Adding sizer to draw() in gratia

[asanders11]

Is it possible to add an argument similar to 'sizer' from your derivSimulCI() and CI fuctions to plot the first derivative of the spline, with sizer=TRUE to color increasing and decreasing parts of the spline?

Thanks!

[gavinsimpson]

@asanders11 I now have sizer-like options available through a new function add_sizer() which works for objects created by derivatives(), as well as new code in draw.derivatives() that allows the sizer-like information to be shown:

That plot was created by

dat <- data_sim("eg1", n = 400, dist = "normal", scale = 2, seed = 42)
mod <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat, method = "REML")

## first derivatives of all smooths using central finite differences
d <- derivatives(mod, type = "central")

draw(d, add_change = TRUE, change_type = "sizer")

with the latest version of gratia here (0.8.1.19 or later)

Does that cover what you were looking for or were you also thinking about plotting smooths with significant periods of change indicated on them too?

[asanders11]

This is great, Gavin..thank you! And yes, I was hoping to plot significant periods of change as well.

[gavinsimpson]

I don't think I can implement this within draw.gam() itself as the way it works is quite complex already. I have implemented this in the draw() codes for smooth_estimates() objects however.

Now you can use smooth_estimates() to evaluate the smooths, then add_sizer() adds the derivative info needed, which the draw() method will recognise and plot:

su_eg4 <- data_sim("eg4", n = 400,  dist = "normal", scale = 2, seed = 1)
su_m_factor_by <- gam(y ~ fac + s(x2, by = fac) + s(x0),
                      data = su_eg4, method = "REML")
smooth_estimates(su_m_factor_by) |>
  add_sizer(derivatives = d, type = "sizer")  |>
  draw(grouped_by = TRUE)

produces:

for example, showing that this works also with the new groped_by argument to group factor-by smooths.

So I'm going to call that closed for now. Hope that's OK? If I've missed something, let me know.

[asanders11]

Appreciate it, Gavin. This is exactly what I needed!

[asanders11]

Hi Gavin - sorry to bring you back to this topic, but do you know when add_sizer() will be added to gratia ? Trying to use it with some data, but it doesn't seem to be in the new update (v 0.8.1). TIA!

[gavinsimpson]

It'll be a few weeks at least before I can get this on CRAN, but you don't need to wait for that; this is in the version on GitHub already, and the README.md file contains instructions on installing the package from the wonderful r-universe repo and build system. https://github.com/gavinsimpson/gratia#installing-gratia