Software

Below are links to software packages that I (with co-authors) have developed. For each, there is a link to the software, as well as the original publication in which the method was described or used. These programs are freely distributed as a service to the scientific community. 

Users of these programs are requested to cite the corresponding papers where the methods were first described

Disclaimer: All of the routines have been tested, but it cannot be guaranteed that they are free of bugs. If errors are identified, please contact DCA to report them. 

Maintained Packages

 

1. geomorph and gmShiny: An R package for statistical shape analysis. This package (written in R) is designed for the collection and analysis of 2D and 3D landmark-based geometric morphometric shape data for 2D and 3D. NOTE: many of the functions described below are incorportated in geomorph (see help files). 

The package may be obtained from the CRAN package repository.

Please cite:

Baken E, M.L. Collyer, A. Kaliontzopoulou, and D.C. Adams. 2021. gmShiny and geomorph v4.0: new graphical interface and enhanced analytics for a comprehensive morphometric experience. Methods in Ecology and Evolution. 12:2355–2363.   

Adams, D.C., M.L. Collyer, A. Kaliontzopoulou, and E.Baken. 2023. Geometric Morphometric Analyses of 2D/3D Landmark Data. vsn. 4.0.6. https://cran.r-project.org/web/packages/geomorph/index.html


2. RRPP: An R package for fitting linear models to high-dimensional data using residual randomization. This package (written in R) is designed for the analysis of linear models using residual randomization. Both ordinary least squares (OLS) and generalized least squares (GLS) models may be examined. Post-hoc tests and graphical visualizaitons are also available. 

The package may be obtained from the CRAN package repository.

Please cite:

Collyer, M.L, and D.C. Adams. 2018. RRPP: An R package for fitting linear models to high-dimensional data using residual randomization. Methods in Ecology and Evolution. 9:1772-1779. 


Contributed Functions

I have written dozens of analytical functions for performing phenotypic and biostatistical analyses. These are incorporated in the geomorph and RRPP packages. For a list of functions, see:

-  geomorph manual
-  RRPP manual 


Software for meta-analysis. This software (distributed by Sinauer Associates) performs fixed effects and random effects meta-analysis for single group, categorical, and continuous meta-analytic models. Please cite: 

Rosenberg, M. S., D. C. Adams, and J. Gurevitch. 2000. MetaWin: Statistical software for meta-analysis. Version 2.0. Sinauer Associates, Sunderland, Massachusetts. 128 pp. 


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ACKNOWLEDGEMENT and DISCLAIMER: Much of the research described in these web pages is supported in part by NSF grant DEB-2140720, and was previously supported by NSF grants DBI-1902511, DEB-1556379, DEB-1257287, DEB-1118884, DEB-0446758, DEB-012228, and their supplements. Any opinions, findings, and conclusions, or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. https://www.nsf.gov