Hello there.
I need to construct an ultrametric phylogenetic tree from a NEXUS file
for run a different program afterwards.
I have tried to run the 'chronopl' command:
tree.ultra <- chronopl(tree, 0, age.min = 1, age.max = NULL,node =
"root", S = 1, tol = 1e-8,CV = FALSE, eval.max = 500, iter.max = 500)
but I get the following error:
Error in nlminb(c(ini.rate, ini.time[unknown.ages]), function(p)
minusploglik(p[EDGES], :
NA/NaN gradient evaluation
As this 'chronopl' command is now replaced by 'chronos' I have tried
to change the parameters to do something similar to the chronopl
command line:
tree.ultra <- chronos(tree, lambda = 1, model = "correlated", quiet
= FALSE, calibration = makeChronosCalib(tree, node = "root", age.min
= 1, age.max = NULL, interactive = FALSE, soft.bounds = FALSE),
control = chronos.control(tol = 1e-8, iter.max = 500, eval.max = 500))
but with these commands I get the following message:
Error in data.frame(node, age.min, age.max, soft.bounds = soft.bounds) :
arguments imply differing number of rows: 1, 0
I also have tried to do this in a simpler way:
tree.ultra <- chronos(tree, lambda = 1, model = "correlated")
But I get this message also:
Setting initial dates...
Fitting in progress... get a first set of estimates
Error en nlminb(start.para, f, g, control = opt.ctrl, lower = LOW,
upper = UP) :
NA/NaN gradient evaluation
Could anyone help me with this problem??
Is anything done in a wrong way?
Thanks a lot
MA
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