rstudio · cderv · Sep 17, 2026 · Sep 17, 2026 · Sep 17, 2026 · Sep 18, 2026
diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,8 @@
 
 - rticles now requires rmarkdown 2.32 or later and Pandoc 2.8 or later, matching rmarkdown's updated minimum Pandoc version ([rstudio/rmarkdown#2623](https://github.com/rstudio/rmarkdown/pull/2623)).
 
+- `agu_article()` now uses Pandoc citeproc with the American Geophysical Union CSL style by default. Existing drafts containing only `agujournal2018.cls` must explicitly set `citation_package: natbib`; the format warns when the selected class and citation backend are incompatible (#606).
+
 - Update `springer_article()` template to version 3 (December 2023): 
   - BREAKING CHANGE: sn-mathphys.bst has been split into Numbered and Author year style namely `sn-mathphys-num.bst` and `sn-mathphys-ay.bst` respectively. Skeleton has been updated. 
     If you have existing article, you need to use `sn-mathphys-num` or `sn-mathphys-ay` option now, instead of `sn-mathphys`.
@@ -38,6 +40,8 @@ supported by the `copernicus.cls`, and fix an issue where the section headers we
 
 ## MINOR CHANGES
 
+- Update `agu_article()` to AGU's September 2025 distribution of `agujournal2019.cls`, current manuscript guidance, and external TrackChanges setup (#606).
+
 - Fix `agu_article()` table rendering with recent LaTeX distributions by using the text-mode table centering helper when available (#606).
 
 - Fix `biometrics_article()` rendering with LaTeX 2026 by preserving the LaTeX kernel's matching `\endtabular` implementation.

diff --git a/R/article.R b/R/article.R
@@ -58,19 +58,100 @@ aea_article <- function(..., keep_tex = TRUE,
   )
 }
 
-#' @section `agu_article`: Format for creating a American Geophysical Union
-#'   (AGU) article. Adapted from
-#'   <https://www.agu.org/publications>.
+#' @section `agu_article`: Format for creating an American Geophysical Union
+#'   (AGU) article. Adapted from AGU's September 2025 LaTeX distribution of
+#'   `agujournal2019.cls` and the official [LaTeX submission
+#'   guidelines](https://www.agu.org/publications/authors/journals/latex-submissions).
+#'
+#'   The default `citation_package = "default"` uses Pandoc citeproc with
+#'   the American Geophysical Union CSL style, following the approach used by
+#'   the Quarto AGU journal format. Use Markdown citation syntax in current
+#'   drafts.
+#'
+#'   New drafts include `agujournal2019.cls`. Existing drafts that retain only
+#'   a project-local `agujournal2018.cls` remain supported but must explicitly
+#'   set `citation_package = "natbib"`. The format warns when the selected
+#'   class and citation backend are incompatible. If both classes are present,
+#'   the current 2019 class is used.
 #' @export
 #' @rdname article
 agu_article <- function(..., keep_tex = TRUE,
-                        citation_package = "natbib", highlight = NULL,
+                        citation_package = "default", highlight = NULL,
                         md_extensions = c("-autolink_bare_uris", "-auto_identifiers")) {
-  pdf_document_format(
+  format <- pdf_document_format(
     "agu",
     keep_tex = keep_tex, highlight = highlight,
     citation_package = citation_package, md_extensions = md_extensions, ...
   )
+
+  pre_processor <- format$pre_processor
+  format$pre_processor <- function(metadata, input_file, runtime, knit_meta,
+                                   files_dir, output_dir) {
+    input_dir <- dirname(input_file)
+    legacy_class <- file.path(input_dir, "agujournal2018.cls")
+    current_class <- file.path(input_dir, "agujournal2019.cls")
+    has_legacy_class <- file.exists(legacy_class)
+    has_current_class <- file.exists(current_class)
+    use_current_class <- !has_legacy_class || has_current_class
+
+    if (!use_current_class && citation_package != "natbib") {
+      warn_once(
+        "rticles.warn_agu_2018_citations",
+        "Detected only 'agujournal2018.cls', which expects ",
+        "`citation_package = \"natbib\"`. The selected '",
+        citation_package,
+        "' backend is unsupported for legacy raw \\citep and \\citet ",
+        "commands. Set natbib explicitly or update the draft to the 2019 class."
+      )
+    } else if (!use_current_class) {
+      warn_once(
+        "rticles.warn_agu_2018",
+        "Detected 'agujournal2018.cls' next to the input file. ",
+        "This class remains supported for backward compatibility, but the ",
+        "article should be updated from the current `rticles::agu_article()` ",
+        "template to use 'agujournal2019.cls' and current AGU guidance."
+      )
+    } else {
+      if (has_legacy_class && has_current_class) {
+        warn_once(
+          "rticles.warn_agu_both_classes",
+          "Detected both 'agujournal2018.cls' and 'agujournal2019.cls' next to ",
+          "the input file. The AGU template will use 'agujournal2019.cls'; you ",
+          "may remove the unused 'agujournal2018.cls' file."
+        )
+      }
+      if (citation_package != "default") {
+        warn_once(
+          "rticles.warn_agu_2019_citations",
+          "The selected 2019 AGU class supports `citation_package = ",
+          "\"default\"` with citeproc and the AGU CSL style. The selected '",
+          citation_package,
+          "' backend is unsupported; the 2019 class does not provide natbib ",
+          "citation commands."
+        )
+      }
+    }
+
+    c(
+      if (is.function(pre_processor)) {
+        pre_processor(
+          metadata, input_file, runtime, knit_meta, files_dir, output_dir
+        )
+      },
+      if (use_current_class) {
+        rmarkdown::pandoc_variable_arg("rticles-agu-2019")
+      },
+      if (citation_package == "default" && is.null(metadata$csl)) {
+        c(
+          "--csl",
+          rmarkdown::pandoc_path_arg(pkg_file_template(
+            "agu", "skeleton", "american-geophysical-union.csl"
+          ))
+        )
+      }
+    )
+  }
+  format
 }
 
