an R package for ShortlivEd RAdionuclide Chronology of recent sediment cores.
To report a problem, email me or use the Github "Issues" tool.
Bruel, R., Sabatier, P., 2020. serac: an R package for ShortlivEd RAdionuclide chronology of recent sediment cores. Journal of Environmental Radioactivity 225, 106449. https://doi.org/10.1016/j.jenvrad.2020.106449
serac is not available on CRAN, but can be downloaded directly from this GitHub repository:
install.packages("devtools")
devtools::install_github("rosalieb/serac", build_vignettes = TRUE)
library(serac)
See the vignette (vignette("serac")) for a complete example of the functionalities of serac. We included in the package an example dataset for Lake Allos (Wilhelm et al., 2012), that allows you to reproduce the age-depth model for the core ALO09P12.
Refer to our paper (Bruel and Sabatier, 2020) for more examples.
Figure 1. Age-depth model for the core ALO09P12 as in Wilhelm et al. (2012), built with the package serac.
If you want to quickly run a first example, here is the main code allowing you to generate an age-depth model:
# Install and load the package and the vignette
devtools::install_github("rosalieb/serac", build_vignettes = TRUE)
library(serac)
vignette("serac")
# Create a folder for the data
dir.create(file.path(getwd(), 'Cores'), showWarnings = FALSE)
dir.create(file.path(paste0(getwd(),'/Cores'), 'serac_example_ALO09P12'), showWarnings = FALSE)
# Write in the main data
write.table(x = serac_example_ALO09P12, file = paste0(getwd(),'/Cores/serac_example_ALO09P12/serac_example_ALO09P12.txt'),col.names = T, row.names = F,sep="\t")
# Including proxy data for this core too
write.table(x = serac_example_ALO09P12_proxy, file = paste0(getwd(),'/Cores/serac_example_ALO09P12/serac_example_ALO09P12_proxy.txt'),col.names = T, row.names = F,sep="\t")
# Code for the age-depth model
model_ALO09P12 <-
serac(name="serac_example_ALO09P12", coring_yr=2009, model=c("CFCS"),
plotphoto=FALSE, minphoto=c(0), maxphoto=c(210),
plot_Pb=T, plot_Am=T, plot_Cs=T, Cher=c(30,40), Hemisphere=c("NH"), NWT=c(51,61),
sedchange=c(75.5),
plot_Pb_inst_deposit=T, inst_deposit=c(20,28,100,107,135,142,158,186),
suppdescriptor=TRUE, descriptor_lab=c("Ca/Fe"),
historic_d=c(20,28,100,107,135,142,158,186),
historic_a=c(1994,1920,1886,1868),
historic_n=c("sept 1994 flood","1920 flood","1886 flood","1868 flood ?"),
min_yr=c(1750),
dmax=c(180),
plotpdf=T, preview=T,
save_code=FALSE)
Code versioning was not done systematically, but starting November 2024, we will specify whenever modifications are done and whether it warrants a change in the version number.
| Version | Date | Comment |
|---|---|---|
| V1.0.0 | Initial release (Bruel and Sabatier, 2020) | |
| V1.1.0 | 2023-03-03 | Modifications: (1) Include detection limits for the radionuclides with the arguments DL_Pb, DL_Cs, and DL_Am. (2) Possibility not to plot the Cesium line with the logical argument plot_Cs_lines. Default = TRUE. |
| V1.2.0 | 2024-11-15) | Possibility to add hiatuses with the argument hiatus. See Issue #4 for details. |