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.
• 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 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
• vismodel() accepts user-defined achromatic receptors
• tcsplot(), tcsvol() & tcspoints(): transparency control passed to user
• getspec() works with OceanView files

pavo 0.5

• updated citation()

MINOR FEATURES AND BUG FIXES

• 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)

pavo 0.3-1

NEW FUNCTIONS

• irrad2flux() and flux2irrad() to convert illuminant measurements

MINOR FEATURES AND BUG FIXES

• 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)

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
• peakshape() minor fixes