 output
- aggspec() if no "by" argument is supplied, applies function to all spectra
- 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
- merge.rspec() combines rspec objects in a single object
- 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
- 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
- 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
- peakshape() minor fixes