cbk.lame.atomify: Estimate element abundances from ion-intensity obtained by...
In misasa/chelyabinsk: Express geochemical datasets

Description Usage Arguments Details Value Examples

Estimate element abundances from ion-intensity obtained by mass spectrometry. Main inputs are element abundance of internal-reference element, ionic_ratio, and ionic_yield. This function accepts a pair of mean and error of ionic ratio such in columns ‘Li7’ and 'Li7_error' and yield a pair of mean and error of element abundance such in columns ‘Li’ and ‘Li_error’.

1 2	cbk.lame.atomify(pmlame, ionic_ratio, ionic_yield, isoref = "Si29", verbose = FALSE)

`pmlame`	A pmlame that includes internal-reference element such for Si with row of acq and column of chem [g/g]. Do not forget to reduce in advance using cbk.lame.reduce.
`ionic_ratio`	A pseudo-pmlame of ion intensity relative to internal-reference isotope with row of acq and column of isomeas [cps/cps]. Rownames should be identical to that of ‘pmlame’. This is like array of I(Li7)/I(Si29), ..., I(Sr88)/I(Si29).
`ionic_yield`	Relative sensitivities of element that were determined by analyses of several reference materials.
`isoref`	Name of internal-reference isotope such as 'Si29'.
`verbose`	Output debug info (default: FALSE).

This function estimate trace-element abundances using following equations. Note that ‘M’ denotes 'pseudo atomic-weight' that corresponds to atomic-weight of an isotope at virtual world where rest of isotopes do not exist (number of other isotopes are zero) but total element abundance and number of the isotope remain the same.

ionic_yield = ionic_ratio / atomic_ratio
ionic_ratio = I(Li7+) / I(Si29+)
atomic_ratio = [Li7] / [Si29]
[Li7] = [Li]/M(Li7)
[Si29] = [Si]/M(Si29)
M(Li7) = m(Li)/R(Li7)
M(Si9) = m(Si)/R(Si29)
[Li] <- ionic_ratio/ionic_yield * [Si]/M(Si29) * M(Li7)

A pmlame of element abundances.

ionic_yield <- data.frame(row.names=c("ionic_yield"), Li7=c(1.027), B11=c(1.76), Si29=c(1), La139=c(77.6))
ionic_ratio <- data.frame(row.names=c('ref_cpx_klb1@1','ref_cpx_klb1@2','trc_meso_allende@10'),Li7=c(5.56389e-04,4.90334e-04,7.02148e-05),B11=c(5.88269e-05,8.64064e-05,1.44872e-04),Si29=c(1,1,1),La139=c(0.000340813,0.000281243,0.000708434))
pmlame0     <- data.frame(row.names=c('ref_cpx_klb1@1','ref_cpx_klb1@2','trc_meso_allende@10'),SiO2=c(520000,520000,600000))
pmlame      <- cbk.lame.reduce(pmlame0)
cbk.lame.atomify(pmlame,ionic_ratio,ionic_yield,isoref='Si29',verbose=TRUE)