hot.dots

This package provides the code used in Fabre et al 2020 (https://doi.org/10.1038/s41559-020-1225-3) to calculate per-landmark rate and variance

Installation

You can install the development version of hot.dots from GitHub with:

# install.packages("devtools")
devtools::install_github("rnfelice/hot.dots")

Example

This is a basic example of how to use these functions

library(hot.dots)
## Import the 3d morphometric data
my.shapes <- read.csv("./shapedata.csv",row.names = 1)
my.shapes <- array.specs(my.shapes,p =  (ncol(my.shapes)/3), k = 3)
# Import the phylogeny
phy1 <- read.nexus("./phy.nex")
#calculate per landmark rates and variance
my.rates <- per_lm_rates(shape.data = my.shapes, phy = phy1)
my.variances <- per_lm_variance(shape.data = my.shapes)

The log10-transformed rate and variance can be plotted using the rgl packages

library(rgl)
#import the mesh file that corresponds to specimen 1 in the `my.shapes` array

spheres3d(my.shapes[,,1], col = my.rates$Rate_Colors)
title3d("Per Landmark Rates")
open3d()

spheres3d(my.shapes[,,1], col = my.variances$Variance_Colors)
title3d("Per Landmark Disparity")