From e868be28ac98a1592ae33de0443a1ef527aeeaba Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Mon, 23 Sep 2024 13:52:28 -0700
Subject: [PATCH] Allow coef to work for delta models #351

---
 DESCRIPTION                   |  2 +-
 NEWS.md                       |  3 +++
 R/methods.R                   | 14 +++++++++++---
 man/coef.sdmTMB.Rd            | 21 +++++++++++++++++++++
 tests/testthat/test-methods.R | 12 ++++++++++++
 5 files changed, 48 insertions(+), 4 deletions(-)
 create mode 100644 man/coef.sdmTMB.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 667d19514..302691204 100644
--- a/DESCRIPTION
+++ b/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"),
diff --git a/NEWS.md b/NEWS.md
index 27124a556..3256deda0 100644
--- a/NEWS.md
+++ b/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
diff --git a/R/methods.R b/R/methods.R
index 58ec21638..314577abe 100644
--- a/R/methods.R
+++ b/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
diff --git a/man/coef.sdmTMB.Rd b/man/coef.sdmTMB.Rd
new file mode 100644
index 000000000..d0060e660
--- /dev/null
+++ b/man/coef.sdmTMB.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods.R
+\name{coef.sdmTMB}
+\alias{coef.sdmTMB}
+\title{Get fixed-effect coefficients}
+\usage{
+\method{coef}{sdmTMB}(object, complete = FALSE, model = 1, ...)
+}
+\arguments{
+\item{object}{The fitted sdmTMB model object}
+
+\item{complete}{Currently ignored}
+
+\item{model}{Linear predictor for delta models. Defaults to the first
+linear predictor.}
+
+\item{...}{Currently ignored}
+}
+\description{
+Get fixed-effect coefficients
+}
diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
index 6b31ba3bf..99a86ffe9 100644
--- a/tests/testthat/test-methods.R
+++ b/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(