readland.shapes: Read landmark data from a shapes object (StereoMorph)

In geomorphR/geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

Read landmark data from a shapes object (StereoMorph)

Description

Read data from an object with class shapes, created by StereoMorph

Usage

readland.shapes(
  Shapes,
  nCurvePts = NULL,
  continuous.curve = NULL,
  scaled = TRUE
)

Arguments

Shapes	An object with class, "shapes"
nCurvePts	A single value (if only one curve) or a string of values (if multiple curves) for culling the number of curve points, using linear interpolation to find equally spaced distances between points. For example, with three curves, nCurvePts = c(20, 50, 10) would return 20, 50, and 10 curve points, respectively. If fixed landmarks are end points of curves, they will not be repeated as additional curve points. Therefore, one should expect in these cases that the number of semilandmarks are fewer than the number of curve points; i.e., choosing 20 curve points might yield 18 semilandmarks. If left NULL, no curve points will be estimated and only fixed landmarks will be read. Note: if less than 3 curve points are chosen for an open curve or less than 4 points are chosen for a closed curve, the number of points will default to 0, as fewer than these make it impossible to develop a curves matrix. A value of 0 can be chosen to omit specific curves when reading in data.
continuous.curve	An optional value or string of values to indicate which curves are closed and whose same start and end point should be treated as a semilandmark. For example, if one wishes to digitize a curve around an eye, for digitizing purposes a point might be initiated to find a curve around the eye and back to the point. This point will be "fixed" without indicating the curve is continuous. One could use this argument to indicate which curves are continuous; e.g., continuous.curve = c(2, 5) to indicate curves 2 and 5 have starting points that are not fixed landmarks but really sliding semilandmarks, as part of a closed curve.
scaled	A logical value (TRUE as default) to indicate whether scaled landmarks and curve points should be used. If any scales are missing, the function will default to scaled = FALSE.

Details

This function reads data from an object with class "shapes", after digitizing specimens using StereoMorph. This function can read in landmarks plus acquire points from curves, if the curves option was used in digitizing. This function is intended for reading data and facilitating the generation of a "curves" matrix for gpagen. It is not intended to influence how one should digitize landmarks using StereoMorph. Each digitizing experience is unique and users might need to edit their own data using StereoMorph functions in some cases; this function will not necessarily overcome all data editing challenges. This function currently works with 2D data only, as the readShapes function of StereoMorph pertains to digitizing images.

The enhanced feature of this function is that it can find a prescribed number of approximately equally spaced semilandmarks along 2D curves (from the many points of Bezier curves in StereoMorph), facilitating rapid gpagen analysis and the flexibility to change the desired number of semilandmarks defining curves. This is only true, however, if the curves option in digitizeImages (StereoMorph) is used.

The user can specify the number of points along curves, whether curves are continuous (closed and without fixed points), and whether landmarks should be scaled, if possible (if scaling was performed while digitizing).

Value

An object of class "geomorphShapes" is a list containing the following

landmarks	A list of specimen by specimen landmarks, arranged with fixed landmarks first and semilandmarks second.
fixed	A vector indicating which landmarks are initially considered "fixed" (but this can be changed).
sliders	A vector indicating which landmarks are initially considered semilandmarks, or "sliders".
curves	A matrix used in gpagen to define how semilandmarks slide by tangents described by flanking points. Each row of the matrix is a series of three points: tangent point 1, slider, tangent point 2. This matrix can be edited. to remove sliding points or add some, if points were originally considered fixed. This matrix is merely a suggestion, based on the curve information read in from a shapes object. Users should be able to rearrange this matrix, as needed.
n	The number of specimens.
p	The number of (both fixed and semi-) landmarks.
k	The number of landmark dimensions, currently only 2.
scaled	Logical value to indicate in landmarks are scaled.

Author(s)

Michael Collyer

See Also

readShapes (from StereoMorph)

Examples

# A true example is not possible, as digitizing experiences are 
# unique, but here is a general set-up
# myShapes <- readShapes("myDigitizingFile") # data from readShapes 
# from StereoMorph 
# myGMdata <- readland.shapes(myShapes) # just reading in the fixed 
# landmarks
# myGMdata <- readland.shapes(myShapes, 
#      nCurvePts = c(10, 15, 5), 
#      continuous.curve = 2) # fixed landmarks plus curve points 
# for three curves, one closed
# myGPA <- gpagen(myGMdata, ProcD = FALSE) # GPA perfomed with 
# minimized bending energy

geomorphR/geomorph documentation built on April 18, 2024, 6:41 p.m.