extract_data: Extracting raw Pb isotope ratio.

In andreabz/pbratios: Processing Pb isotope ratio data

Description

Extracts raw 208Pb/207Pb, 206Pb/207Pb, 208Pb/206Pb and 207Pb/206Pb data from the raw .csv file produced by Perkin Elmer Elan ICP-MS.

Usage

extract_data(filename, report = c("short", "long"))

Arguments

filename

A data set saved in csv format with "," as field separator and "." as decimal separator. Such file can be obtained from the .rep report provided by the instrument by opening it with a spreadsheet editor and saving it as .csv file using a local setting = EN-US or equivalent. The function identifies standard samples for bracketing when labelled as “SRM” and substitutes their names with “SRM981_X” where X is a progressive integer. Similarly, QC samples “CRM” are renamed as “CRM482_X”.

report

A string referring to the type of report generated by the instrument Accepted values are "short" or "long". Short reports have only information about the sample ID, data and time of the measure, a summary with average intensities and finally, the intensity values for each replicate. Long reports contain also information of the "short" counterpart and also some information about the measurement conditions. Additionally, the summary section is reported after the intensity values for each replicates. These reports are tipically produced when working in isotope ratio mode.

Value

A data.table containing raw intensities and raw Pb isotope ratios for each sample. Provided isotope ratios are 208Pb/207Pb, 206Pb/207Pb, 208Pb/206Pb and 207Pb/206Pb. Note that these ratios have still to be inspected for outliers, summarised and corrected for mass bias.

Examples

file.short <- system.file("extdata", "sednya_2015.csv", package = "pbratios")
sednya.2015 <- extract_data(file.short, report = "short")

file.long <- system.file("extdata", "spmnya_2012.csv", package = "pbratios")
spmnya.2012 <- extract_data(file.long, report = "long")

andreabz/pbratios documentation built on May 12, 2019, 2:42 a.m.