Title:	Impute Missing Rare Earth Element Data in Zircon
Version:	0.0.5
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>.
License:	MIT + file LICENSE
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.2.3
Suggests:	testthat (≥ 3.0.0)
Config/testthat/edition:	3 janitor, tidyselect,
Imports:	tibble, dplyr, magrittr, tidyr, stringr, purrr, rlang, broom
Depends:	R (≥ 4.0)
URL:	https://github.com/cicarrascog/imputeREE
BugReports:	https://github.com/cicarrascog/imputeREE/issues
NeedsCompilation:	no
Packaged:	2023-06-22 01:00:06 UTC; ccarr
Author:	Carlos Carrasco Godoy [aut, cre]
Maintainer:	Carlos Carrasco Godoy <carlos.carrasco@anu.edu.au>
Repository:	CRAN
Date/Publication:	2023-06-22 07:20:02 UTC

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling rhs(lhs).

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

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)

Clean variable names that have prefixes or suffixes

Description

This is a helper function

Usage

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

Arguments

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

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

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

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
)

Arguments

Value

a data frame

Rare earth element list

Description

A string vector containing the elemental symbols for REE.

Usage

REE_Elements

Format

Rare earth element list

Rare earth element list

Description

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

Usage

REE_plus_Y_Elements

Format

Rare earth element + Y list

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")

Arguments

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)

Arguments

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)

Arguments

Value

a data frame or tibble

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)

Arguments

Value

A data frame

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)

Arguments

Value

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

Examples

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

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
)

Arguments

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
)

Arguments

Value

a data frame

Denormalize chrodrite Normalize to ppm

Description

Denormalize chrodrite Normalize to ppm

Usage

element_denorm(dat, method = PalmeOneill2014CI)

Arguments

Value

A dataframe

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)

Arguments

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')

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
)

Arguments

Value

a dataframe

See Also

Other model REE: modelChondrite_lattice(), modelZhong(), model_REE()

Examples

Ballard_et_al_Zircon %>%  modelChondrite_Onuma(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
)

Arguments

Value

a dataframe

See Also

Other model REE: modelChondrite_Onuma(), modelZhong(), model_REE()

Examples

Ballard_et_al_Zircon %>%  modelChondrite_lattice(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
)

Arguments

Value

a dataframe

See Also

Other model REE: modelChondrite_Onuma(), modelChondrite_lattice(), model_REE()

Examples

Ballard_et_al_Zircon %>%  modelZhong(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
)

Arguments

Value

a dataframe

See Also

Other model REE: modelChondrite_Onuma(), modelChondrite_lattice(), modelZhong()

Examples

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