Package 'imputeREE' reference manual

Title:	Impute Missing Rare Earth Element Data in Zircon
Description:	Set of functions to impute missing rare earth data, calculate La and Pr concentrations and Ce anomalies in zircons based on the Chondrite-Onuma and Chondrite-Lattice of Carrasco-Godoy and Campbell (2023) <doi:10.1007/s00410-023-02025-9> and the Logarithmic regression from Zhong et al. (2019) <doi:10.1007/s00710-019-00682-y>.
Authors:	Carlos Carrasco Godoy [aut, cre]
Maintainer:	Carlos Carrasco Godoy <[email protected]>
License:	MIT + file LICENSE
Version:	0.0.5
Built:	2024-08-27 04:36:52 UTC
Source:	https://github.com/cicarrascog/imputeree

Add ionic radius and chondrite and mantle values, Z and Mass

Description

This is a helper function to work with Element_norm() and Element_denorm(). Add Ionic Radius to data and chondrite values. For now, only supports 3+ in eight-fold coordination for REE, Zr and Y.Values are from Shannon(1976), McDonough and Sun (1995) and Palme and O'Neill (2014).

Usage

add_element_data(dat)
add_element_data(dat)

Arguments

dat

Long data REE format

Value

A data frame

Add_ID

Description

Add an unique ID per observation and checks that is not overwriting an existing column. If the column already exist, it will take no action. This is a wrapper of tibble::rowid_to_column() that checks that not columns is overwritten.

Usage

add_ID(dat, ID = "rowid")
add_ID(dat, ID = "rowid")

Arguments

`dat`	a tibble or a dataframe
`ID`	Name of column to use for rownames. 'rowid' is used if none is specified. er parameters passed onto the `tibble::rowid_to_column()` function

Value

a data frame

Add Chondrite or Mantle values for normalization.

Description

This is a helper function to work with Element_norm() and Element_denorm(). Takes long pivoted data to match element name and add normalizing values from the Element_data dataset.

Usage

add_IonicRadii(dat, method = ShannonRadiiVIII_Coord_3plus)
add_IonicRadii(dat, method = ShannonRadiiVIII_Coord_3plus)

Arguments

`dat`	a dataframe or tibble.
`method`	Ionic Radii from Shannon, 1976

Value

a data frame or tibble

Add Chondrite or Mantle values for normalization.

Description

This is a helper function to work with Element_norm() and Element_denorm(). Takes long pivoted data to match element name and add normalizing values from the Element_data dataset.

Usage

add_NormValues(dat, chondrite = PalmeOneill2014CI)
add_NormValues(dat, chondrite = PalmeOneill2014CI)

Arguments

`dat`	Dataframe or tibble. doc
`chondrite`	PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI

Value

a data frame or tibble

Zircon Rare earth Element Data from Ballard et al. 2001 and 2002.

Description

Trace element data from selected zircons from the data of Ballard et al. 2001 and 2002.

Usage

Ballard_et_al_Zircon
Ballard_et_al_Zircon

Format

A data frame with 210 rows and 18 variables:

Reference: Reference of the data
Deposit: Deposit associated with the data
Zr_Y_ppm: Y concentrations in ppm
Zr_P_ppm: P concentrations in ppm
Zr_La_ppm: La concentrations in ppm
Zr_Ce_ppm: Ce concentrations in ppm
Zr_Pr_ppm: Pr concentrations in ppm
Zr_Nd_ppm: Nd concentrations in ppm
Zr_Sm_ppm: Sm concentrations in ppm
Zr_Eu_ppm: Eu concentrations in ppm
Zr_Gd_ppm: Gd concentrations in ppm
Zr_Tb_ppm: Tb concentrations in ppm
Zr_Dy_ppm: Dy concentrations in ppm
Zr_Ho_ppm: Ho concentrations in ppm
Zr_Er_ppm: Er concentrations in ppm
Zr_Tm_ppm: Tm concentrations in ppm
Zr_Yb_ppm: Yb concentrations in ppm
Zr_Lu_ppm: Lu concentrations in ppm

