The script revbayes.github.io/tutorials/biogeo/scripts/run_epoch_phy.Rev throws the following error:
RevBayes version (1.0.9)
Build from development (6d8432) on Wed Aug 15 15:17:14 CEST 2018
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> source("run_epoch_phy.Rev")
Processing file "run_epoch_phy.Rev"
Successfully read one character matrix from file 'data/n6/silversword.mol.nex'
Successfully read one character matrix from file 'data/n6/silversword.n6.range.nex'
Attempting to read the contents of file "silversword.tre"
Successfully read file Error: Argument or label mismatch for function call.
Provided call:
dnPhyloCTMCClado (TimeTree<stochastic> 'tree',
RateGenerator<deterministic> 'Q',
CladogeneticProbabilityMatrix<deterministic> 'cladoProbs',
RealPos<deterministic> 'branchRates',
RealPos[]<constant> 'rootFrequencies',
String<constant> 'type',
Natural<constant> 'nSites' )
Correct usage is:
dnPhyloCTMCClado (Tree<any> tree,
RateGenerator|RateGenerator[]<any> Q,
CladogeneticProbabilityMatrix|CladogeneticProbabilityMatrix[]<deterministic> cladoProbs,
Simplex<any> rootFrequencies,
RealPos|RealPos[]<any> branchRates,
RealPos[]<any> siteRates,
Probability<any> pInv,
Natural<any> nSites,
String<any> type {valid options: "DNA"|"RNA"|"AA"|"Pomo"|"Protein"|"Standard"|"NaturalNumbers"},
Bool<any> treatAmbiguousAsGap,
Bool<any> storeInternalNodes,
Bool<any> gapMatchClamped)
Error: Problem processing line 231 in file "run_epoch_phy.Rev"
Many thanks for reporting the problem and for sharing your efforts debugging. The tutorial file for run_epoch_phy.Rev is now correct. The other three biogeography scripts were not affected.
The script
revbayes.github.io/tutorials/biogeo/scripts/run_epoch_phy.Rev
throws the following error:EDIT: The exact call triggering the error is:
It seems that the simplex function is not changing the type of the variable.