MC.Xsc.statistics: Size and Power for the One Sample RAD Probability-Mean Test...

In HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Description

This Monte-Carlo simulation procedure provides the power and size of the one sample RAD probability-mean test, using the Generalized Wald-type statistic.

Usage

MC.Xsc.statistics(Nrs, numMC = 10, fit, pi0 = NULL, type = "ha", siglev = 0.05)

Arguments

Nrs	A vector specifying the number of reads/sequence depth for each sample.
numMC	Number of Monte-Carlo experiments. In practice this should be at least 1,000.
fit	A list (in the format of the output of dirmult function) containing the data parameters for evaluating either the size or power of the test.
pi0	The RAD-probability mean vector. If the type is set to "hnull" then pi0 is set by the sample in fit.
type	If "hnull": Computes the size of the test. If "ha": Computes the power of the test. (default)
siglev	Significance level for size of the test / power calculation. The default is 0.05.

Details

Note: Though the test statistic supports an unequal number of reads across samples, the performance has not yet been fully tested.

Value

Size of the test statistics (under "hnull") or power (under "ha") of the test.

Examples

	data(saliva)
	data(throat) 
	data(tonsils)
	
	### Get a list of dirichlet-multinomial parameters for the data
	fit.saliva <- DM.MoM(saliva) 
	fit.throat <- DM.MoM(throat)
	fit.tonsils <- DM.MoM(tonsils) 
	
	### Set up the number of Monte-Carlo experiments
	### We use 1 for speed, should be at least 1,000
	numMC <- 1
	
	### Generate the number of reads per sample
	### The first number is the number of reads and the second is the number of subjects
	nrs <- rep(15000, 25)
	
	### Computing size of the test statistics (Type I error)
	pval1 <- MC.Xsc.statistics(nrs, numMC, fit.tonsils, fit.saliva$pi, "hnull")
	pval1
	
	### Computing Power of the test statistics (Type II error)
	pval2 <- MC.Xsc.statistics(nrs, numMC, fit.throat, fit.tonsils$pi)
	pval2

Example output

Loading required package: dirmult

Attaching package: 'HMP'

The following object is masked from 'package:dirmult':

    weirMoM

[1] 0.5
[1] 1

HMP documentation built on Aug. 31, 2019, 5:05 p.m.