Package index • pavo

Processing, Organisation, and Simulation

Functions for importing, processing, and/or simulating spectral data

aggspec(): Aggregate reflectance spectra

as.rspec() is.rspec(): Convert data to an rspec object

as.rimg() is.rimg(): Convert data to an rimg object

is.colspace(): Test if object is of class 'colspace'

is.vismodel(): Test if object is of class 'vismodel'

getspec(): Import spectra files

getimg(): Import image data

irrad2flux() flux2irrad(): Converts between irradiance and photon (quantum) flux

merge(<rspec>): Merge two rspec objects

procimg(): Process images

procspec(): Process spectra

spec2rgb(): Spectrum to rgb colour conversion

subset(<rspec>) subset(<colspace>) subset(<vismodel>): Subset rspec, vismodel, and colspace objects

simulate_spec(): Simulate a spectrum

as.cimg(<rimg>) rimg2magick(): Convert images between class rimg and cimg or magick-image

Visualisation

Functions for visualising spectral data, including the results of visual modelling

plot(<colspace>): Plot spectra in a colourspace

plot(<rimg>): Plot unprocessed or colour-classified images

plot(<rspec>): Plot spectra

plot(<sensmod>): Plot absorbance spectra from sensmodel()

plotsmooth(): Plot loess smoothed curves

aggplot(): Plot aggregated reflectance spectra

axistetra(): Plot reference axes in a static tetrahedral colourspace

explorespec(): Plot spectral curves

legendtetra(): Add legend to a static tetrahedral colourspace

points(<colspace>): Plot points in a colourspace

projplot() projpoints(): 2D projection of a tetrahedral colourspace

sensdata(): Retrieve or plot in-built spectral sensitivity data

tcsplot() tcspoints() tcsvol(): Interactive plot of a tetrahedral colourspace

Analysis

Functions for analysing spectral data

adjacent(): Run an adjacency and boundary strength analysis

bootcoldist(): Bootstrap colour distance confidence intervals

classify(): Identify colour classes in an image for adjacency analyses

coldist(): Colour distances

colspace(): Model spectra in a colorspace

jnd2xyz(): Convert JND distances into perceptually-corrected Cartesian coordinates

jndrot(): Rotate Cartesian coordinates obtained from jnd2xyz()

peakshape(): Peak shape descriptors

sensmodel(): Modeling spectral sensitivity

summary(<colspace>): Colourspace data summary

summary(<rimg>): Image summary

summary(<rspec>): Colourimetric variables

summary(<vismodel>): Visual model summary

vismodel(): Visual models

vol(): Plot a tetrahedral colour space

voloverlap(): Colour volume overlap

Data

Included example datasets

flowers: Reflectance spectra from a suite of native Australian flowers, collected around Cairns, Queensland.

sicalis: Spectral curves from three body regions of stripe-tailed yellow finch (Sicalis citrina) males

teal: Angle-resolved reflectance data for the iridescent wing patch of a male green-winged teal (Anas carolinensis)