estimate.missing.landmarks: Estimate the location of missing landmarks

In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

Estimate the location of missing landmarks

Description

This function is a wrapper for geomorph:estimate.missing, which adds records of the specimens and landmarks altered by the imputation of missing landmarks.

Usage

estimate.missing.landmarks(A, na.value = NA, verbose = TRUE, ...)

Arguments

A	A 3-dimensional array containing XY shape coordinates for multiple specimens, or a list containing such as an array and data provenance.
na.value	A numeric value to treat as missing data, (NA). For example, tpsDig2 (starting with version 2.18) records missing landmarks as coordinate values of -1.0. Setting na.value = -1 will provide compatibility with these data.
verbose	A logical argument specifying whether to display metrics each during each iteration.

Details

Additional arguments are passed to geomorph::estimate.missing.

Value

Returns a list with coords, provenance, and any other potential list elements from the input.

Source

Dave Angelini [e-mail] [aut, cre]

References

Adams and M.L. Collyer and A. Kaliontzopoulou. 2020. Geomorph: Software for geometric morphometric analyses. R package version 3.2.1. D.C. (Link)

Rohlf, FJ. 2015. The tps series of software. Hystrix 26, 9–12. (Link)

Examples

j <- data("Jadera", package = "borealis")

j$coords[30,,c(1:3)] <- NA
j$coords[37,,c(1,4)] <- NA

j2 <- estimate.missing.landmarks(j)
cat(j2$provenance$estimate.missing.landmarks)
landmark.plot(j2, specimen.number = 1:4, axes = TRUE)

aphanotus/borealis documentation built on Nov. 4, 2022, 8:44 p.m.