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Morphometrics - Statistics - Programming

Imaging Software:
  • FIJI - Version of ImageJ with preloaded plugins
  • Base ImageJ - Software for processing and editing images
  • StereoMorph - R package to digitize landmarks and generate 3D images from multiple 2D pictures
  • WinDig - Software for digitizing points on electronic files

Random Number Generators:
  • Random.org - Program for generating random numbers

Geometric Morphometrics Software:
  • Morphometrics at Stony Brook - Comprehensive guide to geometric morphometrics software. For individual programs, I recommend the tps series developed by Jim Rohlf at Stony Brook. See:
  • tpsDIG2 - Program to digitize landmarks on digital images
  • tpsRelw - Program that performs procrustes superimposition and principal component analysis (PCA) of landmark data
  • tpsRegr - Program that performs procrustes superimposition and regression analysis of landmark data
  • tpsSplin - Program to visually compare pairs of specimens using deformation grids (thin-plate spline)
  • tpsPLS - Program that performs a partial least-squares analysis to explore the covariance between a set of variables and variation in shape or between two shapes
  • tpsUtil - Utility program for tps software

Other Geometric Morphometrics Software:
  • GeoMorph - R package for geometric morphometrics
  • Geometric Morphometrics Tools Package
  • IMP-Integrated Morphometrics Software
  • Morpheus et al.
  • MorphoJ- Geometric Morphometrics software
  • Morphologika
  • SlicerMorph Project

3D Morphological Analysis / Micro-CT Scanning:
  • 3D Slicer
  • SlicerMorph Project
  • SlicerMorph bioRxiv Article
  • SlicerMorph Tutorials

Online Geometric Morphometrics Books:
  • Guia Practica de Morfometria Geometrica - ResearchGate link to PDF guide on Geometric Morphometrics in Spanish.

Online Statistics and Quantitative Analysis Books:
  • Analisis Multivariado para Datos Biologicos - Teoria y Su Aplicacion Utilizando R - ResearchGate link to PDF book on Multivariate Analysis in Spanish.

Statistics:
  • jamovi - A free, open-source “3rd generation” statistical spreadsheet
  • Past- Free Statistical Software Program
  • VassarStats-Wonderful online statistics package
  • www.statisticshowto.com/benjamini-hochberg-procedure/ - Benjamini-Hochberg Procedure for correcting for multiple tests
  • Statistics Kingdom - Website for basic statistical analysis and graphing. Runs analyses online.

R Links, Tutorials, and Books:
  • The R Project for Statistical Computing
  • R Studio- Interface for using R.
  • R Tutorial- An Online R Tutorial.
  • Learning R- PDF of book by Ricard Cotton.
  • Modern Statistics with R. Online book by Mans Thulin.
  • Modern Statistics for Modern Biology. Online book on Statistics in R and Bioconductor by Susan Holmes and Wolfgang Huber.
  • R for Data Science- Online version of book by Wickham & Grolemund.
  • R Graphics Cookbook- Online version of book by Winston Chang.
  • R Markdown- R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire, Garrett Grolemund.
  • Beyond Multiple Linear Regression. Applied Generalized Linear Models and Multilevel Models in R. Online book by Paul Roback and Julie Legler.

Population Dynamics & Simulation Software:
  • Populus- Simluations of Population Biology.





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  • Home
  • Research
    • Lab Data
  • Freshw Fish West Ecu
  • Publications
  • Protocols
  • Tutorials & Code
  • People
  • Lab Pictures
  • Courses
  • Links
    • Biological Organizations
    • DePaul/Local Links
    • DNA/Molecular Biology
    • Ecuador / Latin America
    • Fish Links
    • Funding
    • Miscellaneous
    • Morphometrics/Statistics/Programming