circacompare_mixed: circacompare_mixed
In circacompare: Analyses of Circadian Data

Description Usage Arguments Value Examples

View source: R/circacompare_mixed.R

circacompare_mixed is similar to circacompare but allows for some simple, user-specified random-effects on the rhythmic parameters of choice.

circacompare_mixed(
  x,
  col_time,
  col_group,
  col_outcome,
  col_id,
  randomeffects = c(),
  period = 24,
  alpha_threshold = 0.05,
  nlme_control = list(),
  nlme_method = "REML",
  verbose = FALSE,
  timeout_n = 10000,
  control = list()
)

`x`	`data.frame`. This is the data.frame which contains the rhythmic data for two groups in a tidy format.
`col_time`	The name of the column within the data.frame, `x`, which contains time in hours at which the data were collected.
`col_group`	The name of the column within the data.frame, `x`, which contains the grouping variable. This should only have two levels.
`col_outcome`	The name of the column within the data.frame, `x`, which contains outcome measure of interest.
`col_id`	The name of the column within the data.frame, `x`, which contains the identifying values for the random effect, such as `subject_id`.
`randomeffects`	which rhythmic parameters to allow random effects. The default is to include no rhythmic parameters.
`period`	The period of the rhythm. For circadian rhythms, leave this as the default value, `24`.
`alpha_threshold`	The level of alpha for which the presence of rhythmicity is considered. Default is to `0.05`.
`nlme_control`	A list of control values for the estimation algorithm to replace the default values returned by the function nlme::nlmeControl. Defaults to an empty list.
`nlme_method`	A character string. If "REML" the model is fit by maximizing the restricted log-likelihood. If "ML" the log-likelihood is maximized. Defaults to "REML".
`verbose`	An optional logical value. If `TRUE` information on the evolution of the iterative algorithm is printed. Default is `FALSE`.
`timeout_n`	The upper limit for the model fitting attempts. Default is `10000`.
`control`	`list`. Used to control the parameterization of the model.

list

# Generate some data with within-id correlation for phase-shift (phi1)
set.seed(99)
phi1_in <- 3.15

mixed_data <- function(n){
  counter <- 1
  for(i in 1:n){
    x <- make_data(k1=0, alpha1=0, phi1=rnorm(1, phi1_in, 0.5), hours=72, noise_sd = 1)
    x$id <- counter
    counter <- counter + 1
    if(i==1){res <- x}else{res <- rbind(res, x)}
  }
  return(res)
}
df <- mixed_data(20)
out <- circacompare_mixed(
  x = df,
  col_time = "time",
  col_group = "group",
  col_outcome = "measure",
  col_id = "id",
  control=list(grouped_params=c("phi"), random_params=c("phi1"))
)
out