isogeochem

isogeochem makes working with carbonate oxygen, carbon, and clumped isotope data reproducible and straightforward. Use it to quickly calculate isotope fractionation factors, and apply paleothermometry equations.

https://github.com/davidbajnai/isogeochem

Keywords

Repository

isogeochem makes working with carbonate oxygen, carbon, and clumped isotope data reproducible and straightforward. Use it to quickly calculate isotope fractionation factors, and apply paleothermometry equations.

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  message = FALSE,
  eval = TRUE,
  fig.path = "man/figures/README-",
  fig.height = 5,
  fig.width = 5,
  dpi = 150,
  out.width = "60%"
)
knitr::opts_knit$set(global.par = TRUE)
r = getOption("repos")
r["CRAN"] = "http://cran.us.r-project.org"
options(repos = r)
```
```{r, include = FALSE}
#> Set global graphic parameters. This code has to be in its own chunk.
par(mfrow = c(1, 1), mar = c(4.5, 4.5, 0.3, 0.3), bg = "white")
```

# isogeochem:  
 Tools for Stable Isotope Geochemistry


[![R-CMD-check](https://github.com/davidbajnai/isogeochem/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/davidbajnai/isogeochem/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/gh/davidbajnai/isogeochem/branch/main/graph/badge.svg?token=srtusVq2Im)](https://app.codecov.io/gh/davidbajnai/isogeochem)
[![CodeFactor](https://www.codefactor.io/repository/github/davidbajnai/isogeochem/badge)](https://www.codefactor.io/repository/github/davidbajnai/isogeochem)
[![repostatus](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN status](https://www.r-pkg.org/badges/version/isogeochem)](https://CRAN.R-project.org/package=isogeochem)
[![CRAN count](https://cranlogs.r-pkg.org/badges/grand-total/isogeochem)](https://cranlogs.r-pkg.org/badges/grand-total/isogeochem)
[![DOI](https://zenodo.org/badge/401782303.svg)](https://zenodo.org/badge/latestdoi/401782303)


`isogeochem` makes working with stable oxygen, carbon, and clumped isotope data straightforward and reproducible. It offers tools to quickly calculate:

* carbonate *δ*18O, *δ*17O, *∆*47, and *∆*48 values at a given temperature
* carbonate growth temperatures from *δ*18O, *∆*47, and *∆*48 values
* isotope fractionation factors, e.g., carbonate/water, quartz/water
* model DIC speciation as a function of temperature, pH, and salinity
* convert between the VSMOW and VPDB scales

The list of available proxy–temperature calibrations is growing with each new released version. 

Please get in touch if you have suggestions to include!

## Getting started

### Installation

Install the released version of `isogeochem` from CRAN.

``` {r, include = FALSE}
if (!require("isogeochem")) install.packages("isogeochem")
```
``` {r, eval = FALSE}
install.packages("isogeochem")
```

Install the development version of `isogeochem` from GitHub.

``` {r, eval = FALSE}
if (!require("devtools")) install.packages("devtools")
if (!require("rmarkdown")) install.packages("rmarkdown")
devtools::install_github("davidbajnai/isogeochem", build_vignettes = TRUE)
```

``` {r, include = FALSE}
library("isogeochem")
```

### Vignettes

Case studies demonstrating the use and scope of the functions in `isogeochem` are
available as vignettes.

``` {r, eval = FALSE}
browseVignettes("isogeochem")
```

## Dual clumped isotope thermometry

Use `D47()` and `D48()` to calculate equilibrium carbonate clumped isotope values (*∆*47, *∆*48) for a given temperature. `temp_D47()` calculates carbonate growth temperatures from *∆*47 values, while `temp_D48()` calculates growth temperature corrected for kinetic effects considering both the *∆*47 and the *∆*48 value.

