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.
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")
)
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
character; the search term
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.
Retention index type: "kovats"
, "linear"
,
"alkane"
, and/or "lee"
. See details for more.
Column polarity: "polar"
and/or "non-polar"
to get RIs calculated for polar or non-polar columns.
Temperature program: "isothermal"
,
"ramp"
, and/or "custom"
.
deprecated. Use query
instead.
logical; should a verbose output be printed on the console?
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/
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, tools:::Rd_expr_doi("10.18434/T4D303").
is.cas
as.cas
if (FALSE) {
myRIs <-
nist_ri(
c("78-70-6", "13474-59-4"),
from = "cas",
type = c("linear", "kovats"),
polarity = "non-polar",
temp_prog = "ramp"
)
myRIs}
Run the code above in your browser using DataLab