Source

Ballard, J. R., Palin, J. M., Williams, I. S., Campbell, I. H., and Faunes, A., 2001, Two ages of porphyry intrusion resolved for the super-giant Chuquicamata copper deposit of northern Chile by ELA-ICP-MS and SHRIMP: Geology, v. 29, p. 383–386. (https://pubs.geoscienceworld.org/gsa/geology/article-abstract/29/5/383/192017/Two-ages-of-porphyry-intrusion-resolved-for-the?redirectedFrom=fulltext)

Ballard, J. R., Palin, M. J., and Campbell, I. H., 2002, Relative oxidation states of magmas inferred from Ce(IV)/Ce(III) in zircon: application to porphyry copper deposits of northern Chile: Contributions to Mineralogy and Petrology, v. 144, p. 347–364. (https://link.springer.com/article/10.1007/s00410-002-0402-5)

Calculate and Impute REE missing data and anomalies.

Description

This is a wrapper for data %>% model_REE() %>% impute_REE() %>% add_parameters()

Usage

calc_all(dat, prefix = NULL, suffix = NULL, chondrite = PalmeOneill2014CI)
calc_all(dat, prefix = NULL, suffix = NULL, chondrite = PalmeOneill2014CI)

Arguments

`dat`	A data frame with REE data in ppm
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm
`chondrite`	an option from: PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI

Value

A data frame. Includes imputed REE, model metrics, and calculated variables.

Examples


Ballard_et_al_Zircon %>% calc_all(prefix = 'Zr_', suffix = '_ppm')


Ballard_et_al_Zircon %>% calc_all(prefix = 'Zr_', suffix = '_ppm')

Clean variable names that have prefixes or suffixes

Description

This is a helper function

Usage

CleanColnames(dat, prefix = NULL, suffix = NULL)
CleanColnames(dat, prefix = NULL, suffix = NULL)

Arguments

`dat`	a data frame
`prefix`	A character of length 1
`suffix`	A character of length 1

Value

A data frame

Corrects for the model deviations of Er, Yb, Lu and Y

Description

Calculated value of Yb, Lu and Y slightly deviates from the linear regression. This function apply a correction to compensates those deviations. This function is wrapped inside model_REE()

Usage

correct_heavy(
  dat,
  Y_correction_fact = 1/0.72,
  Ho_correction_fact = 1,
  Er_correction_fact = 1/0.974,
  Tm_correction_fact = 1,
  Yb_correction_fact = 1/0.907,
  Lu_correction_fact = 1/0.926
)
correct_heavy(
  dat,
  Y_correction_fact = 1/0.72,
  Ho_correction_fact = 1,
  Er_correction_fact = 1/0.974,
  Tm_correction_fact = 1,
  Yb_correction_fact = 1/0.907,
  Lu_correction_fact = 1/0.926
)

Arguments

`dat`	A dataframe
`Y_correction_fact`	a number: correction factor for underestimated Y. 1/ 0.72 by default.
`Ho_correction_fact`	a number: correction factor for Ho. 1 by default.
`Er_correction_fact`	a number: correction factor for underestimated Er. 1/0.974 by default.
`Tm_correction_fact`	a number: correction factor for Tm. 1 by default.
`Yb_correction_fact`	a number: correction factor for underestimated Yb. 1/0.907 by default.
`Lu_correction_fact`	a number: correction factor for underestimated Lu. 1/0.926 by default.

Value

a data frame

Corrects for the model deviations of Yb, Lu and Y

Description

Calculated value of Yb, Lu and Y slightly deviates from the linear regression. This function apply a correction to compensates those deviations. This function is wrapped inside model_REE()

Usage

correct_middle(
  dat,
  Nd_correction_fact = 1/0.989,
  Sm_correction_fact = 1/1.022,
  Gd_correction_fact = 1/1.033,
  Tb_correction_fact = 1/1.05,
  Dy_correction_fact = 1/1.032,
  Pr_correction_fact = 1/0.918
)
correct_middle(
  dat,
  Nd_correction_fact = 1/0.989,
  Sm_correction_fact = 1/1.022,
  Gd_correction_fact = 1/1.033,
  Tb_correction_fact = 1/1.05,
  Dy_correction_fact = 1/1.032,
  Pr_correction_fact = 1/0.918
)

Arguments

`dat`	A dataframe
`Nd_correction_fact`	a number: correction factor for underestimated Nd 1/0.0.989
`Sm_correction_fact`	a number: correction factor for overestimated Sm 1/1.022
`Gd_correction_fact`	a number: correction factor for overestimated Gd 1/1.033
`Tb_correction_fact`	a number: correction factor for overestimated Tb 1/1.050
`Dy_correction_fact`	a number: correction factor for overestimated Dy 1/1.032
`Pr_correction_fact`	a number: correction factor for overestimated Pr 1/0.918

Value

a data frame

Element data for calculations

Description

A dataset containing CI and Mantle values for normalization for selected elements. The data used is from IUPAC, Palme and O'Neill (2014), and McDonough and Sun (1995). Ionic Radii are from Shannon (1976).