 #' @section `amq_article`: Ce format a été adapté du format du bulletin de

diff --git a/inst/rmarkdown/templates/agu/resources/template.tex b/inst/rmarkdown/templates/agu/resources/template.tex
@@ -1,39 +1,18 @@
-%% March 2018
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% AGUJournalTemplate.tex: this template file is for articles formatted with LaTeX
+% AGU article template adapted from the September 2025 distribution of
+% agujournal2019.cls. Existing rticles drafts may retain agujournal2018.cls.
 %
-% This file includes commands and instructions
-% given in the order necessary to produce a final output that will
-% satisfy AGU requirements, including customized APA reference formatting.
-%
-% You may copy this file and give it your
-% article name, and enter your text.
-%
-%
-% Step 1: Set the \documentclass
-%
-% There are two options for article format:
-%
-% PLEASE USE THE DRAFT OPTION TO SUBMIT YOUR PAPERS.
-% The draft option produces double spaced output.
-%
-
-%% To submit your paper:
+% Prefer the current class deterministically when both local classes exist.
+$if(rticles-agu-2019)$
+\documentclass[$for(classoption)$$classoption$$sep$,$endfor$]{agujournal2019}
+
+% The 2019 class leaves revision packages to the document. The 2018 class
+% already loads trackchanges and ulem, so reloading them would clash.
+\usepackage[inline]{trackchanges}
+\usepackage{soul}
+$else$
 \documentclass[$for(classoption)$$classoption$$sep$,$endfor$]{agujournal2018}
-\usepackage{apacite}
-\usepackage{url} %this package should fix any errors with URLs in refs.
-%%%%%%%
-% As of 2018 we recommend use of the TrackChanges package to mark revisions.
-% The trackchanges package adds five new LaTeX commands:
-%
-%  \note[editor]{The note}
-%  \annote[editor]{Text to annotate}{The note}
-%  \add[editor]{Text to add}
-%  \remove[editor]{Text to remove}
-%  \change[editor]{Text to remove}{Text to add}
-%
-% complete documentation is here: http://trackchanges.sourceforge.net/
-%%%%%%%
+$endif$
 
 
 %% Enter journal name below.
@@ -113,6 +92,8 @@
 
 $if(csl-refs)$
 % Pandoc citation processing
+\providecommand{\phantomsection}{}
+\providecommand{\hypertarget}[2]{#2}
 $if(pandoc318)$
 %From Pandoc 3.1.8
 % definitions for citeproc citations
@@ -281,13 +262,13 @@
 
 %  List up to three key points (at least one is required)
 %  Key Points summarize the main points and conclusions of the article
-%  Each must be 100 characters or less with no special characters or punctuation
+%  Each must be 140 characters or fewer with no special characters or punctuation
 
 % Example:
 % \begin{keypoints}
 % \item	List up to three key points (at least one is required)
 % \item	Key Points summarize the main points and conclusions of the article
-% \item	Each must be 100 characters or less with no special characters or punctuation
+% \item	Each must be 140 characters or fewer with no special characters or punctuation
 % \end{keypoints}
 
 \begin{keypoints}
@@ -312,16 +293,14 @@
 $abstract$
 \end{abstract}
 $if(plain_language_summary)$
-\noindent{\bf Plain language summary}\vskip-\parskip
-
-\noindent{$plain_language_summary$}
-\vskip18pt
+\section*{Plain Language Summary}
+$plain_language_summary$
 $endif$
 $body$
 
-$if(bibliography)$
+$if(natbib)$$if(bibliography)$
 \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
-$endif$
+$endif$$endif$
 
 $for(include-after)$
 $include-after$