Using state space models to understand trait evolution in fossil lineages

The main script file to run all the analyses (and create figures) in the linked publication is "Theriot SSM analysis - Zenodo.R" This script calls directly another R script file that has a couple of functions that it needs: "needed functions - Zenodo.R" In addition, the main script file reads the following data files: inso_June.txt - June solar insolation in W/m^2 at Yellowstone Lake for the last 16 Kyr Theriot2006_PinusContortusPollenData.csv - relative abundance of Pinus contortus over the past 13.6 Kyr Theriot2006_spines.txt - data on spine counts from Theriot et al. 2006 To run the analyses, place all the files in the same directory, make that the working directory in R, and then source the main script file ("Theriot SSM analysis - Zenodo.R"). That script file will read the other data and scripts as needed. Reference Theriot, E. C., S. C. Fritz, C. Whitlock, and D. J. Conley. 2006. Late Quaternary rapid morphological evolution of an endemic diatom in Yellowstone Lake, Wyoming. Paleobiology 32(1):38-54.