Usage

Element_Data
Element_Data

Format

A data frame with 77 rows and 11 variables:

Z: Atomic Number
Element_name: Element Symbol
Atomic_Mass: Atomic Mass from IUPAC
Unit: Measure Unit of the Concentrations, ppm = parts per million, pct = percentage
PalmeOneill2014CI: Chondrite values from Palme and Oneil (2014)
PalmeOneill2014CI_RSD: Uncertainty from chondrite values from Palme and O'Neill (2014) as RSD (Relative standard Deviation)
PalmeOneill2014Mantle: Primitive Mantle values from Palme and O'Neill (2014)
PalmeOneill2014Mantle_RSD: Uncertainty from Primitive Mantle Values from Palme and O'Neill (2014) as RSD (Relative standard Deviation)
McDonough1995CI: Chondrite values from McDonough and Sun (1995)
ShannonRadiiVIII_Coord_3plus: Shannon (1976) Ionic Radii for elements in Eight-fold coordination and 3+ charge
Z_Zhong: numbers assigned by Zhong et al. (2019) for a logarithmic regression to calculate Zircon REE.

...

Source

IUPAC Website (https://iupac.org/)

Palme, H., and O’Neill, H. St. C., 2014, 3.1 - Cosmochemical Estimates of Mantle Composition, in Holland, H. D. and Turekian, K. K. eds., Treatise on Geochemistry (Second Edition): Oxford, Elsevier, p. 1-39.(doi:10.1016/B978-0-08-095975-7.00201-1)

McDonough, W. F., and Sun, S. -s., 1995, The composition of the Earth: Chemical Geology, v. 120, p. 223-253.(doi:10.1016/0009-2541(94)00140-4)

Shannon, R. D., 1976, Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides: Acta Crystallographica Section A, v. 32, p. 751-767. doi:10.1107/S0567739476001551

Zhong, S., Seltmann, R., Qu, H., and Song, Y., 2019, Characterization of the zircon Ce anomaly for estimation of oxidation state of magmas: a revised Ce/Ce* method: Mineralogy and Petrology, v. 113, no. 6, p. 755–763. doi:10.1007/s00710-019-00682-y

Denormalize chrodrite Normalize to ppm

Description

Denormalize chrodrite Normalize to ppm

Usage

element_denorm(dat, method = PalmeOneill2014CI)
element_denorm(dat, method = PalmeOneill2014CI)

Arguments

`dat`	A dataframe
`method`	an option from: 'PalmeOneill2014CI', 'Oneill2014Mantle', 'McDonough1995CI'

Value

A dataframe

Calculate normalized values for a list of elements

Description

Element norm normalize values according to published values for the Primitive mantle and chondrites. By defect, it uses the values from Palme and O'Neill (2014). By default, REE + Y list is provided

Usage

Element_norm(
  data,
  return = "rect",
  chondrite = PalmeOneill2014CI,
  prefix = NULL,
  suffix = NULL,
  Element_list = REE_plus_Y_Elements
)
Element_norm(
  data,
  return = "rect",
  chondrite = PalmeOneill2014CI,
  prefix = NULL,
  suffix = NULL,
  Element_list = REE_plus_Y_Elements
)

Arguments

`data`	a data frame
`return`	a character from: "rect" for a wide data return,"raw" for a long data return,"append" to append the results to the input data
`chondrite`	an option from: PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm
`Element_list`	a character vector: indicating the elements that should be normalized. REE + Y by default

Value

a data frame

Impute Rare earth elements

Description

Imputes missing REE after modelling. Expect the output of 'model_REE()' function. Only missing values are replaced.

