Create a ggplot summary of gap statistic results
Create a ggplot summary of gap statistic results
plot_clusgap(clusgap, title = "Gap Statistic results")
clusgap |
(Required).
An object of S3 class |
title |
(Optional). Character string.
The main title for the graphic.
Default is |
A ggplot plot object.
The rendered graphic should be a plot of the gap statistic score
versus values for k, the number of clusters.
# Load and process data
data("soilrep")
soilr = rarefy_even_depth(soilrep, rngseed=888)
print(soilr)
sample_variables(soilr)
# Ordination
sord = ordinate(soilr, "DCA")
# Gap Statistic
gs = gapstat_ord(sord, axes=1:4, verbose=FALSE)
# Evaluate results with plots, etc.
plot_scree(sord)
plot_ordination(soilr, sord, color="Treatment")
plot_clusgap(gs)
print(gs, method="Tibs2001SEmax")
# Non-ordination example, use cluster::clusGap function directly
library("cluster")
pam1 = function(x, k){list(cluster = pam(x, k, cluster.only=TRUE))}
gs.pam.RU = clusGap(ruspini, FUN = pam1, K.max = 8, B = 60)
gs.pam.RU
plot(gs.pam.RU, main = "Gap statistic for the 'ruspini' data")
mtext("k = 4 is best .. and k = 5 pretty close")
plot_clusgap(gs.pam.RU)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.