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ASTR schema: Naming conventions

VG.ASTRschema.0.0.2.Rmd

ASTR follows the following naming and data conventions, which are described in detail in this vignette.

Data preparation

  • All variable names are case sensitive.
  • Decimals can only be read when indicated by a decimal point (0.5), as opposed to decimal commas (0,5).
  • Apostrophes and any other special characters should be avoided in the sample/variable names.

Analytical Data columns naming

All columns that contain element and oxide compositions and analytical errors, isotopic values, or ratios derived therefrom should be named using the following conventions.

  • Only Latin characters can be supported in the column names, (i.e. δ and ε will not be identified).

  • The names of oxides and trace elements are self-explanatory (e.g. SiO2 or Si). Total iron, if given, should be expressed as: FeOtot or Fe2O3tot. Loss on ignition, where known, should be expressed as LOI.

  • Units for values should follow element or oxide, as _<unit>. Units supported include all SI units, as well as ppm, ppb, ppt, %, wt%, at%, w/w%, ‰, counts, and cps, noted as such.

  • Where known, specify wt% and at% instead of using %. For ‘per mille’, use the symbol ‰.

  • For isotopic ratios, use simple forms such as 206Pb/204Pb, 87Sr/86Sr, 147Sm/144Nd, eNd or d18O.

  • If you have columns with Pb isotope model calculations in your dataset prior to importing data, ensure the names do not contain a dash (‘-’) or underscore (‘_’) and specify these columns as context in the read_archem() function. The function pb_iso_age_model() can calculate model ages, µ (238U/204Pb), and κ (232Th/238U) values using the Stacey & Kramers (1975), Cumming & Richards (1975), and Albarede & Juteau (1984) systems within ASTR.

  • The following notations will be automatically identified and replaced with NA, unless you explicitly define other values in read_archem(): ‘NA’, ‘N.A.’, ‘N/A’, ‘na’, ‘n/a’, ‘-’, and ‘n.d.’. Values containing common excel error messages (#DIV/0!, #VALUE!, #REF!, #NAME?, #NUM!, #N/A, and #NULL!) are also replaced by NA automatically.

  • Analytical precision should be indicated in the column name as: _err2SD, _errSD, _err2SD%, _errSD%, _errSE, _err2SE without indicating the unit. The unit will be inferred from the corresponding composition column. SD, 2SD, SE, and 2SE can be expressed in absolute or relative values. We strongly recommend that the uncertainty is included in the data table, and properly noted following the conventions described.

Components Accepted formats
Oxides and elements SiO2 ; Si
Total iron FeOtot ; Fe2O3tot
Loss on ignition LOI
Isotopic ratios 206Pb/204Pb ; 87Sr/86Sr ; 147Sm/144Nd ; d18O
Units for value _wt% ; _at%
Analytical precision _err2SD ; _errSD ; _errSD% ; _errSD% ; _errSE ; _err2SE

References

Albarede, F., & Juteau, M. (1984). Unscrambling the lead model ages. Geochimica Et Cosmochimica Acta, 48(1), 207–212. https://doi.org/10.1016/0016-7037(84)90364-8
Cumming, G. L., & Richards, J. R. (1975). Ore lead isotope ratios in a continuously changing earth. Earth and Planetary Science Letters, 28(2), 155–171. https://doi.org/10.1016/0012-821X(75)90223-X
Stacey, J. S., & Kramers, J. D. (1975). Approximation of terrestrial lead isotope evolution by a two-stage model. Earth and Planetary Science Letters, 26(2), 207–221. https://doi.org/10.1016/0012-821X(75)90088-6