Contains all code used to do analyse the case study data, run the simulation study and visualise the results.
The main scripts of interest are:
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simulate_1000_data_sets.R
Simulates data that can be used for simulation studies. It uses simulate_data_Rcpp.R, and the data was used for the simulation study.
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ascrRcpp_build_script.R
This script creates the package ascrRcpp, which is an custom R package with compiled Rcpp code to fit the ASCR models.
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varying_fits_to_real_data.R
This script fits 35 models
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bootstrap_real_data.R
This scripts creates 999 bootstrapped data sets, and fits the best model to all.
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create_grid_Albers.R
Create a spatial grid that is used for the fitting, based on the Albers projection.
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fitting_to_simulated_data.R
Fits models to simulated data for the simlation study.
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hidden_functions.R
Contains some hidden functions required for other scripts.
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nll.R
Derives the negative log likelihood using ascrRcpp.
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main_Rcpp.R
Fits an ASCR model to data using the ascrRcpp package.
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process_data_august 2020.R
Processes the raw data.
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fits_1_35_nlminb_n=443.Rdata
An Rdata file containing the results of 35 ASCR models with varying density specifications.
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detections_31-08-2010_successful_loc.csv
A matrix of detections for every included call for every detector that was involved with the detection, where TRUE indicates a positive detection;
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received_levels_31-08-2010_successful_loc.csv
A matrix of received sound levels for every included call for every detector that was involved with the detection, and NA otherwise;
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bearings_31-08-2010_successful_loc.csv
A matrix of bearings for every included call for every detector that was involved with the detection, and -1 otherwise;
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DASARs.txt
Some information on the DASARs.