ActExtendCosinor_long {ActCR}  R Documentation 
Extended cosinor model based on sigmoidally transformed cosine curve using antilogistic transformation.This function is a whole dataset
wrapper for ActExtendCosinor
.
ActExtendCosinor_long( count.data, window = 1, lower = c(0, 0, 1, 0, 3), upper = c(Inf, Inf, 1, Inf, 27) )
count.data 

window 
The calculation needs the window size of the data. E.g window = 1 means each epoch is in oneminute window. window size as an argument. 
lower 
A numeric vector of lower bounds on each of the five parameters (in the order of minimum, amplitude, alpha, beta, acrophase) for the NLS. If not given, the default lower bound for each parameter is set to 
upper 
A numeric vector of upper bounds on each of the five parameters (in the order of minimum, amplitude, alpha, beta, acrophase) for the NLS. If not given, the default lower bound for each parameter is set to 
A data.frame
with the following 5 columns
ID 
ID 
ndays 
number of days 
minimum 
Minimum value of the of the function. 
amp 
amplitude, a measure of half the extend of predictable variation within a cycle. This represents the highest activity one can achieve. 
alpha 
It determines whether the peaks of the curve are wider than the troughs: when alpha is small, the troughs are narrow and the peaks are wide; when alpha is large, the troughs are wide and the peaks are narrow. 
beta 
It dertermines whether the transformed function rises and falls more steeply than the cosine curve: large values of beta produce curves that are nearly square waves. 
acrotime 
acrophase is the time of day of the peak in the unit of the time (hours) 
F_pseudo 
Measure the improvement of the fit obtained by the nonlinear estimation of the transformed cosine model 
UpMesor 
Time of day of switch from low to high activity. Represents the timing of the rest activity rhythm. Lower (earlier) values indicate increase in activity earlier in the day and suggest a more advanced circadian phase. 
DownMesor 
Time of day of switch from high to low activity. Represents the timing of the restactivity rhythm. Lower (earlier) values indicate decline in activity earlier in the day, suggesting a more advanced circadian phase. 
MESOR 
A measure analogous to the MESOR of the cosine model (or half the deflection of the curve) can be obtained from mes=min+amp/2. However, it goes through the middle of the peak, and is therefore not equal to the MESOR of the cosine model, which is the mean of the data. 
counts_1 = example_activity_data$count[c(1:12),] cos_all_1 = ActExtendCosinor_long(count.data = counts_1, window = 1) counts_10 = cbind(counts_1[,1:2], as.data.frame(t(apply(counts_1[,c(1:2)], 1, FUN = bin_data, window = 10, method = "average")))) cos_all_10 = ActExtendCosinor_long(count.data = counts_10, window = 10)