README.md

In pvermees/PbPbRedux: Pb-Pb data processing for meteorite geochronology

PbPbRedux

TIMS Pb/Pb data reduction software

Installation

To install PbPbRedux from GitHub, you need the remotes package. If this is not installed on your system, then you can do so as follows:

install.packages('remotes')

Once remotes is installed, PbPbRedux can be installed as follows:

remotes::install_github('pvermees/PbPbRedux')

Examples

Using the example input files in the inst folder of this GitHub repository:

Example 1: all samples use the same blank

# load the package:
library(PbPbRedux)

# load the input files:
smp <- read.csv('samples1.csv',header=TRUE)
blk <- read.csv('blanks1.csv',header=TRUE)
spk <- read.csv('spikes.csv',header=TRUE)

# process the data:
tab <- process(samples=smp,blanks=blk,spikes=spk)

Example 2: each aliquot has its own blank

This is the same code as in the previous example, but using different input files. See the inst folder for details:

library(PbPbRedux)
smp <- read.csv('samples2.csv',header=TRUE)
blk <- read.csv('blanks2.csv',header=TRUE)
spk <- read.csv('spikes.csv',header=TRUE)
tab <- process(samples=smp,blanks=blk,spikes=spk)

Example 3: individual blanks with shared covariance matrix

Now we load an extra file of blanks, whose covariance matrix is used as a measure of dispersion for the individual blank measurements:

library(PbPbRedux)
smp <- read.csv('samples2.csv',header=TRUE)
blk <- read.csv('blanks2.csv',header=TRUE)
spk <- read.csv('spikes.csv',header=TRUE)

# load 15 replicate blank values:
cblk <- read.csv('blanks1.csv',header=TRUE)

tab <- process(samples=smp,blanks=blk,spikes=spk,cblanks=cblk)

To view the documentation of the process function:

?process

Saving and plotting the results:

The output table can be saved to a comma separated variable file using the basic write.csv function:

write.csv(tab,file='results.csv',row.names=FALSE)

You can either open this file in a spreadsheet application for further processing, or you can continue working in R. For example, plotting the results as an isochron using the IsoplotR package:

library(IsoplotR)

# change the default 238U/235U ratio to a meteoritic value:
settings('iratio','U238U235',137.786,0.015)

# using IsoplotR's undocumented 'as.PbPb' function to convert
# the output table into a PbPb data object, where ierr=4 specifies
# that errors are provided as 2se % values:
PbPb <- IsoplotR:::as.PbPb(tab,format=2,ierr=4)

# plot as an inverse isochron (type ?isochron for additional options):
isochron(PbPb,exterr=FALSE)

Individual aliquots can be removed from the isochron using standard R syntax:

omit <- c(1:3,6,8) # aliquots to omit from the isochron
PbPb <- IsoplotR:::as.PbPb(tab[-omit,],format=2,ierr=4)
isochron(PbPb,exterr=FALSE)

pvermees/PbPbRedux documentation built on Aug. 27, 2023, 11:22 a.m.