correlation_tree: Correlation tree

In abichat/correlationtree: Functions about correlation tree

Description

Compute the correlation tree from an abundance table.

Usage

correlation_tree(
  table,
  col = 1,
  matrix = FALSE,
  remove = TRUE,
  fill = FALSE,
  transformation = "1-x",
  ...
)

Arguments

table	a dataframe or a matrix.
col	integer giving the column to be passed as row names.
matrix	logical. Is table a matrix? Default to FALSE.
remove	logical. If TRUE (default), shared zeros between species are removed for the computation of the pairwise correlation coefficients.
fill	logical. If TRUE, NA are set to 0. Default to FALSE.
transformation	function or character. Transformation to apply to each element of the matrix.
...	arguments to be passed to cor such as method (see details).

Details

For method: one of "pearson" (default), "kendall", or "spearman".

Value

correlation_tree returns a "phylo" object.

Examples

df <- data.frame(Clade = letters[1:4],
                 v = c(3, 0, 0, 3),
                 w = c(4, 5, 7, 0),
                 x = c(8, 5, 5, 0),
                 y = c(1, 8, 0, 0),
                 z = c(3, 5, 2, 2))
plot(correlation_tree(df, method = "spearman"))

abichat/correlationtree documentation built on March 11, 2020, 3:55 p.m.