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phyloToricAMatrix -- construct the design matrix of a group-based phylogenetic model

Description

i1 : phyloToricAMatrix(4, {{1, 2}},CFNmodel)

o1 = | 1 0 0 1 1 0 0 1 |
     | 0 1 1 0 0 1 1 0 |
     | 1 1 1 1 0 0 0 0 |
     | 0 0 0 0 1 1 1 1 |
     | 1 1 0 0 1 1 0 0 |
     | 0 0 1 1 0 0 1 1 |
     | 1 0 1 0 1 0 1 0 |
     | 0 1 0 1 0 1 0 1 |
     | 1 0 0 1 0 1 1 0 |
     | 0 1 1 0 1 0 0 1 |

              10       8
o1 : Matrix ZZ   <-- ZZ

Ways to use phyloToricAMatrix:

  • phyloToricAMatrix(Graph,Model)
  • phyloToricAMatrix(LeafTree,Model)
  • phyloToricAMatrix(ZZ,List,Model)

For the programmer

The object phyloToricAMatrix is a method function.


The source of this document is in /build/reproducible-path/macaulay2-1.25.05+ds/M2/Macaulay2/packages/PhylogeneticTrees.m2:1071:0.