Package ‘chelyabinsk’ · Chelyabinsk allows you to handle comprehensive geochemical dataset. As a ﬁrst step, you plot REE and SPIDER diagram using appropriate normalization

Package ‘chelyabinsk’June 23, 2017

Type PackageTitle Express geochemical datasetsVersion 1.0Date 2016-09-29Author Tak KunihiroMaintainer Tak Kunihiro Description R package for geochemical datasetsLicense GPL (>= 2)RoxygenNote 6.0.1Imports testthat, roxygen2, dplyr, jpeg, png, XML, yaml, urltools

R topics documented:chelyabinsk-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cbk.balance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3cbk.category . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3cbk.convector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4cbk.convert.casteml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4cbk.download.casteml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5cbk.download.casteml.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6cbk.download.image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7cbk.exec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8cbk.iso . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9cbk.lame.acqify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9cbk.lame.atomify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10cbk.lame.colMeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11cbk.lame.colSds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12cbk.lame.delivery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12cbk.lame.drop.chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13cbk.lame.drop.dharma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14cbk.lame.drop.stone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14cbk.lame.dump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15cbk.lame.fetch.error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16cbk.lame.merge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16cbk.lame.merge.error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17cbk.lame.normalize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18cbk.lame.reduce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

1

2 chelyabinsk-package

cbk.lame.regulate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19cbk.lame.rep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20cbk.lame.stat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20cbk.lame.texify1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21cbk.path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21cbk.periodic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22cbk.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22cbk.plot.balance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23cbk.plot.lead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24cbk.plot.lithium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25cbk.plot.message . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25cbk.plot.oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26cbk.plot.ree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27cbk.plot.spider . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28cbk.plot.spots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29cbk.plot.trace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29cbk.read.casteml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30cbk.read.dflame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31cbk.read.ionml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32cbk.read.tblame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33cbk.read.yaml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33cbk.ref . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34cbk.texify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35cbk.vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35cbk.write.casteml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36cbk.write.tblame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37cbk.write.yaml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37ionml.convert.ioncsv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38ionml.convert.qtegracsv2ioncsv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39ionml.read.laicpqms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39ionml.read.session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Index 42

chelyabinsk-package Express element distribution using comprehensive geochemicaldatasets

Description

Chelyabinsk allows you to handle comprehensive geochemical dataset. As a first step, you plot REEand SPIDER diagram using appropriate normalization. Then, using both in-situ and whole-rockdatasets, you obtain element quantitative-distribution among phases with mass-balance calculation.

cbk.balance 3

cbk.balance Do mass balance calculation

Description

Do mass balance calculation

Usage

cbk.balance(datain, element, phase, mode, density)

Arguments

datain Element abundances with row "WR"

element Vector of string such for c("Ba", "Nb", "La"...)

phase Vector of name of phases such for c("ol", "pig")

mode Vector of modal abundance of phases with label

density Vector of density of phases with label

Value

Element abundances with rows of remainder and series of quantity, and columns of density andmode

See Also

cbk.lame.normalize

cbk.category Suggest categories to plot

Description

Suggest categories to plot

Usage

cbk.category(pmlfile_or_stone = NULL)

Arguments

pmlfile_or_stone

A CASTEML file that exits locally or stone-ID (or pmlame) to survey cate-gories. Default is NULL and return all categories regardless their plotability.

Value

Categories in preferred order

4 cbk.convert.casteml

Examples

pmlfile

cbk.download.casteml 5

Arguments

pmlfile File path to CASTEML file.

category Category specifier that is passed to casteml convert.

force Flag to force convert again.

verbose Output debug info (default: TRUE).

format Format specifier that is passed to casteml convert.

Value

Path of the converted file.

See Also

casteml convert and https://github.com/misasa/casteml

Examples

pmlfile

6 cbk.download.casteml.1

Details

An user should specify Recursive and recursive option not a part of argument ‘stone’ but explicitly.

Value

Path to CASTEML file that was downloaded.

See Also

casteml download, https://github.com/misasa/casteml, and cbk.convert.casteml

Examples

stone

cbk.download.image 7

Details

This function was created on 2017-04-11 to download CASTEML file by its own from Medusa andthe first argument can only accept single ‘stone’ unlike cbk.download.casteml can accept an arrayconsists of stones.

Value

Path to CASTEML file that was downloaded.

