,
Rafael Maia [aut] ,
Hugo Gruson [aut] ,
John Endler [aut],
Chad Eliason [aut],
Pierre-Paul Bitton [aut] | Title: | Perceptual Analysis, Visualization and Organization of Spectral Colour Data |
|---|---|
| Description: | A cohesive framework for the spectral and spatial analysis of colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013) <doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019) <doi:10.1111/2041-210X.13174>. |
| Authors: | Thomas White [aut, cre] ,
Rafael Maia [aut] ,
Hugo Gruson [aut] ,
John Endler [aut],
Chad Eliason [aut],
Pierre-Paul Bitton [aut] |
| Maintainer: | Thomas White <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 2.10.0 |
| Built: | 2024-11-08 15:28:27 UTC |
| Source: | https://github.com/rmaia/pavo |
Calculate summary variables from the adjacency (Endler 2012) and boundary-strength (Endler et al. 2018) analyses, along with overall pattern contrast (Endler & Mielke 2005).
adjacent( classimg, xpts = NULL, xscale = NULL, bkgID = NULL, polygon = NULL, exclude = c("none", "background", "object"), coldists = NULL, hsl = NULL )adjacent( classimg, xpts = NULL, xscale = NULL, bkgID = NULL, polygon = NULL, exclude = c("none", "background", "object"), coldists = NULL, hsl = NULL )
classimg |
(required) an xyz matrix, or list of matrices, in which x and
y correspond to spatial (e.g. pixel) coordinates, and z is a numeric code
specifying a colour-class. Preferably the result of |
xpts |
an integer specifying the number of sample points along the x
axis, from which the evenly-spaced sampling grid is constructed (if
required). Defaults to the smallest dimension of |
xscale |
(required) an integer or list of integers equal in length to classimg()
specifying the true length of the x-axis, in preferred units. Not required,
and ignored, only if image scales have been set via |
bkgID |
an integer or vector specifying the colour-class ID number(s) of
pertaining to the background alone, for relatively homogeneous and
uniquely-identified backgrounds (e.g. the matte background of pinned
specimens). Examine the attributes of, or call |
polygon |
a data.frame of x-y coordinates delineating a closed polygon
that separates the focal object from the background. Not required, and
ignored, if the focal object outline is specified using |
exclude |
the portion of the scene to be excluded from the analysis, if any.
|
coldists |
a data.frame specifying the visually-modelled chromatic (dS)
and/or achromatic (dL) distances between colour-categories. The first two
columns should be named 'c1' and 'c2', and specify all possible
combinations of numeric colour-class ID's (viewable by calling
|
hsl |
data.frame specifying the hue, saturation, and luminance of color
patch elements, as might be estimated via |
You can customise the type of parallel processing used by this function with
the future::plan() function. This works on all operating systems, as well
as high performance computing (HPC) environment. Similarly, you can customise
the way progress is shown with the progressr::handlers() functions
(progress bar, acoustic feedback, nothing, etc.)
a data frame of summary variables:
'k': The number of user-specified colour and/or luminance classes.
'N': The grand total (sum of diagonal and off-diagonal) transitions.
'n_off': The total off-diagonal transitions.
'p_i': The overall frequency of colour class i.
'q_i_j': The frequency of transitions between all colour classes i
and j, such that sum(q_i_j) = 1.
't_i_j': The frequency of off-diagonal (i.e. class-change transitions)
transitions i and j, such that sum(t_i_j) = 1.
'm': The overall transition density (mean transitions), in units
specified in the argument xscale.
'm_r': The row-wise transition density (mean row transitions), in
user-specified units.
'm_c': The column-wise transition density (mean column transitions), in
user-specified units.
'A': The transition aspect ratio (< 1 = wide, > 1 = tall).
'Sc': Simpson colour class diversity, Sc = 1/(sum(p_i^2)). If all
colour and luminance classes are equal in relative area, then Sc = k.
'St': Simpson transition diversity, St = 1/sum(t_i_j^2).
'Jc': Simpson colour class diversity relative to its achievable maximum.
Jc = Sc/k.
'Jt': Simpson transition diversity relative to its achievable maximum.
Jt = St/(k*(k-1)/2).
'B': The animal/background transition ratio, or the ratio of class-change
transitions entirely within the focal object and those involving the object
and background,
B = sum(O_a_a / O_a_b).
'Rt': Ratio of animal-animal and animal-background transition
diversities, Rt = St_a_a / St_a_b.
'Rab': Ratio of animal-animal and background-background transition
diversities, Rt = St_a_a / St_b_b.
'm_dS', 's_dS', 'cv_dS': weighted mean, sd, and coefficient of variation
of the chromatic boundary strength.
'm_dL', 's_dL', 'cv_dL': weighted mean, sd, and coefficient of variation
of the achromatic boundary strength.
'm_hue', 's_hue', 'var_hue': circular mean, sd, and variance of overall
pattern hue (in radians).
'm_sat', 's_sat', 'cv_sat': weighted mean, sd, and coefficient variation
of overall pattern saturation.
'm_lum', 's_lum', 'cv_lum': weighted mean, sd, and coefficient variation
of overall pattern luminance.
Thomas E. White [email protected]
Endler, J. A. (2012). A framework for analysing colour pattern geometry: adjacent colours. Biological Journal Of The Linnean Society, 107(2), 233-253.
Endler, J. A., Cole G., Kranz A. (2018). Boundary Strength Analysis: Combining color pattern geometry and coloured patch visual properties for use in predicting behaviour and fitness. Methods in Ecology and Evolution, 9(12), 2334-2348.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
classify(), summary.rimg(), procimg()
# Set a seed, for reproducibility set.seed(153) # Run the adjacency analysis on a single image of a butterfly papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio_class <- classify(papilio, kcols = 4) papilio_adj <- adjacent(papilio_class, xscale = 100) # Expand on the above, by including (fake) color distances and hsl values # of colour elements in the image # Generate fake color distances distances <- data.frame( c1 = c(1, 1, 1, 2, 2, 3), c2 = c(2, 3, 4, 3, 4, 4), dS = c(5.3, 3.5, 5.7, 2.9, 6.1, 3.2), dL = c(5.5, 6.6, 3.3, 2.2, 4.4, 6.6) ) # Generate some fake hue, saturation, luminance values hsl_vals <- data.frame( patch = seq_len(4), hue = c(1.5, 2.2, 1.0, 0.5), lum = c(10, 5, 7, 3), sat = c(3.5, 1.1, 6.3, 1.3) ) # Run the full analysis, including the white background's ID papilio_adj <- adjacent(papilio_class, xscale = 100, bkgID = 1, coldists = distances, hsl = hsl_vals ) # Run an adjacency analysis on multiple images. # First load some images of coral snake colour patterns snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) # Automatically colour-classify the coral snake patterns snakes_class <- classify(snakes, kcols = 3) # Run the adjacency analysis, with varying real-world scales for each image snakes_adj <- adjacent(snakes_class, xpts = 120, xscale = c(50, 55))# Set a seed, for reproducibility set.seed(153) # Run the adjacency analysis on a single image of a butterfly papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio_class <- classify(papilio, kcols = 4) papilio_adj <- adjacent(papilio_class, xscale = 100) # Expand on the above, by including (fake) color distances and hsl values # of colour elements in the image # Generate fake color distances distances <- data.frame( c1 = c(1, 1, 1, 2, 2, 3), c2 = c(2, 3, 4, 3, 4, 4), dS = c(5.3, 3.5, 5.7, 2.9, 6.1, 3.2), dL = c(5.5, 6.6, 3.3, 2.2, 4.4, 6.6) ) # Generate some fake hue, saturation, luminance values hsl_vals <- data.frame( patch = seq_len(4), hue = c(1.5, 2.2, 1.0, 0.5), lum = c(10, 5, 7, 3), sat = c(3.5, 1.1, 6.3, 1.3) ) # Run the full analysis, including the white background's ID papilio_adj <- adjacent(papilio_class, xscale = 100, bkgID = 1, coldists = distances, hsl = hsl_vals ) # Run an adjacency analysis on multiple images. # First load some images of coral snake colour patterns snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) # Automatically colour-classify the coral snake patterns snakes_class <- classify(snakes, kcols = 3) # Run the adjacency analysis, with varying real-world scales for each image snakes_adj <- adjacent(snakes_class, xpts = 120, xscale = c(50, 55))
Combines and plots spectra (by taking the average and the standard deviation, for example) according to an index or a vector of identities.
aggplot( rspecdata, by = NULL, FUN.center = mean, FUN.error = sd, lcol = NULL, shadecol = NULL, alpha = 0.2, legend = FALSE, ... )aggplot( rspecdata, by = NULL, FUN.center = mean, FUN.error = sd, lcol = NULL, shadecol = NULL, alpha = 0.2, legend = FALSE, ... )
rspecdata |
(required) a data frame, possibly of class |
by |
(required) either a single value specifying the range of spectra
within the data frame to be combined (for example, |
FUN.center |
the function to be applied to the groups of spectra,
calculating a measure of central tendency (defaults to |
FUN.error |
the function to be applied to the groups of spectra,
calculating a measure of variation (defaults to |
lcol |
colour of plotted lines indicating central tendency. |
shadecol |
colour of shaded areas indicating variance measure. |
alpha |
transparency of the shaded areas. |
legend |
automatically add a legend. |
... |
additional graphical parameters to be passed to plot. |
Plot containing the lines and shaded areas of the groups of spectra.
Rafael Maia [email protected]
Chad Eliason [email protected]
Montgomerie R (2006) Analyzing colors. In: Hill G, McGraw K (eds) Bird coloration. Harvard University Press, Cambridge, pp 90-147.
# Load reflectance data data(sicalis) # Create grouping variable based on spec names bysic <- gsub("^ind[0-9].", "", names(sicalis)[-1]) # Plot using various error functions and options aggplot(sicalis, bysic) aggplot(sicalis, bysic, FUN.error = function(x) quantile(x, c(0.0275, 0.975))) aggplot(sicalis, bysic, shadecol = spec2rgb(sicalis), lcol = 1) aggplot(sicalis, bysic, lcol = 1, FUN.error = function(x) sd(x) / sqrt(length(x)))# Load reflectance data data(sicalis) # Create grouping variable based on spec names bysic <- gsub("^ind[0-9].", "", names(sicalis)[-1]) # Plot using various error functions and options aggplot(sicalis, bysic) aggplot(sicalis, bysic, FUN.error = function(x) quantile(x, c(0.0275, 0.975))) aggplot(sicalis, bysic, shadecol = spec2rgb(sicalis), lcol = 1) aggplot(sicalis, bysic, lcol = 1, FUN.error = function(x) sd(x) / sqrt(length(x)))
Combines spectra (by taking the average, for example) according to an index or a vector of identities.
aggspec(rspecdata, by = NULL, FUN = mean, trim = TRUE)aggspec(rspecdata, by = NULL, FUN = mean, trim = TRUE)
rspecdata |
(required) a data frame, possibly of class |
by |
(required) either a single value specifying the range of spectra
within the data frame to be combined (for example, |
FUN |
the function to be applied to the groups of spectra. (defaults to
|
trim |
logical. if |
A data frame of class rspec containing the spectra after applying
the aggregating function.
Chad Eliason [email protected]
Montgomerie R (2006) Analyzing colors. In: Hill G, McGraw K (eds) Bird coloration. Harvard University Press, Cambridge, pp 90-147.
data(teal) # Average every two spectra teal.sset1 <- aggspec(teal, by = 2) plot(teal.sset1) # Create factor and average spectra by levels 'a' and 'b' ind <- rep(c("a", "b"), times = 6) teal.sset2 <- aggspec(teal, by = ind) plot(teal.sset2)data(teal) # Average every two spectra teal.sset1 <- aggspec(teal, by = 2) plot(teal.sset1) # Create factor and average spectra by levels 'a' and 'b' ind <- rep(c("a", "b"), times = 6) teal.sset2 <- aggspec(teal, by = ind) plot(teal.sset2)
Converts an array of RGB values, a cimg object, or a magick-image object,
to an rimg object.
as.rimg(object, name = "img") ## Default S3 method: as.rimg(object, name = "img") ## S3 method for class 'cimg' as.rimg(object, name = "img") is.rimg(object)as.rimg(object, name = "img") ## Default S3 method: as.rimg(object, name = "img") ## S3 method for class 'cimg' as.rimg(object, name = "img") is.rimg(object)
object |
(required) a three-dimensional array containing RGB values. |
name |
the name(s) of the image(s). |
an object of class rimg for use in further pavo functions
a logical value indicating whether the object is of class rimg
Thomas E. White [email protected]
Hugo Gruson [email protected]
# Generate some fake image data fake <- array( c( as.matrix(rep(c(0.2, 0.4, 0.6), each = 250)), as.matrix(rep(c(0.4, 0.7, 0.8), each = 250)), as.matrix(rep(c(0.6, 0.1, 0.2), each = 250)) ), dim = c(750, 750, 3) ) # Inspect it head(fake) # Determine if is an rimg object is.rimg(fake) # Convert to rimg object and check again fake2 <- as.rimg(fake) is.rimg(fake2)# Generate some fake image data fake <- array( c( as.matrix(rep(c(0.2, 0.4, 0.6), each = 250)), as.matrix(rep(c(0.4, 0.7, 0.8), each = 250)), as.matrix(rep(c(0.6, 0.1, 0.2), each = 250)) ), dim = c(750, 750, 3) ) # Inspect it head(fake) # Determine if is an rimg object is.rimg(fake) # Convert to rimg object and check again fake2 <- as.rimg(fake) is.rimg(fake2)
Converts data frames or matrices containing spectral data to rspec
object
as.rspec( object, whichwl = NULL, interp = TRUE, lim = NULL, exceed.range = TRUE ) is.rspec(object)as.rspec( object, whichwl = NULL, interp = TRUE, lim = NULL, exceed.range = TRUE ) is.rspec(object)
object |
(required) a data frame or matrix containing spectra to process. |
whichwl |
a numeric or character vector specifying which column contains
wavelengths. If |
interp |
whether to interpolate wavelengths in 1-nm bins (defaults to
|
lim |
vector specifying wavelength range to interpolate over (e.g.
