regimeMatrix: Create a matrix that defines models for batch analysis
In maticce: Mapping Transitions in Continuous Character Evolution

Description Usage Arguments Details Value Note Author(s) See Also Examples

regimeMatrix is a recursive function that returns a matrix of n columns by k rows, where n is a number of items and k is the number of all possible permutations of those items, up to a maximum number of items defined by maxNodes, and including a row with zero items.

1 2	regimeMatrix(n, maxNodes)

`n`	An integer between 1 and `maxNodes`
`maxNodes`	An integer between 1 and n; at `n` = `maxNodes`, `regimeMatrix` will return a matrix of 2^`n` rows.

Typically, this function is called by regimeVectors, but it may be useful to call this function if you are interested in defining an arbitrary set of models that doesn't include all possible models in the

A matrix of n columns by k rows, where n is a number of items and k is the number of all possible permutations of those items, up to a maximum number of items defined by maxNodes, and including a row with zero items

Use of regimeMatrix or regimeMaker to generate tailored sets of regimes is not currently integrated smoothly with runBatchHansen, but for the time being they can be used to create regimes for manual analysis.

Andrew Hipp ahipp@mortonarb.org

regimeMaker, paintBranches

  # allowing all possible permutations of changes at 15 nodes will be quite time-consuming:
  print(paste("Number of models =", dim(regimeMatrix(15,15))[1]))
  # paring that down to all possible permutations of changes at 15 nodes, 
  # up to a maximum of 5 changes, is much more manageable:
  print(paste("Number of models =", dim(regimeMatrix(15,5))[1]))