From d351e31ec1533cd67300d8ee80132c9e14bc75b3 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 21:37:03 +0100
Subject: [PATCH 01/12] Move fitting functions into fit

---
 R/defaults.R | 32 ---------------------------
 R/fit.R      | 62 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 R/generics.R |  3 +++
 _pkgdown.yml |  6 ++++-
 4 files changed, 70 insertions(+), 33 deletions(-)
 create mode 100644 R/fit.R

diff --git a/R/defaults.R b/R/defaults.R
index ab096aac3..144244092 100644
--- a/R/defaults.R
+++ b/R/defaults.R
@@ -23,35 +23,3 @@ epidist_stancode.default <- function(data, ...) {
     "See methods(epidist_stancode) for available methods"
   )
 }
-
-#' Default method used for interface using `brms`
-#'
-#' @inheritParams epidist
-#' @inheritParams epidist_formula
-#' @rdname epidist.default
-#' @method epidist default
-#' @family defaults
-#' @export
-epidist.default <- function(data, formula = brms::bf(mu ~ 1),
-                            family = "lognormal", prior = NULL,
-                            backend = "cmdstanr", fn = brms::brm, ...) {
-  epidist_validate(data)
-  epidist_family <- epidist_family(data, family)
-  epidist_formula <- epidist_formula(
-    data = data, family = epidist_family, formula = formula
-  )
-  epidist_prior <- epidist_prior(
-    data = data, family = family, formula = epidist_formula, prior
-  )
-  epidist_stancode <- epidist_stancode(
-    data = data, family = epidist_family, formula = epidist_formula
-  )
-  fit <- fn(
-    formula = epidist_formula, family = epidist_family, prior = epidist_prior,
-    stanvars = epidist_stancode, backend = backend, data = data, ...
-  )
-
-  class(fit) <- c(class(fit), "epidist_fit")
-
-  return(fit)
-}
diff --git a/R/fit.R b/R/fit.R
new file mode 100644
index 000000000..4285380b1
--- /dev/null
+++ b/R/fit.R
@@ -0,0 +1,62 @@
+#' Fit epidemiological delay distributions using a `brms` interface
+#'
+#' @inheritParams epidist_validate
+#' @param formula A formula object created using `brms::bf`. A formula must be
+#' provided for the distributional parameter `mu` common to all `brms` families.
+#' Optionally, formulas may also be provided for additional distributional
+#' parameters.
+#' @param family A description of the response distribution and link function to
+#' be used in the model. Every family function has a link argument allowing
+#' users to specify the link function to be applied on the response variable.
+#' If not specified, default links are used. For details of supported families
+#' see [brmsfamily()].
+#' @param prior One or more `brmsprior` objects created by [brms::set_prior()]
+#' or related functions. These priors are passed to [epidist_prior()] in the
+#' `prior` argument. We recommend caution and the use of prior predictive checks
+#' for specifying prior distributions.
+#' @param backend Character string naming the package to use as the backend for
+#' fitting the Stan model. Options are `"rstan"` and `"cmdstanr"` (the default).
+#' This option is passed directly through to `fn`.
+#' @param fn The internal function to be called. By default this is `brms::brm`,
+#' which performs inference for the specified model. Other options
+#' `brms::make_stancode`, which returns the Stan code for the specified model,
+#' and `brms::make_standata` which returns the data passed to Stan. These
+#' options may be useful for model debugging and extensions.
+#' @param ... Additional arguments for method.
+#' @family fit
+#' @export
+epidist <- function(data, formula, family, prior, backend, fn, ...) {
+  UseMethod("epidist")
+}
+
+#' Default method used for interface using `brms`
+#'
+#' @inheritParams epidist
+#' @inheritParams epidist_formula
+#' @rdname epidist.default
+#' @method epidist default
+#' @family fit
+#' @export
+epidist.default <- function(data, formula = brms::bf(mu ~ 1),
+                            family = "lognormal", prior = NULL,
+                            backend = "cmdstanr", fn = brms::brm, ...) {
+  epidist_validate(data)
+  epidist_family <- epidist_family(data, family)
+  epidist_formula <- epidist_formula(
+    data = data, family = epidist_family, formula = formula
+  )
+  epidist_prior <- epidist_prior(
+    data = data, family = family, formula = epidist_formula, prior
+  )
+  epidist_stancode <- epidist_stancode(
+    data = data, family = epidist_family, formula = epidist_formula
+  )
+  fit <- fn(
+    formula = epidist_formula, family = epidist_family, prior = epidist_prior,
+    stanvars = epidist_stancode, backend = backend, data = data, ...
+  )
+  
+  class(fit) <- c(class(fit), "epidist_fit")
+  
+  return(fit)
+}
diff --git a/R/generics.R b/R/generics.R
index cd5d70147..99fde2d6c 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -26,6 +26,7 @@ epidist_validate <- function(data) {
 epidist_stancode <- function(data, ...) {
   UseMethod("epidist_stancode")
 }
+<<<<<<< HEAD
 