Usage

impute_REE(data, prefix = NULL, suffix = NULL, rsquared = 0.95)
impute_REE(data, prefix = NULL, suffix = NULL, rsquared = 0.95)

Arguments

`data`	A dataframe resulting from 'model_ree()'
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm
`rsquared`	A numerical value between 0 and 1. Tolerance to mis-fitting models. set as 0.9 by default.

Details

By default, exclude models with R-squared lower than 0.95. This limit is flexible and method dependent. As guidelines, the Chondrite-Lattice mthod should consider R-squared > 0.95 for at least 3 points. The Chondrite-Onuma method should consider R-squared >0.98 for at least 4 points.

Value

A dataframe

Examples


Ballard_et_al_Zircon %>%
dplyr::slice(1:100) %>%
model_REE(prefix = 'Zr', suffix = 'ppm') %>%
impute_REE(prefix = 'Zr', suffix = 'ppm')



Ballard_et_al_Zircon %>%
dplyr::slice(1:100) %>%
model_REE(prefix = 'Zr', suffix = 'ppm') %>%
impute_REE(prefix = 'Zr', suffix = 'ppm')

Model REE + Y contents using different methods.

Description

This function models REE + Y using different methods. The Chondrite-Lattice method use a linear regression between the REE (+Y) chondrite-normalized and the missfit term from the lattice strain equation (ri/3 + r0/6)(ri-r0)^2. The Chondrite-Onuma method use the quadratic relationship between the ionic radii and chondrite normalized REE values. The method of Zhong et al. (2019) use a logaritmic relationship between the atomic number of the REE and the chondrite normalized REE. For details in the lattice strain theory, see Blundy and Wood 1994. For more details in the imputation methods see Carrasco-Godoy and Campbell (2023), and Zhong et al. (2019)

Usage

model_REE(
  dat,
  method = 1,
  long_format = F,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  r0 = 0.84,
  chondrite = PalmeOneill2014CI,
  estimate_r0 = FALSE,
  r0_step = 0.01,
  r0_min = 0.01,
  r0_max = 0.15,
  prefix = NULL,
  suffix = NULL,
  Calibrate = T,
  Pr_correction_fact = 1/0.918,
  Y_correction_fact = 1/0.72,
  Dy_correction_fact = 1/1.032,
  Ho_correction_fact = 1,
  Er_correction_fact = 1/0.974,
  Tm_correction_fact = 1,
  Yb_correction_fact = 1/0.8785,
  Lu_correction_fact = 1/0.8943,
  Nd_correction_fact = 1/0.989,
  Sm_correction_fact = 1/1.022,
  Gd_correction_fact = 1/1.033,
  Tb_correction_fact = 1/1.05
)
model_REE(
  dat,
  method = 1,
  long_format = F,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  r0 = 0.84,
  chondrite = PalmeOneill2014CI,
  estimate_r0 = FALSE,
  r0_step = 0.01,
  r0_min = 0.01,
  r0_max = 0.15,
  prefix = NULL,
  suffix = NULL,
  Calibrate = T,
  Pr_correction_fact = 1/0.918,
  Y_correction_fact = 1/0.72,
  Dy_correction_fact = 1/1.032,
  Ho_correction_fact = 1,
  Er_correction_fact = 1/0.974,
  Tm_correction_fact = 1,
  Yb_correction_fact = 1/0.8785,
  Lu_correction_fact = 1/0.8943,
  Nd_correction_fact = 1/0.989,
  Sm_correction_fact = 1/1.022,
  Gd_correction_fact = 1/1.033,
  Tb_correction_fact = 1/1.05
)