|
exceed.range |
logical. Should data be interpolated to the limits
specified by |
an object of class rspec for use in further pavo functions
a logical value indicating whether the object is of class rspec
Chad Eliason [email protected]
# Generate some fake reflectance data fakedat <- data.frame(wl = 300:700, refl1 = rnorm(401), refl2 = rnorm(401)) head(fakedat) # Determine if is rspec object is.rspec(fakedat) # Convert to rspec object fakedat2 <- as.rspec(fakedat) is.rspec(fakedat2) head(fakedat2)# Generate some fake reflectance data fakedat <- data.frame(wl = 300:700, refl1 = rnorm(401), refl2 = rnorm(401)) head(fakedat) # Determine if is rspec object is.rspec(fakedat) # Convert to rspec object fakedat2 <- as.rspec(fakedat) is.rspec(fakedat2) head(fakedat2)
Plots reference x, y and z arrows showing the direction of the axes in a static tetrahedral colourspace plot.
axistetra( x = 0, y = 1.3, size = 0.1, arrowhead = 0.05, col = par("fg"), lty = par("lty"), lwd = par("lwd"), label = TRUE, adj.label = list(x = c(0.003, 0), y = c(0.003, 0.003), z = c(0, 0.003)), label.cex = 1, label.col = NULL )axistetra( x = 0, y = 1.3, size = 0.1, arrowhead = 0.05, col = par("fg"), lty = par("lty"), lwd = par("lwd"), label = TRUE, adj.label = list(x = c(0.003, 0), y = c(0.003, 0.003), z = c(0, 0.003)), label.cex = 1, label.col = NULL )
x, y
|
position of the legend relative to plot limits (usually a value between 0 and 1, but because of the perspective distortion, values greater than 1 are possible) |
size |
length of the arrows. Can be either a single value (applied for x, y and z) or a vector of 3 separate values for each axis. |
arrowhead |
size of the arrowhead. |
col, lty, lwd
|
graphical parameters for the arrows. |
label |
logical, include x, y and z labels (defaults to |
adj.label |
position adjustment for the labels. a list of 3 named objects for x, y and z arrows, each with 2 values for x and y adjustment. |
label.cex, label.col
|
graphical parameters for the labels. |
axistetra adds reference arrows showing the direction of the
3-dimensional axes in a static tetrahedral colourspace plot.
Rafael Maia [email protected]
data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") plot(tcs.sicalis) axistetra()data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") plot(tcs.sicalis) axistetra()
Uses a bootstrap procedure to generate confidence intervals for the mean colour distance between two or more samples of colours
bootcoldist(vismodeldata, by, boot.n = 1000, alpha = 0.95, raw = FALSE, ...)bootcoldist(vismodeldata, by, boot.n = 1000, alpha = 0.95, raw = FALSE, ...)
vismodeldata |
(required) quantum catch colour data.
Can be the result from |
by |
(required) a numeric or character vector indicating the group to which each row from the object belongs to. |
boot.n |
number of bootstrap replicates (defaults to 1000) |
alpha |
the confidence level for the confidence intervals (defaults to 0.95) |
raw |
should the full set of bootstrapped distances (equal in length to boot.n) be returned, instead of the summary distances and CI's? Defaults to FALSE. |
... |
other arguments to be passed to |
You can customise the type of parallel processing used by this function with
the future::plan() function. This works on all operating systems, as well
as high performance computing (HPC) environment. Similarly, you can customise
the way progress is shown with the progressr::handlers() functions
(progress bar, acoustic feedback, nothing, etc.)
a matrix including the empirical mean and bootstrapped
confidence limits for dS (and dL if achromatic = TRUE), or a data.frame
of raw bootstraped dS (and dL if achromatic = TRUE) values equal in length to boot.n.
Maia, R., White, T. E., (2018) Comparing colors using visual models. Behavioral Ecology, ary017 doi:10.1093/beheco/ary017
# Run the receptor-noise limited model, using the visual phenotype # of the blue tit data(sicalis) vm <- vismodel(sicalis, achromatic = "bt.dc", relative = FALSE) gr <- gsub("ind..", "", rownames(vm)) bootcoldist(vm, by = gr, n = c(1, 2, 2, 4), weber = 0.1, weber.achro = 0.1) # Run the same again, though as a simple colourspace model data(sicalis) vm <- vismodel(sicalis, achromatic = "bt.dc") space <- colspace(vm) gr <- gsub("ind..", "", rownames(space)) bootcoldist(space, by = gr) # Estimate bootstrapped colour-distances for a more 'specialised' model, # like the colour hexagon data(flowers) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) flowers.hex <- colspace(vis.flowers, space = "hexagon") pop_group <- c(rep("pop_1", nrow(flowers.hex) / 2), rep("pop_2", nrow(flowers.hex) / 2)) bootcoldist(flowers.hex, by = pop_group)# Run the receptor-noise limited model, using the visual phenotype # of the blue tit data(sicalis) vm <- vismodel(sicalis, achromatic = "bt.dc", relative = FALSE) gr <- gsub("ind..", "", rownames(vm)) bootcoldist(vm, by = gr, n = c(1, 2, 2, 4), weber = 0.1, weber.achro = 0.1) # Run the same again, though as a simple colourspace model data(sicalis) vm <- vismodel(sicalis, achromatic = "bt.dc") space <- colspace(vm) gr <- gsub("ind..", "", rownames(space)) bootcoldist(space, by = gr) # Estimate bootstrapped colour-distances for a more 'specialised' model, # like the colour hexagon data(flowers) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) flowers.hex <- colspace(vis.flowers, space = "hexagon") pop_group <- c(rep("pop_1", nrow(flowers.hex) / 2), rep("pop_2", nrow(flowers.hex) / 2)) bootcoldist(flowers.hex, by = pop_group)
Classify image pixels into discrete colour classes.
classify( imgdat, method = c("kMeans", "kMedoids"), kcols = NULL, refID = NULL, interactive = FALSE, plotnew = FALSE, col = "red", ... )classify( imgdat, method = c("kMeans", "kMedoids"), kcols = NULL, refID = NULL, interactive = FALSE, plotnew = FALSE, col = "red", ... )
imgdat |
(required) image data. Either a single image, or a series of images
stored in a list. Preferably the result of |
method |
methods for image segmentation/classification.
|
kcols |
the number of discrete colour classes present in the input image(s).
Can be a single integer when only a single image is present, or if kcols is identical for all
images. When passing a list of images, |
refID |
either the numeric index or name of a 'reference' image, for use when passing a list of images. Other images will be k-means classified using centres identified in the single reference image, thus helping to ensure that homologous pattern elements will be reliably classified between images, if so desired. |
interactive |
interactively specify the colour-category 'centers', for k-means clustering.
When |
plotnew |
Should plots be opened in a new window when |
col |
the color of the marker points, when |
... |
additional graphical parameters when |
You can customise the type of parallel processing used by this function with
the future::plan() function. This works on all operating systems, as well
as high performance computing (HPC) environment. Similarly, you can customise
the way progress is shown with the progressr::handlers() functions
(progress bar, acoustic feedback, nothing, etc.)
A matrix, or list of matrices, of class rimg containing the colour
class classifications ID at each pixel location. The RGB values corresponding to
cluster centres (i.e. colour classes) are stored as object attributes.
Since the kmeans process draws on random numbers to find initial
cluster centres when interactive = FALSE, use set.seed() if reproducible
cluster ID's are desired between runs.
Thomas E. White [email protected]
# Single image papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio_class <- classify(papilio, kcols = 4) # Multiple images, with interactive classification and a reference image snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) if (interactive()) { snakes_class <- classify(snakes, refID = "snake_01", interactive = TRUE) }# Single image papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio_class <- classify(papilio, kcols = 4) # Multiple images, with interactive classification and a reference image snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) if (interactive()) { snakes_class <- classify(snakes, refID = "snake_01", interactive = TRUE) }
Calculates colour distances. When data are the result of vismodel(), it
applies the receptor-noise model of Vorobyev et al. (1998) to calculate
colour distances with noise based on relative photoreceptor densities. It
also accepts colspace() data in which case unweighted Euclidean distances,
CIE2000 distances (cielab and cielch only), or Manhattan distances (coc model only)
are returned.
coldist( modeldata, noise = c("neural", "quantum"), subset = NULL, achromatic = FALSE, qcatch = NULL, n = c(1, 2, 2, 4), weber = 0.1, weber.ref = "longest", weber.achro = 0.1 )coldist( modeldata, noise = c("neural", "quantum"), subset = NULL, achromatic = FALSE, qcatch = NULL, n = c(1, 2, 2, 4), weber = 0.1, weber.ref = "longest", weber.achro = 0.1 )
modeldata |
(required) quantum catch colour data. Can be the result from
|
noise |
how the noise will be calculated (ignored for
|
subset |
If only some of the comparisons should be returned, a character vector of length 1 or 2 can be provided, indicating which samples are desired. The subset vector must match the labels of the input samples, but partial matching (and regular expressions) are supported. |
achromatic |
Logical. If |
qcatch |
if the object is of class |
n |
photoreceptor densities for the cones used in visual modeling. must
have same length as number of columns (excluding achromatic receptor if
used; defaults to the Pekin robin Leiothrix lutea densities:
|
weber |
The Weber fraction(s) to be used (often also referred to as
receptor noise, or e). The noise-to-signal ratio |
weber.ref |
the cone class used to obtain the empirical estimate of the
Weber fraction used for the |
weber.achro |
the Weber fraction to be used to calculate achromatic
contrast, when |
A data frame containing up to 4 columns. The first two
(patch1, patch2) refer to the two colors being contrasted; dS is the
chromatic contrast (delta S) and dL is the achromatic contrast (delta L).
Units of dS JND's in the receptor-noise model, unweighted Euclidean
distances in colorspace models, and Manhattan distances in the
colour-opponent-coding space. Units of dL vary, and are either simple
contrast, Weber contrast, or Michelson contrast, as indicated by the output
message.
Generic di- tri- and tetra-chromatic
colspace objects were previously passed through the receptor-noise
limited model to return noise-weighted Euclidean distances. This behaviour
has been amended, and generic spaces now return unweighted Euclidean
distances. Equivalent results to the former behaviour can be attained by
sending the results of vismodel() directly to coldist() , as
previously, which also offers greater flexibility and reliability. Thus
coldist() now returns unweighted Euclidean distances for colspace
objects (with the exception of Manhattan distances for the coc space, and CIE2000,
distances for CIELab and CIELCh spaces), and noise-weighted Euclidean distances
for vismodel objects.
Thomas E. White [email protected]
Rafael Maia [email protected]
Vorobyev, M., Osorio, D., Bennett, A., Marshall, N., & Cuthill, I. (1998). Tetrachromacy, oil droplets and bird plumage colours. Journal Of Comparative Physiology A-Neuroethology Sensory Neural And Behavioral Physiology, 183(5), 621-633.
Hart, N. S. (2001). The visual ecology of avian photoreceptors. Progress In Retinal And Eye Research, 20(5), 675-703.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
Olsson, P., Lind, O., & Kelber, A. (2015) Bird colour vision: behavioural thresholds reveal receptor noise. Journal of Experimental Biology, 218, 184-193.
Lind, O. (2016) Colour vision and background adaptation in a passerine bird, the zebra finch (Taeniopygia guttata). Royal Society Open Science, 3, 160383.
Olsson, P., Lind, O., & Kelber, A. (2017) Chromatic and achromatic vision: parameter choice and limitations for reliable model predictions. Behavioral Ecology, doi:10.1093/beheco/arx133
# Dichromat data(flowers) vis.flowers <- vismodel(flowers, visual = "canis", relative = FALSE) didist.flowers <- coldist(vis.flowers, n = c(1, 2)) # Trichromat vis.flowers <- vismodel(flowers, visual = "apis", relative = FALSE) tridist.flowers <- coldist(vis.flowers, n = c(1, 2, 1)) # Trichromat, colour-hexagon model (euclidean distances) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) hex.flowers <- colspace(vis.flowers, space = "hexagon") hexdist.flowers <- coldist(hex.flowers) # Trichromat, colour-opponent-coding model (manhattan distances) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE) coc.flowers <- colspace(vis.flowers, space = "coc") hexdist.flowers <- coldist(coc.flowers) # Tetrachromat data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv", relative = FALSE) tetradist.sicalis.n <- coldist(vis.sicalis)# Dichromat data(flowers) vis.flowers <- vismodel(flowers, visual = "canis", relative = FALSE) didist.flowers <- coldist(vis.flowers, n = c(1, 2)) # Trichromat vis.flowers <- vismodel(flowers, visual = "apis", relative = FALSE) tridist.flowers <- coldist(vis.flowers, n = c(1, 2, 1)) # Trichromat, colour-hexagon model (euclidean distances) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) hex.flowers <- colspace(vis.flowers, space = "hexagon") hexdist.flowers <- coldist(hex.flowers) # Trichromat, colour-opponent-coding model (manhattan distances) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE) coc.flowers <- colspace(vis.flowers, space = "coc") hexdist.flowers <- coldist(coc.flowers) # Tetrachromat data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv", relative = FALSE) tetradist.sicalis.n <- coldist(vis.sicalis)
Models reflectance spectra in a colorspace. For information on plotting
arguments and graphical parameters, see plot.colspace().
colspace( vismodeldata, space = c("auto", "di", "tri", "tcs", "hexagon", "coc", "categorical", "ciexyz", "cielab", "cielch", "segment"), qcatch = NULL, ... )colspace( vismodeldata, space = c("auto", "di", "tri", "tcs", "hexagon", "coc", "categorical", "ciexyz", "cielab", "cielch", "segment"), qcatch = NULL, ... )
vismodeldata |
(required) quantum catch color data. Can be either the
result from |
space |
Which colorspace/model to use. Options are:
|
qcatch |
Which quantal catch metric is being inputted. Only used when
input data is NOT an output from |
... |
additional arguments passed to |
Rafael Maia [email protected]
Thomas White [email protected]
Smith T, Guild J. (1932) The CIE colorimetric standards and their use. Transactions of the Optical Society, 33(3), 73-134.
