Allow coef to work for delta models #351

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9007
+Version: 0.6.0.9008
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,8 @@
 # sdmTMB (development version)
 
+* Add `model` (linear predictor number) argument to coef() method. Also,
+  write documentation for `?coef.sdmTMB`. #351
+
 * Add helpful error message if some coordinates in make_mesh() are NA. #365
 
 * Add informative message if fitting with an offset but predicting with offset

R/methods.R

@@ -45,12 +45,20 @@ fitted.sdmTMB <- function(object, ...) {
 #'
 #' @param object The fitted sdmTMB model object
 #' @param complete Currently ignored
+#' @param model Linear predictor for delta models. Defaults to the first
+#'   linear predictor.
 #' @param ... Currently ignored
 #' @importFrom stats coef
 #' @export
-#' @noRd
-coef.sdmTMB <- function(object, complete = FALSE, ...) {
-  x <- tidy(object)
+coef.sdmTMB <- function(object, complete = FALSE, model = 1, ...) {
+  if (is_delta(object)) {
+    assert_that(length(model) == 1L)
+    model <- as.integer(model)
+    assert_that(model %in% c(1L, 2L))
+    msg <- paste0("Returning coefficients from linear predictor ", model, " based on the `model` argument.")
+    cli_inform(msg)
+  }
+  x <- tidy(object, model = model)
   out <- x$estimate
   names(out) <- x$term
   out

tests/testthat/test-methods.R

@@ -27,6 +27,18 @@ test_that("coef and vcov and confint work", {
   expect_true(grepl("Estimate", colnames(x))[3])
 })
 
+test_that("coef works with delta models and informs as needed", {
+  skip_on_cran()
+  fit <- sdmTMB(
+    density ~ depth,
+    data = pcod_2011, spatial = "off",
+    family = delta_gamma()
+  )
+  expect_message(x <- coef(fit), regexp = "model")
+  expect_message(x <- coef(fit, model = 1), regexp = "model")
+  expect_message(x <- coef(fit, model = 2), regexp = "model")
+})
+
 test_that("various methods work", {
   skip_on_cran()
   fit <- sdmTMB(