jjackson-eco/timeline_demonstration

a sequence of signals preceding population collapse

Analysis for

Multivariate signals of population collapse in a high-throughput ecological experiment

Cerini, F., Jackson, J., Childs, D.Z., & Clements, C.F.

2023-11-20

Repository created by John Jackson and Francesco Cerini

---

This directory contains scripts and analysis data for our work on an empirical demonstration of a sequence of signals preceding a population collapse in the ciliate Paramecium caudatum. For the manuscript please see the Authorea entry. Package version info for this analysis is given below.

Analysis scripts can be found in the code/ sub-repository, manuscript figures and output in the output/ sub-repository, and analysis data in the data/ sub-repository.

Scripts are labeled A and B in order of the analysis, and are as follows:

1. A_data_cleaning.R - Data cleaning, seasonal decomposition and supplementary figures.
2. B_timeline_demonstration_fullanalysis.R - Full analysis for the study, including pre-analysis (autocorrelation and basis dimension selection), modelling and predicitions using GAM for the timeseries, EWS analysis, and figure plotting.

System Information and Package Versions

Click here to expand

R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.9

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggpubr_0.6.0     patchwork_1.1.2  MASS_7.3-60      mgcv_1.9-0       nlme_3.1-162     EWSmethods_1.1.2 lubridate_1.9.2  forcats_1.0.0   
 [9] stringr_1.5.0    dplyr_1.1.2      purrr_1.0.1      readr_2.1.4      tidyr_1.3.0      tibble_3.2.1     ggplot2_3.4.2    tidyverse_2.0.0 

loaded via a namespace (and not attached):
 [1] gtable_0.3.3       rstatix_0.7.2      lattice_0.21-8     tzdb_0.4.0         quadprog_1.5-8     vctrs_0.6.3        tools_4.3.1       
 [8] generics_0.1.3     curl_5.0.2         parallel_4.3.1     fansi_1.0.4        xts_0.13.1         pkgconfig_2.0.3    Matrix_1.6-1.1    
[15] lifecycle_1.0.3    compiler_4.3.1     munsell_0.5.0      codetools_0.2-19   carData_3.0-5      pillar_1.9.0       car_3.1-2         
[22] seasonal_1.9.0     iterators_1.0.14   abind_1.4-5        foreach_1.5.2      fracdiff_1.5-2     tidyselect_1.2.0   stringi_1.7.12    
[29] tseries_0.10-54    splines_4.3.1      grid_4.3.1         colorspace_2.1-0   cli_3.6.1          magrittr_2.0.3     utf8_1.2.3        
[36] broom_1.0.5        withr_2.5.0        scales_1.2.1       backports_1.4.1    forecast_8.21      x13binary_1.1.57-3 timechange_0.2.0  
[43] TTR_0.24.3         infotheo_1.2.0.1   quantmod_0.4.24    nnet_7.3-19        timeDate_4022.108  ggsignif_0.6.4     zoo_1.8-12        
[50] hms_1.1.3          urca_1.3-3         lmtest_0.9-40      rlang_1.1.1        Rcpp_1.0.11        glue_1.6.2         rstudioapi_0.15.0 
[57] R6_2.5.1