Westland S, Ripamonti C, Cheung V. (2012). Computational colour science using MATLAB. John Wiley & Sons.
Chittka L. (1992). The colour hexagon: a chromaticity diagram based on photoreceptor excitations as a generalized representation of colour opponency. Journal of Comparative Physiology A, 170(5), 533-543.
Chittka L, Shmida A, Troje N, Menzel R. (1994). Ultraviolet as a component of flower reflections, and the colour perception of Hymenoptera. Vision research, 34(11), 1489-1508.
Troje N. (1993). Spectral categories in the learning behaviour of blowflies. Zeitschrift fur Naturforschung C, 48, 96-96.
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
Kelber A, Vorobyev M, Osorio D. (2003). Animal colour vision - behavioural tests and physiological concepts. Biological Reviews, 78, 81 - 118.
Backhaus W. (1991). Color opponent coding in the visual system of the honeybee. Vision Research, 31, 1381-1397.
Endler, J. A. (1990) On the measurement and classification of color in studies of animal color patterns. Biological Journal of the Linnean Society, 41, 315-352.
data(flowers) # Model a dichromat viewer in a segment colourspace vis.flowers <- vismodel(flowers, visual = "canis") di.flowers <- colspace(vis.flowers, space = "di") # Model a honeybee viewer in the colour hexagon vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) hex.flowers <- colspace(vis.flowers, space = "hexagon") # Model a trichromat (the honeybee) in a Maxwell triangle vis.flowers <- vismodel(flowers, visual = "apis") tri.flowers <- colspace(vis.flowers, space = "tri") plot(tri.flowers) # Model a tetrachromat (the Blue Tit) in a tetrahedral colourspace vis.flowers <- vismodel(flowers, visual = "bluetit") tcs.flowers <- colspace(vis.flowers, space = "tcs") # Model a housefly in the 'categorical' colourspace vis.flowers <- vismodel(flowers, visual = "musca", achro = "md.r1") cat.flowers <- colspace(vis.flowers, space = "categorical")data(flowers) # Model a dichromat viewer in a segment colourspace vis.flowers <- vismodel(flowers, visual = "canis") di.flowers <- colspace(vis.flowers, space = "di") # Model a honeybee viewer in the colour hexagon vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) hex.flowers <- colspace(vis.flowers, space = "hexagon") # Model a trichromat (the honeybee) in a Maxwell triangle vis.flowers <- vismodel(flowers, visual = "apis") tri.flowers <- colspace(vis.flowers, space = "tri") plot(tri.flowers) # Model a tetrachromat (the Blue Tit) in a tetrahedral colourspace vis.flowers <- vismodel(flowers, visual = "bluetit") tcs.flowers <- colspace(vis.flowers, space = "tcs") # Model a housefly in the 'categorical' colourspace vis.flowers <- vismodel(flowers, visual = "musca", achro = "md.r1") cat.flowers <- colspace(vis.flowers, space = "categorical")
Plots one or multiple spectral curves in the same graph to rapidly compare groups of spectra.
explorespec( rspecdata, by = 1, scale = c("equal", "free"), legpos = "topright", ... )explorespec( rspecdata, by = 1, scale = c("equal", "free"), legpos = "topright", ... )
rspecdata |
(required) a data frame, possibly of class |
by |
number of spectra to include in each graph (defaults to 1) |
scale |
defines how the y-axis should be scaled. |
legpos |
legend position control. Either a vector containing |
... |
additional parameters to be passed to plot |
Spectral curve plots
Number of plots presented per page depends on the number of graphs produced.
Pierre-Paul Bitton [email protected]
data(sicalis) explorespec(sicalis, 3) explorespec(sicalis, 3, ylim = c(0, 100), legpos = c(500, 80))data(sicalis) explorespec(sicalis, 3) explorespec(sicalis, 3, ylim = c(0, 100), legpos = c(500, 80))
Dataset containing reflectance measurements from 36 native Australian angiosperm species, indicated by column names.
data(flowers)data(flowers)
An object of class rspec (inherits from data.frame) with 401 rows and 37 columns.
Thomas White [email protected]
Dalrymple, R., L., Kemp, D. J., Flores-Moreno, H., Laffan, S. W., White, T. E., Hemmings, F. A., Tindall, M. L., & Moles, A. T. (2015). Birds, butterflies and flowers in the tropics are not more colourful than those at higher latitudes. Global Ecology and Biogeography, 24(12), 1424-1432. doi:10.1111/geb.12368
White, T. E., Dalrymple, R. L., Herberstein, M. E., & Kemp, D. J. (2017). The perceptual similarity of orb-spider prey lures and flowers colours. Evolutionary Ecology, 31(1), 1-20. doi:10.1007/s10682-016-9876-x
Dalrymple, R. L., Flores-Moreno, H., Kemp, D. J., White, T. E., Laffan, S. W., Hemmings, F. A., Tindall, M. L., & Moles, A. T. (2018). Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration. Ecological Monographs, 88(2), 204-224.
Finds and imports PNG, JPEG, and/or BMP images.
getimg(imgpath = getwd(), subdir = FALSE, subdir.names = FALSE, max.size = 1)getimg(imgpath = getwd(), subdir = FALSE, subdir.names = FALSE, max.size = 1)
imgpath |
(required) either the full file-path or URL to an image (including extension), or the path to a folder in which multiple image files are located. Mixed file formats within a folder are accepted. |
subdir |
should subdirectories within the |
subdir.names |
should subdirectory path be included in the name of the
images? (defaults to |
max.size |
maximum size of all images to be allowed in memory, in GB. Defaults to
|
a image, or list of images, of class rimg, for use in further
pavo functions.
Thomas E. White [email protected]
# Single image papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) # Multiple images snakes <- getimg(system.file("testdata/images/snakes", package = "pavo"))# Single image papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) # Multiple images snakes <- getimg(system.file("testdata/images/snakes", package = "pavo"))
Finds and imports spectra files from a folder. Currently works for reflectance files generated in Ocean Optics SpectraSuite (USB2000, USB4000 and Jaz spectrometers), CRAIC software (after exporting) and Avantes (before or after exporting).
getspec( where = getwd(), ext = "txt", lim = c(300, 700), decimal = ".", sep = NULL, subdir = FALSE, subdir.names = FALSE, ignore.case = TRUE )getspec( where = getwd(), ext = "txt", lim = c(300, 700), decimal = ".", sep = NULL, subdir = FALSE, subdir.names = FALSE, ignore.case = TRUE )
where |
Folder in which files are located (defaults to current working directory). |
ext |
File extension to be searched for, without the "." (defaults to
|
lim |
A vector with two numbers determining the wavelength limits to be
considered (defaults to |
decimal |
Character to be used to identify decimal plates
(defaults to |
sep |
Column delimiting characters to be considered in addition to the default (which are: tab, space, and ";") |
subdir |
Should subdirectories within the |
subdir.names |
Should subdirectory path be included in the name of the
spectra? (defaults to |
ignore.case |
Should the extension search be case insensitive? (defaults
to |
You can customise the type of parallel processing used by this function with
the future::plan() function. This works on all operating systems, as well
as high performance computing (HPC) environment. Similarly, you can customise
the way progress is shown with the progressr::handlers() functions
(progress bar, acoustic feedback, nothing, etc.)
A data frame, of class rspec, containing individual imported
spectral files as columns.
Reflectance values are interpolated to the nearest wavelength integer.
Rafael Maia [email protected]
Hugo Gruson [email protected]
Gruson H, White TE, Maia R (2019) lightr: import spectral data and metadata in R. Journal of Open Source Software, 4(43), 1857, doi:10.21105/joss.01857.
lightr::lr_get_spec() for a more flexible version of this function
(e.g. uninterpolated wavelengths), and lightr::lr_get_metadata() for the retrieval
and import of spectral metadata.
See https://docs.ropensci.org/lightr/ for the complete, and up-to-date, list
of supported file formats.
# Import and inspect example spectral data with a range of set to 400-700nm. rspecdata <- getspec(system.file("testdata", package = "lightr"), ext = "ttt", lim = c(400, 700)) head(rspecdata)# Import and inspect example spectral data with a range of set to 400-700nm. rspecdata <- getspec(system.file("testdata", package = "lightr"), ext = "ttt", lim = c(400, 700)) head(rspecdata)
Conveniently convert single objects of class rimg to class cimg (from the
package imager) or magick-image (from the package magick), both of which
contains a suite of useful image-processing capabilities.
## S3 method for class 'rimg' as.cimg(image) rimg2magick(image)## S3 method for class 'rimg' as.cimg(image) rimg2magick(image)
image |
an object of class |
an image of the specified class
Attributes (e.g. scales, color-classes) will not be preserved following
conversion from class rimg, so it's best to use early in the analysis workflow.
Thomas E. White [email protected]
Hugo Gruson [email protected]
papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) # Convert from class rimg to cimg if (requireNamespace("imager", quiety = TRUE)) { papilio_cimg <- rimg2cimg(papilio) class(papilio_cimg) } # Convert from class rimg to magick-image papilio_magick <- rimg2magick(papilio) class(papilio_magick)papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) # Convert from class rimg to cimg if (requireNamespace("imager", quiety = TRUE)) { papilio_cimg <- rimg2cimg(papilio) class(papilio_cimg) } # Convert from class rimg to magick-image papilio_magick <- rimg2magick(papilio) class(papilio_magick)
Some spectrometers will give illuminant values in units of irradiance
(μWatt.cm-2),
but physiological models require illuminants in units of photon (quantum) flux
(μmol.s-1.m-2).
The functions irrad2flux() and flux2irrad() allows for easy conversion of
rspec objects between these units.
irrad2flux(rspecdata) flux2irrad(rspecdata)irrad2flux(rspecdata) flux2irrad(rspecdata)
rspecdata |
(required) a rspec object containing illuminant values. |
a converted rspec object.
Rafael Maia [email protected]
Test if object is of class 'colspace'
is.colspace(object)is.colspace(object)
object |
an R object |
a logical value indicating whether the object is of class colspace
Test if object is of class 'vismodel'
is.vismodel(object)is.vismodel(object)
object |
an R object |
a logical value indicating whether the object is of class vismodel.
Converts a coldist() output into Cartesian coordinates that are
perceptually-corrected (i.e. noise-weighted Euclidean distances)
jnd2xyz( coldistres, center = TRUE, rotate = TRUE, rotcenter = c("mean", "achro"), ref1 = "l", ref2 = "u", axis1, axis2 )jnd2xyz( coldistres, center = TRUE, rotate = TRUE, rotcenter = c("mean", "achro"), ref1 = "l", ref2 = "u", axis1, axis2 )
coldistres |
(required) the output from a |
center |
logical indicating if the data should be centered on its centroid
(defaults to |
rotate |
logical indicating if the data should be rotated (defaults to |
rotcenter |
should the vectors for rotation be centered in the achromatic center ("achro") or the data centroid ("mean", the default)? |
ref1 |
the cone to be used as a the first reference. May be |
ref2 |
the cone to be used as a the second reference. May be |
axis1 |
A vector of length number of cones minus 1 composed of 0's and
1's, with 1's representing the axes (x, y, z) to rotate around. Defaults to
c(1, 1, 0) in 3 dimensions, such that the rotation aligns with the xy plane,
and c(1, 0) in 2 dimentions, such that the rotation is centered on the x
axis. Ignored if |
axis2 |
A vector of length number of cones minus 1 composed of 0's and
1's, with 1's representing the axes (x, y, z) to rotate around. Defaults to
c(0, 0, 1) in 3 dimensions, such that the rotation aligns with the z axis,
and c(0, 1) in 2 dimentions, such that the rotation is centered on the y
axis. Ignored if |
Rafael Maia [email protected]
Pike, T.W. (2012). Preserving perceptual distances in chromaticity diagrams. Behavioral Ecology, 23, 723-728.
