testSP {dowser} | R Documentation |
testSP
performs an SP test
testSP(
switches,
permuteAll = FALSE,
from = NULL,
to = NULL,
dropzeroes = TRUE,
bylineage = FALSE,
pseudocount = 0,
alternative = c("greater", "two.sided", "less"),
tip_switch = 20,
exclude = FALSE
)
switches |
Data frame from findSwitches |
permuteAll |
Permute among trees? |
from |
Include only switches from this state? |
to |
Include only switches to this state? |
dropzeroes |
Drop switches with zero counts? |
bylineage |
Perform test for each lineage individually? |
pseudocount |
Pseudocount for P value calculations |
alternative |
Perform one-sided ( |
tip_switch |
maximum tip/switch ratio |
exclude |
exclude clones with tip/switch ratio > |
Output data table columns: RECON = SP for observed data PERMUTE = SP for permuted data DELTA = RECON - PERMUTE PLT = p value for DELTA < 0 PGT = p value for DELTA < 0
FROM
: State going from.
TO
: State going to.
RECON
: SP for observed data.
PERMUTE
: SP for permuted data.
DELTA
: RECON - PERMUTE.
PLT
: p value that DELTA < 0
PGT
: p value that DELTA > 0
STAT
: Statistic used (SP).
REP
: Bootstrap repetition.
REPS
: Total number of ootstrap repetition.
A list containing a tibble
with mean SP statistics, and another
with SP statistics per repetition.
Uses output from findSwitches. Related to testPS and testSC.
## Not run:
igphyml <- "~/apps/igphyml/src/igphyml"
data(ExampleAirr)
ExampleAirr$sample_id = sample(ExampleAirr$sample_id)
clones = formatClones(ExampleAirr, trait="sample_id")
btrees = findSwitches(clones[1:2], bootstraps=10, nproc=1,
igphyml=igphyml, trait="sample_id")
testSP(btrees$switches)
## End(Not run)