permuvec: perfom permutation testing on angles and distances between...

In zarquon42b/Morpho: Calculations and Visualisations Related to Geometric Morphometrics

perfom permutation testing on angles and distances between subgroups of two major groups.

Description

perform permutation test on length and angle of the vectors connecting the subgroup means of two groups: e.g. compare if length and angle between sex related differences in two populations differ significantly.

Usage

permuvec(
  data,
  groups,
  subgroups = NULL,
  rounds = 9999,
  scale = TRUE,
  tol = 1e-10,
  mc.cores = parallel::detectCores()
)

Arguments

data	array or matrix containing data.
groups	factors of firs two grouping variables.
subgroups	factors of the subgrouping.
rounds	number of requested permutation rounds
scale	if TRUE: data will be scaled by pooled within group covarivance matrix. Otherwise Euclidean distance will be used for calculating distances.
tol	threshold for inverting covariance matrix.
mc.cores	integer: determines how many cores to use for the computation. The default is autodetect. But in case, it doesn't work as expected cores can be set manually.Parallel processing is disabled on Windows due to occasional errors.

Details

This function calculates means of all four subgroups and compares the residual vectors of the major grouping variables by angle and distance.

Value

angle	angle between the vectors of the subgroups means
dist	distances between subgroups
meanvec	matrix containing the means of all four subgroups
permutangles	vector containing angles (in radians) from random permutation
permudists	vector containing distances from random permutation
p.angle	p-value of angle between residual vectors
p.dist	p-value of length difference between residual vectors
subdist	length of residual vectors connecting the subgroups

means.

Examples

data(boneData)
proc <- procSym(boneLM)
pop <- name2factor(boneLM,which=3)
sex <- name2factor(boneLM,which=4)
## use non scaled distances by setting \code{scale = FALSE}
## and only use first 10 PCs
perm <- permuvec(proc$PCscores[,1:10], groups=pop, subgroups=sex,
                 scale=FALSE, rounds=100, mc.cores=2)


## visualize if the amount of sexual dimorphism differs between
# (lenghts of vectors connecting population specific sex's averages)
# differs between European and Chines
hist(perm$permudist, xlim=c(0,0.1),main="measured vs. random distances",
     xlab="distances")
points(perm$dist,10,col=2,pch=19)#actual distance
text(perm$dist,15,label=paste("actual distance\n
     (p=",perm$p.dist,")"))
## not significant!!

## visualize if the direction of sexual dimorphism
# (angle between vectors connecting population specific sex's averages)
# differs between European and Chines
hist(perm$permutangles, main="measured vs. random angles",
     xlab="angles")
points(perm$angle,10,col=2,pch=19)#actual distance
text(perm$angle,15,label=paste("actual distance\n
    (p=",perm$p.angle,")"))
## also non-significant

zarquon42b/Morpho documentation built on Jan. 28, 2024, 2:11 p.m.