fitdiscrete error with new String7 from CSV #205
Description
If you read the trait data with CSV.read, it automatically makes the strings String7 type, which throws an error when running fitdiscrete:
julia> s1 = fitdiscrete(net1, :ERSM, species, df; optimizeQ=false)
ERROR: MethodError: no method matching fitdiscrete(::HybridNetwork, ::Symbol, ::Vector{String7}, ::DataFrame; optimizeQ::Bool)
Closest candidates are:
fitdiscrete(::HybridNetwork, ::Symbol, ::Array{String}, ::DataFrame) got unsupported keyword argument "optimizeQ"
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/Upx5A/src/traitsLikDiscrete.jl:467
fitdiscrete(::HybridNetwork, ::Symbol, ::Array{String}, ::DataFrame, ::Any; kwargs...)
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/Upx5A/src/traitsLikDiscrete.jl:467
fitdiscrete(::HybridNetwork, ::PhyloNetworks.SubstitutionModel, ::RateVariationAcrossSites, ::DataFrame; kwargs...)
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/Upx5A/src/traitsLikDiscrete.jl:433
...
Stacktrace:
[1] top-level scope
@ REPL[69]:1
julia> typeof(species)
Vector{String7} (alias for Array{String7, 1})
In here, they provide a solution when reading the data frame (use stringtype=String), but they also suggest using AbstractString rather than String in the definition of the function.