align.procrustes: Generalized Procrustes alignment with interactive outlier...

In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

Generalized Procrustes alignment with interactive outlier detection and removal

Description

GPA is performed by a call to gpagen. If outlier.analysis = TRUE then the function will display the results of plotOutliers, then warp grids for the most extreme shapes. The user is prompted to select a certain number of extreme shapes to exclude from a repeated Procrustes alignment. This processes is iterative, until the user indicates that it should stop or no shapes are requested for removal.

Usage

align.procrustes(
  A,
  curves = NULL,
  show.plot.gpa = TRUE,
  outlier.analysis = FALSE,
  display.outliers = 4,
  output.gdf = TRUE,
  ...
)

Arguments

A	A list or 3-dimensional array containing XY shape coordinates for multiple specimens.
curves	An optional matrix defining which landmarks should be treated as semilandmarks by gpagen.
show.plot.gpa	A logical value specifying whether to plot the Procrustes-aligned landmarks.
outlier.analysis	A logical value specifying whether to perform interactive outlier analysis. Alternatively, a numeric vector can be provided indicating the index positions of specimens to remove. A character vector of specimen names can also be provided, indicating the specimens to remove.
display.outliers	The number of outlier shapes to display in the interactive outlier analysis.
output.gdf	A logical value specifying whether to return output with a list structure that includes an element, gdf, containing a geomorph.data.frame of shape coordinates and metadata (the default).

Value

Returns a list with Procrustes-aligned coordinates in coords, centroid size in Csize. All other elements from gpagen are in the the element gpagen. Any other list elements in the input are retained. Data provenance is also retained in provenance and updated with details of the GPA..

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)

Examples

data("Bombus.forewings", package = "borealis")

fw.gpa <- align.procrustes(Bombus.forewings)

fw.gpa <- align.procrustes(Bombus.forewings, show.plot.gpa = FALSE)
plot(fw.gpa$gpagen)

fw.gpa <- align.procrustes(Bombus.forewings, outlier.analysis = TRUE)
fw.gpa <- align.procrustes(Bombus.forewings, outlier.analysis = 57)
fw.gpa <- align.procrustes(Bombus.forewings,
                           outlier.analysis = c("FJ190828-002","DRA190718-001"),
                           print.progress = FALSE )

names(fw.gpa$provenance)
cat(fw.gpa$provenance$align.procrustes)

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