-
GM Preliminaries
- Geomorph Data Types
- Reading Data
-
Data Manipulation
- Geomorph Data Frame
- Combine Landmark Configurations (combine.subsets)
- Interlandmark Distances (interlmkdist)
- Rotate or Flip Landmark Configurations (rotate.coords)
- Create 3D Array (arrayspecs)
- Convert Array to Matrix (two.d.array)
- Estimating Missing Landmarks
- Outlier Identification
- Standardizing Articulations
- Symmetric Shape Generation
- R Data Basics
-
Procrustes Analysis
- GPA Introduction
- GPA with fixed landmarks
- GPA with curve semilandmarks
- GPA with surface semilandmarks
- gpagen Advanced Options
-
Analytics
- Linear Models
-
Shape Patterns
- Two-block Partial Least Squares (two.b.pls)
- Integration Test
- Modularity Test
- Overall Integration for a Set of Traits
- Phylogenetic Integration (phylo.int)
- Phylogenetic Modularity (phylo.mod)
- Global Integration
- Comparison of Modularity (compare.CR)
- Comparison of Integration (compare.pls)
- Comparison of Overall Integration
-
Phylogenetic Comparative Methods
- Phylogenetic ANOVA/Regression (ProcD.pgls)
- Compare Evolutionary Rates (compare.evol.rates)
- Compare Multiple Evolutionary Rates (compare.multi.evol.rates)
- Phylogenetic Morphological Integration (phylo.int)
- Phylogenetic Modularity (phylo.mod)
- Assessing Phylogenetic Signal (physignal)
- Assessing Phylogenetic Signal Effect Size (physignal.z)
- Comparing Phylogenetic Signal Effect Sizes (compare.physignal.z)
- Visualizations
- Common Workflows
Plot Allometry
Mark A. Conaway
Introduction
plotAllometry()
- \(fit\): A procD.lm fit.
- \(size\): A vector of centroid sizes, the same length as the number of observations in the fit.
- \(logsz\): A logical (TRUE or FALSE) value to indicate whether to first find the logarithm of size.
- \(method\): The method of allometric visualization, which includes CAC, PredLine, RegScore, and size.shape (PCA). See below for more details.
Important Note!