Pathogen-induced alterations in fine-scale movement behaviour predict impaired reproductive success

This R-Project contains the following code files (in folder R):

01_movement_data_cleaning: Code to clean the raw ATLAS tracking data

02_nestbox_data_cleaning: Code to clean nest box control sheets

03_pathogen_data_cleaning: Code to clean the laboratory results for blood parasites PCRs

04_ctmm_models: Code to prepare data, applying continuous time movement models (incl. model selection) on movement data. Moreover, track reconstruction is performed

05_Neural_Network: Code to perform Neural Networks for classification of behavioural states

06_behavioural classification_analyses: Code to analyse Neural Network output

07_HSF: Code for Habitat Selection Functions (HSF)

08_ISSF: : Code for integrated Step Selection Functions (iSSF)

09_breeding_success_HSF: Multivariate model to perform on HSF estimates

10_breeding_success_ISSF: Multivariate model to perform on iSSF estimates

This repository contains the following data files (in folder data-raw) :

Nestboxes_2021: Nest box monitoring sheets 2021

Nestboxes_2022: Nest box monitoring sheets 2022

Nestboxes_2023: Nest box monitoring sheets 2023

Starlings_ring: Starling ringing data

pathogen_data: Blood parasite infection data