Plot the estimates of random effects with confidence intervals
Usage
## S3 method for class 'random.effects'
plot(x, by = NULL, interval="confidence", level = 0.95, xlab = NULL, ylab = NULL,
xlim = NULL, ylim = NULL, pch=19, col.points='red', col.seg=gray(0.5), ...)
Arguments
x
"random.effects" object
by
defines the element to be plotted
interval
Define the interval to be used. See details
level
the confidence level required
xlab
a title for the x axis
ylab
a title for the y axis
ylim
the x limits of the plot
xlim
the y limits of the plot
pch
either an integer specifying a symbol or a single character
to be used as the default in plotting points
col.points
a specification for the default plotting color points
col.seg
a specification for the default plotting color segments
...
Arguments to be passed to method, such as plot
Details
interval
If interval='hpd' is plotted the posterior mean of the random effects with credibility interval.
The credibility interval for this case is obtained from the sample using the function HPDinterval
of the package coda. If interval='confidence', the credibility interval is obtained from normal distribution
quantile (qnorm((1-level)/2,mean,sd). By default is interval='confidence'
Examples
# Not run
data(sensory)
Consumer <- factor(sensory$consumer)
Sacarose <- factor(sensory$sacarose)
#### Model
# Not run
dex1 <- Bayesthresh(cor ~ (1|Consumer) + Sacarose, Write=TRUE,
burn = 10, jump = 2, ef.iter = 10, data=sensory)
rand <- random.effects(dex1, HPDinterval=TRUE)
plot(rand, interval='hpd')
plot(rand)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(Bayesthresh)
Loading required package: lme4
Loading required package: Matrix
Loading required package: MASS
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: mvtnorm
Loading required package: matrixcalc
Loading required package: coda
Attaching package: 'coda'
The following object is masked from 'package:VGAM':
nvar
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Bayesthresh/plot.random.effects.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.random.effects
> ### Title: Plot random effects of model
> ### Aliases: plot.random.effects
> ### Keywords: plot.random.effects random.effects
>
> ### ** Examples
>
>
> # Not run
> data(sensory)
>
> Consumer <- factor(sensory$consumer)
> Sacarose <- factor(sensory$sacarose)
>
> #### Model
> # Not run
> dex1 <- Bayesthresh(cor ~ (1|Consumer) + Sacarose, Write=TRUE,
+ burn = 10, jump = 2, ef.iter = 10, data=sensory)
>
> rand <- random.effects(dex1, HPDinterval=TRUE)
> plot(rand, interval='hpd')
> plot(rand)
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