 #' Fit epidemiological delay distributions using a `brms` interface
 #'
@@ -57,3 +58,5 @@ epidist_stancode <- function(data, ...) {
 epidist <- function(data, formula, family, prior, backend, fn, ...) {
   UseMethod("epidist")
 }
+=======
+>>>>>>> 4cb6f81e (Move fitting functions into fit.R)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index cf80bfada..3848f00ab 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -57,10 +57,14 @@ reference:
   desc: Functions related to specifying custom `brms` formula
   contents:
   - has_concept("formula")
-- title: Priors
+- title: Prior distributions
   desc: Functions for specifying prior distributions
   contents:
   - has_concept("prior")
+- title: Model fitting
+  desc: Functions for fitting delay distribution models
+  contents:
+  - has_concept("fit")
 - title: Latent individual model
   desc: Specific methods for the latent individual model
   contents:

From ab8ce1d20bfcc74700e0e6097700dd45c1b30c8e Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 21:37:26 +0100
Subject: [PATCH 02/12] Create stancode.R

---
 R/defaults.R | 13 -------------
 R/generics.R |  3 +++
 R/stancode.R | 28 ++++++++++++++++++++++++++++
 _pkgdown.yml |  6 +++++-
 4 files changed, 36 insertions(+), 14 deletions(-)
 create mode 100644 R/stancode.R

diff --git a/R/defaults.R b/R/defaults.R
index 144244092..e8fa85a35 100644
--- a/R/defaults.R
+++ b/R/defaults.R
@@ -10,16 +10,3 @@ epidist_validate.default <- function(data, ...) {
     "See methods(epidist_validate) for available methods"
   )
 }
-
-#' Default method for defining model specific Stan code
-#'
-#' @inheritParams epidist_stancode
-#' @param ... Additional arguments passed to method.
-#' @family defaults
-#' @export
-epidist_stancode.default <- function(data, ...) {
-  cli_abort(
-    "No epidist_stancode method implemented for the class ", class(data), "\n",
-    "See methods(epidist_stancode) for available methods"
-  )
-}
diff --git a/R/generics.R b/R/generics.R
index 99fde2d6c..007b153e2 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -10,6 +10,7 @@
 epidist_validate <- function(data) {
   UseMethod("epidist_validate")
 }
+<<<<<<< HEAD
 
