correlationTest - 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.

Value¶

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

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.

See also¶

Uses output from getTrees.