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volcalc 2.0.0
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@Aariq Aariq released this 22 Sep 13:33
v2.0.0
8fa1dd6

This version includes big (breaking) changes in how the package works! Please
read the changelog below carefully and check function documentation and examples
to see the new usage of functions.

  • Change output of get_fx_groups() and calc_vol() from data frame to tibble
  • get_fx_groups() and calc_vol() no longer depend on KEGG or take KEGG compound IDs or pathway IDs. Instead, calc_vol() accepts a path to a .mol file as input.
  • calc_vol() is vectorized and accepts multiple compounds as input.
  • Moved SIMPOL.1 calculations out of calc_vol() and into to their own function, simpol1(), to pave the way for future expansions using other methods. The "manual" workflow is now .mol file |> ChemmineR::read.SDFset() |> get_fx_groups() |> simpol1()
  • The output of calc_vol() (and simpol1()) now contains a column called log10_P instead of log_Sum, equivalent to log_Sum + the coefficient for b_0(T)
  • Output of calc_vol() now contains a column with the inputs, named whatever is supplied to from (eg. a column called mol_path containing paths to mol files)
  • A new function, get_mol_kegg(), replaces save_compound_mol() for downloading mol files from KEGG
  • Added pkgdown website
  • get_fx_groups() now only counts the smallest set of smallest rings (#57)
  • Fixed a bug that caused the number of phenols to be miscounted. Rather than counting phenols, get_fx_groups now counts aromatic hydroxyl groups (e.g. phenols) to more closely align with Pankow & Asher (2008) (#46)
  • package now has a hex logo!
  • Fixes a bug in volcalc introduced by a bug-fix in ChemmineR v3.53.1 (#54)
  • The volatility column in the output of calc_vol() has been renamed to rvi (relative volatility index)
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