Author: David Bajnai
Contributors: Julian Tödter
License:
GPL-3
isogeochem aims to make working with stable oxygen, carbon, and
clumped isotope data reproducible and straightforward. It offers tools
to quickly calculate:
- equilibrium carbonate δ18O, δ17O, ∆47, and ∆48 values
- carbonate growth temperatures from δ18O, ∆47, and ∆48 values
- isotope fractionation factors, e.g., between carbonate and water
- model DIC speciation as a function of temperature, pH, and salinity
- convert between the VSMOW and VPDB scales
Look at the .pdf manual for the available list of calibrations and mineralogies.
This package is work in progress. Please get in touch if you have any suggestions! Contributors are acknowledged.
This package is not on CRAN yet.
You can install the development
version from Github with devtools:
if (!require("devtools")) install.packages("devtools")
devtools::install_github("davidbajnai/isogeochem")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.
library(isogeochem)
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)d17O_c() calculates equilibrium carbonate oxygen isotope values
(δ18O, δ17O, ∆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.
library(isogeochem)
if (!require("shades")) install.packages("shades")
# Model equilibrium calcite
temp = seq(0, 50, 10) # temperature range: 0—50 °C
d18O_H2O = -1
d18Op = prime(d17O_c(temp, d18O_H2O, eq18 = "Daeron19")[, 1])
D17O = prime(d17O_c(temp, d18O_H2O, eq18 = "Daeron19")[, 3])
# Model progressing meteoric diagenetic alteration
em_equi = d17O_c(10, d18O_H2O, eq18 = "Daeron19") # equilibrium endmember
em_diag = d17O_c(25, -10, 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])
## Plot in ∆17O vs d'18O space ##
plot(0, type = "l", axes = TRUE, ylim = c(-0.1,-0.04), xlim = c(15, 40),
xlab = expression(delta * "'" ^ 18 * "O"[c] * " (‰, VSMOW)"),
ylab = expression(Delta ^ 17 * "O (‰, VSMOW)"),
lty = 0, font = 1, cex.lab = 1, las = 1)
# Plot the equilibrium curve and points
lines(d18Op, D17O, col = "purple", lwd = 2)
points(d18Op, D17O, col = shades::gradient(c("blue", "red"), length(temp)),
pch = 19, cex = 1.2)
# Plot the mixing model between the equilibrium and diagenetic endmembers
lines(prime(mix[, 1]), mix[, 2], col = "tan4", lty = 2, lwd = 2)
points(prime(mix[, 1]), mix[, 2],
col = shades::gradient(c("#3300CC", "tan4"), length(seq(0, 10, 1))),
pch = 18, cex = 1.2)
# Add labels to the plot
text(d18Op + 0.5, D17O, paste(temp, "°C"), pos = 4, cex = 1,
col = shades::gradient(c("blue", "red"), length(temp)))
text(prime(mix[, 1]), mix[, 2], paste(mix[, 3], "%"), pos = 1, cex = 0.5,
col = shades::gradient(c("#3300CC", "tan4"), length(seq(0, 10, 1))))Use isogeochem to calculate isotope fractionation factors at given
temperatures.
# calcite/water – using Daëron et al. (2021)
a18_c_H2O(temp = 25, min = "calcite", eq = "Daeron19")
# calcite/water – using Kim and O'Neil (1997)
a18_c_H2O(temp = 25, min = "calcite", eq = "KO97")
# aragonite/water – using Grossman & Ku (1986) modified by Dettman et al. (1999)
a18_c_H2O(temp = 25, min = "aragonite", eq = "GK86")
# water/hydroxide ion – using Zeebe (2021)
a18_H2O_OH(temp = 25, eq = "Z21-X3LYP")Case studies demonstrating the use and scope of the functions are available as vignettes
browseVignettes("isogeochem")# Convert between the VSMOW and VPDB scales:
to_VPDB(10)
# Convert between classical delta and delta prime values:
prime(10)
unprime(9.95)Within isogeochem you have quick access to important datasets.
| Name | Description | Reference |
|---|---|---|
devilshole |
The original Devils Hole carbonate d18O time series | Winograd et al. (2006) |
LR04 |
A benthic foraminifera d18O stack | Lisiecki & Raymo (2005) |
GTS2020 |
An abridged version of the GTS2020 oxygen isotope stack | Grossman & Joachimski (2020) |
There are several other R packages that complement isogeochem and are
worth checking out:
viridisLite and viridis
produce color-blind and black-and-white printer friendly color scales.
seasonalclumped
can be used to reconstruct temperature and salinity variations from
seasonal oxygen and clumped isotope records.
deeptime adds geological
timescales to ggplots.