Maia, R., White, T. E., (2018) Comparing colors using visual models. Behavioral Ecology, ary017 doi:10.1093/beheco/ary017
# Load floral reflectance spectra data(flowers) # Estimate quantum catches visual phenotype of a Blue Tit vis.flowers <- vismodel(flowers, visual = "bluetit") # Estimate noise-weighted colour distances between all flowers cd.flowers <- coldist(vis.flowers) # Convert points to Cartesian coordinates in which Euclidean distances are # noise-weighted. jnd2xyz(cd.flowers)# Load floral reflectance spectra data(flowers) # Estimate quantum catches visual phenotype of a Blue Tit vis.flowers <- vismodel(flowers, visual = "bluetit") # Estimate noise-weighted colour distances between all flowers cd.flowers <- coldist(vis.flowers) # Convert points to Cartesian coordinates in which Euclidean distances are # noise-weighted. jnd2xyz(cd.flowers)
Adds a legend to a static tetrahedral colourspace plot.
legendtetra(x = 0.8, y = 1.2, ...)legendtetra(x = 0.8, y = 1.2, ...)
x, y
|
position of the legend relative to plot limits (usually a value between 0 and 1, but because of the perspective distortion, values greater than 1 are possible) |
... |
additional arguments passed to |
legendtetra() adds a legend to a static tetrahedral colourspace plot.
for additional information on which arguments are necessary and how they are used,
see legend().
Rafael Maia [email protected]
data(sicalis) vis_sicalis <- vismodel(sicalis) tcs_sicalis <- colspace(vis_sicalis) cols <- c("#1B9E77", "#D95F02", "#7570B3") plot(tcs_sicalis, col = cols) legendtetra( legend = c("Crown", "Throat", "Breast"), col = cols, pch = 16 )data(sicalis) vis_sicalis <- vismodel(sicalis) tcs_sicalis <- colspace(vis_sicalis) cols <- c("#1B9E77", "#D95F02", "#7570B3") plot(tcs_sicalis, col = cols) legendtetra( legend = c("Crown", "Throat", "Breast"), col = cols, pch = 16 )
Merges two rspec objects into a single rspec object.
## S3 method for class 'rspec' merge(x, y, ...)## S3 method for class 'rspec' merge(x, y, ...)
x, y
|
(required) |
... |
additional class arguments. |
an object of class rspec for use with pavo functions.
Will use by = "wl" if unspecified, or automatically append wl to the
by argument if one is specified.
Chad Eliason [email protected]
# Load angle-resolved reflectance data for a green-winged teal, and # split it in two data(teal) teal1 <- teal[, c(1, 2:5)] teal2 <- teal[, c(1, 6:13)] # Merge the two split datasets back into one, with a shared 'wl' column teal.mer <- merge(teal1, teal2, by = "wl") # Examine the results, and compare the original to the (identical) # reconstructed version plot(teal.mer) plot(teal) identical(teal.mer, teal) # Or an equivalent method, which also allows for the merging of more than one rspec # object at a time (simply add further objects to the list()) teal.mer2 <- do.call(merge, list(teal1, teal2)) # Check equivalence identical(teal.mer2, teal)# Load angle-resolved reflectance data for a green-winged teal, and # split it in two data(teal) teal1 <- teal[, c(1, 2:5)] teal2 <- teal[, c(1, 6:13)] # Merge the two split datasets back into one, with a shared 'wl' column teal.mer <- merge(teal1, teal2, by = "wl") # Examine the results, and compare the original to the (identical) # reconstructed version plot(teal.mer) plot(teal) identical(teal.mer, teal) # Or an equivalent method, which also allows for the merging of more than one rspec # object at a time (simply add further objects to the list()) teal.mer2 <- do.call(merge, list(teal1, teal2)) # Check equivalence identical(teal.mer2, teal)
Calculates height, location and width of peak at the reflectance midpoint (FWHM).
Note: bounds should be set wide enough to incorporate all minima in spectra. Smoothing
spectra using procspec() is also recommended.
peakshape( rspecdata, select = NULL, lim = NULL, plot = TRUE, ask = FALSE, absolute.min = FALSE, ... )peakshape( rspecdata, select = NULL, lim = NULL, plot = TRUE, ask = FALSE, absolute.min = FALSE, ... )
rspecdata |
(required) a data frame, possibly of class |
select |
specification of which spectra to plot. Can be a numeric vector
or factor (e.g., |
lim |
a vector specifying the wavelength range to analyze. |
plot |
logical. Should plots indicating calculated parameters be returned?
(Defaults to |
ask |
logical, specifies whether user input needed to plot multiple plots
when number of spectra to analyze is greater than 1 (defaults to |
absolute.min |
logical. If |
... |
additional arguments to be passed to plot. |
a data frame containing column names (id); peak height (max value, B3), location (hue, H1) and full width at half maximum (FWHM), as well as half widths on left (HWHM.l) and right side of peak (HWHM.r). Incl.min column indicates whether user-defined bounds incorporate the actual minima of the spectra. Function will return a warning if not.
Chad Eliason [email protected]
Rafael Maia [email protected]
Hugo Gruson [email protected]
data(teal) peakshape(teal, select = 3) peakshape(teal, select = 10) # Use wavelength bounds to narrow in on peak of interest peakshape(teal, select = 10, lim = c(400, 550))data(teal) peakshape(teal, select = 3) peakshape(teal, select = 10) # Use wavelength bounds to narrow in on peak of interest peakshape(teal, select = 10, lim = c(400, 550))
Plots reflectance spectra in the appropriate colourspace.
## S3 method for class 'colspace' plot(x, ...)## S3 method for class 'colspace' plot(x, ...)
x |
(required) an object of class |
... |
additional graphical options, which vary by modeled
Also see |
A colourspace plot appropriate to the input data.
Rafael Maia [email protected]
Thomas White [email protected]
Chad Eliason [email protected]
Smith T, Guild J. (1932) The CIE colorimetric standards and their use. Transactions of the Optical Society, 33(3), 73-134.
Westland S, Ripamonti C, Cheung V. (2012). Computational colour science using MATLAB. John Wiley & Sons.
Chittka L. (1992). The colour hexagon: a chromaticity diagram based on photoreceptor excitations as a generalized representation of colour opponency. Journal of Comparative Physiology A, 170(5), 533-543.
Chittka L, Shmida A, Troje N, Menzel R. (1994). Ultraviolet as a component of flower reflections, and the colour perception of Hymenoptera. Vision research, 34(11), 1489-1508.
Troje N. (1993). Spectral categories in the learning behaviour of blowflies. Zeitschrift fur Naturforschung C, 48, 96-96.
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
Kelber A, Vorobyev M, Osorio D. (2003). Animal colour vision - behavioural tests and physiological concepts. Biological Reviews, 78, 81 - 118.
Backhaus W. (1991). Color opponent coding in the visual system of the honeybee. Vision Research, 31, 1381-1397.
Endler, J. A. (1990) On the measurement and classification of color in studies of animal color patterns. Biological Journal of the Linnean Society, 41, 315-352.
data(flowers) data(sicalis) # Dichromat vis.flowers <- vismodel(flowers, visual = "canis") di.flowers <- colspace(vis.flowers, space = "di") plot(di.flowers) # Colour hexagon vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) hex.flowers <- colspace(vis.flowers, space = "hexagon") plot(hex.flowers, sectors = "coarse") # Tetrahedron (static) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") plot(tcs.sicalis) # Tetrahedron (interactive) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") tcsplot(tcs.sicalis, size = 0.005) ## Add points to interactive tetrahedron patch <- rep(c("C", "T", "B"), 7) tcs.crown <- subset(tcs.sicalis, "C") tcs.breast <- subset(tcs.sicalis, "B") tcsplot(tcs.crown, col = "blue") tcspoints(tcs.breast, col = "red") ## Plot convex hull in interactive tetrahedron tcsplot(tcs.sicalis, col = "blue", size = 0.005) tcsvol(tcs.sicalis)data(flowers) data(sicalis) # Dichromat vis.flowers <- vismodel(flowers, visual = "canis") di.flowers <- colspace(vis.flowers, space = "di") plot(di.flowers) # Colour hexagon vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, achromatic = "l", bkg = "green" ) hex.flowers <- colspace(vis.flowers, space = "hexagon") plot(hex.flowers, sectors = "coarse") # Tetrahedron (static) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") plot(tcs.sicalis) # Tetrahedron (interactive) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") tcsplot(tcs.sicalis, size = 0.005) ## Add points to interactive tetrahedron patch <- rep(c("C", "T", "B"), 7) tcs.crown <- subset(tcs.sicalis, "C") tcs.breast <- subset(tcs.sicalis, "B") tcsplot(tcs.crown, col = "blue") tcspoints(tcs.breast, col = "red") ## Plot convex hull in interactive tetrahedron tcsplot(tcs.sicalis, col = "blue", size = 0.005) tcsvol(tcs.sicalis)
Plot unprocessed or colour-classified image data. If the images are in a list, they will be stepped through one by one.
## S3 method for class 'rimg' plot(x, axes = TRUE, col = NULL, ...)## S3 method for class 'rimg' plot(x, axes = TRUE, col = NULL, ...)
x |
(required) an image of class rimg, or list thereof. |
axes |
should axes be drawn? (defaults to |
col |
optional vector of colours when plotting colour-classified images. Defaults to the mean RGB values of the k-means centres (i.e. the average 'original' colours). |
... |
additional graphical parameters. Also see |
an image plot.
Thomas E. White [email protected]
papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) plot(papilio) papilio_class <- classify(papilio, kcols = 4) plot(papilio_class) # Multiple images snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) plot(snakes) snakes_class <- classify(snakes, kcols = 3) plot(snakes_class)papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) plot(papilio) papilio_class <- classify(papilio, kcols = 4) plot(papilio_class) # Multiple images snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) plot(snakes) snakes_class <- classify(snakes, kcols = 3) plot(snakes_class)
Plots reflectance spectra in different arrangements.
## S3 method for class 'rspec' plot( x, select = NULL, type = c("overlay", "stack", "heatmap"), varying = NULL, n = 100, labels = FALSE, labels.stack = NULL, labels.cex = 1, wl.guide = TRUE, ... )## S3 method for class 'rspec' plot( x, select = NULL, type = c("overlay", "stack", "heatmap"), varying = NULL, n = 100, labels = FALSE, labels.stack = NULL, labels.cex = 1, wl.guide = TRUE, ... )
x |
(required) a data frame, possibly an object of class |
select |
specification of which spectra to plot. Can be a numeric vector
or factor (e.g., |
type |
what type of plot should be drawn. Possibilities are:
|
varying |
a numeric vector giving values for y-axis in
|
n |
number of bins with which to interpolate colors and |
labels |
logical. Add labels identifying each spectrum to the outer plot
margin? Defaults to |
labels.stack |
a vector of labels for spectra when |
labels.cex |
size of the text labels when |
wl.guide |
logical determining whether visible light spectrum should be added to the x-axis. |
... |
additional arguments passed to |
Thomas White [email protected]
Hugo Gruson [email protected]
Chad Eliason [email protected]
# Load angle-resolved reflectance data for a green-winged teal data(teal) # Create an overlay plot (default) plot(teal) # Create an stacked spectral plot plot(teal, type = "stack") # Create a reflectance heatmap plot(teal, type = "heatmap")# Load angle-resolved reflectance data for a green-winged teal data(teal) # Create an overlay plot (default) plot(teal) # Create an stacked spectral plot plot(teal, type = "stack") # Create a reflectance heatmap plot(teal, type = "heatmap")
sensmodel()
Plot absorbance spectra from sensmodel()
## S3 method for class 'sensmod' plot( x, select = NULL, type = c("overlay", "stack", "heatmap"), varying = NULL, n = 100, labels = FALSE, labels.stack = NULL, labels.cex = 1, wl.guide = TRUE, ... )## S3 method for class 'sensmod' plot( x, select = NULL, type = c("overlay", "stack", "heatmap"), varying = NULL, n = 100, labels = FALSE, labels.stack = NULL, labels.cex = 1, wl.guide = TRUE, ... )
x |
(required) a data frame, possibly an object of class |
select |
specification of which spectra to plot. Can be a numeric vector
or factor (e.g., |
type |
what type of plot should be drawn. Possibilities are:
|
varying |
a numeric vector giving values for y-axis in
|
n |
number of bins with which to interpolate colors and |
labels |
logical. Add labels identifying each spectrum to the outer plot
margin? Defaults to |
labels.stack |
a vector of labels for spectra when |
labels.cex |
size of the text labels when |
wl.guide |
logical determining whether visible light spectrum should be added to the x-axis. |
... |
additional arguments passed to |
# Blue tit visual system based on Hart et al (2000) bluesens <- sensmodel(c(371, 448, 502, 563), beta = FALSE, lambdacut = c(330, 413, 507, 572), oiltype = c("T", "C", "Y", "R"), om = TRUE ) plot(bluesens) # Alternatively, you can specify your own ylab plot(bluesens, ylab = "absor.")# Blue tit visual system based on Hart et al (2000) bluesens <- sensmodel(c(371, 448, 502, 563), beta = FALSE, lambdacut = c(330, 413, 507, 572), oiltype = c("T", "C", "Y", "R"), om = TRUE ) plot(bluesens) # Alternatively, you can specify your own ylab plot(bluesens, ylab = "absor.")
