knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = rmarkdown::pandoc_available() )
Different maps can be compared using the procrustesMap()
function where one map is compared to another.
We'll read in the H3N2 2004 map as an example map
library(Racmacs) map_file <- system.file("extdata/h3map2004.ace", package = "Racmacs") map <- read.acmap(map_file) view(map)
We can use the procrustesMap()
function to compare the top 2 optimization runs.
pc_run12 <- procrustesMap( map = map, comparison_map = map, optimization_number = 1, comparison_optimization_number = 2 ) view(pc_run12)
We can also compare 3D map solutions to 2D map solutions. Firstly we will create a 3D version of our map with a fresh set of optimizations (choosing only 10 runs here for speed).
map3d <- optimizeMap( map = map, number_of_dimensions = 3, number_of_optimizations = 10, minimum_column_basis = "none" )
Now we will run procrustes map on the 3d version and view the result, by default an extra grid is drawn showing the dimensions to which the comparison map was constrained.
pc_3d2d <- procrustesMap( map = map3d, comparison_map = map ) view(pc_3d2d)
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