plot.metadiag {bamdit} | R Documentation |
Generic plot function for metadiag object in bamdit
Description
This function plots the observe data in the ROC (Receiving Operating Charachteristics) space with the posterior predictive contours. The predictive curves are approximated using a non-parametric smoother or with a parametric model. For the parametric model the current implementation supports only a logistic link function. The marginal posterior predictive distributions are ploted outside the ROC space.
Usage
## S3 method for class 'metadiag'
plot(
x,
parametric.smooth = TRUE,
level = c(0.5, 0.75, 0.95),
limits.x = c(0, 1),
limits.y = c(0, 1),
kde2d.n = 25,
color.line = "red",
title = paste("Posterior Predictive Contours (50%, 75% and 95%)"),
marginals = TRUE,
bin.hist = 30,
color.hist = "lightblue",
S = 500,
color.pred.points = "lightblue",
color.data.points = "blue",
...
)
Arguments
x |
The object generated by the metadiag function. |
parametric.smooth |
Indicates if the predictive curve is a parametric or non-parametric. |
level |
Credibility levels of the predictive curve. If parametric.smooth = FALSE, then the probability levels are estimated from the nonparametric surface. |
limits.x |
Numeric vector of length 2 specifying the x-axis limits. The default value is c(0, 1). |
limits.y |
Numeric vector of length 2 specifying the x-axis limits. The default value is c(0, 1). |
kde2d.n |
The number of grid points in each direction for the non-parametric density estimation. Can be scalar or a length-2 inter vector. |
color.line |
Color of the predictive contour line. |
title |
Optional parameter for setting a title in the plot. |
marginals |
Plot the posterior marginal predictive histograms. |
bin.hist |
Number of bins of the marginal histograms. |
color.hist |
Color of the histograms. |
S |
Number of predictive rates to be plotted. |
color.pred.points |
Color of the posterior predictive rates. |
color.data.points |
Color of the data points. |
... |
... |
See Also
Examples
## Not run:
library(bamdit)
data("glas")
glas.t <- glas[glas$marker == "Telomerase", 1:4]
glas.m1 <- metadiag(glas.t, # Data frame
re = "normal", # Random effects distribution
re.model = "DS", # Random effects on D and S
link = "logit", # Link function
sd.Fisher.rho = 1.7, # Prior standard deviation of correlation
nr.burnin = 1000, # Iterations for burnin
nr.iterations = 10000, # Total iterations
nr.chains = 2, # Number of chains
r2jags = TRUE) # Use r2jags as interface to jags
plot(glas.m1, # Fitted model
level = c(0.5, 0.75, 0.95), # Credibility levels
parametric.smooth = TRUE) # Parametric curve
# Plot results: based on a non-parametric smoother of the posterior predictive rates .......
plot(glas.m1, # Fitted model
level = c(0.5, 0.75, 0.95), # Credibility levels
parametric.smooth = FALSE) # Non-parametric curve
# Using the pipe command in the package dplyr and changing some colors .......
library(dplyr)
glas.t %>%
metadiag(re = "normal", re.model ="SeSp") %>%
plot(parametric.smooth = FALSE,
S = 100,
color.data.points = "green",
color.pred.points = "blue",
color.line = "black")
## End(Not run)