Arguments

`dat`	A data frame with REE data in ppm
`method`	a number. a choice of `1` for Chondrite Lattice or `2` for Zhong et al. (2019) or `3` for Chondrite-Onuma method.
`long_format`	If T, rectangular long data is returned.
`exclude`	a string: vector including elements that should be omitted from modelling. La, Ce and Eu are the default. Ce and Eu should be always included
`r0`	A number: ionic radii of the lattice site r0. By default is 0.87 A, the median value obtained by Carrasco-Godoy and Campbell.
`chondrite`	an option from: PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI
`estimate_r0`	If T, r0 is estimated using a method similar to the one from Loader et al. 2022.
`r0_step`	If r0 is estimated, this define the step for iteration. smaller step heavily increases the computing time.
`r0_min`	Minimun value from which the iteration starts. Calculated from r0.
`r0_max`	Maximun value at which iteration ends. Calculated from r0.
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm
`Calibrate`	Logical (T or F). If True, the model is calibrated using the correction factors. By default it is the reciprocal of the median REE from the work of Carrasco-Godoy and Campbell is used.
`Pr_correction_fact`	a number: correction factor for overestimated Pr 1/0.918
`Y_correction_fact`	a number: correction factor for underestimated Y. 1/ 0.72 by default.
`Dy_correction_fact`	a number: correction factor for overestimated Dy 1/1.032
`Ho_correction_fact`	a number: correction factor for Ho. 1 by default.
`Er_correction_fact`	a number: correction factor for underestimated Er. 1/0.97 by default.
`Tm_correction_fact`	a number: correction factor for Tm. 1 by default.
`Yb_correction_fact`	a number: correction factor for underestimated Yb. 1/0.8785 by default.
`Lu_correction_fact`	a number: correction factor for underestimated Lu. 1/0.8943 by default.
`Nd_correction_fact`	a number: correction factor for underestimated Nd 1/0.0.989
`Sm_correction_fact`	a number: correction factor for overestimated Sm 1/1.022
`Gd_correction_fact`	a number: correction factor for overestimated Gd 1/1.033
`Tb_correction_fact`	a number: correction factor for overestimated Tb 1/1.050

Value

a dataframe

Examples


Ballard_et_al_Zircon %>%  model_REE(prefix = 'Zr', suffix = 'ppm')


Ballard_et_al_Zircon %>%  model_REE(prefix = 'Zr', suffix = 'ppm')

Model REE contents using the Chondrite-Lattice method of Carrasco-Godoy and Campbell (2023)

Description

This function apply the Chondrite-Lattice method which is a linear regression between the misfit parameter from the lattice strain equation and the logarithm of their chondrite normalized values. At least 2 points are required to use this method. This method is based on the work of Blundy and Wood (1994) but using chondrite normalized values as noted by Carrasco-Godoy and Campbell (2023). Refer to Carrasco-Godoy and Campbell (2023) for details.

Usage

modelChondrite_lattice(
  dat,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  Calibrate = T,
  prefix = NULL,
  suffix = NULL,
  r0 = 0.87,
  chondrite = PalmeOneill2014CI,
  Pr_correction_fact = 1/0.918,
  Y_correction_fact = 1/0.72,
  Dy_correction_fact = 1/1.032,
  Ho_correction_fact = 1,
  Er_correction_fact = 1/0.974,
  Tm_correction_fact = 1,
  Yb_correction_fact = 1/0.8785,
  Lu_correction_fact = 1/0.8943,
  Nd_correction_fact = 1/0.989,
  Sm_correction_fact = 1/1.022,
  Gd_correction_fact = 1/1.033,
  Tb_correction_fact = 1/1.05
)
modelChondrite_lattice(
  dat,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  Calibrate = T,
  prefix = NULL,
  suffix = NULL,
  r0 = 0.87,
  chondrite = PalmeOneill2014CI,
  Pr_correction_fact = 1/0.918,
  Y_correction_fact = 1/0.72,
  Dy_correction_fact = 1/1.032,
  Ho_correction_fact = 1,
  Er_correction_fact = 1/0.974,
  Tm_correction_fact = 1,
  Yb_correction_fact = 1/0.8785,
  Lu_correction_fact = 1/0.8943,
  Nd_correction_fact = 1/0.989,
  Sm_correction_fact = 1/1.022,
  Gd_correction_fact = 1/1.033,
  Tb_correction_fact = 1/1.05
)

