correlationTest {dowser} | R Documentation |
correlationTest
performs root-to-tip regression date randomization test
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
)
clones |
A |
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. |
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.
A tibble
with the same columns as clones, but additional
columns corresponding to test statistics for each clone.
Uses output from getTrees
.