regimeMaker {maticce} | R Documentation |
This function utilizes a matrix of the format returned by regimeMatrix
to define the models it is going to create. Then, it paints these models onto the trees provided and returns a list suitable for further analysis.
regimeMaker(ouchTrees, regMatrix, nodeMembers)
ouchTrees |
A list of ouch-style trees |
regMatrix |
A model by nodes matrix of the format returned by regimeMatrix
|
nodeMembers |
A list of individuals defining the nodes specified in regMatrix
|
The easiest way to use this function will usually be to utilize regimeMatrix
to create the matrix input as regMatrix
and manually prune or add rows. See the example below.
A list with three items:
regList |
A list of lists of regimes, with the number of first-order items corresponding to the number of trees in ouchTrees ,
the number of second-order items corresponding to the number of models being tested.
In the example below, regs$regList[[2]][[4]] is the fourth model defined on the second tree.
|
nodeMatrix |
A boolean matrix with rows corresponding to the trees in ouchTrees and columns corresponding to the nodes specified in regMatrix ;
cells indicate by TRUE or FALSE whether a node is present in each of the trees being analyzed.
|
regMatrix |
A list of regimeMatrix -format matrices that define the models applicable for each tree in ouchTrees , with missing nodes designated by NAs.
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Use of regimeMatrix
or regimeMaker
to generate tailored sets of regimes is not currently integrated smoothly with runBatchHansen
,
but for the time being they can be used to create regimes for manual analysis.
Andrew L. Hipp <ahipp@mortonarb.org>
data(carex) # tree comes in in phylo format, but we need an ouchtree object trees <- lapply(carex$ovales.bayesTrees[1:10], ape2ouch) # if we are interested in comparing the single-change models that allow changes only at nodes 1, 2, 4, 5, and 8, as well as the no-change model, we could do: mat <- regimeMatrix(n = 8, maxNodes = 1)[c(1,2,4,5,8,9), ] # the 9th row is the no-change model #... then we make regimes based on that regime matrix... regs <- regimeMaker(trees, mat, carex$ovales.nodes) #... and paint the regimes from tree 1 onto tree 1 either singly... plot(trees[[1]], regime = regs$regList[[1]][[1]]) #... or in a layout: plot(trees[[1]], regime = regs$regList[[1]])