read.morphologika {geomorph}

Read landmark data from Morphologika file(s)

Description

Read Morphologika file (*.txt) to obtain landmark coordinates and specimen information

Usage

read.morphologika(filelist)

Arguments

filelist

The name of a Morphologika *.txt file containing two- or three-dimensional landmark data. Alternatively, a character vector of names of Morphologika *.txt file (such as made using list.files)

Details

This function reads a *.txt file in the Morphologika format containing two- or three-dimensional landmark coordinates. Morphologika files are text files in one of the standard formats for geometric morphometrics (see O'Higgins and Jones 1998,2006). If multiple morphologika files are specified (containing the same number of landmarks for all specimens), function returns a single object for files.

If the headers "labels", "labelvalues" and "groups" are present, then a data matrix containing all individual specimen information is returned. If the header "wireframe" is present, then a matrix of the landmark addresses for the wireframe is returned (see plotRefToTarget option 'links'). If the header "polygon" is present, then a matrix of the landmark addresses for the polygon wireframe is returned (see polygon3d or polygon).

NOTE: For multiple morphologika files that each contain only a single specimen (such as those exported from Stratovan Checkpoint software), one can add specimen names to the returned 3D array by: dimnames(mydata)[[3]] <- gsub (".txt", "", filelist)).

Value

Function returns a (p x k x n) array of the coordinate data. If other optional headers are present in the file (e.g. "[labels]" or "[wireframe]") function returns a list containing the "coords" array, and data matrix of "labels" and or "wireframe".

Author(s)

Emma Sherratt & Erik Otarola-Castillo

References

O'Higgins P and Jones N (1998) Facial growth in Cercocebus torquatus: An application of three dimensional geometric morphometric techniques to the study of morphological variation. Journal of Anatomy. 193: 251-272

O'Higgins P and Jones N (2006) Tools for statistical shape analysis. Hull York Medical School.