Plot smooths from GAMs

Plotting smooths

To illustrate how to use plot_smooths(), let’s first prepare some dummy data with a factor variable and run gam() on this data. The gam model includes a reference smooth s(x2), a by-factor difference smooth s(x2, by = fac), and a smooth s(x0).

set.seed(10)
data <- gamSim(4)
#> Factor `by' variable example
model <- gam(
    y ~
        fac +
        s(x2) +
        s(x2, by = fac) +
        s(x0),
    data = data
)

We can now plot the estimated smooths for the two levels of fac. The function supports factors with more than 2 levels.

plot_smooths(
    model = model,
    series = x2,
    comparison = fac
) +
    theme(legend.position = "top")

Plotting a single smooth

It is also possible to plot a single smooth.

model_2 <- gam(
    y ~
        s(x0),
    data = data
)

plot_smooths(
    model = model_2,
    series = x0
)

Plotting interactions

It is very likely that the model will contain interactions. It is possible to plot models with interactions by specifying faceting with the facet_terms argument.

simdata <- simdat %>%
    filter(
    Subject %in% c("a01", "a08", "a15", "c01", "c08", "c15")
) %>%
    mutate(
    GroupCondition = interaction(Group, Condition)
)

model_inter <- bam(
    Y ~
        GroupCondition +
        s(Time, by = GroupCondition),
    data = simdata
)

plot_smooths(
    model = model_inter,
    series = Time,
    comparison = Group,
    facet_terms = Condition,
    split = list(GroupCondition = c("Group", "Condition"))
) +
    theme(legend.position = "top")

To plot just one or some of the facets, you should use the conditions argument. This argument takes a list of quosures with quos().

plot_smooths(
    model = model_inter,
    series = Time,
    comparison = Group,
    facet_terms = Condition,
    conditions = quos(Condition == -1),
    split = list(GroupCondition = c("Group", "Condition"))
) +
    theme(legend.position = "top")

plot_smooths(
    model = model_inter,
    series = Time,
    comparison = Group,
    facet_terms = Condition,
    conditions = quos(Condition %in% c(-1, 3)),
    split = list(GroupCondition = c("Group", "Condition"))
) +
    theme(legend.position = "top")

Plotting the difference smooth

The difference smooth can be plotted with plot_difference(). Portions of the difference smooth that do not include 0 are shaded in red.

plot_difference(
  model,
  series = x2,
  difference = list(fac = c("1", "2"))
)

To plot a difference smooth from a model with factor interactions, it is possible to specify the two levels to compare from the factor interaction (the argument split is not supported in plot_difference()).

plot_difference(
  model_inter,
  Time,
  difference = list(GroupCondition = c("Children.1", "Adults.1"))
)

plot_difference(
  model_inter,
  Time,
  difference = list(GroupCondition = c("Children.3", "Adults.3"))
)