Arguments

`dat`	A data frame with REE data in ppm
`exclude`	a string: vector including elements that should be omitted from modelling. La, Ce and Eu are the default. Ce and Eu should be always included
`Calibrate`	Logical (T or F). If True, the model is calibrated using the correction factors. By default it is the reciprocal of the median REE from the work of Carrasco-Godoy and Campbell is used.
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm
`r0`	A number: ionic radii of the lattice site r0. By default is 0.87 A, the median value obtained by Carrasco-Godoy and Campbell.
`chondrite`	an option from: PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI
`Pr_correction_fact`	a number: correction factor for overestimated Pr 1/0.918
`Y_correction_fact`	a number: correction factor for underestimated Y. 1/ 0.72 by default.
`Dy_correction_fact`	a number: correction factor for overestimated Dy 1/1.032
`Ho_correction_fact`	a number: correction factor for Ho. 1 by default.
`Er_correction_fact`	a number: correction factor for underestimated Er. 1/0.97 by default.
`Tm_correction_fact`	a number: correction factor for Tm. 1 by default.
`Yb_correction_fact`	a number: correction factor for underestimated Yb. 1/0.8785 by default.
`Lu_correction_fact`	a number: correction factor for underestimated Lu. 1/0.8943 by default.
`Nd_correction_fact`	a number: correction factor for underestimated Nd 1/0.0.989
`Sm_correction_fact`	a number: correction factor for overestimated Sm 1/1.022
`Gd_correction_fact`	a number: correction factor for overestimated Gd 1/1.033
`Tb_correction_fact`	a number: correction factor for overestimated Tb 1/1.050

Value

a dataframe

Examples

Ballard_et_al_Zircon %>%  modelChondrite_lattice(prefix = 'Zr', suffix = 'ppm')
Ballard_et_al_Zircon %>%  modelChondrite_lattice(prefix = 'Zr', suffix = 'ppm')

Model REE contents using the Chondrite-Onuma method of Carrasco-Godoy and Campbell (2023)

Description

This function apply the Chondrite-Onuma method which is a quadratic regression between the ionic radius of the REE and the logarithm of their chondrite normalized values. At least 3 non-linear points are required to use this method. This method is based on the work of Onuma et al. (1968) but using chondrite normalized values as noted by Carrasco-Godoy and Campbell (2023). Refer to Carrasco-Godoy and Campbell (2023) for details.

Usage

modelChondrite_Onuma(
  dat,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  Calibrate = T,
  chondrite = PalmeOneill2014CI,
  prefix = NULL,
  suffix = NULL,
  Pr_correction_fact = 1/1,
  Nd_correction_fact = 1/1.026486418,
  Sm_correction_fact = 1/0.971111041,
  Gd_correction_fact = 1/0.95928241,
  Tb_correction_fact = 1/1.000985745,
  Dy_correction_fact = 1/1.030049321,
  Ho_correction_fact = 1/1.018711009,
  Er_correction_fact = 1/0.996610693,
  Tm_correction_fact = 1/1.053205463,
  Yb_correction_fact = 1/0.982656111,
  Lu_correction_fact = 1/0.952608321,
  Y_correction_fact = 1/0.665380561
)
modelChondrite_Onuma(
  dat,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  Calibrate = T,
  chondrite = PalmeOneill2014CI,
  prefix = NULL,
  suffix = NULL,
  Pr_correction_fact = 1/1,
  Nd_correction_fact = 1/1.026486418,
  Sm_correction_fact = 1/0.971111041,
  Gd_correction_fact = 1/0.95928241,
  Tb_correction_fact = 1/1.000985745,
  Dy_correction_fact = 1/1.030049321,
  Ho_correction_fact = 1/1.018711009,
  Er_correction_fact = 1/0.996610693,
  Tm_correction_fact = 1/1.053205463,
  Yb_correction_fact = 1/0.982656111,
  Lu_correction_fact = 1/0.952608321,
  Y_correction_fact = 1/0.665380561
)

Arguments

`dat`	A data frame with REE data in ppm
`exclude`	a string: vector including elements that should be omitted from modelling. La, Ce and Eu are the default. Ce and Eu should be always included
`Calibrate`	Logical (T or F). If True, the model is calibrated using the correction factors. By default it is the reciprocal of the median REE from the work of Carrasco-Godoy and Campbell is used.
`chondrite`	an option from: PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm
`Pr_correction_fact`	a number: correction factor for overestimated Pr 1/0.918
`Nd_correction_fact`	a number: correction factor for underestimated Nd 1/0.0.989
`Sm_correction_fact`	a number: correction factor for overestimated Sm 1/1.022
`Gd_correction_fact`	a number: correction factor for overestimated Gd 1/1.033
`Tb_correction_fact`	a number: correction factor for overestimated Tb 1/1.050
`Dy_correction_fact`	a number: correction factor for overestimated Dy 1/1.032
`Ho_correction_fact`	a number: correction factor for Ho. 1 by default.
`Er_correction_fact`	a number: correction factor for underestimated Er. 1/0.97 by default.
`Tm_correction_fact`	a number: correction factor for Tm. 1 by default.
`Yb_correction_fact`	a number: correction factor for underestimated Yb. 1/0.8785 by default.
`Lu_correction_fact`	a number: correction factor for underestimated Lu. 1/0.8943 by default.
`Y_correction_fact`	a number: correction factor for underestimated Y. 1/ 0.72 by default.