See Also

casteml download, https://github.com/misasa/casteml, and cbk.convert.casteml cbk.download.casteml

Examples

stone

8 cbk.exec

See Also

casteml download, https://github.com/misasa/casteml, and cbk.convert.casteml

Examples

pmlfile

cbk.iso 9

cbk.iso Return properties of isotope

Description

Return properties of isotope. It is in a form of pmlame.

Usage

cbk.iso(isomeas = NULL, property = "weight")

Arguments

isomeas A name of isotope such as ‘Li7’ and ‘Rb87’.property A name of PROPERTY that is one of ‘proton’, ‘nucleon’, ‘weight’, ‘ratio’,

‘symbol’, or ‘pseudo.atomic.weight’.

Value

A scalar of property or pmlame of isotope table

See Also

cbk.periodic, isotope.m, isotope_constant.m

Examples

cbk.iso()cbk.iso('Li7')cbk.iso('Li7','ratio')

cbk.lame.acqify Create pmlame with acqlist from one with stonelist

Description

Create pmlame with acqlist from one with stonelist

Usage

cbk.lame.acqify(reflame, acqlist, stonify_regexp = "@[[:digit:]]+$",verbose = FALSE)

Arguments

reflame A pmlame of reference with row of stone such as ‘ref_cpx_klb1’ and column ofchem such as ‘Sr’ [g/g].

acqlist List of analysis such as ‘ref_cpx_klb1@1’.stonify_regexp A regexp string to stonefy analyses. Matched string will be stripped off from

acqlist to have stonelist.verbose Output debug info (default: FALSE).

10 cbk.lame.atomify

Value

A pmlame with row of analysis and columns of chem [g/g].

Examples

reflame

cbk.lame.colMeans 11

• M(Li7) = m(Li)/R(Li7)

• M(Si9) = m(Si)/R(Si29)

Li

12 cbk.lame.delivery

cbk.lame.colSds Return standard deviation of each chem

Description

Return standard deviation of each chem

Usage

cbk.lame.colSds(pmlame, stonify_regexp = "@[[:digit:]]+$")

Arguments

pmlame A pmlame with row of stone and column of chem [g/g].

stonify_regexp A regexp string to be stripped off to stonefy analyses. Matched string will bestripped off from acqlist to have stonelist.

Value

A pmlame with standard deviation value of each column

Examples

pmlame

cbk.lame.drop.chem 13

Details

With ion Si29 intensity 3.85e+05 [cps], element SiO2 abundance 59 wt estimated to be 1.25 ppm.

Value

Delivery rate of element from solid target to detector.

Examples

pmlame0

14 cbk.lame.drop.stone

cbk.lame.drop.dharma Remove rows where all values are NA

Description

Remove rows where all values are NA

Usage

cbk.lame.drop.dharma(pmlame, column = FALSE, verbose = FALSE)

Arguments


column Flag to remove columns

verbose Output debug info (default: FALSE).

Value

A pmlame without removed rows

Examples

pmlfile

cbk.lame.dump 15

See Also

cbk.lame.drop.stone

Examples

pmlame

16 cbk.lame.merge

cbk.lame.fetch.error Extract error columns from pmlame as errorlame

Description

Extract error columns from pmlame as errorlame

Usage

cbk.lame.fetch.error(pmlame, chem = NULL)

Arguments

pmlame A pmlame with both mean and error.

chem Target chem you want to extract.

Value

An errorlame that is a pmlame of only error colums with label of ‘chem’ such as ‘Li7’ instead of‘Li7_error’. Note that columns that exist in input will be returned.

Examples

pmlame

cbk.lame.merge.error 17

Examples

pmlame1

18 cbk.lame.reduce

cbk.lame.normalize Return normalized element abundances

Description

Return normalized element abundances. Note that only elements that exist both in pmlame andreflame are processed. See also "Geochemical Modelling..." by Janousek et al. (2015)

Usage

cbk.lame.normalize(pmlame, reflame, suffix_after_chem = NULL,verbose = FALSE)

Arguments


reflame A pmlame of a reference. This can be a pmlame of multiple references.suffix_after_chem

String to recognize column of errors. Feed "_error" when necessary. As ofFebruary 18, 2017, this exists only for compatibility.


Value

A ref-normalized daraframe with only elements defined in ref.

