pir_plot: show models names' abbreviations

[richelbilderbeek]

Currently, the pir_plots show model names as used in the R code:

Instead, I'd prefer human-friendly abbreviations.

I suggest to do the same renaming as in e.g. 'Table 11: Evidences of figure 2'. From pirouette_article/scripts/example_5.R I copy-paste:

df_evidences$site_model_name <- plyr::revalue(df_evidences$site_model_name, c("JC69" = "JC", "TN93" = "TN"))
df_evidences$clock_model_name <- plyr::revalue(
  df_evidences$clock_model_name,
  c("strict" = "Strict", "relaxed_log_normal" = "RLN")
)
df_evidences$tree_prior_name <- plyr::revalue(
  df_evidences$tree_prior_name,
  c(
    "yule" = "Yule", 
    "birth_death" = "BD", 
    "coalescent_bayesian_skyline" = "CBS", 
    "coalescent_constant_population" = "CCP", 
    "coalescent_exp_population" = "CEP"
  )
)

[richelbilderbeek]

Fixed: