R documentation
‘Saturnin’
March 26, 2006
R topics documented:
acnk . . . . . .
ap.saturation . .
filter.out . . . .
load.file . . . .
millicat . . . .
mz.saturation .
normalize2total
r2clip . . . . .
zr.saturation . .
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1
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5
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10
A/CNK values (Shand 1943)
acnk
Description
Calculates alumina saturation index (A/CNK) of Shand (1943)
Usage
acnk(what)
Arguments
what
.
.
.
.
.
.
.
.
.
numeric matrix with millications.
Details
Classic Shand’s (1943) values termed alumina saturation index.
Value
A vector with the results.
1
2
ap.saturation
Author(s)
Vojtech Janousek, [email protected]
References
Shand (1943) Eruptive Rocks. John Wiley & Sons
See Also
millicat
Apatite saturation
ap.saturation
Description
Calculates apatite saturation temperatures for observed whole-rock major-element compositions.
Prints also phosphorus saturation levels for the given major- element compositions and assumed
magma temperature.
Usage
ap.saturation(Si=WR[,"SiO2"],ACNK=WR[,"A/CNK"],
P2O5=data.matrix(WR)[,""P2O5""],T=750)
Arguments
Si
SiO2 contents in the melt (wt. %)
ACNK
vector with A/CNK (mol %) values
P2O5
vector with P2 O5 concentrations
T
assumed magma temperature in C
Details
* Calculates phosphorus saturation levels following Harrison & Watson (1984):
ln(DP ) =
8400 + 26400(SiO2 − 0.5)
− 3.1 − 12.4(SiO2 − 0.5)
T
P2 O5 .HW =
42
DP
where ’T’ = absolute temperature (K), ’DP ’ = distribution coefficient for phosphorus between
apatite and melt and ’SiO2 ’ is the weight fraction of silica in the melt, SiO2 wt. %/100.
These formulae were shown to be valid only for metaluminous rocks, i.e. A/CNK < 1, and were
modified for peraluminous rocks (A/CNK > 1) by Bea et al. (1992):
P2 O5 .Bea = P2 O5 .HW e
6429(A/CN K−1)
(T −273.15)
3
ap.saturation
and Pichavant et al. (1992):
P2 O5 .P V = P2 O5 .HW + (A/CN K − 1)e
−5900
−3.22SiO2 +9.31
T
Note that the phosphorus saturation concentrations are not returned by the function but printed only.
* Calculates saturation temperatures in C using the observed P2 O5 concentrations (Harrison &
Watson, 1984):
T.HW =
8400 + 26400(SiO2 − 0.5)
− 273.15
ln( P242O5 ) + 3.1 + 12.4(SiO2 − 0.5)
for peraluminous rocks (A/CNK > 1) the equation of Bea et al. (1992) needs to be solved for ’T’
(in K) by iterations:
42
P2 O5 .Bea =
e
8400+26400(SiO2 −0.5)
−3.1−12.4(SiO2 −0.5)
T
e
6429(A/CN K−1)
(T −273.15)
as is that of Pichavant et al. (1992):
42
P2 O5 .P V =
e
8400+26400(SiO2 −0.5)
−3.1−12.4(SiO2 −0.5)
T
+ (A/CN K − 1)e
−5900
−3.22SiO2 +9.31
T
Value
Returns a matrix ’results’ with the following columns:
A/CNK
A/CNK values
Tap.sat.C.H+W
saturation T of Harrison & Watson (1984) in C
Tap.sat.C.Bea
saturation T of Bea et al. (1992) in C, peraluminous rocks only
Tap.sat.C.Pich
saturation T of Pichavant et al. (1992) in C, peraluminous rocks only
Author(s)
Vojtech Janousek, [email protected]
References
Bea F, Fershtater G B & Corretgé L G (1992) The geochemistry of phosphorus in granite rocks and
the effects of aluminium. Lithos 29: 43-56
Harrison T M & Watson E B (1984) The behavior of apatite during crustal anatexis: equilibrium
and kinetic considerations. Geochim Cosmochim Acta 48: 1467-1477
Pichavant M, Montel J M & Richard L R (1992) Apatite solubility in peraluminous liquids: experimental data and extension of the Harrison-Watson model. Geochim Cosmochim Acta 56: 38553861
4
load.file
filter.out
Extracting specified columns of a data frame/matrix
Description
This function returns samples for which are available the specified data columns in a matrix/data
frame.
Usage
filter.out(where, what)
Arguments
where
name of the matrix/data frame
what
character vector with names of the columns to be extracted
Details
Returns columns ’what’ for samples from ’where’, for which all the values are greater than zero.
Value
Matrix with the extracted elements.
Author(s)
Vojtech Janousek, [email protected]
Examples
filter.out(WR,c("SiO2","Al2O3","FeO"))
load.file
Loading a data file
Description
Loads data stored in a tab-delimited ASCII text file.
Usage
load.file()
5
millicat
Details
In the text file, the first line contains names for the variables/data columns (except for the first one
that is automatically assumed to contain the sample names). Hence the first line must have one item
less than the following ones. The data rows start with sample name and do not have to be all of the
same length (the rest of the row is filled by ’NA’ automatically).
Missing values (’NA’) are allowed anywhere in the data file (naturally apart from sample and column
names).
The data files can be practically freeform, i.e. no specified oxides/elements are required and no
exact order of these is to be adhered to. Extra columns not required by the calculation algorithms
are ignored. Analyses can contain as many numeric columns as necessary, the names of oxides and
trace elements are self-explanatory (e.g. ’SiO2’, ’Fe2O3’, ’Rb’, ’Nd’).
Note that names of variables are case sensitive in R and that each of the sample and variable names
need to be unique.
Value
Data frame with the loaded data
Author(s)
Vojtech Janousek, [email protected]
Millications
millicat
Description
Returns millications.
Usage
millicat(what=WR)
Arguments
what
numeric matrix with the whole-rock data
Details
The calculated values are Si, Ti, Al, Fe3, Fe2, Fe, Mn, Mg, Ca, Na, K, P, Li.
Elementi = 1000
Oxidei (wt.%)
∗ x(Elementi )
M W (Oxidei )
Where: MW = molecular weight of the Oxide[i], x = number of atoms of Element[i] in the formula
Value
Numeric matrix with the millications
Author(s)
Vojtech Janousek, [email protected]
6
mz.saturation
mz.saturation
Monazite saturation (Montel 1993)
Description
Calculates monazite saturation temperatures for given major-element compositions and LREE contents of the magma.
Usage
mz.saturation(cats = millicat(WR), H2O = 3, Xmz = 0,83)
Arguments
cats
numeric matrix; whole-rock data recast to millications
H2O
assumed water contents of the magma
Xmz
mole fractions of the REE-phosphates in monazite
Details
This function uses saturation model of Montel (1993). The formulae are as follows:
P
LREE =
REEi
( at.weight(REEi)
)
Xmz
where REEi : La, Ce, Pr, Nd, Sm, Gd.
Dmz = 100
T mz.sat.C =
N a + K + Li + 2Ca
1
.
Al
Al + Si
13318
√
− 273.15
9.5 + 2.34Dmz + 0.3879 H2 O − ln(LREE)
Value
Returns a matrix ’results’ with the following columns:
Dmz
distribution coefficient
Tmz.sat.C
monazite saturation temperature
Author(s)
Vojtech Janousek, [email protected]
References
Montel J M (1993) A model for monazite/melt equilibrium and application to the generation of
granitic magmas. Chem Geol 110: 127-146
7
normalize2total
normalize2total
Recast to given sum
Description
Recasts the selected data to a fixed sum.
Usage
normalize2total(what, total = 100)
Arguments
what
numeric matrix.
total
a sum the data should be normalized to.
Details
The function returns the selected elements/oxides (columns in the data matrix ’WR’) normalized to
the required sum.
Value
Numeric vector/matrix with the results.
Author(s)
Vojtech Janousek, [email protected]
Examples
normalize2total(major,1)
r2clip
Copy results to clipboard
Description
Copies the specified variable (typically the most recently calculated results) to a clipboard.
Usage
r2clip(what=results)
Arguments
what
Value
None.
a variable to be copied, can be either a vector, a matrix or a data frame.
8
zr.saturation
Author(s)
Vojtech Janousek, [email protected]
zr.saturation
Zircon saturation (Watson + Harrison 1983)
Description
Calculates zircon saturation temperatures for the observed major-element data and Zr concentrations. Returns also Zr saturation levels for the given major-element compositions and assumed
magma temperature.
Usage
zr.saturation(cats = millicat(WR), T = 750, Zr = subset(WR, Zr>0, "Zr"))
Arguments
cats
numeric matrix; whole-rock data recast to millications
T
assumed temperature of the magma in C
Zr
numeric vector with Zr concentrations
Details
Calculates Zr saturation concentration at the specified temperature. Given ’T’ is the estimated
absolute temperature (K) of the magma and ’M’ is a cationic ratio:
M = 100
N a + K + 2Ca
Al.Si
it can be written Watson & Harrison 1983):
DZr = e(−3.8−0.85(M −1)+
12900
)
T
The Zr saturation level is then given by:
Zr.sat =
497644
DZr
On the other hand, the saturation temperature can be obtained from the observed Zr concentration
and magma composition (assuming no zircon inheritance)
DZr =
T Zr.sat.C =
497644
Zr
12900
− 273.15
ln(DZr ) + 3.8 + 0.85(M − 1)
9
zr.saturation
Value
Returns a matrix ’results’ with the following columns:
M
cationic ratios
Zr
observed Zr concentrations
Zr.sat
saturation levels of Zr for assumed temperature
TZr.sat.C
zircon saturation temperatures in C
Author(s)
Vojtech Janousek, [email protected]
References
Watson E B & Harrison M (1983) Zircon saturation revisited: temperature and composition effects
in a variety of crustal magma types. Earth Planet Sci Lett 64: 295-304
Index
∗Topic file
load.file, 4
r2clip, 7
∗Topic internal
acnk, 1
filter.out, 3
millicat, 5
normalize2total, 6
∗Topic manip
ap.saturation, 2
mz.saturation, 5
zr.saturation, 8
acnk, 1
ap.saturation, 2
filter.out, 3
load.file, 4
millicat, 1, 5
mz.saturation, 5
normalize2total, 6
r2clip, 7
Shand (acnk), 1
zr.saturation, 8
10