See Also

cbk.ref and cbk.periodic

Examples

pmlame

cbk.lame.regulate 19

Value

A pmlame with converted columns

Examples

pmlfile

20 cbk.lame.stat

cbk.lame.rep Replicate pmlame in horizontal or vertical direction

Description

Replicate pmlame in horizontal or vertical direction

Usage

cbk.lame.rep(pmlame, times, direction = NULL)

Arguments

pmlame A pmlame to be replicated

times Number of replication

direction Direction to make replicate (‘h’ or ‘v’). This function guesses direction to bereplicated when pmlame is single row or column.

Value

A pmlame with repeated column or row.

Examples

pmlame0

cbk.lame.texify1 21

See Also

cbk.lame.colMeans and cbk.lame.colSds

Examples

pmlame

22 cbk.plot

Value

An absolute path of files stored in local library

Examples

dflame.csv

cbk.plot.balance 23

Arguments

pmlfile_or_stone

A CASTEML file that exits locally or stone-ID (or pmlame).

opts List of further options for plot. Two options such as ‘list(legendp=TRUE, Re-cursivep=FALSE)’ are available.

category Category specifier that is passed to casteml convert.

Value

A pmlame used to plot the diagram.

See Also

cbk.plot.trace

Examples

cbk.plot(c("20141106120733-593074","20141106120433-380274","20141106120509-983968"))cbk.plot(cbk.path("20081202172326.hkitagawa.pml"))cbk.plot(cbk.path("20081202172326.hkitagawa.pml"),category="trace")cbk.plot(cbk.path("20081202172326.hkitagawa.pml"),category="lead")cbk.plot(cbk.path("20130528105235-594267.pml"),category="trace")cbk.plot(cbk.path("20130528105235-594267.pml"),category="lithium")cbk.plot(cbk.path("20130528105235-594267.pml"),category="oxygen")cbk.plot(cbk.path("20081202172326.hkitagawa.pml"),opts=list(legendp=FALSE))

cbk.plot.balance Balance quantity of elements in whole rock and phases

Description

Balance quantity of elements in whole rock and phases. This calculates quantity of elements in eachphases from mode and element abundances of each phase. Then from calculated whole-rock (WR)quantity of element by summation and measured WR quantity of element, this estimates surplus ordeficit of elements.

Usage

cbk.plot.balance(pmlame_or_file, reflame_or_file, modeinfo, verbose = TRUE)

Arguments

pmlame_or_file A pmlame or CASTEML file with element abundance of phases without mea-sured WR

reflame_or_file

A pmlame or CASTEML file with element abundance of measured WR

modeinfo A pmlame or TBLAME.csv with mode and density of phases including WR


24 cbk.plot.lead

Value

A pmlame with element quantities and mode of phases

Examples

reflame

cbk.plot.lithium 25

cbk.plot.lithium Read CASTEML file and create lithium diagram

Description

Read CASTEML dataframe and create lithium diagram. This function does not save the createddiagram. You should prepare a canvas in advance.

Usage

cbk.plot.lithium(pmlfile_or_stone, opts = NULL, verbose = FALSE,pch = NULL, col = NULL)

Arguments

pmlfile_or_stone


opts List of further options for plot. See cbk.plot.


pch Array of symbol (default: NULL)

col Array of color (default: NULL)

Value

@return A pmlame used to plot the diagram.

See Also

https://github.com/misasa/casteml

Examples

pmlfile

26 cbk.plot.oxygen

Arguments

pmlfile_or_stone

A CASTEML file that exits locally or stone-ID (or pmlame)

text Message to be displayed on diagram. When it is with special caractors, quote itin advance.

Value

Dataframe used to plot the diagram

Examples

pmlame

cbk.plot.ree 27

cbk.plot.ree Read CASTEML file and create REE diagram

Description

Read CASTEML dataframe and create REE diagram. This function tris to blow errorbar. If you donot see errorbar, check pmlame that you feed.

Usage

cbk.plot.ree(pmlfile_or_stone, opts = NULL, tableunit = "none",reference = "Wasson.1988", verbose = FALSE, ...)

Arguments

pmlfile_or_stone



tableunit Unit to toss to cbk.read.casteml.

reference Reference of element abundance.


... Graphical options that are passed to matplot and legend, such as ‘col’ and ‘pch’.

Value

@return A pmlame used to plot the diagram.

