manateessm: R code for fitting the manatee counts state space model of Scolardi et al. (2024)

Contents

Files in this repository:

• manateessm_main.r: the main R script to follow. It loads all required libraries, compiles the C++ script, reads in the data .txt file, does all the required pre-processing, fits the Poisson-Gaussian state space model (SSM) used in Scolardi et al. (2024), and creates a few results figures.
• manateessm_data.txt: simulated data meant to mimic the Sarasota Bay Region data. It has 100 rows, representing time points at a monthly resolution, and includes the following variables as columns:
  • month: time stamp with format YYYY-MM
  • manatee_counts: the count response variable, with NAs for months without any survey
  • number_surveys: the number of aerial surveys run in each month
  • surveyor_experience: a dummy variable representing the experience of the surveyors, with coding 1 = experienced and 0 = less experienced
  • temperature: monthly maximum water temperature
• PoiGauAR1SSM.cpp: a C++ script defining the joint (negative log-) likelihood of the SSM
• this README.

Version History

This is manateessm version 0.1. This is the initial release on GitHub.

References

Scolardi, K. M., Aeberhard, W. H., and Wilkinson, K. A. (2024) Long-term aerial monitoring of Florida manatees, Trichechus manatus latirostris, in a diverse Gulf Coast environment. Submitted