nist_ri: Retrieve retention indices from NIST

In ropensci/webchem: Chemical Information from the Web

Retrieve retention indices from NIST

Description

This function scrapes NIST for literature retention indices given a query or vector of queries as input. The query can be a cas number, IUPAC name, or International Chemical Identifier (inchikey), according to the value of the from argument. Retention indices are stored in tables by type, polarity and temperature program (temp_prog). The function can take multiple arguments for these parameters and will return any retention times matching the specified criteria in a single table.

If a non-cas query is provided, the function will try to resolve the query by searching the NIST WebBook for a corresponding CAS number. If from == "name", phonetic spellings of Greek stereo-descriptors (e.g. "alpha", "beta", "gamma") will be automatically converted to the corresponding letters to match the form used by NIST. If a CAS number is found, it will be returned in a tibble with the corresponding information from the NIST retention index database.

Usage

nist_ri(
  query,
  from = c("cas", "inchi", "inchikey", "name"),
  type = c("kovats", "linear", "alkane", "lee"),
  polarity = c("polar", "non-polar"),
  temp_prog = c("isothermal", "ramp", "custom"),
  cas = NULL,
  verbose = getOption("verbose")
)

Arguments

query	character; the search term
from	character; type of search term. can be one of "name", "inchi", "inchikey", or "cas". Using an identifier is preferred to "name" since NA is returned in the event of multiple matches to a query. Using an identifier other than a CAS number will cause this function to run slower as CAS numbers are used as internal identifiers by NIST.
type	Retention index type: "kovats", "linear", "alkane", and/or "lee". See details for more.
polarity	Column polarity: "polar" and/or "non-polar" to get RIs calculated for polar or non-polar columns.
temp_prog	Temperature program: "isothermal", "ramp", and/or "custom".
cas	deprecated. Use query instead.
verbose	logical; should a verbose output be printed on the console?

Details

The types of retention indices included in NIST include Kovats ("kovats"), Van den Dool and Kratz ("linear"), normal alkane ("alkane"), and Lee ("lee"). Details about how these are calculated are available on the NIST website: https://webbook.nist.gov/chemistry/gc-ri/

Value

returns a tibble of literature RIs with the following columns:

• query is the query provided to the NIST server

• cas is the CAS number or unique record identified used by NIST

• RI is retention index

• type is the type of RI (e.g. "kovats", "linear", "alkane", or "lee")

• polarity is the polarity of the column (either "polar" or "non-polar")

• temp_prog is the type of temperature program (e.g. "isothermal", "ramp", or "custom")

• column is the column type, e.g. "capillary"

• phase is the stationary phase (column phase)

• length is column length in meters

• gas is the carrier gas used

• substrate

• diameter is the column diameter in mm

• thickness is the phase thickness in µm

• program. various columns depending on the value of temp_prog

• reference is where this retention index was published

• comment. I believe this denotes the database these data were aggregated from

Note

Copyright for NIST Standard Reference Data is governed by the Standard Reference Data Act, https://www.nist.gov/srd/public-law.

References

NIST Mass Spectrometry Data Center, William E. Wallace, director, "Retention Indices" in NIST Chemistry WebBook, NIST Standard Reference Database Number 69, Eds. P.J. Linstrom and W.G. Mallard, National Institute of Standards and Technology, Gaithersburg MD, 20899, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18434/T4D303")}.

See Also

is.cas as.cas

Examples

## Not run: 
myRIs <-
  nist_ri(
    c("78-70-6", "13474-59-4"),
    from = "cas",
    type = c("linear", "kovats"),
    polarity = "non-polar",
    temp_prog = "ramp"
  )
myRIs
## End(Not run)

ropensci/webchem documentation built on Feb. 23, 2024, 6:28 p.m.