Geom for predictions
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$summary.fixed
for an inla object fit
## S3 method for class 'prediction' gg(data, mapping = NULL, ribbon = TRUE, alpha = 0.3, bar = FALSE, ...)
data |
A prediction object, usually the result of a |
mapping |
a set of aesthetic mappings created by |
ribbon |
If TRUE, plot a ribbon around the line based on the upper and lower 2.5 percent quantiles. |
alpha |
The ribbons numeric alpha level in |
bar |
If TRUE plot boxplot-style summary for each variable. |
... |
Arguments passed on to |
Concatenation of a geom_line
value and optionally a geom_ribbon
value.
Other geomes for inla and inlabru predictions:
gg.data.frame()
,
gg.matrix()
,
gg()
,
gm()
if (bru_safe_inla()) { # Generate some data input.df <- data.frame(x = cos(1:10)) input.df <- within(input.df, y <- 5 + 2 * cos(1:10) + rnorm(10, mean = 0, sd = 0.1)) # Fit a model with fixed effect 'x' and intercept 'Intercept' fit <- bru(y ~ x, family = "gaussian", data = input.df) # Predict posterior statistics of 'x' xpost <- predict(fit, data = NULL, formula = ~x_latent) # The statistics include mean, standard deviation, the 2.5% quantile, the median, # the 97.5% quantile, minimum and maximum sample drawn from the posterior as well as # the coefficient of variation and the variance. xpost # For a single variable like 'x' the default plotting method invoked by gg() will # show these statisics in a fashion similar to a box plot: ggplot() + gg(xpost) # The predict function can also be used to simulataneously estimate posteriors # of multiple variables: xipost <- predict(fit, data = NULL, formula = ~ c( Intercept = Intercept_latent, x = x_latent ) ) xipost # If we still want a plot in the previous style we have to set the bar parameter to TRUE p1 <- ggplot() + gg(xipost, bar = TRUE) p1 # Note that gg also understands the posterior estimates generated while running INLA p2 <- ggplot() + gg(fit$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") }
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