UM.eqtest: Equality tests for two multinomial samples

In mlysy/MADPop: MHC Allele-Based Differencing Between Populations

Equality tests for two multinomial samples

Description

Generate multinomial samples from a common probability vector and calculate the Chi-square and Likelihood Ratio test statistics.

Usage

UM.eqtest(N1, N2, p0, nreps, verbose = TRUE)

Arguments

N1	Size of sample 1.
N2	Size of sample 2.
p0	Common probability vector from which to draw the multinomial samples. Can also be a matrix, in which case each simulation randomly draws with replacement from the rows of p0.
nreps	Number of replications of the simulation.
verbose	Logical. If TRUE prints message every 5000 replications.

Details

The chi-squared and likelihood ratio test statistics are calculated from multinomial samples (Y_1^1, Y_2^1), \ldots, (Y_1^M, Y_2^M), where

Y_k^m \stackrel{\textrm{ind}}{\sim} \textrm{Multinomial}(N_k, p_0^m),

where p_0^m is the mth row of p0.

Value

An nreps x 2 matrix with the simulated chi-squared and LR values.

Examples

# bootstrapped p-value calculation against equal genotype proportions
# in lakes Michipicoten and Simcoe

# contingency table
popId <- c("Michipicoten", "Simcoe")
ctab <- UM.suff(fish215[fish215$Lake %in% popId,])$tab
ctab

# MLE of probability vector
p.MLE <- colSums(ctab)/sum(ctab)
# sample sizes
N1 <- sum(ctab[1,]) # Michipicoten
N2 <- sum(ctab[2,]) # Simcoe

# bootstrapped test statistics (chi^2 and LRT)
T.boot <- UM.eqtest(N1 = N1, N2 = N2, p0 = p.MLE, nreps = 1e3)

# observed test statistics
T.obs <- c(chi2 = chi2.stat(ctab), LRT = LRT.stat(ctab))
# p-values
rowMeans(t(T.boot) > T.obs)

mlysy/MADPop documentation built on Feb. 28, 2024, 12:29 p.m.