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 andphylo
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
.