otolith: Identification of fish otolith using digital images

Description Usage Arguments Details Value References

Sample curvillinear semi-landmarks on a closed outline, using either the 'comb' or the 'equally-spaced' methods.

1 2	comb(outdata, nd = 50, plot = FALSE, label = FALSE) equaldist(outdata, nd = 50, plot = FALSE, label = FALSE)

`outdata`	outline data. a matrix consists of xy coordinates. works on both 4-connected and 8-connected outline.
`nd`	numeric. Number of equally spaced divides along the outline for each part of the outline.
`plot`	logical. Whether to plot
`label`	logical. Whether to label the plot

comb divides the outline into two parts by principal PC axis, a 'comb' is then used to guide the sampling of the semi-landmarks. See reference for 'comb' method explanations.

comb produces errorneous results for complex outline with high outline curvature, e.g. at the 'excisura' site of some fish otoliths, thus, the equaldist method is preferable for fish otoliths and is used in the img2landmark wrapper.

equaldist divides the outline in similar way as comb, then semi -landmarks are sampled in equal intervals in each part, along the outline.

semi-landmarks sampled and the plot of the sampled semi-landmarks on the outline if plot=TRUE

Ponton, D. (2006). Is geometric morphometrics efficient for comparing otolith shape of different fish species?. Journal of Morphology, 267(6), 750-757.

Sheets, H. D., Covino, K. M., Panasiewicz, J. M., & Morris, S. R. (2006). Comparison of geometric morphometric outline methods in the discrimination of age-related differences in feather shape. Frontiers in Zoology, 3(1), 1-12.

jinyung/otolith documentation built on May 19, 2019, 10:36 a.m.