Example code used in Mapping the physiological changes in sleep regulation across infancy and young childhood, Webb et al. (2024) PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1012541.
Sleep_Model_PRF.m is the main file, which implements the combined Phillips and Robinson-Forger model of the sleep/wake switch, sleep homeostatic process, and circadian pacemaker.
Sleep_Model_PRF.m defines the model parameter values p, then calls the model via Run_prf_2023.m for a set time T. Run_prf_2023.m runs the model for 4 weeks as a warm up to remove any transients, the using the last model state as the initial value solves for time T, and extracts the last 2 weeks of the model output. The model is called via phillips_forger_model_2023.m, which also calls light_func.m and sigmoid.m.
The Matlab function Get_sleep_results_2023.m calculates a number of sleep behaviour summary measurements, including the probability of being asleep per 30 minute window for the last 7 days of the model produced time series.
The R function cost_func_mtrx in cost_func_mtrx.R calculates the cost function value (Equation 13 of Webb et al. (2024)) for provided model produced sleep probabilities with a single set of sleep probability data.
The sleep-wake time series from the four datasets (Figure 1 Webb et al (2024)) are provided in data/sleep-wake-data, and the sleep probabilities used for the cost function and model fitting are provided in data/sleep-prob-data.
All four datasets are in public domain: Dataset 1 (Github repository https://github.com/jiuguangw/Agenoria, commit be11a8e on 30/12/2021, used for academic purposes under CC BY-NC-SA 4.0), Dataset 2 (Github repository https://github.com/jitney86/Baby-data-viz, commit d92043f on 11/8/2017, used for academic purposes under MIT license), Dataset 3 (Infant #01 in Figure 1 of Jenni et al. (2006) Infant Behavior and Development, 29(2):143-52), and Dataset 4 (Figure 3 of McGraw et al. (1999) Sleep 22:303-310).