See Also


Examples

pmlfile

28 cbk.plot.spider

cbk.plot.spider Read CASTEML file and create spider diagram

Description

Read CASTEML dataframe and create spider diagram. This function does not save the createddiagram. You should prepare a canvas in advance.

Usage

cbk.plot.spider(pmlfile_or_stone, opts = NULL, tableunit = "none",property = "atomicnumber", reference = "Wasson.1988", verbose = FALSE,pch = NULL, col = NULL)

Arguments

pmlfile_or_stone




property Property to align x-axis to pass to cbk.periodic.

reference Reference of element abundance




Value


See Also


Examples

pmlfile

cbk.plot.spots 29

cbk.plot.spots Read CASTEML file and create spots diagram

Description

Read CASTEML dataframe and create spots diagram. This function does not save the createddiagram. You should prepare a canvas in advance.

Usage

cbk.plot.spots(pmlfile_or_surface, opts = NULL, imagefile = NULL,verbose = FALSE, pch = NULL, col = NULL)

Arguments

pmlfile_or_surface



imagefile Image shown on background of analyzed spots.




Value


See Also


Examples

pmlfile

30 cbk.read.casteml

Arguments

pmlfile_or_stone




Value


See Also


Examples

pmlfile

cbk.read.dflame 31

See Also

cbk.convert.casteml, cbk.read.dflame, and https://github.com/misasa/casteml

Examples

pmlfile

32 cbk.read.ionml

Examples

pmlfile

cbk.read.tblame 33

cbk.read.tblame Read csvfile created by casteml convert with column ‘unit’

Description

Read csvfile with row ‘unit’, that is also referred as ‘tblame’.

Usage

cbk.read.tblame(tblame, tableunit = "none", verbose = TRUE)

Arguments

tblame A csvfile with columns of chem and rows of stone, with 2nd row ‘unit’.

tableunit Output unit that will be resolved by cbk.convector (default: "none").


Details

This internally calls read.csv, take out row of ‘unit’ and normalized by the ‘unit’ row.

Value

A pmlame with unit organized.

See Also

cbk.read.dflame, https://github.com/misasa/casteml, and cbk.convector.

cbk.read.yaml Read a pmlame stored in yamlfile.

Description

Read a pmlame stored in yamlfile.

Usage

cbk.read.yaml(yamlfile, verbose = TRUE)

Arguments

yamlfile A yamlfile with pmlame, that is with columns of chem and rows of stone.


Details

This function restores rownames using a column with label ‘rownames’.


34 cbk.ref

Value

A pmlame with columns of chem and rows of stone.

See Also

cbk.write.yaml, cbk.read.casteml.

cbk.ref Return element abundances of reference

Description

Return element abundances of reference. The reference includes "Wasson.1988", "McDonough.1995",and "Boynton.1989".

[1] Wasson, J. T., and Kallemeyn, G. W. (1988). Compositions of chondrites. Phil. Trans. Roy. Soc.London A, 325, 535-544. [2] McDonough, W., and Sun, S. (1995). The composition of the earth.Chemical Geology, 120(3-4), 223-253. [3] Janousek, V. et al. (2015). Geochemical Modelling ofIgneous Processes–Principles And Recipes in R Language. Springer

Usage

cbk.ref(analysis, tableunit = "none", property = NULL)

Arguments

analysis A name of reference that is one of "Wasson.1988", "McDonough.1995", and"Boynton.1989".

tableunit Output unit that will be resolved by ‘cbk.convector’. (default: "none")

property A numeric vector of element property with label that serves as sort key (default:NULL). You can feed output from ‘cbk.periodic’.

Value

A pmlame of element abundances

See Also

cbk.periodic

Examples

cbk.ref("Boynton.1989","ppm")cbk.ref("Wasson.1988","ppm",cbk.periodic('atomicnumber'))cbk.ref("Wasson.1988","ppm",cbk.periodic('volatility'))cbk.ref("McDonough.1995","ppm",cbk.periodic('volatility'))

cbk.texify 35

cbk.texify Convert CASTEML file to multple texfiles

Description

Convert CASTEML file to multple texfiles. This function splits chem and parse the datasets sepa-ratedly.

Usage

cbk.texify(pmlfile_or_stone, outfile = "table-auto.tex", chem = NULL,ncol = 11, verbose = FALSE)

Arguments

pmlfile_or_stone


outfile File path to texfile.

chem List of chem such as c("Li","Si","Ca","Ca.1","Rb").

ncol Number of columns per a table.

verbose Output debug info.

