Simulation Data & R scripts for: "Introducing recurrent events analyses to assess species interactions based on camera trap data: a comparison with time-to-first-event approaches"

Files descriptions:

All csv files refer to results from the different models (PAMM, AARs, Linear models, MRPPs) on each iteration of the simulation. One row being one iteration. 
"results_perfect_detection.csv" refers to the results from the first simulation part with all the observations.
"results_imperfect_detection.csv" refers to the results from the first simulation part with randomly thinned observations to mimick imperfect detection.

ID_run: identified of the iteration (N: number of sites, D_AB: duration of the effect of A on B, D_BA: duration of the effect of B on A, AB: effect of A on B, BA: effect of B on A, Se: seed number of the iteration).
PAMM30: p-value of the PAMM running on the 30-days survey.
PAMM7: p-value of the PAMM running on the 7-days survey.
AAR1: ratio value for the Avoidance-Attraction-Ratio calculating AB/BA.
AAR2: ratio value for the Avoidance-Attraction-Ratio calculating BAB/BB.
Harmsen_P: p-value from the linear model with interaction Species1*Species2 from Harmsen et al. (2009).
Niedballa_P: p-value from the linear model comparing AB to BA (Niedballa et al. 2021).
Karanth_permA: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species A (Karanth et al. 2017).
MurphyAB_permA: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021).    
MurphyBA_permA: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021).    
Karanth_permB: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species B (Karanth et al. 2017).
MurphyAB_permB: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021).    
MurphyBA_permB: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021).    
    

"results_int_dir_perf_det.csv" refers to the results from the second simulation part, with all the observations.
"results_int_dir_imperf_det.csv" refers to the results from the second simulation part, with randomly thinned observations to mimick imperfect detection.
ID_run: identified of the iteration (N: number of sites, D_AB: duration of the effect of A on B, D_BA: duration of the effect of B on A, AB: effect of A on B, BA: effect of B on A, Se: seed number of the iteration).
p_pamm7_AB: p-value of the PAMM running on the 7-days survey testing for the effect of A on B.
p_pamm7_AB: p-value of the PAMM running on the 7-days survey testing for the effect of B on A.
AAR1: ratio value for the Avoidance-Attraction-Ratio calculating AB/BA.
AAR2_BAB: ratio value for the Avoidance-Attraction-Ratio calculating BAB/BB.
AAR2_ABA: ratio value for the Avoidance-Attraction-Ratio calculating ABA/AA.
Harmsen_P: p-value from the linear model with interaction Species1*Species2 from Harmsen et al. (2009).
Niedballa_P: p-value from the linear model comparing AB to BA (Niedballa et al. 2021).
Karanth_permA: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species A (Karanth et al. 2017).
MurphyAB_permA: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021).    
MurphyBA_permA: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021).    
Karanth_permB: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species B (Karanth et al. 2017).
MurphyAB_permB: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021).    
MurphyBA_permB: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021).    
    

Scripts files description:
1_Functions: R script containing the functions:
    - MRPP from Karanth et al. (2017) adapted here for time efficiency.
    - MRPP from Murphy et al. (2021) adapted here for time efficiency.
    - Version of the ct_to_recurrent() function from the recurrent package adapted to process parallized on the simulation datasets.
    - The simulation() function used to simulate two species observations with reciprocal effect on each other.
2_Simulations: R script containing the parameters definitions for all iterations (for the two parts of the simulations), the simulation paralellization and the random thinning mimicking imperfect detection.
3_Approaches comparison: R script containing the fit of the different models tested on the simulated data.
3_1_Real data comparison: R script containing the fit of the different models tested on the real data example from Murphy et al. 2021.
4_Graphs: R script containing the code for plotting results from the simulation part and appendices.
5_1_Appendix - Check for similarity between codes for Karanth et al 2017 method: R script containing Karanth et al. (2017) and Murphy et al. (2021) codes lines and the adapted version for time-efficiency matter and a comparison to verify similarity of results.
5_2_Appendix - Multi-response procedure permutation difference: R script containing R code to test for difference of the MRPPs approaches according to the species on which permutation are done.