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Erik Otárola-Castillo | SOFTWARE

Harvard Fellow

Department of Human Evolutionary Biology, Harvard University

Iowa State University



Department of Human Evolutionary Biology
Harvard University
11 Divinity Ave
Cambridge, MA 02138
Phone 631-796-7331

E-mail: eotarolacastillo@fas.harvard.edu


Below you can find software programs which I have written (in R) to conduct methods I developed or implemented. Programs are freely available to the scientific community. These programs have been tested and debugged but I cannot gurantee that they are completely bug free. If errors are found, please contact me.


  geomorph: Geometric morphometric analysis of 2d/3d landmark data   

 "geomorph" is an R package containing programs to read, manipulate, and digitize landmark data; generate shape variables via Procrustes analysis for points, curves and surface data, perform statistical analyses of shape variation and covariation, and provide graphical depictions of shapes and patterns of shape variation. Geomorph can be downloaded freely from the Comprehensive R Archive Network (CRAN).

    geomorph package in CRAN


Please cite: Adams Dean C. and Erik Otárola-Castillo 2012, Package 'geomorph': Geometric morphometric analysis of 2d/3d landmark data. R package version 1.0



  Ontogenetic Allometry Trajectory Significance Test  

 Program to conduct significance testing of ontogenetic-allometry trajectories using residual randomization and within-age category sample size bootstrap (implementing work in, Anderson, M. J., and C. J. F. Ter Braak, 2003; Collyer, M. L., and D. C. Adams. 2007; Piras, P., P. Colangelo, D.C. Adams, A. Buscalioni, J. Cubo, T. Kotsakis, C. Meloro, and P. Raia. 2010; KP McNulty, SR Frost, DS Strait 2006).




  Multivariate: 2Block Partial LS and Ordinations   

General programs I wrote to conduct 2Block Partial Least Squares (from Rohlf and Corti 2000 systematic biology), Principal Components Analysis, Principal Coordinates Analysis, Correspondence Analysis, Canonical Correspondence Analysis, and Redundancy Analysis.




  Major Axis Regression  

Program to calculate slope of major axis regression using the variance covariance matrix of x and y. Can include W matrix for Phylogenetic correction




  Multivariate t-test (parametric and by permutation)  

Program to conduct a Multivariate t-test (Hotelling's T^2). Code includes traditional paramteric test with examples, and its non parametric counterpart under permutation.

    multivariate t test.r




 As the size of sampling units increase, so do the number of taxa. The rarefaction method (Sanders 1968, Hulbert 1971) can be used to assess whether diversity comparison between samples of varying sizes is possible. This R program operationalizes rarefaction and provides an example.




  Speedy Permutation Test  

Program to conduct simple (univariate) permutation test between 2 groups. Two versions, in "for loop" and a spedier version. Dataset: Difference in means of some trait (1:50) between 2 populations (A,B)




  Genetic Drift Illustration  

R program illustrates Genetic Drift in a population. "Real Time" plot shows the change in the frequency of two alleles in a population over several generations due to random sampling.











© 2012 Erik Otárola-Castillo| Web Design by Erik Otárola-Castillo