Value

Vector of file path to texfiles.

See Also

cbk.lame.texify1

cbk.vector Convert dataframe with label to vector with label

Description

Convert dataframe with label to vector with label. It seems that this conversion is necessary forcalcuration.

Usage

cbk.vector(df)

Arguments

df A dataframe with label

Details

This is written at initial stage of development. May be not that useful.

36 cbk.write.casteml

Value

A vector with label

Examples

cbk.vector(data.frame(row.names=c("density"), ol=c(3.300), pig=c(3.400), WR=c(3.3)))

cbk.write.casteml Write a pmlame to CASTEML file

Description

Write a pmlame to CASTEML file

Usage

cbk.write.casteml(pmlame, outfile = NULL, verbose = TRUE)

Arguments


outfile File path to casteml file


Value

File path to a casteml file

See Also

cbk.read.casteml

Examples

pmlame0

cbk.write.tblame 37

cbk.write.tblame Write pmlame as TBLAME.csv

Description

Write pmlame as TBLAME.csv

Usage

cbk.write.tblame(pmlame, outfile, verbose = TRUE)

Arguments


outfile Path of TBLAME.csv, which is a csvfile with rows of stone and columns ofchem.


Value

Path of TBLAME.csv

See Also

write.csv, cbk.read.tblame, and https://github.com/misasa/casteml

cbk.write.yaml Write a pmlame to yamlfile.

Description

Write a pmlame to yamlfile.

Usage

cbk.write.yaml(pmlame, outfile = NULL, verbose = TRUE)

Arguments


outfile Path to yamlfile with a pmlame.


Details

This function uses yaml::as.yaml to save pmlame. Since yaml::as.yaml drops rownames, thisfunction stores rownames using a column with label ‘rownames’.


38 ionml.convert.ioncsv

Value

Path to yamlfile.

See Also

cbk.read.yaml and cbk.write.casteml.

ionml.convert.ioncsv Convert IONCSV to IONML

Description

Convert IONCSV to IONML. This program assumes extensions of IONCSV and IONML to be‘.ion’ and ‘.xml’, respectively.

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

Usage

ionml.convert.ioncsv(ioncsv, outfile = NULL, force = FALSE)

Arguments

ioncsv Name of IONCSV.

outfile Name of IONML that will be created.

force Flag to force convert again.

Value

Name of IONML that was created.

See Also

ionml.convert.qtegracsv2ioncsv

Examples

ioncsv

ionml.convert.qtegracsv2ioncsv 39

ionml.convert.qtegracsv2ioncsv

Convert LAICPQMS-type QTEGRACSV by Analyte G2 with iCAP-Qto IONCSV

Description

Convert LAICPQMS-type QTEGRACSV by Analyte G2 with iCAP-Q to IONCSV. Filter metadataout and append column of cycle number.

This program assumes extensions of LAICPQMS-type QTEGRACSV and IONCSV to be ‘.csv’and ‘.ion’, respectively.

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

Usage

ionml.convert.qtegracsv2ioncsv(acqfile, outfile = NULL, force = FALSE)

Arguments

acqfile Name of LAICPQMS-type QTEGRACSV exported form Qtegra

outfile Name of IONCSV that will be created

force Flag to force convert again

Value

Name of IONCSV that was created

See Also

ionml-laicpqms.plx

Examples

acqfile

40 ionml.read.session

Usage

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

Arguments

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’.


ionml Read IONML file instead of IONCSV (default: TRUE).

Details

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 theBASELINE is subtracted from the main signal. The main signal is normalized by ‘ref’. Thisfunction returns the BASELINE subtracted and reference normalized ‘ionic-ratio’ with statisticalinformation at the bottom of the table. Detection limit is defined by 3 times standard error ofBASELINE measument.

