TendrilPerm {Tendril}

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)