correlationTest: Run date randomization test for temporal signal on a set of...
In dowser: B Cell Receptor Phylogenetics Toolkit

correlationTest

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:

data: airrClone object, same as input but with additional columns "cluster" which correspond to permutation cluster, and "divergence."
slope: Slope of linear regression between divergence and time.
correlation: Correlation between divergence and time.
p: p value of correlation compared to permuted correlations.
random_correlation: Mean correlation of permutation replicates.
min_p: Minimum p value of data, determined by either the number of distinct clade/timepoint combinations or number of permutations.
nposs: Number of possible distinct timepoint/clade combinations.
nclust: Number of clusters used in permutation. If perm_type="uniform" this is the number of tips.
p_gt/p_lt: P value that permuted correlations are greater or less than observed correlation. Only returned if alternative = "two.sided"
test_trees: The phylo tree objects used, possibly with resolved polytomies.