 #' Define model specific Stan code
 #'
@@ -60,3 +61,5 @@ epidist <- function(data, formula, family, prior, backend, fn, ...) {
 }
 =======
 >>>>>>> 4cb6f81e (Move fitting functions into fit.R)
+=======
+>>>>>>> 8cb24d62 (Create stancode.R)
diff --git a/R/stancode.R b/R/stancode.R
new file mode 100644
index 000000000..674941e2e
--- /dev/null
+++ b/R/stancode.R
@@ -0,0 +1,28 @@
+#' Define model specific Stan code
+#'
+#' This function is used within [epidist()] to create any custom Stan code which
+#' is injected into `brms` via the `stanvars` argument. It is unlikely that
+#' as a user you will need this function, but we export it nonetheless to be
+#' transparent about what exactly is happening inside of a call to [epidist()].
+#'
+#' @inheritParams epidist_validate
+#' @param ... Additional arguments passed to method.
+#' @rdname epidist_stancode
+#' @family stan
+#' @export
+epidist_stancode <- function(data, ...) {
+  UseMethod("epidist_stancode")
+}
+
+#' Default method for defining model specific Stan code
+#'
+#' @inheritParams epidist_stancode
+#' @param ... Additional arguments passed to method.
+#' @family stan
+#' @export
+epidist_stancode.default <- function(data, ...) {
+  cli_abort(
+    "No epidist_stancode method implemented for the class ", class(data), "\n",
+    "See methods(epidist_stancode) for available methods"
+  )
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 3848f00ab..f23a4db96 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -61,8 +61,12 @@ reference:
   desc: Functions for specifying prior distributions
   contents:
   - has_concept("prior")
+- title: Stan code
+  desc: Functions for specifying custom Stan code to put into `brms`
+  contents:
+  - has_concept("stan") 
 - title: Model fitting
-  desc: Functions for fitting delay distribution models
+  desc: Functions for fitting delay distribution models using `brms`
   contents:
   - has_concept("fit")
 - title: Latent individual model

From 5c784904371e4811a955a90819cb89353a4c5af5 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 21:38:27 +0100
Subject: [PATCH 03/12] Create validate.R

---
 R/defaults.R | 13 +------------
 R/generics.R |  4 ++++
 R/validate.R | 25 +++++++++++++++++++++++++
 _pkgdown.yml |  4 ++++
 4 files changed, 34 insertions(+), 12 deletions(-)
 create mode 100644 R/validate.R

diff --git a/R/defaults.R b/R/defaults.R
index e8fa85a35..8b1378917 100644
--- a/R/defaults.R
+++ b/R/defaults.R
@@ -1,12 +1 @@
-#' Default method for data validation
-#'
-#' @inheritParams epidist_validate
-#' @param ... Additional arguments passed to method.
-#' @family defaults
-#' @export
-epidist_validate.default <- function(data, ...) {
-  cli_abort(
-    "No epidist_validate method implemented for the class ", class(data), "\n",
-    "See methods(epidist_validate) for available methods"
-  )
-}
+
diff --git a/R/generics.R b/R/generics.R
index 007b153e2..6dcf9628e 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 #' Validate a data object for use with [epidist()]
 #'
 #' This function validates that the provided `data` is suitable to run a
@@ -63,3 +64,6 @@ epidist <- function(data, formula, family, prior, backend, fn, ...) {
 >>>>>>> 4cb6f81e (Move fitting functions into fit.R)
 =======
 >>>>>>> 8cb24d62 (Create stancode.R)
+=======
+
+>>>>>>> 006aeb64 (Create validate.R)
diff --git a/R/validate.R b/R/validate.R
new file mode 100644
index 000000000..1ce7dbb21
--- /dev/null
+++ b/R/validate.R
@@ -0,0 +1,25 @@
+#' Validate a data object for use with [epidist()]
+#'
+#' This function validates that the provided `data` is suitable to run a
+#' particular `epidist` model. This may include checking the class of `data`,
+#' and that it contains suitable columns.
+#'
+#' @param data A `data.frame` containing line list data.
+#' @family validate
+#' @export
+epidist_validate <- function(data) {
+  UseMethod("epidist_validate")
+}
+
+#' Default method for data validation
+#'
+#' @inheritParams epidist_validate
+#' @param ... Additional arguments passed to method.
+#' @family validate
+#' @export
+epidist_validate.default <- function(data, ...) {
+  cli_abort(
+    "No epidist_validate method implemented for the class ", class(data), "\n",
+    "See methods(epidist_validate) for available methods"
+  )
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index f23a4db96..61f1dbd5d 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -41,6 +41,10 @@ reference:
   desc: Functions for preprocessing data
   contents:
   - has_concept("preprocess")
+- title: Validation
+  desc: Functions used to check validity of package objects
+  contents:
+  - has_concept("validate")
 - title: S3 generics
   desc: S3 generics for delay modelling
   contents:

