octopucs {octopucs} | R Documentation |
The global function of the "octopucs" package is to estimate support for hierarchical clusters throughout the dendrogram's topology, considering their repeatability, integrity, and contamination based on bootstrapping procedures.
octopucs(data, n=NULL, prop=NULL, resample = TRUE, distance =NULL,
method=NULL, orientation=NULL, disp = NULL, lab.pos=NULL,
sep.lab=NULL, xlim=NULL, ylim=NULL, verbose=NULL)
data |
A matrix whose rows (sites/conditions) will be grouped based on the columns (species/elements). |
n |
The number of bootstrap repetitions. |
prop |
Proportion of information used in the bootstrapping procedures. When matrices contain more than 18 columns, it refers to (i) the proportion of columns used in every run to produce a new grouping array when "resample=TRUE" and (ii) the number of cells in the body of the matrix (1–prop; e.g., 1–0.8=0.2) that will be replaced with column averages when "resample=FALSE". When matrices contain less than 18 columns, the procedure with "resample=FALSE" will be forced. In such a scenario, "prop" corresponds to the number of cells in the body of the matrix (1–prop; e.g., 1–0.8=0.2) that will be replaced in the bootstrapping procedures. |
resample |
When TRUE, "octopucs" will select random subsets of columns in every bootstrap run to produce a new grouping array. When FALSE, "octopucs" will replace cells in the body of the matrix with column averages instead of entire columns (see description for "prop" for further details). |
distance |
Distance method to be used (default="bray"). Options include those of the function "vegdist" ("vegan"): "manhattan", "euclidean", "canberra", "bray", "kulczynski", "gower", "morisita", "horn", "mountford", "jaccard", "raup", "binomial", "chao", "altGower", "cao" and "mahalanobis", as well as those referred in Koleff et al. (2003), available either by name or number: 1 or "w", 2 or "-1", 3 or "c", 4 or "wb", 5 or "r", 6 or "I", 7 or "e", 8 or "t", 9 or "me", 10 or "j", 11 or "sor", 12 or "m", 13 or "-2", 14 or "co", 15 or "cc", 16 or "g", 17 or "-3", 18 or "1", 19 or "", 20 or "hk", 21 or "rlb", 22 or "sim", 23 or "gl", 24 or "z". For open distance metrics (not restricted to zero-one ranges), the axis is re-scaled to cover a zero-one range. If so, the axis will be labeled a "Similarity (rescaled)"; if no re-scaling is necessary, the label will appear as "Similarity". |
method |
Agglomerative procedure for hierarchical clustering, including: "average" (=UPGMA), "ward.D", "ward.D2", "single", "complete", "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC). |
orientation |
Orientation of the plot (default="r": right; metric in the x-axis is similarity). "l" = left-wise orientation (metric in the x-axis is dissimilarity). "d" = down-wise orientation (metric in the y-axis is dissimilarity). |
disp |
Result display in the dendrogram (default="sig"; only supported nodes will populated with given results). "all" = all nodes will be populated with support metrics, with significantly supported nodes in blue/red and non-significantly supported nodes in black. |
lab.pos |
This argument modifies the position of the labels relative to the tips of the dendrogram (sites/conditions). |
sep.lab |
This argument modifies the position of supporting values from the nodes and lines in the dendrogram. |
xlim |
Limits of the x-axis. |
ylim |
Limits of the y-axis. |
verbose |
TRUE = display all relevant setup values used in the analysis. FALSE = display only the dendrogram with marked significantly grouped clusters. |
"octopucs" generates a list object that contains:
$gcluster |
hclust output of the generalized clustered dendrogram. |
$support |
Table with the support value for every group and subgroup across the topology of the generalized clustered dendrogram. |
$grps |
List with the memberships of every group and subgroup in the topology. |
Roger Guevara (roger.guevara@inecol.mx) & Ian MacGregor-Fors (ian.macgregor@helsinki.fi)
Koleff, P., Gaston, K.J., Lennon, J. J. 2003. Measuring beta diversity for presence-absence data. Journal of Animal Ecology 71:367. https://doi.org/10.1046/j.1365-2656.2003.00710.x
data(dune)
octopucs(dune, n=100, prop=0.8,
resample=TRUE,distance="bray",
method="average", disp = "sig",
verbose=TRUE)