Commit ac82f7bb authored by sonitaR's avatar sonitaR
Browse files

final Monday codes

parent a23ecf8b
......@@ -97,7 +97,6 @@ plot(h.clust.sim)
h.clust.com <- hclust(d, method = "complete")
plot(h.clust.com)
# (5) CHOOSING AND PLOTTING THE BEST DENDROGRAM AND INTERPRETING IT
# Load necessary packages
require(cluster)
......@@ -117,6 +116,7 @@ complete.coph <- cophenetic(h.clust.com)
cor(d, complete.coph)
# average
average.coph <- cophenetic(h.clust.av)
cor(d, average.coph)
......@@ -344,21 +344,23 @@ heatmap(as.matrix(env.de), Rowv=dend, symm=TRUE, margin=c(3,3))
# (6) INTERPRET. How to find what is different in one group from the others?
# USe the vegan function "tabasco"
tabasco(env1, ordclust)
tabasco(env1, ordclust, scale = "row")
# THE END ################################################################################
##########################################################################################
# Report tips
##########################################################################################
# - Report in the methods the type of clustering analysis used, the algorythm used
# to compute the association coefficients, the clustering method used,
# - Describe in METHODS:
# - What were the aims of your clustering analysis
# - The type of clustering analysis used, the algorythm used
# to compute the association coefficients, the branch linkage method used,
# and the strategy used to identify the number of significant clusters identified
# - Describe in RESULTS
# Whehter there is any grouping of the sites apparent according to their community
# - Describe in RESULTS:
# Whether there is any grouping of the sites apparent according to their community
# structure.
# - Whehter there is any grouping of the sites apparent according to their environmental
# - Whether there is any grouping of the sites apparent according to their environmental
# characteristics.
# - What species and common environemental characteristics appear to be separating the
# - What species and common environmental characteristics appear to be separating the
# groups?
##########################################################################################
......
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