LM_relativepos_check: Check the relative positions for a set of landmarks, compared...

In fruciano/GeometricMorphometricsMix: Miscellaneous functions useful for geometric morphometrics

Check the relative positions for a set of landmarks, compared to a reference specimen

Description

The function compares the relative position of a set of landmarks to the one observed in a reference specimen. It also outputs which coordinates do not much the pattern observed in the reference specimen.

Usage

LM_relativepos_check(
  Dataset,
  LM_to_check,
  reference_specimen = 1,
  only_by_landmark_order = FALSE,
  use_specimen_names = TRUE
)

Arguments

Dataset	k x p x n array of k landmarks and p dimensions for n observations (specimens).
LM_to_check	Vector with the indices of which landmarks of Dataset should be tested
reference_specimen	The index of the specimen to use as reference (by default, the first).
only_by_landmark_order	If TRUE, each landmark in LM_to_check will be tested relative to the next in LM_to_check; otherwise all the pairwise relative positions between landmarks will be run
use_specimen_names	whether the names of specimens in Dataset should be used for the output

Details

Compare relative positions of landmarks to the one observed in a reference specimen. This function is useful to identify specimens with switched landmark positions and similar problems when a dataset has been collected using consistent criteria (e.g., a set of fish body pictures, with the mouth-tail axis approximately horizontal for all specimens).

For instance, if we want to check that landmarks 1, 2, and 3 are all aligned along the y coordinate in 2D, we will use a specimen (usually the first), checking that it has been landmarked correctly. Then, we will run the function on landmarks 1, 2, and 3 (by setting LM_to_check=c(1, 2, 3)). The function will output a list of which specimens seem to be problematic and which landmarks and coordinates for these specimens seem problematic. The putatively problematic coordinates will be indicated with "0". Clearly, if we are only interested in 1, 2, and 3 being along y, it will not matter if in some case we will find "0" under Coord1, but only if we find a "0" under Coord2.

Value

The function outputs a list with the following elements:

potentially_problematic_idx

Indices of potentially problematic specimens

potentially_problematic_LMs

List of potentially problematic landmarks and coordinates for the specimens in potentially_problematic_idx

Notice

Generally, it is better to use this function with a small number of carefully selected landmarks, instead of running it on all landmarks at the same time.

The parameter only_by_landmark_order allows to set whether all combinations of landmarks should be tested (default), or not.

If only_by_landmark_order is set to TRUE, each landmark in LM_to_check will be only tested with the next one. For instance if LM_to_check=c(1,2,3) the function will only compare the first landmark with the second, and the second with the third.

If the function cannot find potentially problematic specimens, a message to this effect will be presented.

fruciano/GeometricMorphometricsMix documentation built on Jan. 31, 2024, 6:24 a.m.