In this repository, we develop a novel break-point analysis tool for population time series data, building on the methods described in Bahlai et al 2015, Ecological Applications. The tool uses the Ricker model as the data-generating process for a dynamic rule, iterates through all break point combinations, and uses information-theoretic decision tools (i.e. Akaike's Information Criteron) to determine best fits. In this repository we develop the tool, simulate data under a variety of conditions to demonstrate the tool, and apply the tool to two case studies: overwintering populations of monarch butterflies and invasions of multicolored Asian ladybeetle. This tool is scripted entirely in R.
dynamic_shift_detector.R - contains functions to detect regime shifts in population time series. The function DSdetector() takes raw time series data and generates a complete report on fits, best fits, break points, and regression parameters for models with best fits
monarch_example.R - applies the dynamic shift detector analysis to monarch overwintering data from Mexico
plot_monarch_figures.R - plots output from monarch example, places outputs in figs folder
harmonia_example.R - applies the dynamic shift detector analysis to harmonia ladybeetle population data from Kellogg Biological Station. Includes data cleaning/manipulation code after Bahlai et al 2015.
plot_harmona_figures.R - plots output from harmonia example, places outputs in figs folder
simulations.R- a set of functions that creates time series data using secified parameters, and then a set of funtions to test if the parameters input match the ones detected by the dynamic shift detector, and the code that creates simulations under a variety of conditions, runs it through the comparison functions, and tallies the outputs, outputs a CSV file to the 'simresults' folder
plot_simulation_results.R - takes the simulation outputs and creates plots based on varying one input at a time to see the DSdetector's performance under differing conditions- outputs figures as PDF vector graphis to the 'figs' folder
casestudydata folder contains data for Harmonia case study. Monarch study data are proprietary
simresults folder contains simpulation output CSVs, in sets of one iteration of each case per file
figs folder PDF versions of all figs produced be scripts are held in this folder
tests folder contains a version of the RSdetector code and test data used in development
writing folder contains bits of writing, abstracts, etc, relevant to presentations and publications on this project
This work is licensed under a Creative Commons Attribution 4.0 International License.