``` {r, label = "Figure1"}
if (!require("shades")) install.packages("shades")

# Model equilibrium carbonate ∆47 and ∆48 values
temp  = seq(0, 100, 10) # temperature range: 0—100 °C
D47eq = D47(temp, eq = "Fiebig21")
D48eq = D48(temp, eq = "Fiebig21")

# Sample data
D47_coral  = 0.617; D47_coral_err  = 0.006
D48_coral  = 0.139; D48_coral_err  = 0.022
D47_speleo = 0.546; D47_speleo_err  = 0.007
D48_speleo = 0.277; D48_speleo_err  = 0.029

## Plot in ∆47 vs ∆48 space ##
plot(0, type = "l", axes = TRUE, ylim = c(0.4, 0.7), xlim = c(0.1, 0.3),
     ylab = expression(Delta[47] * " (CDES90, ‰)"),
     xlab = expression(Delta[48] * " (CDES90, ‰)"),
     lty = 0, font = 1, cex.lab = 1, las = 1)

# Plot the equilibrium curve and points
lines (D48eq, D47eq, col = "purple", lwd = 2)
points(D48eq, D47eq, col = shades::gradient(c("blue", "red"), length(temp)),
       pch = 19, cex = 1.2)

# Plot the sample data,
# ... the kinetic slopes,
# ... and calculate growth temperatures corrected for kinetic effects
# ... using a single function!
temp_D48(D47_coral, D48_coral, D47_coral_err, D48_coral_err, ks = -0.6,
         add = TRUE, col = "seagreen", pch = 15)
temp_D48(D47_speleo, D48_speleo, D47_speleo_err, D48_speleo_err, ks = -1,
         add = TRUE, col = "darkorange", pch = 17)

# Add labels to the plot
text(D48(temp, eq = "Fiebig21"), D47(temp, eq = "Fiebig21"), paste(temp, "°C"),
     col = shades::gradient(c("blue", "red"), length(temp)), pos = 4, cex = 0.8)
```

## Triple oxygen isotopes

`d17O_c()` calculates equilibrium carbonate oxygen isotope values (*δ*18O, *δ*17O, *∆*17O) for a given temperature and ambient water composition. Use the `mix_d17O()` function to calculate mixing curves in triple oxygen isotope space, e.g., for modeling diagenesis.

``` {r, label = "Figure2"}
if (!require("shades")) install.packages("shades")

# Model equilibrium *calcite* precipitating from seawater
temp_sw  = seq(0, 50, 10) # temperature range: 0—50 °C
d18O_sw = 0 # d18O value of seawater
D17O_sw = -0.004 # D17O value of seawater
d18Op = prime(d17O_c(temp_sw, d18O_sw, D17O_sw, eq18 = "Daeron19")[, 1])
D17O  = d17O_c(temp_sw, d18O_sw, D17O_sw, eq17 = "Wostbrock20", eq18 = "Daeron19")[, 3]

# Model progressing meteoric diagenetic alteration
d18O_ds = -8 # d18O value of diagenetic fluid
D17O_ds = 0.020 # D17O value of diagenetic fluid
em_equi = d17O_c(temp = 10, d18O_H2O = d18O_sw, D17O_H2O = D17O_sw,
                 eq17 = "Wostbrock20", eq18 = "Daeron19") # equilibrium endmember
em_diag = d17O_c(temp = 80, d18O_H2O = d18O_ds, D17O_H2O = D17O_ds,
                 eq17 = "Wostbrock20", eq18 = "Daeron19") # diagenetic endmember
mix = mix_d17O(d18O_A = em_equi[1], d17O_A = em_equi[2],
               d18O_B = em_diag[1], d17O_B = em_diag[2], step = 25)

## Plot in ∆17O vs d'18O space ##
plot(0, type = "l", ylim = c(-0.1, 0.05), xlim = c(-10, 40), 
     xlab = expression(delta * "'" ^ 18 * "O (‰, VSMOW)"),
     ylab = expression(Delta ^ 17 * "O (‰, VSMOW)"),
     lty = 0, font = 1, cex.lab = 1, las = 1)

# Plot meteoric waters from the build-in dataset
points(prime(meteoric_water$d18O), D17O(meteoric_water$d18O, meteoric_water$d17O),
       col = "lightblue1", pch = 20)
text(-4, 0.05, "meteoric water", pos = 4, col = "lightblue1")

