TendrilPerm: Tendril permutations

In Karpefors/Tendril: Compute and Display Tendril Plots

Tendril permutations

Description

Function to compute the permutations of one specified tendril, starting from a specific day. Permutations are simulated under the null hypothesis. Thus, on average, there will be an equal number of events on each treatment arm.

Usage

TendrilPerm(tendril, PermTerm, n.perm = 100, perm.from.day = 1,
  pi.low = 0.1, pi.high = 0.9)

Arguments

tendril	an object of class tendril as produced by Tendril()
PermTerm	the name of the type of event (tendril) to calculate permutations on
n.perm	the number of permutations. Default 100
perm.from.day	the starting day for the permutation calculations. Default 1
pi.low	percentile low value. Default 0.1
pi.high	percentile high value. Default 0.9

Details

Make permutation analysis to a specific type of event, as specified in PermTerm.

Value

The function return an object of class TendrilPerm containing all the input data and a dataframe of permutation results. Use:

data$perm.data

and

data$tendril.pi

and

data$tendril

to access the permutations, percentiles dataframes, and tendril data respectively

Examples

# Create tendril
tendril <- Tendril(mydata = TendrilData,
  rotations = Rotations,
  AEfreqThreshold = 9,
  Tag = "Comment",
  Treatments = c("placebo", "active"),
  Unique.Subject.Identifier = "subjid",
  Terms = "ae",
  Treat = "treatment",
  StartDay = "day",
  SubjList = SubjList,
  SubjList.subject = "subjid",
  SubjList.treatment = "treatment"
)

# Compute permutations
perm.data <- TendrilPerm(tendril = tendril,
  PermTerm="AE40",
  n.perm = 200,
  perm.from.day = 1)

# Plot results
plot(perm.data)
plot(perm.data, percentile = TRUE)

Karpefors/Tendril documentation built on June 12, 2022, 9:22 p.m.