Plots spectral curves with various levels of loess smoothing to help decide which
loess parameters are best for subsequently smoothing the data (e.g. via procspec()).
plotsmooth( rspecdata, minsmooth = 0.05, maxsmooth = 0.2, curves = 5, specnum = "ALL", ask = TRUE )plotsmooth( rspecdata, minsmooth = 0.05, maxsmooth = 0.2, curves = 5, specnum = "ALL", ask = TRUE )
rspecdata |
(required) a data frame, possibly of class |
minsmooth |
the minimum f value of the loess function to visualize (defaults to |
maxsmooth |
the maximum f value of the loess function to visualize (defaults to |
curves |
the number of curves to display on the same plot (defaults to |
specnum |
the number of spectral curves, from the data frame, to visualize (defaults to |
ask |
logical. if |
Series of plot with curves processed with varying level of loess smoothing
Pierre-Paul Bitton [email protected]
# Load reflectance spectra data(sicalis) # Visualise the spectral reflectance curves across a range of smoothing levels plotsmooth(sicalis, minsmooth = 0.05, maxsmooth = 0.1, curves = 7, specnum = 6)# Load reflectance spectra data(sicalis) # Visualise the spectral reflectance curves across a range of smoothing levels plotsmooth(sicalis, minsmooth = 0.05, maxsmooth = 0.1, curves = 7, specnum = 6)
Add points to a colourspace plot
## S3 method for class 'colspace' points(x, ...)## S3 method for class 'colspace' points(x, ...)
x |
(required) an object of class |
... |
additional graphical options. See |
points.colspace adds points to a colourspace plot.
Rafael Maia [email protected]
Thomas White [email protected]
Specify scales, resize, and/or define focal objects within images.
procimg( image, resize = NULL, rotate = NULL, scaledist = NULL, outline = FALSE, reclass = NULL, smooth = FALSE, iterations = 1L, col = "red", obj_dist = NULL, obj_width = NULL, eye_res = NULL, plotnew = FALSE, ... )procimg( image, resize = NULL, rotate = NULL, scaledist = NULL, outline = FALSE, reclass = NULL, smooth = FALSE, iterations = 1L, col = "red", obj_dist = NULL, obj_width = NULL, eye_res = NULL, plotnew = FALSE, ... )
image |
(required) image data. Either a single image array, or a number of images
stored in a list. Preferably the result of |
resize |
an integer specifying a percentage for resizing images, if so desired. E.g. 50 to half the size of an image, 200 to double it. |
rotate |
an integer specifying the angle of image rotation, in degrees. Images are rotated around the centre, and linearly interpolated. |
scaledist |
an integer, or numeric vector equal in length to the number of images, specifying the length of the scale in the image(s). Image(s) will then be presented, and the user asked to select either end of the scale corresponding to the input value. |
outline |
interactively specify the focal object in an image by clicking around its outline. The xy-coordinates of the resulting closed polygon are saved as an attribute, for use in generating a masking layer & separating animals/plants from backgrounds in further analyses. This is particularly useful when backgrounds are complex, such as in natural settings. |
reclass |
interactively specify an area on a colour-classified image that is
to be reclassified as the numeric value provided. e.g. when |
smooth |
should the polygon specified when |
iterations |
the number of smoothing iterations, when |
col |
the color of the marker points and/or line, when using interactive options. |
obj_dist, obj_width, eye_res
|
blur the image to model the visual acuity of non-human animals as per Caves & Johnsen (2018)'s AcuityView 2.0 algorithm. The procedure requires three arguments; obj_dist is the real-world distance between the viewer and the focal object in the image in the image, obj_width is the real-world width of the entire image; eye_res is the minimum resolvable angle of the viewer in degrees. All three arguments are numeric, and any units of measurement are suitable for obj_dist and obj_width, but they must match. Note that this is the more flexible v2.0 implementation meaning that any rectangular image is suitable; it need not be square with dimensions a power of 2. If using this capability, please cite Caves & Johnsen (2018), as per the included reference, and see note below. |
plotnew |
should plots be opened in a new window? Defaults to |
... |
additional graphical parameters. Also see |
an image, or list of images, for use in further
pavo functions.
There are several caveats that should be considered when using the AcuityView algorithm. First and foremost, the converted image is not what the animal actually sees. For example, it does not account for edge enhancement and other processing by the retina and brain that may alter an image. It does, however, show what spatial information can be detected and then processed by the visual system. Second, the converted image is static, which does not allow one to assess how movement may reveal the presence of an otherwise indiscernible object. Third, AcuityView makes several assumptions about the Modulation Transfer Function (MTF), which describes how the optical system affects image contrast as a function of the level of detail. These assumptions include that the MTF is constant over the region of the retina that views the scene, is circularly symmetrical, and is wavelength independent. For a full discussion and details, please do read Caves & Johnsen (2018).
Thomas E. White [email protected]
Caves, E. M., & Johnsen, S. (2018). AcuityView: An r package for portraying the effects of visual acuity on scenes observed by an animal. Methods in Ecology and Evolution, 9(3), 793-797 doi:10.1111/2041-210X.12911.
Chaikin, G. 1974. An algorithm for high speed curve generation. Computer Graphics and Image Processing 3, 346-349.
if (interactive()) { # Interactively add a scale to a single image papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio <- procimg(papilio, scaledist = 10) # Interactively assign individual scales to each image, # after slightly reducing their size (to 90% of original). snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) snakes <- procimg(snakes, scaledist = c(10, 14), resize = 90) # Model the appearance of a butterfly given the reduced visual acuity of another # animal viewer as per the AcuityView algorithm. Here our butterfly is 60 cm away, # the image width is 10 cm, and the minimum resolvable angle of the viewer is 0.2-degrees. tiger <- getimg(system.file("testdata/images/tiger.png", package = "pavo")) tiger_acuity <- procimg(tiger, obj_dist = 60, obj_width = 10, eye_res = 0.2) }if (interactive()) { # Interactively add a scale to a single image papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio <- procimg(papilio, scaledist = 10) # Interactively assign individual scales to each image, # after slightly reducing their size (to 90% of original). snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) snakes <- procimg(snakes, scaledist = c(10, 14), resize = 90) # Model the appearance of a butterfly given the reduced visual acuity of another # animal viewer as per the AcuityView algorithm. Here our butterfly is 60 cm away, # the image width is 10 cm, and the minimum resolvable angle of the viewer is 0.2-degrees. tiger <- getimg(system.file("testdata/images/tiger.png", package = "pavo")) tiger_acuity <- procimg(tiger, obj_dist = 60, obj_width = 10, eye_res = 0.2) }
Applies normalization and/or smoothing to spectra for further analysis or plotting.
procspec( rspecdata, opt = c("none", "smooth", "maximum", "minimum", "bin", "sum", "center"), fixneg = c("none", "addmin", "zero"), span = 0.25, bins = 20 )procspec( rspecdata, opt = c("none", "smooth", "maximum", "minimum", "bin", "sum", "center"), fixneg = c("none", "addmin", "zero"), span = 0.25, bins = 20 )
rspecdata |
(required) a data frame, possibly of class |
opt |
what type of processing options to apply. User can select multiple options by providing a vector. Possibilities are:
|
fixneg |
how to handle negative values. Possibilities are:
|
span |
sets the smoothing parameter used by |
bins |
sets the number of equally sized wavelength bins for |
A data frame of class rspec with the processed data.
Chad Eliason [email protected]
Cuthill, I., Bennett, A. T. D., Partridge, J. & Maier, E. 1999. Plumage reflectance and the objective assessment of avian sexual dichromatism. The American Naturalist, 153, 183-200.
Montgomerie R. 2006. Analyzing colors. In Hill, G.E, and McGraw, K.J., eds. Bird Coloration. Volume 1 Mechanisms and measurements. Harvard University Press, Cambridge, Massachusetts.
White, T. E., Dalrymple, R. L., Noble D. W. A., O'Hanlon, J. C., Zurek, D. B., Umbers, K. D. L. 2015. Reproducible research in the study of biological coloration. Animal Behaviour, 106, 51-57.
data(teal) plot(teal, select = 10) # Smooth data to remove noise teal.sm <- procspec(teal, opt = "smooth", span = 0.25) plot(teal.sm, select = 10) # Normalize to max of unity teal.max <- procspec(teal, opt = c("max")) plot(teal.max, select = 10)data(teal) plot(teal, select = 10) # Smooth data to remove noise teal.sm <- procspec(teal, opt = "smooth", span = 0.25) plot(teal.sm, select = 10) # Normalize to max of unity teal.max <- procspec(teal, opt = c("max")) plot(teal.max, select = 10)
Produces a 2D projection plot of points in a tetrahedral colour space
Adds points to a tetrahedral colorspace projection
projplot(tcsdata, ...) projpoints(tcsdata, ...)projplot(tcsdata, ...) projpoints(tcsdata, ...)
tcsdata |
(required) tetrahedral color space coordinates, possibly a result from |
... |
additional parameters to be passed to the plotting of data points. |
projplot() creates a 2D plot of color points projected from the tetrahedron
to its encapsulating sphere, and is ideal to visualize differences in hue.
projpoints() creates points in a projection color space plot
produced by projplot().
projplot() uses the Mollweide projection, and not the Robinson projection, which
has been used in the past. Among other advantages, the Mollweide projection preserves area
relationships within latitudes without distortion.
Rafael Maia [email protected]
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") projplot(tcs.sicalis, pch = 16, col = setNames(rep(seq_len(3), 7), rep(c("C", "T", "B"), 7)))data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") projplot(tcs.sicalis, pch = 16, col = setNames(rep(seq_len(3), 7), rep(c("C", "T", "B"), 7)))
Retrieve (as an rspec object) or plot pavo's in-built spectral sensitivity data.
sensdata( visual = c("none", "all", "avg.uv", "avg.v", "bluetit", "ctenophorus", "star", "pfowl", "apis", "canis", "cie2", "cie10", "musca", "drosophila", "habronattus", "rhinecanthus"), achromatic = c("none", "all", "bt.dc", "ch.dc", "st.dc", "md.r1", "dm.r1", "ra.dc", "cf.r"), illum = c("none", "all", "bluesky", "D65", "forestshade"), trans = c("none", "all", "bluetit", "blackbird"), bkg = c("none", "all", "green"), plot = FALSE, ... )sensdata( visual = c("none", "all", "avg.uv", "avg.v", "bluetit", "ctenophorus", "star", "pfowl", "apis", "canis", "cie2", "cie10", "musca", "drosophila", "habronattus", "rhinecanthus"), achromatic = c("none", "all", "bt.dc", "ch.dc", "st.dc", "md.r1", "dm.r1", "ra.dc", "cf.r"), illum = c("none", "all", "bluesky", "D65", "forestshade"), trans = c("none", "all", "bluetit", "blackbird"), bkg = c("none", "all", "green"), plot = FALSE, ... )
visual |
visual systems. Options are:
|
achromatic |
the sensitivity data used to calculate luminance (achromatic) receptor stimulation. Options are:
|
illum |
illuminants. Options are:
|
trans |
Ocular transmission data. Options are:
|
bkg |
background spectra. Options are:
|
plot |
should the spectral data be plotted, or returned instead (defaults to |
... |
additional graphical options passed to |
An object of class rspec (when plot = FALSE), containing
a wavelength column "wl" and spectral data binned at 1 nm intervals from 300-700 nm.
Thomas E. White [email protected]
Rafael Maia [email protected]
Sharkey, C. R., Blanco, J., Leibowitz, M. M., Pinto-Benito, D., & Wardill, T. J. (2020). The spectral sensitivity of Drosophila photoreceptors. Scientific reports, 10(1), 1-13.
# Plot the honeybee's receptors sensdata(visual = "apis", ylab = "Absorbance", plot = TRUE) # Plot the average UV vs V avian receptors sensdata(visual = c("avg.v", "avg.uv"), ylab = "Absorbance", plot = TRUE) # Retrieve the CIE colour matching functions as an rspec object ciedat <- sensdata(visual = c("cie2", "cie10"))# Plot the honeybee's receptors sensdata(visual = "apis", ylab = "Absorbance", plot = TRUE) # Plot the average UV vs V avian receptors sensdata(visual = c("avg.v", "avg.uv"), ylab = "Absorbance", plot = TRUE) # Retrieve the CIE colour matching functions as an rspec object ciedat <- sensdata(visual = c("cie2", "cie10"))
Models spectral sensitivity (with oil droplets; optional) based on peak cone sensitivity according to the models of Govardovskii et al. (2000) and Hart & Vorobyev (2005).
sensmodel( peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NULL, oiltype = NULL, beta = TRUE, om = NULL, integrate = TRUE, sensnames = paste0("lmax", peaksens) )sensmodel( peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NULL, oiltype = NULL, beta = TRUE, om = NULL, integrate = TRUE, sensnames = paste0("lmax", peaksens) )
peaksens |
(required) a vector with peak sensitivities for the cones to model. |
range |
a vector of length 2 for the range over which to calculate the spectral sensitivities (defaults to 300nm to 700nm). |
lambdacut |
a vector of same length as peaksens that lists the cut-off
wavelength value for oil droplets. Needs either |
Bmid |
a vector of same length as peaksens that lists the gradient of line tangent to the absorbance spectrum of the oil droplets. See Hart and Vorobyev (2005). |
oiltype |
a list of same length as peaksens that lists the oil droplet types (currently accepts only "T", C", "Y", "R", "P") when Bmid is not known. Calculates Bmid based on the regression equations found in Hart ad Vorobyev (2005). |
beta |
logical. If |
om |
a vector of same length as |
integrate |
logical. If |
sensnames |
A vector equal in length to |
A data frame of class rspec containing each cone model as a column.
