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peRiodiCS

Code for periodic versions of cubic splines and restricted cubic splines. The functions transform a numeric (time) variable x into a new basis, to model with either a periodic variant of cubic splines or periodic restricted cubic spline.

Install from GitHub with:

library(devtools)
install_github("crtahlin/peRiodiCS")

Example models for different variants:

# load example data; see help("viral_east_mediteranean")
data("viral_east_mediteranean")

# calculate location of knots to use
Knots <- Hmisc::rcspline.eval(x = viral_east_mediteranean$EpiWeek,
                              nk = 5, knots.only = TRUE)
                       
### RCS - restricted cubic splines (non-periodic, just for reference) #########
# model viral infections vs weeks
model_rcs <- glm(RSV ~ Hmisc::rcspline.eval(EpiWeek, inclx = TRUE, knots = Knots), data = viral_east_mediteranean)

# plot model (with many points, to make it smooth)
plot_per_mod(Model = model_rcs, XvarName = "EpiWeek", Smooth = TRUE)

### periodic RCS ##############################################################
# model viral infections vs weeks
model_rcs_per <- glm(RSV ~ rcs_per(EpiWeek, knots = Knots), data = viral_east_mediteranean)

# plot model (with many points, to make it smooth)
plot_per_mod(Model = model_rcs_per, XvarName = "EpiWeek", Smooth = TRUE)
                                  
### periodic CS (cubic spline) ###############################################
# model viral infections vs weeks
model_cs_per <- glm(RSV ~ cs_per(EpiWeek, knots = Knots), data = viral_east_mediteranean)

# plot model (with many points, to make it smooth)
plot_per_mod(Model = model_cs_per, XvarName = "EpiWeek", Smooth = TRUE)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.