# Plot the composition of the fluids
points(prime(d18O_sw), D17O_sw, col = "darkmagenta", pch = 8) # seawater
text(prime(d18O_sw), D17O_sw, "seawater", pos = 4, col = "darkmagenta")
points(prime(d18O_ds), D17O_ds, col = "deeppink", pch = 8) # diagenetic fluid
text(prime(d18O_ds), D17O_ds, "diagenetic fluid", pos = 4, col = "deeppink")

# Plot the equilibrium curve and points
lines(d18Op, D17O, col = "darkmagenta", lwd = 2)
points(d18Op, D17O, pch = 19, cex = 1.2, 
       col = shades::gradient(c("blue", "red"), length(temp_sw)))
text(d18Op, D17O, paste(temp_sw, "°C"), pos = 4, cex = 0.8, 
     col = shades::gradient(c("blue", "red"), length(temp_sw)))
text(30, -0.05, paste("equilibrium calcite \nfrom seawater"),
     pos = 3, col = "darkmagenta")

# Plot the mixing model between the equilibrium and diagenetic endmembers
lines(prime(mix[, 1]), mix[, 2], col = "deeppink", lty = 3, lwd = 2)
points(prime(mix[, 1]), mix[, 2], pch = 18, cex = 1.5, 
       col = shades::gradient(c("#3300CC", "deeppink"), length(mix[, 2])))
text(prime(mix[, 1]), mix[, 2], paste(mix[, 3], "%", sep = ""), pos = 2, cex = 0.8, 
     col = shades::gradient(c("#3300CC", "deeppink"), length(mix[, 3])))
text(22, -0.09, paste("progressing", "\ndiagenetic alteration", "\n(recrystallisation) at 80°C", sep =""),
     pos = 2, col = "deeppink")
```

## Thermometry

Use `isogeochem` to calculate crystallization temperatures from carbonate *δ*18O and *∆*47 values.

``` {r}
# Temperature from D47 with or without errors
temp_D47(D47_CDES90 = 0.601, eq = "Petersen19")
temp_D47(D47_CDES90 = 0.601,
         D47_error = 0.008 ,
         eq = "Anderson21")

# Temperature from d18O
temp_d18O(
  d18O_c_VSMOW = 30,
  d18O_H2O_VSMOW = 0,
  min = "calcite",
  eq = "Watkins13")
```

## Fractionation factors

Use `isogeochem` to calculate 16O/18O fractionation factors at given temperatures.

``` {r, label = "Figure3"}
if (!require("viridisLite")) install.packages("viridisLite")

plot(0, type = "l", las = 1, yaxt = "n", 
     xlim = c(10, 30), ylim = c(-30, 50),
     xlab = "Temperature (°C)",
     ylab = expression("Equilibrium enrichment in "^18*"O relative to H"[2]*"O (‰)"))
axis(2, seq(-30, 50, 10), las = 1)

temps = seq(10, 30, 1)
d18O_H2O_VSMOW = 0
cols = viridisLite::viridis(7, option = "C")

text(10, 45, expression("CO"[2]*" (aq)"), col = cols[1], adj = c(0, 0))
lines(temps, A_from_a(a18_CO2aq_H2O(temps), d18O_H2O_VSMOW),
      lwd = 2, lty = 2, col = cols[1])
text(10, 35, expression("HCO"[3]^"–"), col = cols[2], adj = c(0, 0))
lines(temps, A_from_a(a18_HCO3_H2O(temps), d18O_H2O_VSMOW),
      lwd = 2, lty = 2, col = cols[2])
text(10, 30, "calcite", col = cols[3], adj = c(0, 0))
lines(temps, A_from_a(a18_c_H2O(temps, "calcite", "Daeron19"), d18O_H2O_VSMOW),
  lwd = 2, lty = 1, col = cols[3])
text(10, 21, expression("CO"[3]^"2–"), col = cols[4], adj = c(0, 0))
lines(temps, A_from_a(a18_CO3_H2O(temps), d18O_H2O_VSMOW),
  lwd = 2, lty = 2, col = cols[4])
text(10, 1, expression("H"[2]*"O"), col = cols[5], adj = c(0, 0))
lines(temps, rep(d18O_H2O_VSMOW, length(temps)),
      lwd = 3, lty = 1, col = cols[5])
text(10, -23, expression("OH"^"–"), col = cols[6], adj = c(0, 0))
lines(temps, B_from_a(a18_H2O_OH(temps, eq = "Z20-X3LYP"), d18O_H2O_VSMOW),
  lwd = 2, lty = 1, col = cols[6])
```

## Utility functions

``` {r}
# Convert between the VSMOW and VPDB scales:
to_VPDB(32)
to_VSMOW(1)

# Convert between classical delta and delta prime values:
prime(10)
unprime(9.95)

# Calculate isotope fractionation factors:
a_A_B(A = 30.40, B = 0.15)
epsilon(a_A_B(A = 30.40, B = 0.15))
```

## Datasets

Within `isogeochem` you have quick access to important datasets.

| Name        | Description                                                     | Reference              |
|-------------|---------------------------------------------------------------- |------------------------|
| `devilshole`| The original Devils Hole carbonate *δ*18O time series| Winograd et al. (2006) |
| `LR04`      | A benthic foraminifera *δ*18O stack                  | Lisiecki & Raymo (2005)|
| `GTS2020`   | An abridged version of the GTS2020 oxygen isotope stack    | Grossman & Joachimski (2020)|
| `meteoric_water`| A compilation of meteoric water *δ*18O and *δ*17O values | Barkan & Luz (2010), Aron et al. (2021)|

For more information on the datasets please have a look at the corresponding documentation, e.g., `?devilshole`

___

## License and citation

Copyright (C) 2023 David Bajnai

This program is free software: you can redistribute it and/or modify it under the terms of the [GNU General Public License version 3](LICENSE.md), or (at your option) any later version. This program is distributed in the hope that it will be useful, but without any warranty.

Follow the citation format provided in [CITATION](CITATION.cff) when referencing `isogeochem`.

___

## See also


There are several other R packages that complement `isogeochem` and are worth checking out:

[`viridisLite`](https://github.com/sjmgarnier/viridisLite) and [`viridis`](https://github.com/sjmgarnier/viridis) produce color-blind and black-and-white printer friendly color scales.

[`clumpedr`](https://github.com/isoverse/clumpedr/) works with [`isoreader`](https://github.com/isoverse/isoreader) to read in raw measurement data and reproducibly process the results to clumped isotope values.

[`seasonalclumped`](https://github.com/nielsjdewinter/seasonalclumped) can be used to reconstruct temperature and salinity variations from seasonal oxygen and clumped isotope records.

[`deeptime`](https://github.com/willgearty/deeptime) adds geological timescales to ggplots.

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
title: 'isogeochem: An R package'
message: 'If you use this R package, you can cite it as below'
type: software
authors:
  - given-names: David
    family-names: Bajnai
    orcid: 'https://orcid.org/0000-0002-4053-5056'
    affiliation: Georg-August-Universität Göttingen
identifiers:
  - type: doi
    value: 10.5281/zenodo.5507224
    description: Concept DOI for all isogeochem versions
  - type: doi
    value: 10.5281/zenodo.7754760
    description: Versioned DOI for isogeochem v1.1.1
repository-code: 'https://github.com/davidbajnai/isogeochem'
abstract: >-
  The isogeochem R package makes working with carbonate
  oxygen, carbon, and clumped isotope data reproducible and
  straightforward. Use it to quickly calculate isotope
  fractionation factors and apply paleothermometry
  equations.
keywords:
  - isotope
  - fractionation
  - oxygen
  - carbon
  - carbonate
  - thermometry
  - clumped
license: GPL-3.0-or-later
version: v1.1.1
date-released: '2023-03-21'

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