Survival and Habitat Quality (SHQ) analysis data and code

This archive contains the source code and data required for reproducing the analyses and figures from the manuscript "A lifetime of experiences: Modeling habitat quality through cumulative effects on individual survival", accepted for publication by the journal Methods in Ecology and Evolution on 2025-04-07. Code and data are included to:

Perform SHQ on simulated dataThe code to simulate data for SHQ is in R/Simulate data.R. The model code to run SHQ is in models/SHQ.txt. The MCMC results from running SHQ on simulated datasets with and without missing values are in the results folder under "SHQsim_withNAs" and "SHQsim_noNAs". These results files can be read into R using the Plotting simulations.R script, which then has code for creating Figure 2. 

Compare known fate vs. SHQCode to simulate data for known fate survival analysis is in R/Simulate data.R. The model code to run known fate survival analysis is in models/Known_fate.txt. The MCMC results from running SHQ and known fate survival analysis on the same simulated dataset are saved as .RDS files in the folder "KFvsSHQ" in the results folder. These results files can be read into R using the Plotting simulations.R script, which then has code for creating Figure 3. 

Complete pronghorn case studyThe GPS collar data for the pronghorn case study are formatted into encounter histories (data/eh.rds). The encounter histories record each day that the pronghorn was alive (1) and dead (0). Fate data are included are formatted to record each animalID and cause of mortality (for each collared (data/fates.rds). Covariate data include daily covariate values for each animalID (data/covariatedata.rds). The code to format encounter histories, fate, and encounter histories is found in R/Pronghorn case study.R. "R/Pronghorn case study.R" has code to prepare data for and run the SHQ analysis. This script also includes the code to create Figures 4, 5, and 6 from those results.