testSP {dowser}

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 one-sided (greater or less) or two.sided test

tip_switch

maximum tip/switch ratio

exclude

exclude clones with tip/switch ratio > tip_switch?

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)