Value

a dataframe

Examples

Ballard_et_al_Zircon %>%  modelChondrite_Onuma(prefix = 'Zr', suffix = 'ppm')
Ballard_et_al_Zircon %>%  modelChondrite_Onuma(prefix = 'Zr', suffix = 'ppm')

Model REE contents using the method of Zhong et al. (2019)

Description

This function apply the logarithmic regression using the method of Zhong et al. (2019). This method considers the relationship between the logarithm of the REE atomic number vs their chondrite normalized values. For more information refer to the Zhong et al. (2019) and Carrasco-Godoy and Campbell (2023) for a discussion of its limitations to calculate La or Ce*.

Usage

modelZhong(
  dat,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  Calibrate = F,
  chondrite = PalmeOneill2014CI,
  prefix = NULL,
  suffix = NULL
)
modelZhong(
  dat,
  exclude = c("La", "Pr", "Ce", "Eu", "Y"),
  Calibrate = F,
  chondrite = PalmeOneill2014CI,
  prefix = NULL,
  suffix = NULL
)

Arguments

`dat`	A data frame with REE data in ppm
`exclude`	a string: vector including elements that should be omitted from modelling. La, Ce and Eu are the default. Ce and Eu should be always included
`Calibrate`	Logical (T or F). If True, the model is calibrated using the correction factors. By default it is the reciprocal of the median REE from the work of Carrasco-Godoy and Campbell is used.
`chondrite`	an option from: PalmeOneill2014CI, Oneill2014Mantle, McDonough1995CI
`prefix`	A prefix in your columns e.g. ICP_La
`suffix`	A suffix in your columns e.g. La_ppm

Value

a dataframe

Examples

Ballard_et_al_Zircon %>%  modelZhong(prefix = 'Zr', suffix = 'ppm')
Ballard_et_al_Zircon %>%  modelZhong(prefix = 'Zr', suffix = 'ppm')

Rare earth element list

Description

A string vector containing the elemental symbols for REE.

Usage

REE_Elements
REE_Elements

Format

Rare earth element list

Description

A string vector containing the elemental symbols for REE and Y.

Usage

REE_plus_Y_Elements
REE_plus_Y_Elements

Format

Rare earth element + Y list

Package 'imputeREE'

Help Index

Add ionic radius and chondrite and mantle values, Z and Mass

Description

Usage

Arguments

Value

Add_ID

Description

Usage

Arguments

Value

Add Chondrite or Mantle values for normalization.

Description

Usage

Arguments

Value

Add Chondrite or Mantle values for normalization.

Description

Usage

Arguments

Value

Zircon Rare earth Element Data from Ballard et al. 2001 and 2002.

Description

Usage

Format

Source

Calculate and Impute REE missing data and anomalies.

Description

Usage

Arguments

Value

Examples

Clean variable names that have prefixes or suffixes

Description

Usage

Arguments

Value

Corrects for the model deviations of Er, Yb, Lu and Y

Description

Usage

Arguments

Value

Corrects for the model deviations of Yb, Lu and Y

Description

Usage

Arguments

Value

Element data for calculations

Description

Usage

Format

Source

Denormalize chrodrite Normalize to ppm

Description

Usage

Arguments

Value

Calculate normalized values for a list of elements

Description

Usage

Arguments

Value

Impute Rare earth elements

Description

Usage

Arguments

Details

Value

Examples

Model REE + Y contents using different methods.

Description

Usage

Arguments

Value

See Also

Examples

Model REE contents using the Chondrite-Lattice method of Carrasco-Godoy and Campbell (2023)

Description

Usage