serac

an R package for ShortlivEd RAdionuclide Chronology of recent sediment cores.

To report a problem, email me or use the Github "Issues" tool.

Citation

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

Download

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)

Get started

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.

Directly skip to your first age-depth model

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::installgithub("rosalieb/serac", buildvignettes = 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'), 'seracexampleALO09P12'), showWarnings = FALSE)

Write in the main data

write.table(x = seracexampleALO09P12, file = paste0(getwd(),'/Cores/seracexampleALO09P12/seracexampleALO09P12.txt'),col.names = T, row.names = F,sep="\t")

Including proxy data for this core too

write.table(x = seracexampleALO09P12proxy, file = paste0(getwd(),'/Cores/seracexampleALO09P12/seracexampleALO09P12proxy.txt'),col.names = T, row.names = F,sep="\t")

Code for the age-depth model

modelALO09P12 <-   serac(name="seracexampleALO09P12", coringyr=2009, model=c("CFCS"),         plotphoto=FALSE, minphoto=c(0), maxphoto=c(210),         plotPb=T, plotAm=T, plotCs=T, Cher=c(30,40), Hemisphere=c("NH"), NWT=c(51,61),         sedchange=c(75.5),         plotPbinstdeposit=T, instdeposit=c(20,28,100,107,135,142,158,186),         suppdescriptor=TRUE, descriptorlab=c("Ca/Fe"),         historicd=c(20,28,100,107,135,142,158,186),         historica=c(1994,1920,1886,1868),         historicn=c("sept 1994 flood","1920 flood","1886 flood","1868 flood ?"),         minyr=c(1750),         dmax=c(180),         plotpdf=T, preview=T,         save_code=FALSE) ```

Version

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.