Pierre-Paul Bitton [email protected]
Chad Eliason [email protected]
Govardovskii VI, Fyhrquist N, Reuter T, Kuzmin DG and Donner K. 2000. In search of the visual pigment template. Visual Neuroscience 17:509-528, doi:10.1017/S0952523800174036
Hart NS, and Vorobyev M. 2005. Modeling oil droplet absorption spectra and spectral sensitivities of bird cone photoreceptors. Journal of Comparative Physiology A. 191: 381-392, doi:10.1007/s00359-004-0595-3
Hart NS, Partridge JC, Cuthill IC, Bennett AT (2000) Visual pigments, oil droplets, ocular media and cone photoreceptor distribution in two species of passerine bird: the blue tit (Parus caeruleus L.) and the blackbird (Turdus merula L.). J Comp Physiol A 186:375-387, doi:10.1007/s003590050437
# Blue tit visual system based on Hart et al (2000) bluesens <- sensmodel(c(371, 448, 502, 563), beta = FALSE, lambdacut = c(330, 413, 507, 572), oiltype = c("T", "C", "Y", "R"), om = TRUE ) # Danio aequipinnatus based on Govardovskii et al. (2000) daniosens <- sensmodel(c(357, 411, 477, 569))# Blue tit visual system based on Hart et al (2000) bluesens <- sensmodel(c(371, 448, 502, 563), beta = FALSE, lambdacut = c(330, 413, 507, 572), oiltype = c("T", "C", "Y", "R"), om = TRUE ) # Danio aequipinnatus based on Govardovskii et al. (2000) daniosens <- sensmodel(c(357, 411, 477, 569))
Dataset containing reflectance measurements from 3 body parts ("C": crown, "B": breast, "T": throat) from seven male stripe-tailed yellow finches (Sicalis citrina)
data(sicalis)data(sicalis)
An object of class rspec (inherits from data.frame) with 401 rows and 22 columns.
Rafael Maia [email protected]
Simulate a naturalistic reflectance, radiance, irradiance, or transmission spectrum. Curves may have sigmoidal (s-shaped) and/or Gaussian (bell-shaped) features. Multiple Gaussian and sigmoidal curves can be combined in a single spectrum, to simulate more complex spectral functions.
simulate_spec( wl_inflect = NULL, wl_peak = NULL, width_sig = 20, width_gauss = 70, skew_gauss = 0, xlim = c(300, 700), ylim = c(0, 100) )simulate_spec( wl_inflect = NULL, wl_peak = NULL, width_sig = 20, width_gauss = 70, skew_gauss = 0, xlim = c(300, 700), ylim = c(0, 100) )
wl_inflect |
A numeric vector specifying the wavelength location (in nm) for one or more inflection point(s) for a 'sigmoid' shaped curve, if desired. |
wl_peak |
A numeric vector specifying the wavelength location (in nm) for one or more inflection point(s) for a 'Gaussian' (or 'bell') shaped curve, if desired. |
width_sig |
A numeric value or vector (if multiple wl_inflect values are specified)
specifying the steepness of the change, for any sigmoidal curve(s). Required when
|
width_gauss |
A numeric value or vector specifying the the full-width at half-maximum
of any Gaussian curve(s). Required when |
skew_gauss |
Skewness parameter for controlling the direction and magnitude of
skew, when simulating for Gaussian curves (ignored when simulating only sigmoidal curves).
Curves will have no skew when |
xlim |
A vector specifying the wavelength range of the simulated spectra. Defaults to
300-700nm ( |
ylim |
A vector specifying the minimum and maximum reflectance values of the resulting
curve. Defaults to 0 - 100 % ( |
An object of class rspec.
Thomas White [email protected]
Hugo Gruson [email protected]
Azzalini A (1985). A class of distributions which includes the normal ones. Scan. J. Stat. 171-178.
# Single ideal 'grey' reflectance spectrum, with 50% reflectance across 300 - 700 nm. reflect0 <- simulate_spec(ylim = c(0, 50)) # Single sigmoidal spectrum, with a low-to-high inflection at 550 nm. reflect1 <- simulate_spec(wl_inflect = 550) # Single Gaussian spectrum, with a peak at 400 nm reflect2 <- simulate_spec(wl_peak = 400) # Combination of both Gaussian (with peak at 340 nm) and sigmoidal (with inflection # at 560 nm) reflect3 <- simulate_spec(wl_inflect = 560, wl_peak = 340) # Double-Gaussian peaks of differing widths reflect4 <- simulate_spec(wl_peak = c(340, 560), width_gauss = c(12, 40)) # Complex spectrum with single sigmoidal peak and multi-Gaussian peaks reflect5 <- simulate_spec(wl_inflect = 575, wl_peak = c(340, 430), width_gauss = c(20, 60)) # Simulate a set of Gaussian reflectance curves with peaks varying between 400-600nm # in increments of 10, then combine into a single rspec object, and plot the result peaks <- seq(400, 600, 10) # Peak locations reflectances <- lapply(seq_along(peaks), function(x) simulate_spec(wl_peak = peaks[x])) # Simulate reflectances <- Reduce(merge, reflectances) # Combine plot(reflectances) # Plot # Simulate a set of Gaussian reflectance curves with a single peak at 500 nm, but # with maximum reflectance varying from 30 to 90% in 10% increments, then combine # into a single rspec object, and plot the result ymax <- lapply(seq(30, 90, 10), function(x) c(0, x)) # Varying reflectance maxima reflectances2 <- lapply(ymax, function(x) simulate_spec(wl_peak = 500, ylim = x)) # Simulate reflectances2 <- Reduce(merge, reflectances2) # Combine plot(reflectances2) # Plot # To simulate non-reflectance spectra (like irradiances or radiances), it's often useful # to explore more 'extreme' parameters. Here's a simple example which simulates # natural daylight, as represented by the D65 standard daylight spectrum. D65_real <- procspec(sensdata(illum = "D65"), opt = "smooth") # Official D65 daylight spectrum D65_sim <- simulate_spec( wl_peak = 400, width_gauss = 1300, skew_gauss = 10, ylim = c(0, 1) ) # Simulated D65 cor.test(D65_real$D65, D65_sim$spec_p400) # >0.99 correlation plot(merge(D65_real, D65_sim), lty = 1:2, ylab = "Irradiance (%)") # Merge and plot the two spectra# Single ideal 'grey' reflectance spectrum, with 50% reflectance across 300 - 700 nm. reflect0 <- simulate_spec(ylim = c(0, 50)) # Single sigmoidal spectrum, with a low-to-high inflection at 550 nm. reflect1 <- simulate_spec(wl_inflect = 550) # Single Gaussian spectrum, with a peak at 400 nm reflect2 <- simulate_spec(wl_peak = 400) # Combination of both Gaussian (with peak at 340 nm) and sigmoidal (with inflection # at 560 nm) reflect3 <- simulate_spec(wl_inflect = 560, wl_peak = 340) # Double-Gaussian peaks of differing widths reflect4 <- simulate_spec(wl_peak = c(340, 560), width_gauss = c(12, 40)) # Complex spectrum with single sigmoidal peak and multi-Gaussian peaks reflect5 <- simulate_spec(wl_inflect = 575, wl_peak = c(340, 430), width_gauss = c(20, 60)) # Simulate a set of Gaussian reflectance curves with peaks varying between 400-600nm # in increments of 10, then combine into a single rspec object, and plot the result peaks <- seq(400, 600, 10) # Peak locations reflectances <- lapply(seq_along(peaks), function(x) simulate_spec(wl_peak = peaks[x])) # Simulate reflectances <- Reduce(merge, reflectances) # Combine plot(reflectances) # Plot # Simulate a set of Gaussian reflectance curves with a single peak at 500 nm, but # with maximum reflectance varying from 30 to 90% in 10% increments, then combine # into a single rspec object, and plot the result ymax <- lapply(seq(30, 90, 10), function(x) c(0, x)) # Varying reflectance maxima reflectances2 <- lapply(ymax, function(x) simulate_spec(wl_peak = 500, ylim = x)) # Simulate reflectances2 <- Reduce(merge, reflectances2) # Combine plot(reflectances2) # Plot # To simulate non-reflectance spectra (like irradiances or radiances), it's often useful # to explore more 'extreme' parameters. Here's a simple example which simulates # natural daylight, as represented by the D65 standard daylight spectrum. D65_real <- procspec(sensdata(illum = "D65"), opt = "smooth") # Official D65 daylight spectrum D65_sim <- simulate_spec( wl_peak = 400, width_gauss = 1300, skew_gauss = 10, ylim = c(0, 1) ) # Simulated D65 cor.test(D65_real$D65, D65_sim$spec_p400) # >0.99 correlation plot(merge(D65_real, D65_sim), lty = 1:2, ylab = "Irradiance (%)") # Merge and plot the two spectra
Calculates rgb values from spectra based on human colour matching functions.
spec2rgb(rspecdata, alpha = 1)spec2rgb(rspecdata, alpha = 1)
rspecdata |
(required) a data frame, possibly of class |
alpha |
alpha value to use for colours (defaults to 1, opaque). |
A character vector consisting of hexadecimal colour values for passing to further plotting functions.
Hugo Gruson [email protected]
Chad Eliason [email protected]
CIE(1932). Commission Internationale de l'Eclairage Proceedings, 1931. Cambridge: Cambridge University Press.
data(teal) spec2rgb(teal) # Plot data using estimated perceived colour plot(teal, col = spec2rgb(teal), type = "overlay")data(teal) spec2rgb(teal) # Plot data using estimated perceived colour plot(teal, col = spec2rgb(teal), type = "overlay")
Subsets various object types based on a given vector or grep partial matching of data names.
## S3 method for class 'rspec' subset(x, subset, ...) ## S3 method for class 'colspace' subset(x, subset, ...) ## S3 method for class 'vismodel' subset(x, subset, ...)## S3 method for class 'rspec' subset(x, subset, ...) ## S3 method for class 'colspace' subset(x, subset, ...) ## S3 method for class 'vismodel' subset(x, subset, ...)
x |
(required) an object of class |
subset |
a string used for partial matching of observations. |
... |
additional attributes passed to |
a subsetted object of the same class as the input object.
if more than one value is given to subset, any spectra that
matches either condition will be included. It's a union, not an
intersect.
Chad Eliason [email protected]
data(sicalis) vis.sicalis <- vismodel(sicalis) tcs.sicalis <- colspace(vis.sicalis, space = "tcs") # Subset all 'crown' patches (C in file names) head(subset(sicalis, "C")) head(subset(sicalis, c("B", "C"))) head(subset(sicalis, "T", invert = TRUE)) subset(vis.sicalis, "C") subset(tcs.sicalis, "C")[, seq_len(5)]data(sicalis) vis.sicalis <- vismodel(sicalis) tcs.sicalis <- colspace(vis.sicalis, space = "tcs") # Subset all 'crown' patches (C in file names) head(subset(sicalis, "C")) head(subset(sicalis, c("B", "C"))) head(subset(sicalis, "T", invert = TRUE)) subset(vis.sicalis, "C") subset(tcs.sicalis, "C")[, seq_len(5)]
Returns the attributes of colspace objects.
## S3 method for class 'colspace' summary(object, by = NULL, ...)## S3 method for class 'colspace' summary(object, by = NULL, ...)
object |
(required) a |
by |
when the input is in |
... |
class consistency (ignored). |
returns all attributes of the data as mapped to the selected colourspace, including
options specified when calculating the visual model. Also return the default
data.frame summary, except when the object is the result of tcspace(),
in which case the following variables are output instead:
centroid.u, .s, .m, .l the centroids of usml coordinates of points.
c.vol the total volume occupied by the points, computed with a convex
hull.
rel.c.vol volume occupied by the points (convex hull volume) relative to
the tetrahedron volume.
colspan.m the mean hue span.
colspan.v the variance in hue span.
huedisp.m the mean hue disparity.
huedisp.v the variance in hue disparity.
mean.ra mean saturation.
max.ra maximum saturation achieved by the group of points.
a.vol colour volume computed with -shapes.
Rafael Maia [email protected]
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
Gruson H. (2020). Estimation of colour volumes as concave hypervolumes using
-shapes. Methods in Ecology and Evolution, 11(8), 955-963
doi:10.1111/2041-210X.13398
# Colour hexagon data(flowers) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, bkg = "green" ) flowers.hex <- hexagon(vis.flowers) summary(flowers.hex) # Tetrahedral model data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") csp.sicalis <- colspace(vis.sicalis) summary(csp.sicalis, by = rep(c("C", "T", "B"), 7))# Colour hexagon data(flowers) vis.flowers <- vismodel(flowers, visual = "apis", qcatch = "Ei", relative = FALSE, vonkries = TRUE, bkg = "green" ) flowers.hex <- hexagon(vis.flowers) summary(flowers.hex) # Tetrahedral model data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") csp.sicalis <- colspace(vis.sicalis) summary(csp.sicalis, by = rep(c("C", "T", "B"), 7))
Returns the attributes of, and optionally plots, an image.
## S3 method for class 'rimg' summary(object, plot = FALSE, axes = TRUE, col = NULL, ...)## S3 method for class 'rimg' summary(object, plot = FALSE, axes = TRUE, col = NULL, ...)
object |
(required) an image of class |
plot |
logical; plot the image and, if the image is color-classified, the colours
corresponding to colour class categories side-by-side? Defaults to |
axes |
should axes be drawn when |
col |
optional vector of colours when plotting colour-classified images with |
... |
additional graphical options when |
Either the RGB values of the k-means centres from the colour-classified image,
or a plot of both the image and specified colours (when plot = TRUE).
Thomas E. White [email protected]
papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio_class <- classify(papilio, kcols = 4) summary(papilio_class) # Plot the colour-classified image alongside the colour class palette summary(papilio_class, plot = TRUE) # Multiple images snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) snakes_class <- classify(snakes, kcols = 3) summary(snakes_class, plot = TRUE)papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo")) papilio_class <- classify(papilio, kcols = 4) summary(papilio_class) # Plot the colour-classified image alongside the colour class palette summary(papilio_class, plot = TRUE) # Multiple images snakes <- getimg(system.file("testdata/images/snakes", package = "pavo")) snakes_class <- classify(snakes, kcols = 3) summary(snakes_class, plot = TRUE)
Calculates all 23 colourimetric variables reviewed in Montgomerie (2006).
