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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
pmlame A pmlame with row of stone and column of chem [g/g].
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
pmlame A pmlame with row of stone and column of chem [g/g].
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.
verbose Output debug info (default: FALSE).
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
verbose Output debug info (default: FALSE).
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
A CASTEML file that exits locally or stone-ID (or pmlame).
opts List of further options for plot. See cbk.plot.
verbose Output debug info (default: FALSE).
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
A CASTEML file that exits locally or stone-ID (or pmlame).
opts List of further options for plot. See cbk.plot.
tableunit Unit to toss to cbk.read.casteml.
reference Reference of element abundance.
verbose Output debug info (default: FALSE).
... 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
https://github.com/misasa/casteml
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
A CASTEML file that exits locally or stone-ID (or pmlame).
opts List of further options for plot. See cbk.plot.
tableunit Unit to toss to cbk.read.casteml.
property Property to align x-axis to pass to cbk.periodic.
reference Reference of element abundance
verbose Output debug info (default: FALSE).
pch Array of symbol (default: NULL)
col Array of color (default: NULL)
Value
A pmlame used to plot the diagram.
See Also
https://github.com/misasa/casteml
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
A CASTEML file that exits locally or stone-ID (or pmlame).
opts List of further options for plot. See cbk.plot.
imagefile Image shown on background of analyzed spots.
verbose Output debug info (default: FALSE).
pch Array of symbol (default: NULL)
col Array of color (default: NULL)
Value
A pmlame used to plot the diagram.
See Also
https://github.com/misasa/casteml
Examples
pmlfile
30 cbk.read.casteml
Arguments
pmlfile_or_stone
A CASTEML file that exits locally or stone-ID (or pmlame).
opts List of further options for plot. See cbk.plot.
tableunit Unit to toss to cbk.read.casteml.
Value
A pmlame used to plot the diagram.
See Also
https://github.com/misasa/casteml
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").
verbose Output debug info (default: TRUE).
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.
verbose Output debug info (default: TRUE).
Details
This function restores rownames using a column with label ‘rownames’.
https://github.com/misasa/casteml
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
A CASTEML file that exits locally or stone-ID (or pmlame).
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
pmlame A pmlame with row of stone and column of chem [g/g].
outfile File path to casteml file
verbose Output debug info (default: TRUE).
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
pmlame A pmlame with row of stone and column of chem [g/g].
outfile Path of TBLAME.csv, which is a csvfile with rows of stone and columns ofchem.
verbose Output debug info (default: FALSE).
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
pmlame A pmlame with row of stone and column of chem [g/g].
outfile Path to yamlfile with a pmlame.
verbose Output debug info (default: TRUE).
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’.
https://github.com/misasa/casteml
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’.
verbose Output debug info (default: FALSE).
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
verbose Output debug info (default: FALSE).
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