Value

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

See Also

ionml.convert.qtegracsv2ioncsv ionml.convert.ioncsv

Examples

pmlfile0

ionml.read.session 41

Usage

ionml.read.session(ionml.xml, t0 = 5, t1 = 20, t2 = 25, t3 = 60,ref = "Si29", error = "sterr", intensityp = FALSE, verbose = FALSE,ionml = TRUE)

Arguments

ionml.xml Paths to IONML.

t0 When baseline starts (default: 5 s, scalar or vector)

t1 When baseline ends (default: 20 s, scalar or vector).

t2 When ion starts (default: 25 s, scalar or vector).

t3 When ion ends (default: 60 s, scalar or vector).

ref Reference ion such as ‘Si29’.

error Use ‘sterr’, ‘DL’, or ‘mix’ as error. When ‘mix’, error is delection limit ‘DL’instead of standard error ‘sderr’ when DL is larger than ‘sderr’.

intensityp Have mean and sd of intensity instead of mean and sderr of ionic ratio


ionml Read IONML file instead of IONCSV (default: TRUE).

Value

Pseudo-pmlame with average and standard error of ionic ratio

See Also

ionml.read.laicpqms

Examples

pmlame0

Index

cbk.balance, 3cbk.category, 3cbk.convector, 4, 31, 33cbk.convert.casteml, 4, 6–8, 31cbk.download.casteml, 5, 7, 31cbk.download.casteml.1, 6cbk.download.image, 7cbk.exec, 8cbk.iso, 9cbk.lame.acqify, 9cbk.lame.atomify, 10cbk.lame.colMeans, 11cbk.lame.colSds, 12cbk.lame.delivery, 12cbk.lame.drop.chem, 13cbk.lame.drop.dharma, 14cbk.lame.drop.stone, 14cbk.lame.dump, 15cbk.lame.fetch.error, 16, 19cbk.lame.merge, 16cbk.lame.merge.error, 17cbk.lame.normalize, 3, 18cbk.lame.reduce, 10, 18cbk.lame.regulate, 19cbk.lame.rep, 20cbk.lame.stat, 20cbk.lame.texify1, 21, 35cbk.path, 21cbk.periodic, 9, 18, 22, 28, 34cbk.plot, 22, 24–30cbk.plot.balance, 23cbk.plot.lead, 24cbk.plot.lithium, 25cbk.plot.message, 25cbk.plot.oxygen, 26cbk.plot.ree, 27cbk.plot.spider, 28cbk.plot.spots, 29cbk.plot.trace, 23, 29cbk.read.casteml, 27, 28, 30, 30, 34, 36cbk.read.dflame, 31, 31, 33cbk.read.ionml, 32cbk.read.tblame, 33, 37

cbk.read.yaml, 33, 38cbk.ref, 18, 34cbk.texify, 35cbk.vector, 35cbk.write.casteml, 36, 38cbk.write.tblame, 37cbk.write.yaml, 34, 37chelyabinsk (chelyabinsk-package), 2chelyabinsk-package, 2

ionml.convert.ioncsv, 38, 40ionml.convert.qtegracsv2ioncsv, 32, 39,

40ionml.read.laicpqms, 39, 41ionml.read.session, 40

read.csv, 33

shell.exec, 8system, 8

write.csv, 37

42

chelyabinsk-packagecbk.balancecbk.categorycbk.convectorcbk.convert.castemlcbk.download.castemlcbk.download.casteml.1cbk.download.imagecbk.execcbk.isocbk.lame.acqifycbk.lame.atomifycbk.lame.colMeanscbk.lame.colSdscbk.lame.deliverycbk.lame.drop.chemcbk.lame.drop.dharmacbk.lame.drop.stonecbk.lame.dumpcbk.lame.fetch.errorcbk.lame.mergecbk.lame.merge.errorcbk.lame.normalizecbk.lame.reducecbk.lame.regulatecbk.lame.repcbk.lame.statcbk.lame.texify1cbk.pathcbk.periodiccbk.plotcbk.plot.balancecbk.plot.leadcbk.plot.lithiumcbk.plot.messagecbk.plot.oxygencbk.plot.reecbk.plot.spidercbk.plot.spotscbk.plot.tracecbk.read.castemlcbk.read.dflamecbk.read.ionmlcbk.read.tblamecbk.read.yamlcbk.refcbk.texifycbk.vectorcbk.write.castemlcbk.write.tblamecbk.write.yamlionml.convert.ioncsvionml.convert.qtegracsv2ioncsvionml.read.laicpqmsionml.read.sessionIndex

Documents

Package ‘chelyabinsk’ · Chelyabinsk allows you to handle comprehensive geochemical dataset. As a ﬁrst step, you plot REE and SPIDER diagram using appropriate normalization