stdCoefs: Standardize coefficients

In shapeR: Collection and Analysis of Otolith Shape Data

Standardize coefficients

Description

Function to standardized the wavelet and Fourier coefficients for a specific parameter such as the fish length. For each country/population a regression coefficient is calculated as a function of fish length. If the slope is significantly different from zero, a correction is made according to Lleonart et al 2000. First ANCOVA is performed: variable ~ pop*length_cm, following a method by Longmore et al 2010. If there is a significant interaction between population and length_cm, then the coefficients are not used and automatically discarded. If there is no interaction, the coefficients are kept and standardized with regards to fish length.

Usage

stdCoefs(object, classes=NA, std.by, std.type = "mean", p.crit = 0.05,bonferroni= FALSE)

Arguments

object	A shapeR object
classes	The classes to be grouped for standardization. Should be the same as used for the statistical tests
std.by	The parameter to be used for standardization. Typically the length of the fish from the master.list.
std.type	The tuning of the standardization. The standardization can be sensitive to what value all the fishes are standardized to. Possible values are: min Standardized as the minimum value of std.by mean Standardized as the mean value of std.by max Standardized as the maximum value of std.by
p.crit	An argument used to select the threshold critera for omitting coefficients which show interaction with fish length. If p.crit = 0.05, all coefficients which have p<0.05 are omitted. If p.crit = 0.01, only coefficients with p<0.01 are omitted.
bonferroni	A logical parameter for performing Bonferroni for multiple testing

Value

A shapeR object with standardized shape coefficients in the slot shape.std

Author(s)

Lisa Anne Libungan

References

Lleonart, J., Salat, J. & Torres, G.J. (2000) Removing allometric effects of body size in morphological analysis. Journal of Theoretical Biology, 205, 85-93.

Longmore, C., Fogarty, K., Neat, F., Brophy, D., Trueman, C., Milton, A. & Mariani, S. (2010) A comparison of otolith microchemistry and otolith shape analysis for the study of spatial variation in a deep-sea teleost, Coryphaenoides rupestris. Environmental Biology of Fishes, 89, 591-605.

Reist, J.D. (1985) An Empirical-Evaluation of Several Univariate Methods That Adjust for Size Variation in Morphometric Data. Canadian Journal of Zoology-Revue Canadienne De Zoologie, 63, 1429-1439.

Examples

data(shape)
shape = stdCoefs(shape,classes="pop","length_cm")

shapeR documentation built on Nov. 22, 2022, 1:07 a.m.