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.
stdCoefs(object, classes=NA, std.by, std.type = "mean", p.crit = 0.05,bonferroni= FALSE)A shapeR object with standardized shape coefficients in the slot shape.std
A shapeR object
The classes to be grouped for standardization. Should be the same as used for the statistical tests
The parameter to be used for standardization. Typically the length of the fish from the master.list.
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
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.
A logical parameter for performing Bonferroni for multiple testing
Lisa Anne Libungan
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.
data(shape)
shape = stdCoefs(shape,classes="pop","length_cm")
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