From 28a9cd32778852f3bc28d8cdb90e0e3bc72046ed Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 21:39:00 +0100
Subject: [PATCH 04/12] Remove defaults.R and generics.R and pkgdown groups

---
 R/defaults.R |  1 -
 R/generics.R | 69 ----------------------------------------------------
 _pkgdown.yml |  8 ------
 3 files changed, 78 deletions(-)
 delete mode 100644 R/defaults.R
 delete mode 100644 R/generics.R

diff --git a/R/defaults.R b/R/defaults.R
deleted file mode 100644
index 8b1378917..000000000
--- a/R/defaults.R
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/R/generics.R b/R/generics.R
deleted file mode 100644
index 6dcf9628e..000000000
--- a/R/generics.R
+++ /dev/null
@@ -1,69 +0,0 @@
-<<<<<<< HEAD
-#' Validate a data object for use with [epidist()]
-#'
-#' This function validates that the provided `data` is suitable to run a
-#' particular `epidist` model. This may include checking the class of `data`,
-#' and that it contains suitable columns.
-#'
-#' @param data A `data.frame` containing line list data.
-#' @family generics
-#' @export
-epidist_validate <- function(data) {
-  UseMethod("epidist_validate")
-}
-<<<<<<< HEAD
-
-#' Define model specific Stan code
-#'
-#' This function is used within [epidist()] to create any custom Stan code which
-#' is injected into `brms` via the `stanvars` argument. It is unlikely that
-#' as a user you will need this function, but we export it nonetheless to be
-#' transparent about what exactly is happening inside of a call to [epidist()].
-#'
-#' @inheritParams epidist_validate
-#' @param ... Additional arguments passed to method.
-#' @rdname epidist_stancode
-#' @family generics
-#' @export
-epidist_stancode <- function(data, ...) {
-  UseMethod("epidist_stancode")
-}
-<<<<<<< HEAD
-
-#' Fit epidemiological delay distributions using a `brms` interface
-#'
-#' @inheritParams epidist_validate
-#' @param formula A formula object created using [brms::bf()]. A formula must be
-#' provided for the distributional parameter `mu` common to all `brms` families.
-#' Optionally, formulas may also be provided for additional distributional
-#' parameters.
-#' @param family A description of the response distribution and link function to
-#' be used in the model. Every family function has a link argument allowing
-#' users to specify the link function to be applied on the response variable.
-#' If not specified, default links are used. For details of supported families
-#' see [brmsfamily()].
-#' @param prior One or more `brmsprior` objects created by [brms::set_prior()]
-#' or related functions. These priors are passed to [epidist_prior()] in the
-#' `prior` argument. We recommend caution and the use of prior predictive checks
-#' for specifying prior distributions.
-#' @param backend Character string naming the package to use as the backend for
-#' fitting the Stan model. Options are `"rstan"` and `"cmdstanr"` (the default).
-#' This option is passed directly through to `fn`.
-#' @param fn The internal function to be called. By default this is
-#' [brms::brm()] which performs inference for the specified model. Other options
-#' [brms::make_stancode()], which returns the Stan code for the specified model,
-#' and [brms::make_standata()] which returns the data passed to Stan. These
-#' options may be useful for model debugging and extensions.
-#' @param ... Additional arguments for method.
-#' @family generics
-#' @export
-epidist <- function(data, formula, family, prior, backend, fn, ...) {
-  UseMethod("epidist")
-}
-=======
->>>>>>> 4cb6f81e (Move fitting functions into fit.R)
-=======
->>>>>>> 8cb24d62 (Create stancode.R)
-=======
-
->>>>>>> 006aeb64 (Create validate.R)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 61f1dbd5d..f5ef239b1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -45,14 +45,6 @@ reference:
   desc: Functions used to check validity of package objects
   contents:
   - has_concept("validate")
-- title: S3 generics
-  desc: S3 generics for delay modelling
-  contents:
-  - has_concept("generics")
-- title: Method default
-  desc: Default methods for S3 generics
-  contents:
-  - has_concept("defaults")
 - title: Family
   desc: Functions related to specifying custom `brms` families
   contents:

