2.9.0

CRAN Release 2.9.0

NEW FEATURES AND SIGNIFICANT CHANGES

• 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 2.7.0

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().

CRAN version 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

CRAN version 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"))

CRAN version 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.

CRAN version 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

CRAN version 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

CRAN version 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 weigted distances rather than cie-distances for cielch model results

CRAN version 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.

CRAN version 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)