## S3 method for class 'rspec' summary(object, subset = FALSE, lim = NULL, wlmin = NULL, wlmax = NULL, ...)## S3 method for class 'rspec' summary(object, subset = FALSE, lim = NULL, wlmin = NULL, wlmax = NULL, ...)
object |
(required) a data frame, possibly an object of class |
subset |
Either |
lim |
The range of wavelengths used in calculations. The default is to use
the entire range in the |
wlmin, wlmax
|
Deprecated. Use the |
... |
class consistency (ignored) |
A data frame containing either 23 or 5 (subset = TRUE) variables described
in Montgomerie (2006) with spectra name as row names.
The colorimetric variables calculated by this function are
described in Montgomerie (2006) with corrections included in the README CLR
file from the May 2008 distribution of the CLR software. Authors should reference
both this package,Montgomerie (2006), and the original reference(s).
Description and notes on the measures:
B1 (Total brightness): Sum of the relative reflectance over the entire spectral range (area under the curve). Frequently used but should be discouraged because values are difficult to compare across studies (B2 is preferred). REF 1-3, 7, 9-11, 13
B2 (Mean brightness): Mean relative reflectance over the entire spectral range. This is preferred to B1 since values are easier to compare across studies. REF 4, 12
B3 (Intensity): Maximum relative reflectance (Reflectance at wavelength of maximum reflectance). Note that may be sensitive to noise near the peak. REF 1, 5, 6
S1 (Chroma): Relative contribution of a spectral range to the total brightness (B1) S1 is arbitrarily divided in 6 measures of chroma based on the wavelength ranges normally associated with specific hues. The values are calculated using the following ranges: S1U (UV, if applicable): lambda min-400nm; S1V (Violet) lambda min-415nm; S1B (Blue) 400nm-510nm; S1G (Green) 510nm-605nm; S1Y (Yellow) 550nm-625nm; S1R (Red) 605nm-lambda max. REF 2, 7, 8, 11-13
S2 (Spectral saturation): Rmax/Rmin This measure is sensitive to spectral noise. Proper interpretation of this value may be difficult for spectra with multiple peaks in the range of interest. REF 1
S3 (Chroma): Reflectance over the Rmax +- 50nm range divided by B1. Values for peaks within 50nm of either the minimum or maximum range of the data will not be comparable since the area under the curve for the area of interest will not always be based on the same wavelength range. Therefore, S3 should be interpreted with caution for peaks in the UV or Red range. REF 11
S4 (Spectral purity): |bmaxneg| , calculated by approximating the derivative of the spectral curve. As such, it is very sensitive to noise and should only be considered when data is adequately smoothed. NAs are returned for curves which do not, at any range of wavelength, decrease in intensity. Therefore, reflectance curves for brown and red surfaces, for example, should not generate a values. REF 1
S5 (Chroma): Similar in design to segment classification measures (see Montgomerie 2006 for details). REF 10
S6 (Contrast): Rmax - Rmin. Because it uses both Rmin and Rmax, this measure may be sensitive to spectral noise. REF 5, 6
S7 (Spectral saturation): Difference between the relative reflectance before and after the wavelength at which reflectance is halfway between its minimum (Rmin) and its maximum (Rmax). Somewhat sensitive to noise and can be misleading when more than one maxima and/or minima are present. REF 3, 9
S8 (Chroma): (Rmax - Rmin)/B2. Because it uses both Rmin and Rmax, this measure may be sensitive to spectral noise. REF 3, 13
S9 (Carotenoid chroma): (R700 - R450)/R700. Should only be used when the colour of the surface is clearly due to carotenoid pigmentation and R450 is lower than R700. Could be sensitive to noise. REF 8
S10 (Peaky chroma): (Rmax - Rmin)/B2 x |bmaxneg|. Should be used with properly smoothed curves. REF 7
H1 (Peak wavelength, hue): Wavelength of maximum reflectance. May be sensitive to noise and may be variable if there is more than one maxima. REF 1, 2, 4, 6, 7, 10-13
H2 (Hue): Wavelength at bmaxneg. Should be calculated using smoothed data. REF 2, 13
H3 (Hue): Wavelength at Rmid. Sensitive to noisy spectra and may be variable if there are more than one maxima and minima. REF 3, 9, 13
H4 (Hue): Similar in design to segment classification measures see Montgomerie (2006) for details. REF 10
H5 (Hue): Wavelength at bmax. Sensitive to noise and may be variable if there is more than one maxima and minima. REF 5
If minimum wavelength is over 400, UV chroma is not computed.
Variables which compute bmax and bmaxneg should be used with caution, for they rely on smoothed curves to remove noise, which would otherwise result in spurious results. Make sure chosen smoothing parameters are adequate.
Smoothing affects only B3, S2, S4, S6, S10, H2, and H5 calculation. All other variables can be reliably extracted using non-smoothed data.
Thomas E. White [email protected]
Pierre-Paul Bitton [email protected]
Rafael Maia [email protected]
Montgomerie R. 2006. Analyzing colors. In Hill, G.E, and McGraw, K.J., eds. Bird Coloration. Volume 1 Mechanisms and measurements. Harvard University Press, Cambridge, Massachusetts.
References describing variables:
1- Andersson, S. 1999. Morphology of uv reflectance in a whistling-thrush: Implications for the study of structural colour signalling in birds. Journal of Avian Biology 30:193-204.
2- Andersson, S., J. Ornborg, and M. Andersson. 1998. Ultraviolet sexual dimorphism and assortative mating in blue tits. Proceedings of the Royal Society B 265:445-450.
3- Andersson, S., S. Pryke, J. Ornborg, M. Lawes, and M. Andersson. 2002. Multiple receivers, multiple ornaments, and a trade-off between agonistic and epigamic signaling in a widowbird. American Naturalist 160:683-691.
4- Delhey, K., A. Johnsen, A. Peters, S. Andersson, and B. Kempenaers. 2003. Paternity analysis reveals opposing selection pressures on crown coloration in the blue tit (Parus caeruleus). Proceedings of the Royal Society B 270:2057-2063.
5- Keyser, A. and G. Hill. 1999. Condition-dependent variation in the blue-ultraviolet coloration of a structurally based plumage ornament. Proceedings of the Royal Society B 266:771-777.
6- Keyser, A.J. and G. Hill. 2000. Structurally based plumage coloration is an honest signal of quality in male blue grosbeaks. Behavioural Ecology 11:202-209.
7- Ornborg, J., S. Andersson, S. Griffith, and B. Sheldon. 2002. Seasonal changes in a ultraviolet structural colour signal in blue tits, Parus caeruleus. Biological Journal of the Linnean Society 76:237-245.
8- Peters, A., A. Denk, K. Delhey, and B. Kempenaers. 2004. Carotenoid-based bill colour as an indicator of immunocompetence and sperm performance in male mallards. Journal of Evolutionary Biology 17:1111-1120.
9- Pryke, S., M. Lawes, and S. Andersson. 2001. Agonistic carotenoid signalling in male red-collared widowbirds: Aggression related to the colour signal of both the territory owner and model intruder. Animal Behaviour 62:695-704.
10- Saks, L., K. Mcgraw, and P. Horak. 2003. How feather colour reflects its carotenoid content. Functional Ecology 17:555-561.
11- Shawkey, M., A. Estes, L. Siefferman, and G. Hill. 2003. Nanostructure predicts intraspecific variation in ultraviolet-blue plumage colour. Proceedings of the Royal Society B 270:1455-1460.
12- Siefferman, L. and G. Hill. 2005. UV-blue structural coloration and competition for nestboxes in male eastern bluebirds. Animal Behaviour 69:67-72.
13- Smiseth, P., J. Ornborg, S. Andersson, and T. Amundsen. 2001. Is male plumage reflectance correlated with paternal care in bluethroats? Behavioural Ecology 12:164-170.
# Load data data(sicalis) # Calculate and display all spectral summary variables summary(sicalis) # Calculate only subset of B2, S8 and H1 as per Andersson (1999) summary(sicalis, subset = TRUE) # Calculate user-specified subset of B1 and H4 summary(sicalis, subset = c("B1", "H4"))# Load data data(sicalis) # Calculate and display all spectral summary variables summary(sicalis) # Calculate only subset of B2, S8 and H1 as per Andersson (1999) summary(sicalis, subset = TRUE) # Calculate user-specified subset of B1 and H4 summary(sicalis, subset = c("B1", "H4"))
Returns the attributes used when calculating a visual model using vismodel()
## S3 method for class 'vismodel' summary(object, ...)## S3 method for class 'vismodel' summary(object, ...)
object |
(required) Results of |
... |
class consistency (ignored) |
Returns all attributes chosen when calculating the visual model, as well as the
default data.frame summary
Rafael Maia [email protected]
Vorobyev, M., Osorio, D., Bennett, A., Marshall, N., & Cuthill, I. (1998). Tetrachromacy, oil droplets and bird plumage colours. Journal Of Comparative Physiology A-Neuroethology Sensory Neural And Behavioral Physiology, 183(5), 621-633.
Hart, N. S. (2001). The visual ecology of avian photoreceptors. Progress In Retinal And Eye Research, 20(5), 675-703.
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") summary(vis.sicalis)data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") summary(vis.sicalis)
Produces an interactive 3D plot of a tetrahedral colourspace using OpenGL capabilities.
Plots points in a tetrahedral colour space
tcsplot( tcsdata, size = 0.02, alpha = 1, col = "black", vertexsize = 0.02, achro = TRUE, achrosize = 0.01, achrocol = "grey", lwd = 1, lcol = "lightgrey", new = FALSE, hspin = FALSE, vspin = FALSE, floor = TRUE, gamut = FALSE ) tcspoints(tcsdata, size = 0.02, col = "black", alpha = 1) tcsvol( tcsdata, type = c("convex", "alpha"), avalue = "auto", col = "black", alpha = 0.2, grid.alpha = 1, grid = TRUE, fill = TRUE, lwd = 1 )tcsplot( tcsdata, size = 0.02, alpha = 1, col = "black", vertexsize = 0.02, achro = TRUE, achrosize = 0.01, achrocol = "grey", lwd = 1, lcol = "lightgrey", new = FALSE, hspin = FALSE, vspin = FALSE, floor = TRUE, gamut = FALSE ) tcspoints(tcsdata, size = 0.02, col = "black", alpha = 1) tcsvol( tcsdata, type = c("convex", "alpha"), avalue = "auto", col = "black", alpha = 0.2, grid.alpha = 1, grid = TRUE, fill = TRUE, lwd = 1 )
tcsdata |
(required) a data frame, possibly a result from the
|
size |
size of the points in the plot (defaults to 0.02) |
alpha |
transparency of points (or volume fill in |
col |
colour of the points in the plot (defaults to black) |
vertexsize |
size of the points at the vertices |
achro |
should a point be plotted at the origin (defaults to |
achrosize |
size of the point at the origin when |
achrocol |
color of the point at the origin |
lwd, lcol
|
graphical parameters for the edges of the tetrahedron. |
new |
should a new 3D plot be called (defaults to |
hspin |
if |
vspin |
if |
floor |
if |
gamut |
logical. Should the polygon showing the possible colours given
visual system and illuminant used in the analysis (defaults to |
type |
accepts a vector of length 1 or 2 with 'p' for points and/or 'l' for lines from the point to the base of the tetrahedron. |
avalue |
if |
grid.alpha |
transparency of the volume polygon grid lines |
grid |
if |
fill |
if |
tcsplot() creates a 3D plot using functions of the package rgl,
based on openGL capabilities. Plot is interactive and can be manipulated with the mouse
(left button: rotate along 'z' axis; right button: rotate along 'x' axis;
third button: zoom).
tcspoints() adds points to the plot. Points are currently plotted
only as spheres to maintain export capabilities.
tcsvol() creates a 3D colour volume within a tcsplot object.
Rafael Maia [email protected]
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
# For plotting data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") tcsplot(tcs.sicalis, size = 0.005) rgl::rgl.postscript("testplot.pdf", fmt = "pdf") rgl::rgl.snapshot("testplot.png") # For adding points patch <- rep(c("C", "T", "B"), 7) tcs.crown <- subset(tcs.sicalis, "C") tcs.breast <- subset(tcs.sicalis, "B") tcsplot(tcs.crown, col = "blue") tcspoints(tcs.breast, col = "red") # For plotting convex hull tcsplot(tcs.sicalis, col = "blue", size = 0.005) tcsvol(tcs.sicalis)# For plotting data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") tcsplot(tcs.sicalis, size = 0.005) rgl::rgl.postscript("testplot.pdf", fmt = "pdf") rgl::rgl.snapshot("testplot.png") # For adding points patch <- rep(c("C", "T", "B"), 7) tcs.crown <- subset(tcs.sicalis, "C") tcs.breast <- subset(tcs.sicalis, "B") tcsplot(tcs.crown, col = "blue") tcspoints(tcs.breast, col = "red") # For plotting convex hull tcsplot(tcs.sicalis, col = "blue", size = 0.005) tcsvol(tcs.sicalis)
Dataset containing reflectance measurements from the wing patch of a single male at different incident angles (15-75 degrees in 5-degree increments).
data(teal)data(teal)
An object of class rspec (inherits from data.frame) with 401 rows and 13 columns.
