readland.tps: Read landmark data from tps file
Description
Read *.tps file to obtain landmark coordinatesUsage
readland.tps(file, specID = c("None", "ID", "imageID"), readcurves = FALSE,
warnmsg = T)Arguments
file
A *.tps file containing two- or three-dimensional landmark data
specID
a character specifying whether to extract the specimen ID names from the ID or IMAGE lines (default is "None").
readcurves
A logical value stating whether CURVES= field and associated coordinate data will be read as semilandmarks (TRUE)
or ignored (FALSE).
warnmsg
A logical value stating whether warnings should be printed
Value
- Function returns a (p x k x n) array, where p is the number of landmark points, k is the number
of landmark dimensions (2 or 3), and n is the number of specimens. The third dimension of this array
contains names for each specimen, which are obtained from the image names in the *.tps file.
Details
This function reads a *.tps file containing two- or three-dimensional landmark coordinates.
Tps files are text files in one of the standard formats for geometric morphometrics (see Rohlf 2010).
Two-dimensional landmarks coordinates are designated by the identifier "LM=", while three-dimensional
data are designated by "LM3=". Landmark coordinates are multiplied by their scale factor if this is
provided for all specimens. If one or more specimens are missing the scale factor, landmarks are treated
in their original units.
Missing data may be present in the file. In this case, they must be designated by 'NA'. The
positions of missing landmarks may then be estimated using estimate.missing.
The user may specify whether specimen names are to be extracted from the 'ID=' field or 'IMAGE=' field
and included in the resulting 3D array.
e.g., for 'ID=' use (file, specID = "ID") and for 'IMAGE=' use (file, specID = "imageID").
The default is specID="None".
If there are curves defined in the file (i.e., CURVES= fields), the option readcurves should be used.
When readcurves = TRUE, the coordinate data for the curves will be returned as semilandmarks and will be appended to
the fixed landmark data. Then the user needs to use define.sliders.2d or define.sliders.3d
to create a matrix designating how the curve points will slide (used by 'curves=' in gpagen).
When readcurves = FALSE, only the landmark data are returned.
NOTE: At present, all other information that can be contained in tps files (comments, variables, radii, etc.)
is ignored.References
Rohlf, F. J. 2010. tpsRelw: Relative warps analysis. Version 1.49. Department of Ecology
and Evolution, State University of New York at Stony Brook, Stony Brook, NY.