optpart (version 3.0-3)

refine: Refining a Classification by Re-Assigning Memberships

Description

Refine allows you to re-assign specific elements of a classification from one class or cluster to another. In the default case, you simply interactively enter sample IDs and give a new cluster assignment. For PCO and NMDS ordinations, you do the assignments with a mouse.

Usage

# S3 method for default
refine(comm,clustering,…)
# S3 method for dsvord
refine(x,clustering,ax=1,ay=2,…)

Arguments

comm

a community data.frame

x

an ordination of class ‘dsvord’

clustering

a clustering identity or membership vector

ax

the X axis of the ordination

ay

the Y axis of the ordination

…

ancillary arguments to allow differing numbers of arguments

Value

a list object of class ‘clustering’ with one component.

clustering

a numeric vector giving the cluster assignment for each sample

References

http://ecology.msu.montana.edu/labdsv/R

Examples

# NOT RUN {
data(shoshveg)
# }
# NOT RUN {
dis.bc <- dsvdis(shoshveg,'bray')
# }
# NOT RUN {
opt.5 <- optpart(5,dis.bc)
# }
# NOT RUN {
nmds.bc <- nmds(dis.bc)
# }
# NOT RUN {
plot(nmds.bc)
# }
# NOT RUN {
res <- refine(nmds.bc,opt.5)
# }