simcosinor

Simulations for the cosinor model.

Lazy install

virtualenv -p python3.7 python37env
source python37env/bin/activate
git clone https://github.com/trislett/simcosinor.git
cd simcosinor
pip install .
cd ..

Some examples

Just run 10000 simulations using the defaults:

simcosinor -e threesubs_modality1

Run the simulations using 24 random times points only.

simcosinor -e threesubs_modality1 -rand -ns 24

Run the simulations with eveningly dispursed time-points, but limited from 11:30am until 11:30pm.

simcosinor -e threesubs_modality1 -rand -ns 72 -sr 11.5 23.5 -er

Run the simulations with randomly dispursed time-points.

simcosinor -e threesubs_modality1 -rand -ns 72 -sr 0 24

Plotting examples

Run simulation and generate plots of the right insula gyrus

simcosinor -e threesubs_modality1 -rand -ps -pp -pw 24 -ppm -roi rh.R_Ig

Console output:

Running 10000 simulations...
ROI = rh.R_Ig
[Metric]		[Mean] [Standard Deviation]
R2		=	0.3062 [0.0832]
Acro24[24.0]	=	16.8039 [0.7275]
-logP		=	12.8674 [4.2322]

Simulation plot:

Residual plot of the cosinor model (used to estimate the error):

Periodogram:

Sliding window (size = 24):

Cosinor plot with permutation testing: