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Hello I would like to compute geodesic distances from random trees for comparison and hypothesis testing with those produced from a given set of trees. I am using dist.multiPhylo() in the 'distory' package, but it seems to be too compute-intensive. To illustrate my point: > lin4 #object consisting of 4 randomly generated trees [1] "(S8: 1.00000, (((S4: 0.28596, S5: 0.28596): 0.63211, (S10: 0.88214, ((S6: 0.49245, S7: 0.49245): 0.24813, S9: 0.74058): 0.14156): 0.03592): 0.03859, ((S1: 0.16950, S2: 0.16950): 0.61358, S3: 0.78308): 0.17357): 0.04335);" [2] "((S6: 0.10938, S2: 0.10938): 0.89062, ((S7: 0.79060, ((S4: 0.31389, S8: 0.31389): 0.31812, (((S1: 0.06153, S3: 0.06153): 0.08642, S10: 0.14795): 0.47444, S9: 0.62238): 0.00962): 0.15860): 0.01336, S5: 0.80396): 0.19604);" [3] "((S7: 0.98617, (S4: 0.90628, (S3: 0.86179, ((S1: 0.17650, S6: 0.17650): 0.48270, ((S10: 0.28064, S5: 0.28064): 0.06352, (S9: 0.00968, S8: 0.00968): 0.33448): 0.31505): 0.20259): 0.04449): 0.07990): 0.01383, S2: 1.00000);" [4] "(((((S6: 0.42675, S3: 0.42675): 0.16273, S8: 0.58948): 0.00542, S5: 0.59490): 0.05023, (S4: 0.19208, S7: 0.19208): 0.45305): 0.35486, (S9: 0.90829, (S10: 0.64179, (S2: 0.36191, S1: 0.36191): 0.27988): 0.26649): 0.09171);" > dist.multiPhylo(lin4) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? If I increase the value of "expressions" from 5000 (default) to 25000 then > options(expressions=25000) > dist.multiPhylo(lin4) Error: protect(): protection stack overflowIs there a way to circumvent these errors? Thank you very much for your time. Juan A. Balbuena --
Dr. Juan A. Balbuena |
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