mcexact {exactLoglinTest} | R Documentation |
This function computes Monte Carlo estimates of conditional P-values for goodness of fit tests for general log-linear models.
mcexact(formula, data, stat = gof, dens = hyper, nosim = 10 ^ 3, method = "bab", savechain = FALSE, tdf = 3, maxiter = nosim, p = NULL, batchsize = NULL) build.mcx.obj(formula, data, stat = gof, dens = hyper, nosim = 10 ^ 3, method = "bab", savechain = FALSE, tdf = 3, maxiter = nosim, p = NULL, batchsize = NULL)
formula |
Null model formula specified as in glm |
data |
Data frame |
stat |
The test statistic, a function of the form function(y, mu.hat)
where y is the observed and mu.hat are the fitted
values. Current default gof is a bivariate function of the
deviance and the Pearson chi-squared. |
dens |
The target density on the log scale up to a constant of
proportionallity. A function of the form
function(y) . Current default is (proportional to) the log of
the generalized hypergeometric density. |
nosim |
Desired number of simulations. |
method |
Possibly two values, the importance sampling method of
Booth and Butler, method = "bab" or the MCMC approach of
Caffo and Booth method = "cab" . |
savechain |
If TRUE saves the values of the chain. |
tdf |
A tuning parameter |
maxiter |
For method = "bab" number of iterations is
different from the number of simulations. maxiter is a
bound on the total number of iterations. |
p |
A tuning parameter for method = "cab" . |
batchsize |
Required batchsizes for method = "cab" . |
Returns a list of class either "bab"
or "cab"
depending
on method
. The list contains all of the inputs plus all
required information to resume the simulation. Generic functions
print
and summary
format the output while update
can be used to resume simulations. mcexact
is the front end while
build.mcx.obj
simply builds the basic object that mcexact
applies to.
simulate.conditional
generates a matrix of simulated tables.
Brian Caffo
Booth and Butler (1999), "An importance sampling algorithm for exact conditional tests in log-linear models", Biometrika 86: 321-332.
Caffo and Booth (2001). "A Markov Chain Monte Carlo Algorithm for Approximating Exact Conditional Probabilities", The Journal of Computational and Graphical Statistics 10: 730-45.
http://www.biostat.jhsph.edu/~bcaffo/downloads.htm
#library(mcexact) set.seed(1) #importance sampling data(residence.dat) mcx <- mcexact(y ~ res.1985 + res.1980 + factor(sym.pair), data = residence.dat) summary(mcx) #mcmc data(pathologist.dat) mcx <- mcexact(y ~ factor(A) + factor(B) + I(A * B), data = pathologist.dat, method = "cab", p = .5, nosim = 10 ^ 4, batchsize = 100) summary(mcx)