habitat_suitability_curves_fda's Introduction

A new look at habitat suitability curves through FDA 👓

A scientific research by Jeremie Boudreault, André St-Hilaire, Normand Bergeron and Fateh Chebana
This project is part of my master studies at Institut National de la Recherche Scientifique
All scripts and data are made freely available here under the Creative Common License
Any questions should be sent to Jeremie.Boudreault [at] ete.inrs [dot] ca

Data

Data consists of a field survey that have been conducted during summer 2017 on the Sainte-Marguerite River (SMR) and Petite-Cascapedia River (PCR) :

data/field-data/* : contains the two raw xlsx files filled after each day of field work.
data/gps/* : locations of the studied sites for the two rivers.

R scripts

Scripts are all from Jeremie Boudreault. They make the use of the R package FDboost for fitting functional regression models (FRM) :

s01_clean_field_data.R : clean the field data spreadsheets and produced cleaned datasets.
s02_compute_salmon_numbers.R: convert measured salmon fork-lengths to number of fry and parr.
s03_select_study_case.R: select optimal data subset for this project.
s04_map_studied_sites.R: map sites studied in this project.
s05_generate_fd_curves.R: generate (functional) curves of availability and selection/preference.
s06_prepare_data_modelling.R: prepare data prior to fit function regression models (FRM).
s07_fit_function_models.R: fit FRMs to curves using a parallelized k-fold cross-validation.
s08_define_optimal_stopping.R: choose optimal early stopping parameter.
s09_compute_coef_bootstrap.R: compute standard-error of FRM coefficients using bootstrap.
s10_plot_frm_coefficients.R: plots intercept and coefficients surfaces from fitted FRM.
s11_build_classical_models.R: build classical local and regional models of HSC.
s12_assess_models_performance.R: calculate some goodness-of-fit metrics for the fitted models.