Chad Eliason [email protected]
Calculates quantum catches at each photoreceptor. Both raw and relative values can be returned, for use in a suite of colourspace and non-colourspace models.
vismodel( rspecdata, visual = c("avg.uv", "avg.v", "bluetit", "ctenophorus", "star", "pfowl", "apis", "canis", "cie2", "cie10", "musca", "drosophila", "segment", "habronattus", "rhinecanthus"), achromatic = c("none", "bt.dc", "ch.dc", "st.dc", "md.r1", "dm.r1", "ra.dc", "cf.r", "ml", "l", "all"), illum = c("ideal", "bluesky", "D65", "forestshade"), trans = c("ideal", "bluetit", "blackbird"), qcatch = c("Qi", "fi", "Ei"), bkg = c("ideal", "green"), vonkries = FALSE, scale = 1, relative = TRUE )vismodel( rspecdata, visual = c("avg.uv", "avg.v", "bluetit", "ctenophorus", "star", "pfowl", "apis", "canis", "cie2", "cie10", "musca", "drosophila", "segment", "habronattus", "rhinecanthus"), achromatic = c("none", "bt.dc", "ch.dc", "st.dc", "md.r1", "dm.r1", "ra.dc", "cf.r", "ml", "l", "all"), illum = c("ideal", "bluesky", "D65", "forestshade"), trans = c("ideal", "bluetit", "blackbird"), qcatch = c("Qi", "fi", "Ei"), bkg = c("ideal", "green"), vonkries = FALSE, scale = 1, relative = TRUE )
rspecdata |
(required) a data frame, possibly of class |
visual |
the visual system to be used. Options are:
|
achromatic |
the sensitivity data to be used to calculate luminance (achromatic) receptor stimulation. Either a vector containing the sensitivity for a single receptor, or one of the options:
|
illum |
either a vector containing the illuminant, or one of the options:
|
trans |
either a vector containing the ocular or environmental transmission spectra, or one of the options:
|
qcatch |
Which quantal catch metric to return. Options are:
|
bkg |
background spectrum. Note that this will have no effect when
|
vonkries |
logical. Should the von Kries colour correction transformation be applied?
(defaults to |
scale |
a value by which the illuminant will be multiplied. Useful for when the
illuminant is a relative value (i.e. transformed to a maximum of 1 or to a percentage),
and does not correspond to quantum flux units
(μmol.s-1.m-2).
Useful values are, for example, 500 (for dim light) and 10000 (for bright
illumination). Note that if |
relative |
should relative quantum catches be returned (i.e. is it a colour
space model? Defaults to |
An object of class vismodel containing the photon catches for each of the
photoreceptors considered. Information on the parameters used in the calculation are also
stored and can be called using the summary.vismodel() function.
Built-in visual, achromatic, illum, bkg and trans are only defined
on the 300 to 700nm wavelength range. If you wish to work outside this range,
you will need to provide your own data.
Thomas E. White [email protected]
Rafael Maia [email protected]
Vorobyev, M., Osorio, D., Bennett, A., Marshall, N., & Cuthill, I. (1998). Tetrachromacy, oil droplets and bird plumage colours. Journal Of Comparative Physiology A-Neuroethology Sensory Neural And Behavioral Physiology, 183(5), 621-633.
Hart, N. S., Partridge, J. C., Cuthill, I. C., Bennett, A. T. D. (2000). Visual pigments, oil droplets, ocular media and cone photoreceptor distribution in two species of passerine bird: the blue tit (Parus caeruleus L.) and the blackbird (Turdus merula L.). Journal of Comparative Physiology A, 186, 375-387.
Hart, N. S. (2001). The visual ecology of avian photoreceptors. Progress In Retinal And Eye Research, 20(5), 675-703.
Barbour H. R., Archer, M. A., Hart, N. S., Thomas, N., Dunlop, S. A., Beazley, L. D, Shand, J. (2002). Retinal characteristics of the Ornate Dragon Lizard, Ctenophorus ornatus.
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.
Chittka L. (1992). The colour hexagon: a chromaticity diagram based on photoreceptor excitations as a generalized representation of colour opponency. Journal of Comparative Physiology A, 170(5), 533-543.
Stockman, A., & Sharpe, L. T. (2000). Spectral sensitivities of the middle- and long-wavelength sensitive cones derived from measurements in observers of known genotype. Vision Research, 40, 1711-1737.
CIE (2006). Fundamental chromaticity diagram with physiological axes. Parts 1 and 2. Technical Report 170-1. Vienna: Central Bureau of the Commission Internationale de l' Eclairage.
Neitz, J., Geist, T., Jacobs, G.H. (1989) Color vision in the dog. Visual Neuroscience, 3, 119-125.
Sharkey, C. R., Blanco, J., Leibowitz, M. M., Pinto-Benito, D., & Wardill, T. J. (2020). The spectral sensitivity of Drosophila photoreceptors. Scientific reports, 10(1), 1-13.
sensdata() to retrieve or plot in-built spectral sensitivity data
used in vismodel()
# Dichromat (dingo) data(flowers) vis.dingo <- vismodel(flowers, visual = "canis") di.dingo <- colspace(vis.dingo, space = "di") # Trichromat (honeybee) data(flowers) vis.bee <- vismodel(flowers, visual = "apis") tri.bee <- colspace(vis.bee, space = "tri") # Tetrachromat (blue tit) data(sicalis) vis.bluetit <- vismodel(sicalis, visual = "bluetit") tcs.bluetit <- colspace(vis.bluetit, space = "tcs") # Tetrachromat (starling), receptor-noise model data(sicalis) vis.star <- vismodel(sicalis, visual = "star", achromatic = "bt.dc", relative = FALSE) dist.star <- coldist(vis.star, achromatic = TRUE) # Estimate quantum catches using a custom trichromatic visual phenotype custom <- sensmodel(c(330, 440, 550)) names(custom) <- c("wl", "s", "m", "l") vis.custom <- vismodel(flowers, visual = custom) tri.custom <- colspace(vis.custom, space = "tri")# Dichromat (dingo) data(flowers) vis.dingo <- vismodel(flowers, visual = "canis") di.dingo <- colspace(vis.dingo, space = "di") # Trichromat (honeybee) data(flowers) vis.bee <- vismodel(flowers, visual = "apis") tri.bee <- colspace(vis.bee, space = "tri") # Tetrachromat (blue tit) data(sicalis) vis.bluetit <- vismodel(sicalis, visual = "bluetit") tcs.bluetit <- colspace(vis.bluetit, space = "tcs") # Tetrachromat (starling), receptor-noise model data(sicalis) vis.star <- vismodel(sicalis, visual = "star", achromatic = "bt.dc", relative = FALSE) dist.star <- coldist(vis.star, achromatic = TRUE) # Estimate quantum catches using a custom trichromatic visual phenotype custom <- sensmodel(c(330, 440, 550)) names(custom) <- c("wl", "s", "m", "l") vis.custom <- vismodel(flowers, visual = custom) tri.custom <- colspace(vis.custom, space = "tri")
Produces a 3D colour volume in tetrahedral colour space when plotting a non-interactive tetrahedral plot.
vol( tcsdata, type = c("convex", "alpha"), avalue = "auto", alpha = 0.2, grid = TRUE, fill = TRUE, new = FALSE, ... )vol( tcsdata, type = c("convex", "alpha"), avalue = "auto", alpha = 0.2, grid = TRUE, fill = TRUE, new = FALSE, ... )
tcsdata |
(required) a data frame, possibly a result from the
|
type |
if "convex", the colour volume is plotted using a convex hull and if "alpha", it is plotted using alphashapes. |
avalue |
if |
alpha |
transparency of volume (if |
grid |
logical. if |
fill |
logical. if |
new |
logical. Should a new plot be started or draw over an open plot?
(defaults to |
... |
additional graphical options. See |
vol() creates a 3D colour volume within a static tetrahedral plot.
Rafael Maia [email protected]
Hugo Gruson
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Stoddard, M. C., & Stevens, M. (2011). Avian vision and the evolution of egg color mimicry in the common cuckoo. Evolution, 65(7), 2004-2013.
Maia, R., White, T. E., (2018) Comparing colors using visual models. Behavioral Ecology, ary017 doi:10.1093/beheco/ary017
Gruson H. (2020). Estimation of colour volumes as concave hypervolumes using
-shapes. Methods in Ecology and Evolution, 11(8), 955-963
doi:10.1111/2041-210X.13398
# For plotting data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") plot(tcs.sicalis) # Convex hull vol(tcs.sicalis, type = "convex") # Alpha-shape if (require("alphashape3d")) { vol(tcs.sicalis, type = "alpha", avalue = 1) }# For plotting data(sicalis) vis.sicalis <- vismodel(sicalis, visual = "avg.uv") tcs.sicalis <- colspace(vis.sicalis, space = "tcs") plot(tcs.sicalis) # Convex hull vol(tcs.sicalis, type = "convex") # Alpha-shape if (require("alphashape3d")) { vol(tcs.sicalis, type = "alpha", avalue = 1) }
Calculates the overlap between the volumes defined by two sets of points in cartesian space.
voloverlap( colsp1, colsp2, type = c("convex", "alpha"), avalue = "auto", plot = FALSE, interactive = FALSE, col = c("blue", "red", "darkgrey"), fill = FALSE, new = TRUE, nsamp = 1000, psize = 0.001, lwd = 1, ... )voloverlap( colsp1, colsp2, type = c("convex", "alpha"), avalue = "auto", plot = FALSE, interactive = FALSE, col = c("blue", "red", "darkgrey"), fill = FALSE, new = TRUE, nsamp = 1000, psize = 0.001, lwd = 1, ... )
colsp1, colsp2
|
(required) data frame, possibly a result from the |
type |
if "convex", the colour volume is plotted using a convex hull and if "alpha", it is plotted using alphashapes. |
avalue |
if |
plot |
logical. Should the volumes and points be plotted? (defaults to |
interactive |
logical. If |
col |
a vector of length 3 with the colours for (in order) the first volume, the second volume, and the overlap. |
fill |
logical. should the two volumes be filled in the plot? (defaults to |
new |
logical. Should a new plot window be called? If |
nsamp |
if |
psize |
if |
lwd |
if |
... |
additional arguments passed to the plot. See |
Calculates the overlap between the volumes defined by two set of points in colourspace. The volume from the overlap is then given relative to:
vsmallest the volume of the overlap divided by the smallest of that defined
by the the two input sets of colour points. Thus, if one of the volumes is entirely
contained within the other, this overlap will be vsmallest = 1.
vboth the volume of the overlap divided by the combined volume of both
input sets of colour points.
If type = "alpha", If used, the output will be different:
s_in1, s_in2 the number of sampled points that fall within each of the volumes
individually.
s_inboth the number of sampled points that fall within both volumes.
s_ineither the number of points that fall within either of the volumes.
psmallest the proportion of points that fall within both volumes divided by the
number of points that fall within the smallest volume.
pboth the proportion of points that fall within both volumes divided by the total
number of points that fall within both volumes.
Stoddard & Stevens (2011) originally obtained the volume overlap through Monte Carlo simulations of points within the range of the volumes, and obtaining the frequency of simulated values that fall inside the volumes defined by both sets of colour points.
Stoddard & Stevens (2011) also return the value of the overlap relative to one of the volumes (in that case, the host species). However, for other applications this value may not be what one expects to obtain if (1) the two volumes differ considerably in size, or (2) one of the volumes is entirely contained within the other. For this reason, we also report the volume relative to the union of the two input volumes, which may be more adequate in most cases.
Rafael Maia [email protected]
Hugo Gruson [email protected]
Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.
Stoddard, M. C., & Stevens, M. (2011). Avian vision and the evolution of egg color mimicry in the common cuckoo. Evolution, 65(7), 2004-2013.
Maia, R., White, T. E., (2018) Comparing colors using visual models. Behavioral Ecology, ary017 doi:10.1093/beheco/ary017
Gruson H. (2020). Estimation of colour volumes as concave hypervolumes using
-shapes. Methods in Ecology and Evolution, 11(8), 955-963
doi:10.1111/2041-210X.13398
data(sicalis) tcs.sicalis.C <- subset(colspace(vismodel(sicalis)), "C") tcs.sicalis.T <- subset(colspace(vismodel(sicalis)), "T") tcs.sicalis.B <- subset(colspace(vismodel(sicalis)), "B") # Convex hull volume voloverlap(tcs.sicalis.T, tcs.sicalis.B, type = "convex") voloverlap(tcs.sicalis.T, tcs.sicalis.C, type = "convex", plot = TRUE) voloverlap(tcs.sicalis.T, tcs.sicalis.C, type = "convex", plot = TRUE, col = seq_len(3)) # Alpha-shape volume if (require("alphashape3d")) { voloverlap(tcs.sicalis.T, tcs.sicalis.B, type = "alpha", avalue = 1) }data(sicalis) tcs.sicalis.C <- subset(colspace(vismodel(sicalis)), "C") tcs.sicalis.T <- subset(colspace(vismodel(sicalis)), "T") tcs.sicalis.B <- subset(colspace(vismodel(sicalis)), "B") # Convex hull volume voloverlap(tcs.sicalis.T, tcs.sicalis.B, type = "convex") voloverlap(tcs.sicalis.T, tcs.sicalis.C, type = "convex", plot = TRUE) voloverlap(tcs.sicalis.T, tcs.sicalis.C, type = "convex", plot = TRUE, col = seq_len(3)) # Alpha-shape volume if (require("alphashape3d")) { voloverlap(tcs.sicalis.T, tcs.sicalis.B, type = "alpha", avalue = 1) }