correlationTest {dowser}R Documentation

Run date randomization test for temporal signal on a set of trees.

Description

correlationTest performs root-to-tip regression date randomization test

Usage

correlationTest(
  clones,
  permutations = 1000,
  minlength = 0.001,
  perm_type = c("clustered", "uniform"),
  time = "time",
  sequence = "sequence_id",
  germline = "Germline",
  verbose = FALSE,
  polyresolve = TRUE,
  alternative = c("greater", "two.sided"),
  storeTree = FALSE,
  nproc = 1
)

Arguments

clones

A tibble object containing airrClone and phylo objects

permutations

Number of permutations to run

minlength

Branch lengths to collapse in trees

perm_type

Permute among single timepoint clades or uniformly among tips

time

Column name holding numeric time information

sequence

Column name holding sequence ID

germline

Germline sequence name

verbose

Print lots of rubbish while running?

polyresolve

Resolve polytomies to have a minimum number of single timepoint clades

alternative

Is alternative that the randomized correlation are greater than or equal to observed, or greater/less than?

storeTree

Store the tree used?

nproc

Number of cores to use for calculations. Parallelizes by tree.

Details

Object returned contains these columns which are added or modified from input:

Value

A tibble with the same columns as clones, but additional columns corresponding to test statistics for each clone.

See Also

Uses output from getTrees.


[Package dowser version 2.1.0 Index]