Lineups

A repository demonstrating the use of lineups for goodness-of-fit testing of animal movement models, including integrated step-selection analyses (ISSAs) and hidden Markov models (HMMs).

Citation for associated paper

Fieberg, J., Signer, J. and S. Freeman. 2023. Evaluating goodness-of-fit of animal movement models using lineups. bioRxiv, doi: https://doi.org/10.1101/2023.09.26.559591.



Directory Structure

├── R                                      # directory containing R code used to generate the models and plots in the associated paper
│   ├── issa_fisher.R                      # code for generating lineups plots from an ISSA
│   ├── issa_fisher.html                   # html version of above file
│   ├── hmm_fisher.R                       # functions for generating lineups plots from an ISSA
│   ├── hmm_fisher.html                    # html version of above file
│   ├── hmm_fisher_script.R                # script that calls functions in hmm_fisher.R
│   └── hmm_fisher_script.html             # html version of above file
├── README.md
├── data
│   ├── fisher_track.rds                   # Formatted fisher data used in ISSA and HMM fitting
│   ├── models
│   │   └── hmm                            # directory containing fitted HMMs
│   │       ├── individual_model_1072.rds  # model fit to single individual's data
│   │       ├── pop_test_1016.rds          # remaining files fit to pooled data, where test data is with pop_test_<test_data>.rds
│   │       ├── pop_test_1072.rds
│   │       └── pop_test_1078.rds
│   └── simulations                        # directory containing data simulated from models
│       ├── issa                           # data simulated from ISSAs
│       │   └── pop_test_1078.rds
│       ├── joined_hmm_issa.rds            # data from here down simulated from HMM models
│       ├── pop_test_1016.rds
│       ├── pop_test_1072.rds
│       └── pop_test_1078.rds
├── figures
│   ├── hmm                                # directory of figures generated from an HMM
│   ├── issf                               # directory of figures generated from an ISSA
│   ├── lineup_correlation_joint.png       # correlation of step lengths & turn angles of simulated trajectories from an HMM and an ISSA
│   ├── lineup_correlation_joint_real.png  # same as above but including the observed data
│   ├── sl_hist.png                        # observed step length histograms of our three fishers
│   ├── sl_ta_correlation.png              # correlation of step lengths & turn angles of observed data
│   ├── ta_hist.png                        # obeserved turn angles histograms of our three fishers
│   └── trajectories.png                   # observed trajectories of our three fishers
└── vignettes                              # directory of vignettes and their related data 
    ├── data
    │   ├── models
    │   └── simulations
    ├── figures
    │   └── hmm_lineup_schema.png
    ├── hmm.R                              # vignette demonstrating lineup-based cross-validation of HMMs
    ├── hmm.html                           # html version of above file
    ├── issa.R                             # vignette demonstrating using the lineup protocol with ISSAs 
    └── issa.html                          # html version of above file