From 8b4dd25eb2af7c96af6b930374b4c24b8b23f0e2 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 10:30:18 +0100
Subject: [PATCH 05/12] Document

---
 man/epidist.Rd                  | 9 ++++-----
 man/epidist.default.Rd          | 9 ++++-----
 man/epidist_stancode.Rd         | 9 ++++-----
 man/epidist_stancode.default.Rd | 9 ++++-----
 man/epidist_validate.Rd         | 9 ++++-----
 man/epidist_validate.default.Rd | 9 ++++-----
 6 files changed, 24 insertions(+), 30 deletions(-)

diff --git a/man/epidist.Rd b/man/epidist.Rd
index 6ace0b497..dbb162aa5 100644
--- a/man/epidist.Rd
+++ b/man/epidist.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generics.R
+% Please edit documentation in R/fit.R
 \name{epidist}
 \alias{epidist}
 \title{Fit epidemiological delay distributions using a \code{brms} interface}
@@ -41,8 +41,7 @@ options may be useful for model debugging and extensions.}
 Fit epidemiological delay distributions using a \code{brms} interface
 }
 \seealso{
-Other generics: 
-\code{\link{epidist_stancode}()},
-\code{\link{epidist_validate}()}
+Other fit: 
+\code{\link{epidist.default}()}
 }
-\concept{generics}
+\concept{fit}
diff --git a/man/epidist.default.Rd b/man/epidist.default.Rd
index 6dac69030..376fb7645 100644
--- a/man/epidist.default.Rd
+++ b/man/epidist.default.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/defaults.R
+% Please edit documentation in R/fit.R
 \name{epidist.default}
 \alias{epidist.default}
 \title{Default method used for interface using \code{brms}}
@@ -49,8 +49,7 @@ options may be useful for model debugging and extensions.}
 Default method used for interface using \code{brms}
 }
 \seealso{
-Other defaults: 
-\code{\link{epidist_stancode.default}()},
-\code{\link{epidist_validate.default}()}
+Other fit: 
+\code{\link{epidist}()}
 }
-\concept{defaults}
+\concept{fit}
diff --git a/man/epidist_stancode.Rd b/man/epidist_stancode.Rd
index 3ed292a52..d86c8010d 100644
--- a/man/epidist_stancode.Rd
+++ b/man/epidist_stancode.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generics.R
+% Please edit documentation in R/stancode.R
 \name{epidist_stancode}
 \alias{epidist_stancode}
 \title{Define model specific Stan code}
@@ -18,8 +18,7 @@ as a user you will need this function, but we export it nonetheless to be
 transparent about what exactly is happening inside of a call to \code{\link[=epidist]{epidist()}}.
 }
 \seealso{
-Other generics: 
-\code{\link{epidist}()},
-\code{\link{epidist_validate}()}
+Other stan: 
+\code{\link{epidist_stancode.default}()}
 }
-\concept{generics}
+\concept{stan}
diff --git a/man/epidist_stancode.default.Rd b/man/epidist_stancode.default.Rd
index 7154370dd..1aa781741 100644
--- a/man/epidist_stancode.default.Rd
+++ b/man/epidist_stancode.default.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/defaults.R
+% Please edit documentation in R/stancode.R
 \name{epidist_stancode.default}
 \alias{epidist_stancode.default}
 \title{Default method for defining model specific Stan code}
@@ -15,8 +15,7 @@
 Default method for defining model specific Stan code
 }
 \seealso{
-Other defaults: 
-\code{\link{epidist.default}()},
-\code{\link{epidist_validate.default}()}
+Other stan: 
+\code{\link{epidist_stancode}()}
 }
-\concept{defaults}
+\concept{stan}
diff --git a/man/epidist_validate.Rd b/man/epidist_validate.Rd
index f30fc94cb..06d52bcbf 100644
--- a/man/epidist_validate.Rd
+++ b/man/epidist_validate.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generics.R
+% Please edit documentation in R/validate.R
 \name{epidist_validate}
 \alias{epidist_validate}
 \title{Validate a data object for use with \code{\link[=epidist]{epidist()}}}
@@ -15,8 +15,7 @@ particular \code{epidist} model. This may include checking the class of \code{da
 and that it contains suitable columns.
 }
 \seealso{
-Other generics: 
-\code{\link{epidist}()},
-\code{\link{epidist_stancode}()}
+Other validate: 
+\code{\link{epidist_validate.default}()}
 }
-\concept{generics}
+\concept{validate}
diff --git a/man/epidist_validate.default.Rd b/man/epidist_validate.default.Rd
index 9c0787ffa..e1c12f87a 100644
--- a/man/epidist_validate.default.Rd
+++ b/man/epidist_validate.default.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/defaults.R
+% Please edit documentation in R/validate.R
 \name{epidist_validate.default}
 \alias{epidist_validate.default}
 \title{Default method for data validation}
@@ -15,8 +15,7 @@
 Default method for data validation
 }
 \seealso{
-Other defaults: 
-\code{\link{epidist.default}()},
-\code{\link{epidist_stancode.default}()}
+Other validate: 
+\code{\link{epidist_validate}()}
 }
-\concept{defaults}
+\concept{validate}

