Biomedical subjects

F James Rohlf

Publications and source records attributed to F James Rohlf.

3 recordsLinked to original sources

PubMed2006

A comment on phylogenetic correction.

Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifact due to phylogeny and there is an expectation that the corrected regression or correlation coefficients will usually be closer to zero. It is shown here that this is not an accurate way to interpret these methods. The effect of taking phylogeny into account is to reduce the variance of the estimated regression or correlation coefficients. Their means are not because since estimates of regression coefficients are unbiased whether or not the correct phylogeny is taken into account. Estimates of correlations are only slightly biased (and in the opposite direction that many expect).

Computer Simulation↗

PubMed2003

Bias and error in estimates of mean shape in geometric morphometrics.

Sampling experiments were performed to investigate mean square error and bias in estimates of mean shape produced by different geometric morphometric methods. The experiments use the isotropic error model, which assumes equal and independent variation at each landmark. The case of three landmarks in the plane (i.e., triangles) was emphasized because it could be investigated systematically and the results displayed on the printed page. The amount of error in the estimates was displayed as RMSE surfaces over the space of all possible configurations of three landmarks. Patterns of bias were shown as vector fields over this same space. Experiments were also performed using particular combinations of four or more landmarks in both two and three dimensions. It was found that the generalized Procrustes analysis method produced estimates with the least error and no pattern of bias. Averages of Bookstein shape coordinates performed well if the longest edge was used as the baseline. The method of moments (Stoyan, 1990, Model. Biomet. J. 32, 843) used in EDMA (Lele, 1993, Math. Geol. 25, 573) exhibits larger errors. When variation is not small, it also shows a pattern of bias for isosceles triangles with one side much shorter than the other two and for triangles whose vertices are approximately collinear causing them to resemble their own reflections. Similar problems were found for the log-distance method of Rao and Suryawanshi (1996, Proc. Nat. Acad. Sci. 95, 4121). These results and their implications for the application of different geometric morphometric methods are discussed.

Animals↗

PubMed2003

Computing the uniform component of shape variation.

Any change in shape of a configuration of landmark points in two or three dimensions includes a uniform component, a component that is a wholly linear (affine) transformation. The formulas for estimating this component have been standardized for two-dimensional data but not for three-dimensional data. We suggest estimating the component by way of the complementarity between the uniform component and the space of partial warps. The component can be estimated by regression in either one space or the other: regression on the partial warps, followed by their removal, or regression on a basis for the uniform component itself. Either of the new methods can be used for both two- and three-dimensional landmark data and thus generalize Bookstein's (1996, pages 153-168 in Advances in morphometrics [L. F. Marcus et al., eds.], Plenum, New York) linearized Procrustes formula for estimating the uniform component in two dimensions.

Algorithms↗