Functions for analysis of stable isotope time series, including the cosine (Balasse 2012; Tornero et al. 2013) and splitting-coalescence-estimation (SCEM, Chazin et al. 2018) methods for modelling season of birth.
Forked from soudeepd/SCEM. Original readme below.
R scripts to perform the Splitting-Coalescence-Estimation Method (cf. Chazin et al., 2018) to model birth seasonality in studies of herd animals.
Hannah Chazin, Soudeep Deb, Joshua Falk, Arun Srinivasan
We introduce improved methods for statistically assessing birth seasonality and intra-annual variation in δ18O from faunal tooth enamel.
The first method estimates input parameters for use with a previously-developed parametric approach (Tornero et al., 2013). The relevant code for this approach is makeFits.R, while makeFitsWrong.R is the code to implement the same method but with given initial conditions for two parameters. The latter can be used to show the disadvantage of the existing approach.
The second method we propose is a new idea that uses a nonparametric clustering procedure to group individuals with similar time series data and estimate birth seasonality based on the clusters. This method is more efficient across different scenarios, especially when less of the tooth row is preserved. The new approach offers a high level of statistical rigor and flexibility in dealing with the time series data produced through intra-individual sampling in isotopic analysis. One can use the function SCEM.R to implement this method.
Example of implementing the above methods for our data (provided as armenia-data.csv) can be found in Usage-Example.R. Other functions in this repository are used internally in the above-mentioned functions.
For any inquiries or questions related to this, please open an issue in this repository. You can also contact us at h.chazin@columbia.edu or sdeb@uchicago.edu.
Chazin, H., Deb, S., Falk, J., and Srinivasan, A. (2018) New Statistical Approaches to Intra‐individual Isotopic Analysis and Modelling of Birth Seasonality in Studies of Herd Animals. Archaeometry, https://doi.org/10.1111/arcm.12432.
Tornero, C., Bălăşescu, A., Ughetto-Monfrin, J., Voinea, V., Balasse, M., 2013. Seasonality and season of birth in early Eneolithic sheep from Cheia (Romania): methodological advances and implications for animal economy. Journal of Archaeological Science 40, 4039–4055. https://doi.org/10.1016/j.jas.2013.05.013