ionml.read.laicpqms: Read IONML originated from Analyte G2 with iCAP-Q
In misasa/chelyabinsk: Express geochemical datasets

Description Usage Arguments Details Value See Also Examples

Read IONML originated from Analyte G2 with iCAP-Q. When IONML is not found, this will create IONML from QTEGRACSV (CSV file exported from Qtegra with identical basename with IONML) via IONCSV stored in temporal dirctory.

The IONCSV consists of columns of time and ion intensities. The first column of each line should be number of ‘cycle’. Colname of the IONCSV should be ‘time’ and name of element followed by atomic weight (‘Si29’ instead of ‘29Si’).

This is a fork from ‘Batch_calc_separated_pdf_2.3.R’. On 2018-07-27, ‘summarise_each’ was replaced by ‘summarise_all’.

1 2	ionml.read.laicpqms(pmlame_or_file, t0 = 5, t1 = 20, t2 = 25, t3 = 60, ref = "Si29", verbose = FALSE, ionml = TRUE)

`pmlame_or_file`	ion-type pmlame or IONML or QTEGRACSV.
`t0`	When baseline starts (default: 5 s).
`t1`	When baseline ends (default: 20 s).
`t2`	When ion starts (default: 25 s).
`t3`	When ion ends (default: 60 s).
`ref`	reference ion such as ‘Si29’.
`verbose`	Output debug info (default: FALSE).
`ionml`	Read IONML file instead of IONCSV (default: TRUE).

Signal between ‘t2’ and ‘t3’ is regarded as main signal from a sample (online). Signal between ‘t0’ and ‘t1’ is regarded as background. Mean of latter is calculated as BASELINE. Then the BASELINE is subtracted from the main signal. The main signal is normalized by ‘ref’. This function returns the BASELINE subtracted and reference normalized ‘ionic-ratio’ with statistical information at the bottom of the table. Detection limit is defined by 3 times standard error of BASELINE measument.

The ion-type pmlame of ion-to-ref ratio online with rows of statistical information.

ionml.convert.qtegracsv2ioncsv ionml.convert.ioncsv

ionmlfile <- cbk.path("ref_cpx_klb1@1.xml")
message(sprintf("The ionmlfile is located at |%s|.",ionmlfile))
pmlfile0  <- ionml.read.laicpqms(ionmlfile)

file     <- cbk.path("ref_cpx_klb1@1.ion")
message(sprintf("The file is located at |%s|.",file))
pmlfile0 <- ionml.read.laicpqms(file,ionml=FALSE)