From 38ec2e7d8cc50fd9de9194c2b96155e1181c0c33 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 10:32:17 +0100
Subject: [PATCH 06/12] Don't need this line

---
 R/fit.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/fit.R b/R/fit.R
index 4285380b1..d1697e3cf 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -32,7 +32,6 @@ epidist <- function(data, formula, family, prior, backend, fn, ...) {
 #' Default method used for interface using `brms`
 #'
 #' @inheritParams epidist
-#' @inheritParams epidist_formula
 #' @rdname epidist.default
 #' @method epidist default
 #' @family fit

From 2f1b406d41647226d7d3d4e6baa9789ae3f7e7c7 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 10:33:20 +0100
Subject: [PATCH 07/12] Standardise providing ... argument to generics

---
 R/validate.R            | 3 ++-
 man/epidist_validate.Rd | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/validate.R b/R/validate.R
index 1ce7dbb21..65d86d884 100644
--- a/R/validate.R
+++ b/R/validate.R
@@ -5,9 +5,10 @@
 #' and that it contains suitable columns.
 #'
 #' @param data A `data.frame` containing line list data.
+#' @param ... Additional arguments passed to method.
 #' @family validate
 #' @export
-epidist_validate <- function(data) {
+epidist_validate <- function(data, ...) {
   UseMethod("epidist_validate")
 }
 
diff --git a/man/epidist_validate.Rd b/man/epidist_validate.Rd
index 06d52bcbf..bccd9b855 100644
--- a/man/epidist_validate.Rd
+++ b/man/epidist_validate.Rd
@@ -4,10 +4,12 @@
 \alias{epidist_validate}
 \title{Validate a data object for use with \code{\link[=epidist]{epidist()}}}
 \usage{
-epidist_validate(data)
+epidist_validate(data, ...)
 }
 \arguments{
 \item{data}{A \code{data.frame} containing line list data.}
+
+\item{...}{Additional arguments passed to method.}
 }
 \description{
 This function validates that the provided \code{data} is suitable to run a

From 79ff399cfe348f384bb8fa8aaf8a69ca5d4b3fe4 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 10:37:24 +0100
Subject: [PATCH 08/12] Remove whitespace

---
 R/fit.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/fit.R b/R/fit.R
index d1697e3cf..b712cf350 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -54,8 +54,6 @@ epidist.default <- function(data, formula = brms::bf(mu ~ 1),
     formula = epidist_formula, family = epidist_family, prior = epidist_prior,
     stanvars = epidist_stancode, backend = backend, data = data, ...
   )
-  
   class(fit) <- c(class(fit), "epidist_fit")
-  
   return(fit)
 }

From 53babbd422def5590e3b2f5ac898a2cc85f032c6 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 11:02:47 +0100
Subject: [PATCH 09/12] Fix R CMD CHECK warning

