Skip to contents

Diagnostic plots for EM fits

Source: R/EM_plot.R
plot.EM.Rd

Produce diagnostic plots of EM fits returned from mixfit.

Usage

# S3 method for class 'EM'
plot(x, size = 1.25, link = c("identity", "logit", "log"), ...)

Arguments

x

EM fit

size

Optional argument passed to ggplot2 routines which control line thickness.

Choice of an applied link function. Can take one of the values identity (default), logit or log.

...

Ignored.

Overlays the fitted mixture density with a histogram and a density plot of the raw sample fitted. Applying a link function can be beneficial, for example a logit (log) link for beta (gamma) mixtures obtained from a Binomial (Poisson) gMAP analysis.

Value

A list of ggplot plots for diagnostics of the EM run. Detailed EM diagnostic plots are included only if the global option RBesT.verbose is set to TRUE. These include plots of the parameters of each component vs the iteration. The plot of the mixture density with a histogram and a density of the fitted sample is always returned.

Customizing ggplot2 plots

The returned plot is a ggplot2 object. Please refer to the "Customizing Plots" vignette which is part of RBesT documentation for an introduction. For simple modifications (change labels, add reference lines, ...) consider the commands found in bayesplot-helpers. For more advanced customizations please use the ggplot2 package directly. A description of the most common tasks can be found in the R Cookbook and a full reference of available commands can be found at the ggplot2 documentation site.

See also

Other EM: mixfit()

Examples


bmix <- mixbeta(rob=c(0.2, 1, 1), inf=c(0.8, 10, 2))
bsamp <- rmix(bmix, 1000)
bfit <- mixfit(bsamp, type="beta", Nc=2)
pl <- plot(bfit)

print(pl$mixdens)

print(pl$mix)


# \donttest{
# a number of additional plots are generated in verbose mode
.user_option <- options(RBesT.verbose=TRUE)
pl_all <- plot(bfit)

# recover previous user options
options(.user_option)

names(pl_all)
#>  [1] "mixdist" "w"       "a"       "b"       "lN"      "Lm"      "N"      
#>  [8] "m"       "Lw"      "lli"     "mixdens" "mixecdf" "mix"    
# [1] "mixdist" "a"   "b"   "w"   "m"   "N"   "Lm"  "lN"  "Lw"  "lli" "mixdens" "mixecdf" "mix"
# }