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volcalc 2.1.0
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@Aariq Aariq released this 15 Dec 17:24
v2.1.0
79c877e
  • The manuscript associated with volcalc is now published in Frontiers in Microbiology 🎉. DOI: 10.3389/fmicb.2023.1267234
  • There are now two vignettes available which can be viewed with browseVignettes("volcalc") or on the package website

Miscelanous changes

  • New example .mol files were added. See ?mol_example()
  • mol_example() no longer takes any arguments and just returns file paths to all example .mol files

Changes to calc_vol() and simpol1()

  • It is now possible to supply input to calc_vol() as a vector of SMILES strings with from = "smiles".
  • Users can now choose from RVI thresholds for non-volatile, low, moderate, and high volatility for clean atmosphere, polluted atmosphere, or soil using the environment parameter of calc_vol().
  • A coefficient for amides has been removed from the "Meredith" method of simpol1() to avoid double-counting amides.
  • The default for the method argument to calc_vol() has now been renamed to "meredith". "simpol1" now uses the original SIMPOL.1 method without additional coefficients added in Meredith et al. (2023).
  • simpol1() gains an argument meredith that controls whether just the functional groups in the original SIMPOL.1 method (Pankow & Asher, 2008) is used or if additional coefficients used in Meredith et al. (2023) are also included.
  • simpol1() now takes into account amide functional groups.

Changes to get_mol_kegg()

  • The pathway_ids argument of get_mol_kegg() now also accepts pathway module IDs (e.g. "M00082").
  • get_mol_kegg() got a significant speed improvement (#84).
  • get_mol_kegg() will skip downloading a .mol file if it is already present by default (override with force=TRUE).

Changes to get_fx_groups()

  • mass column renamed to molecular_weight and addition of an exact_mass column.
  • change to how non-aromatic carbon double bonds are counted. Now using SMARTS pattern "C=C"
  • now returns hydroxyl_total and hydroxyl_aliphatic instead of hydroxyl_groups
  • now returns rings_total and rings_aliphatic instead of rings
  • Now captures all functional groups in the SIMPOL.1 method except "number of carbons on the acid side of an amide". This version adds these previously missing groups used by simpol1():
    • C=C-C=O in a non-aromatic ring
    • non-aromatic carbon double bonds
    • aromatic amines
    • primary, secondary, and tertiary amides
    • hydroperoxides
    • carbonylperoxyacids
    • carbonylperoxynitrates
    • alkyl, alicyclic, and aromatic ethers (in addition to total ethers)
    • nitrophenols
    • nitroesters
  • changed ether to ether_alkyl and added ether_total (matching any R-O-R)
  • slight change to the SMARTS pattern to capture sulfonate groups to also capture conjugate sulfonic acids
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