summary.gSlc: Summary of the generalized additive mixed model fit produced...

Description Usage Arguments Details Author(s) References See Also Examples

View source: R/summary.gSlc.r

Description

A graphical table showing, for key model parameters, the Markov chain Monte Carlo samples, diagnostic plots and numerical summaries.

Usage

1
2
## S3 method for class 'gSlc'
summary(object,colour=TRUE,paletteNumber=1,...)

Arguments

object

A gSlc() fit object.

colour

Boolean flag:
TRUE = produce a colour graphical table,
FALSE = produce a black and white graphical table .

paletteNumber

If colour = TRUE then there there are two possible colour palettes. These are determined by whether paletteNumber is set to 1 or 2. The default is paletteNumber=1.

...

place-holder for additional arguments.

Details

The columns of the graphical table are:

1. parameter name,
2. trace plot of the Markov chain Monte Carlo sample,
3. plot of Markov chain Monte Carlo sample against its lag 1 sample,
4. sample autocorrelation function,
5. kernel density estimate of the posterior density function,
6. posterior mean and 95% credible interval.

Author(s)

Tung Pham [email protected] and Matt Wand [email protected].

References

Pham, T.H. and Wand, M.P. (2018). Generalized additive mixed model analysis via gammSlice. Australian and New Zealand Journal of Statistics, in press.

See Also

gSlc, plot.gSlc

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
library(gammSlice)
set.seed(39402) ; m <- 100 ; n <- 2
beta0True <- 0.5 ; betaxTrue <- 1.7 ; sigsqTrue <- 0.8
idnum <- rep(1:m,each=n) ; x <- runif(m*n)
U <- rep(rnorm(m,0,sqrt(sigsqTrue)),each=n)
mu <- 1/(1+exp(-(beta0True+betaxTrue*x+U)))
y <- rbinom((m*n),1,mu)
fit1 <- gSlc(y ~ x,random = list(idnum = ~1),family = "binomial",
             control = gSlc.control(nBurn=150,nKept=100,nThin=1))
summary(fit1)
summary(fit1,paletteNumber = 2)
summary(fit1,colour = FALSE)

## Not run: 
# Re-fit with higher Markov chain Monte Carlo sample:

fit2 <- gSlc(y ~ x,random = list(idnum = ~1),family = "binomial")
summary(fit2)
summary(fit2,paletteNumber = 2)
summary(fit2,colour = FALSE)

## End(Not run)

gammSlice documentation built on May 21, 2018, 9:03 a.m.