Improve ggeffects compatibility #203

Now works with:
- + (1 | factor)
- + s(other_covariate)

Adding unit tests

R/methods.R

@@ -205,7 +205,8 @@ Effect.sdmTMB <- function(focal.predictors, mod, ...) {
     coefficients = coefs,
     vcov = vc,
     family = fam,
-    formula = formula(mod)
+    # formula = formula(mod) # includes random intercepts...
+    formula = remove_s_and_t2(mod$split_formula[[1]]$fixedFormula)
   )
   effects::Effect.default(focal.predictors, mod, ..., sources = args)
 }

tests/testthat/test-ggeffect.R

@@ -0,0 +1,51 @@
+test_that("ggeffects + sdmTMB", {
+  skip_on_cran()
+  skip_on_ci()
+  skip_if_not_installed("INLA")
+  skip_if_not_installed("ggeffects")
+  skip_if_not_installed("ggplot2")
+
+  d <- pcod_2011
+  d$fyear <- as.factor(d$year)
+  fit <- sdmTMB(present ~ depth_scaled + I(depth_scaled^2) + fyear,
+    data = d,
+    mesh = pcod_mesh_2011,
+    family = binomial()
+  )
+  g <- ggeffects::ggeffect(fit, "depth_scaled [-2.5:2.5, by=.1]")
+  expect_true(inherits(g, "ggeffects"))
+  plot(g)
+
+  e <- effects::effect("depth_scaled", fit)
+  e
+  expect_true(inherits(e, "eff"))
+
+  fit2 <- sdmTMB(present ~ depth_scaled + I(depth_scaled^2) + (1 | fyear),
+    data = d,
+    mesh = pcod_mesh_2011,
+    family = binomial()
+  )
+  effects::effect("depth_scaled", fit2)
+  g <- ggeffects::ggeffect(fit2, "depth_scaled [-2.5:2.5, by=.1]")
+  plot(g)
+  expect_true(inherits(g, "ggeffects"))
+
+  fit3 <- sdmTMB(present ~ s(year, k = 3) + depth_scaled + I(depth_scaled^2),
+    data = d,
+    mesh = pcod_mesh_2011,
+    family = binomial()
+  )
+  effects::effect("depth_scaled", fit3)
+  g <- ggeffects::ggeffect(fit3, "depth_scaled [-2.5:2.5, by=.1]")
+  plot(g)
+  expect_true(inherits(g, "ggeffects"))
+
+  fit4 <- sdmTMB(present ~ s(depth_scaled, k = 4),
+    data = d,
+    mesh = pcod_mesh_2011,
+    family = binomial()
+  )
+  expect_error({
+    effects::effect("depth_scaled", fit4)
+  }, regexp = "missing")
+})