testSP {dowser}  R Documentation 
Performs SP (switch proportion) test on switch data
Description
testSP
performs an SP test
Usage
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
)
Arguments
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 onesided ( 
tip_switch 
maximum tip/switch ratio 
exclude 
exclude clones with tip/switch ratio > 
Details
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.
Value
A list containing a tibble
with mean SP statistics, and another
with SP statistics per repetition.
See Also
Uses output from findSwitches. Related to testPS and testSC.
Examples
## 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)