TWT cannot handle underscores in the names of variables in the YAML file

[hugocastelan]

TWT does not accept variable names with underscores in the names of lineages in the YAML file. The same happens if there are underscores in other variables

Example of a part of the YAML file:

# -----------------------------------------------------
# LINEAGES: early sampling
# -----------------------------------------------------

Lineages:

  Present_DRC:
    type: virus
    sampling.time: 0.0
    location: DRC
    replicates: 10

  Present_Cameroon:
    type: virus
    sampling.time: 0.0
    location: Cameroon
    replicates: 10

  Present_GabonEG:
    type: virus
    sampling.time: 0.0
    location: GabonEG
    replicates: 10

The error is the following: it occurs when underscores are used in the variables in the YAML file.:

plot(inner)
 path<-"~/Documents/projects/mugration_project/endemic_model_VIH_DRC.yaml"
 model<- Model$new(yaml.load_file(path))

Error in FUN(X[[i]], ...) : 
  Error: underscore characters are reserved, please modify Lineage namePresent_DRC

[ArtPoon]

This does not seem to be a problem now