inlabru (version 2.1.9)

gg.prediction: Geom for predictions

Description

This geom serves to visualize prediction objects which usually results from a call to predict.bru. Predictions objects provide summary statistics (mean, median, sd, ...) for one or more random variables. For single variables (or if requested so by setting bar = TRUE), a boxplot-style geom is constructed to show the statistics. For multivariate predictions the mean of each variable (y-axis) is plotted agains the row number of the varriable in the prediction data frame (x-axis) using geom_line. In addition, a geom_ribbon is used to show the confidence interval.

Note: gg.prediction also understands the format of INLA-style posterior summaries, e.g. fit$summary.fixed for an inla object fit

Usage

# S3 method for prediction
gg(data, mapping = NULL, ribbon = TRUE, alpha = 0.3,
  bar = FALSE, ...)

Arguments

data

A prediction object, usually the result of a predict.bru call.

mapping

a set of aesthetic mappings created by aes or aes_. These are passed on to geom_line.

ribbon

If TRUE, plot a ribbon around the line based on the upper and lower 2.5 percent quantiles.

alpha

The ribbons numeric alpha level in [0,1].

bar

If TRUE plot boxplot-style summary for each variable.

...

Arguments passed on to geom_line.

Value

Concatenation of a geom_line value and optionally a geom_ribbon value.

See Also

Other geomes for inla and inlabru predictions: gg.data.frame, gg.matrix, gg, gm

Examples

# NOT RUN {
# Generate some data

input.df <- data.frame(x=cos(1:10))
input.df <- within(input.df, y <- 5 + 2*cos(1:10) + rnorm(10, mean=0, sd=0.1))

# Fit a model with fixed effect 'x' and intercept 'Intercept'

fit <- bru(y ~ x, "gaussian", input.df)

# Predict posterior statistics of 'x'

xpost = predict(fit, formula = ~ x)

# The statistics include mean, standard deviation, the 2.5% quantile, the median,
# the 97.5% quantile, minimum and maximum sample drawn from the posterior as well as
# the coefficient of variation and the variance.

xpost

# For a single variable like 'x' the default plotting method invoked by gg() will
# show these statisics in a fashion similar to a box plot:
ggplot() + gg(xpost)


# The predict function can also be used to simulatenneously estimate posteriors
# of multiple variables:

xipost = predict(fit, formula = ~ data.frame(post = c(Intercept, x)))
xipost

# If we still want a plot in the previous style we have to set the bar parameter to TRUE

rownames(xipost) = c("Intercept","x")
p1 = ggplot() + gg(xipost, bar = TRUE)
p1

# Note that gg also understands the posterior estimates generated while running INLA

p2 = ggplot() + gg(fit$summary.fixed, bar = TRUE)
multiplot(p1, p2)

# By default, if the prediction has more than one row, gg will plot the column 'mean' against
# the row index. This is for instance usefuul for predicting and plotting function
# but not very meaningful given the above example:

ggplot() + gg(xipost)

# For ease of use we can also type

plot(xipost)

# This type of plot will show a ribbon around the mean, which viszualizes the upper and lower
# quantiles mentioned above (2.5 and 97.5%). Plotting the ribbon can be turned of using the
# \code{ribbon} parameter

ggplot() + gg(xipost, ribbon = FALSE)

# Much like the other geomes produced by gg we can adjust the plot using ggplot2 style
# commands, for instance

ggplot() + 
  gg(xipost) +
  gg(xipost, mapping = aes(y = median), ribbon = FALSE, color = "red")

# }