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Plot derivatives of smooths

Source: R/draw-methods.R
draw.derivatives.Rd

Plot derivatives of smooths

Usage

# S3 method for class 'derivatives'
draw(
  object,
  select = NULL,
  scales = c("free", "fixed"),
  add_change = FALSE,
  change_type = c("change", "sizer"),
  alpha = 0.2,
  change_col = "black",
  decrease_col = "#56B4E9",
  increase_col = "#E69F00",
  lwd_change = 1.5,
  ncol = NULL,
  nrow = NULL,
  guides = "keep",
  angle = NULL,
  differentiate_factor_smooths = TRUE,
  ...
)

# S3 method for class 'partial_derivatives'
draw(
  object,
  select = NULL,
  scales = c("free", "fixed"),
  alpha = 0.2,
  ncol = NULL,
  nrow = NULL,
  guides = "keep",
  angle = NULL,
  ...
)

Arguments

object

a fitted GAM, the result of a call to mgcv::gam().

select

character, logical, or numeric; which smooths to plot. If NULL, the default, then all model smooths are drawn. Numeric select indexes the smooths in the order they are specified in the formula and stored in object. Character select matches the labels for smooths as shown for example in the output from summary(object). Logical select operates as per numeric select in the order that smooths are stored.

scales

character; should all univariate smooths be plotted with the same y-axis scale? If scales = "free", the default, each univariate smooth has its own y-axis scale. If scales = "fixed", a common y axis scale is used for all univariate smooths.

Currently does not affect the y-axis scale of plots of the parametric terms.

add_change

logical; should the periods of significant change be highlighted on the plot?

change_type

character; the type of change to indicate. If "change", no differentiation is made between periods of significant increase or decrease. If "sizer", the periods of increase and decrease are differentiated in the resulting plot.

alpha

Deprecated; use gratia_theme_get() theme settings instead. Numeric; alpha transparency for confidence or simultaneous interval.

change_col, decrease_col, increase_col

Deprecated; use gratia_theme_get() theme settings instead. Colour specifications to use for indicating periods of change. col_change is used when change_type = "change", while col_decrease and col_increase are used when `change_type = "sizer"“.

lwd_change

Deprecated; use gratia_theme_get() theme settings instead. Numeric; the linewidth to use for the change indicators.

ncol, nrow

numeric; the numbers of rows and columns over which to spread the plots

guides

character; one of "keep" (the default), "collect", or "auto". Passed to patchwork::plot_layout()

angle

numeric; the angle at which the x axis tick labels are to be drawn passed to the angle argument of ggplot2::guide_axis().

differentiate_factor_smooths

logical; should colour be used to differentiate the levels of the factors involved in random factor smooths (bs = "fs") or constrained factor smooths (bs = "sz")? If TRUE, the factor(s) are used to define groups and mapped to the colour aesthetic.

...

additional arguments passed to patchwork::wrap_plots().

Label layout

Pass label_control = draw_label_control(...) to draw() to wrap discrete axis labels and legend text, stagger discrete tick labels, or adjust legend and colour-bar layout. Settings apply to each panel, including unwrapped plot lists. See draw_label_control() for the available settings.

Examples

load_mgcv()
# Simulate an additive Gaussian response and fit a GAM
dat <- data_sim("eg1", n = 200, scale = 1, seed = 42)
mod <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat, method = "REML")

# Estimate and plot the rate of change of one smooth
df <- derivatives(mod, select = "s(x2)", type = "central")
draw(df)