permudist: performs permutation testing for group differences.

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

performs permutation testing for group differences.

Description

This function compares the distance between two groupmeans to the distances obtained by random assignment of observations to this groups.

Usage

permudist(
  data,
  groups,
  rounds = 1000,
  which = NULL,
  p.adjust.method = "none",
  median = FALSE
)

Arguments

data	array or matrix containing data
groups	factors determining grouping.
rounds	number of permutations
which	integer (optional): in case the factor levels are > 2 this determins which factorlevels to use
p.adjust.method	method to adjust p-values for multiple comparisons see p.adjust.methods for options.
median	logical: if TRUE, comparison will be median instead of mean.

Value

dist	distance matrix with distances between actual group means
p.adjust.method	method used for p-value adjustion
p.value	distance matrix containing pairwise p-values obtained by comparing the actual distance to randomly acquired distances

Examples

data(boneData)
proc <- procSym(boneLM)
groups <- name2factor(boneLM,which=3)
perm <- permudist(proc$PCscores[,1:10], groups=groups, rounds=10000)

## now we concentrate only on sex dimorphism between Europeans
groups <- name2factor(boneLM,which=3:4)
levels(groups)
perm1 <- permudist(proc$PCscores, groups=groups,which=3:4, rounds=10000)

Morpho documentation built on Feb. 16, 2023, 10:51 p.m.