Description Details Author(s) References See Also Examples
Performs Monte Carlo hypothesis tests. It allows a couple of different sequential stopping boundaries (a truncated sequential probability ratio test boundary and a boundary proposed by Besag and Clifford, 1991). Gives valid p-values and confidence intervals on p-values.
Package: | MChtest |
Type: | Package |
Version: | 1.0-3 |
Date: | 2019-05-14 |
License: | GPL |
Use MCbound
to create sequential stopping boundaries. These may take considerable set-up time, but once the
stopping boundary is calculated then it can be used in MCtest
to save time in computation of Monte Carlo
hypothesis tests. The idea of the truncated sequential probability ratio test boundary is that it takes many resamples if
the true p-value (i.e., the one from an infinite resample size) is close to the significance level (e.g., 0.05),
but takes much fewer if the true p-value is far from the significance level.
Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Besag, J. and Clifford, P. (1991). Sequential Monte Carlo p-values. Biometrika. 78: 301-304.
Fay, M.P., Kim, H-J. and Hachey, M. (2007). Using truncated sequential probability ratio test boundaries for Monte Carlo implementation of hypothesis tests. Journal of Computational and Graphical Statistics. 16(4):946-967.
Precalculated MCbound: MCbound.precalc1
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Create a stopping boundary
##### May take a long time if Nmax is large
B<-MCbound("tsprt",c(alpha0=.001,beta0=.01,Nmax=99,p0=.04,p1=.06))
## do Monte Carlo test
x<-data.frame(y=1:100,z=rnorm(100),group=c(rep(1,50),rep(2,50)))
stat<-function(x){ cor(x[,1],x[,2]) }
### nonparametric bootstrap test on correlation between y and z
### low p-value means that such a large correlation unlikely due to chance
resamp<-function(x){ n<-dim(x)[[1]] ; x[sample(1:n,replace=TRUE),] }
MCtest(x,stat,resamp,bound=B)
## Package comes with a large precalculated MC bound as the default
## the precalculated bound is good for testing at the 0.05 level
MCtest(x,stat,resamp)
|
MCtest using MCbound of
type= tsprt with parms=
alpha0 beta0 Nmax p0 p1
0.001 0.010 99.000 0.040 0.060
p-value= 0.6666667
99 percent confidence interval (on p-value):
0.1435687 0.9771157
MCtest using MCbound of
type= tsprt with parms=
p0 p1 alpha0 beta0 Nmax
6.144961e-02 4.000000e-02 1.000000e-04 1.000000e-04 9.999000e+03
p-value= 0.5227259
99 percent confidence interval (on p-value):
0.3241731 0.7086698
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