---
 R/latent_individual.R                             | 3 ++-
 man/epidist_validate.epidist_latent_individual.Rd | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/latent_individual.R b/R/latent_individual.R
index 55c8d7211..86146e106 100644
--- a/R/latent_individual.R
+++ b/R/latent_individual.R
@@ -72,10 +72,11 @@ as_latent_individual.data.frame <- function(data) {
 #' `data.frame` with the correct columns.
 #'
 #' @param data A `data.frame` containing line list data
+#' @param ... ...
 #' @method epidist_validate epidist_latent_individual
 #' @family latent_individual
 #' @export
-epidist_validate.epidist_latent_individual <- function(data) {
+epidist_validate.epidist_latent_individual <- function(data, ...) {
   assert_true(is_latent_individual(data))
   assert_latent_individual_input(data)
   assert_names(
diff --git a/man/epidist_validate.epidist_latent_individual.Rd b/man/epidist_validate.epidist_latent_individual.Rd
index 81d82e537..986b13ded 100644
--- a/man/epidist_validate.epidist_latent_individual.Rd
+++ b/man/epidist_validate.epidist_latent_individual.Rd
@@ -4,10 +4,12 @@
 \alias{epidist_validate.epidist_latent_individual}
 \title{Validate latent individual model data}
 \usage{
-\method{epidist_validate}{epidist_latent_individual}(data)
+\method{epidist_validate}{epidist_latent_individual}(data, ...)
 }
 \arguments{
 \item{data}{A \code{data.frame} containing line list data}
+
+\item{...}{...}
 }
 \description{
 This function checks whether the provided \code{data} object is suitable for

From 264e95f7f2b7516f3833a1a1089e8d5c5a1fe8a2 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 21:41:10 +0100
Subject: [PATCH 10/12] Return NULL by default for stancode

---
 R/stancode.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/stancode.R b/R/stancode.R
index 674941e2e..669e7cf22 100644
--- a/R/stancode.R
+++ b/R/stancode.R
@@ -21,8 +21,5 @@ epidist_stancode <- function(data, ...) {
 #' @family stan
 #' @export
 epidist_stancode.default <- function(data, ...) {
-  cli_abort(
-    "No epidist_stancode method implemented for the class ", class(data), "\n",
-    "See methods(epidist_stancode) for available methods"
-  )
+  return(NULL)
 }

From 934c204c796263de5d75f614dde7203a3671050a Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 22:02:58 +0100
Subject: [PATCH 11/12] Add test of Stan code NULL case

---
 tests/testthat/test-stancode.R | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 tests/testthat/test-stancode.R

diff --git a/tests/testthat/test-stancode.R b/tests/testthat/test-stancode.R
new file mode 100644
index 000000000..898740509
--- /dev/null
+++ b/tests/testthat/test-stancode.R
@@ -0,0 +1,3 @@
+test_that("epidist_stancode.default returns NULL", { # nolint: line_length_linter.
+  expect_null(epidist_stancode(data.frame()))
+})

From ff01e8aefd97328e768cfda4dca4fd3df7d37fb8 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Tue, 15 Oct 2024 23:12:58 +0100
Subject: [PATCH 12/12] Add test for stanvars class

---
 tests/testthat/test-latent_individual.R | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-latent_individual.R b/tests/testthat/test-latent_individual.R
index 9aafac4c5..5675c4c96 100644
--- a/tests/testthat/test-latent_individual.R
+++ b/tests/testthat/test-latent_individual.R
@@ -50,5 +50,12 @@ test_that("epidist_validate.epidist_latent_individual returns FALSE for incorrec
 })
 
 test_that("epidist_stancode.epidist_latent_individual produces valid stanvars", { # nolint: line_length_linter.
-  expect_equal(1, 1)
+  epidist_family <- epidist_family(prep_obs)
+  epidist_formula <- epidist_formula(
+    prep_obs, epidist_family, formula = brms::bf(mu ~ 1)
+  )
+  stancode <- epidist_stancode(
+    prep_obs, family = epidist_family, formula = epidist_formula
+  )
+  expect_s3_class(stancode, "stanvars")
 })