From ab1b7ca41705b9b64d755a3522096d84b77d086d Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 11:35:02 +0000
Subject: [PATCH 01/11] Add 3 families and bf as reexports

---
 NAMESPACE     |  7 +++++++
 R/reexports.R | 15 +++++++++++++++
 _pkgdown.yml  |  3 +++
 3 files changed, 25 insertions(+)
 create mode 100644 R/reexports.R

diff --git a/NAMESPACE b/NAMESPACE
index 83cc4fcb4..c7d355347 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -23,11 +23,13 @@ S3method(epidist_formula_model,epidist_latent_model)
 S3method(epidist_model_prior,default)
 S3method(epidist_stancode,default)
 S3method(epidist_stancode,epidist_latent_model)
+export(Gamma)
 export(add_mean_sd)
 export(as_epidist_latent_model)
 export(as_epidist_linelist_data)
 export(as_epidist_naive_model)
 export(assert_epidist)
+export(bf)
 export(epidist)
 export(epidist_diagnostics)
 export(epidist_family)
@@ -42,6 +44,7 @@ export(epidist_stancode)
 export(is_epidist_latent_model)
 export(is_epidist_linelist_data)
 export(is_epidist_naive_model)
+export(lognormal)
 export(new_epidist_latent_model)
 export(new_epidist_linelist_data)
 export(new_epidist_naive_model)
@@ -52,10 +55,13 @@ export(simulate_exponential_cases)
 export(simulate_gillespie)
 export(simulate_secondary)
 export(simulate_uniform_cases)
+export(weibull)
 import(ggplot2)
 importFrom(brms,bf)
+importFrom(brms,lognormal)
 importFrom(brms,prior)
 importFrom(brms,stanvar)
+importFrom(brms,weibull)
 importFrom(checkmate,assert_class)
 importFrom(checkmate,assert_data_frame)
 importFrom(checkmate,assert_date)
@@ -75,6 +81,7 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(lubridate,days)
 importFrom(lubridate,is.timepoint)
+importFrom(stats,Gamma)
 importFrom(stats,as.formula)
 importFrom(stats,setNames)
 importFrom(tibble,tibble)
diff --git a/R/reexports.R b/R/reexports.R
new file mode 100644
index 000000000..d4a60e421
--- /dev/null
+++ b/R/reexports.R
@@ -0,0 +1,15 @@
+#' @importFrom brms lognormal
+#' @export
+brms::lognormal
+
+#' @importFrom brms weibull
+#' @export
+brms::weibull
+
+#' @importFrom stats Gamma
+#' @export
+stats::Gamma
+
+#' @importFrom brms bf
+#' @export
+brms::bf
diff --git a/_pkgdown.yml b/_pkgdown.yml
index a371ea562..7d0e1cf9c 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -84,3 +84,6 @@ reference:
 - title: Diagnostic functions
   contents:
   - has_concept("diagnostics")
+- title: Reexported functions
+  contents:
+  - reexports

From f0095201d56f75e768f4eb40ee61a82cde5a6192 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 11:46:57 +0000
Subject: [PATCH 02/11] Use lognormal() as default and document it

---
 R/epidist.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/epidist.R b/R/epidist.R
index 74c1632e1..c7d5035ae 100644
--- a/R/epidist.R
+++ b/R/epidist.R
@@ -9,8 +9,9 @@
 #' @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()].
+#' If not specified, default links are used. For details of all supported
+#' families see [brmsfamily()]. Commonly used, such as [lognormal()], are also
+#' reexported as part of `epidist`.
 #' @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.
@@ -34,7 +35,7 @@ epidist <- function(data, formula, family, prior, fn, ...) {
 #' @family fit
 #' @export
 epidist.default <- function(data, formula = mu ~ 1,
-                            family = "lognormal", prior = NULL,
+                            family = lognormal(), prior = NULL,
                             fn = brms::brm, ...) {
   assert_epidist(data)
   epidist_family <- epidist_family(data, family)

From 5ed11899473648128016162660c1fce41a720a6c Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 11:51:33 +0000
Subject: [PATCH 03/11] Use lognormal() not "lognormal"

---
 R/family.R                             | 2 +-
 tests/testthat/test-int-latent_model.R | 2 +-
 tests/testthat/test-utils.R            | 4 ++--
 vignettes/faq.Rmd                      | 7 ++++---
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/R/family.R b/R/family.R
index a3758f45b..9512b9019 100644
--- a/R/family.R
+++ b/R/family.R
@@ -8,7 +8,7 @@
 #' @inheritParams epidist
 #' @family family
 #' @export
-epidist_family <- function(data, family = "lognormal", ...) {
+epidist_family <- function(data, family = lognormal(), ...) {
   assert_epidist(data)
   family <- brms:::validate_family(family) # nolint
   class(family) <- c(family$family, class(family))
diff --git a/tests/testthat/test-int-latent_model.R b/tests/testthat/test-int-latent_model.R
index db269ffe1..c7f1d9870 100644
--- a/tests/testthat/test-int-latent_model.R
+++ b/tests/testthat/test-int-latent_model.R
@@ -86,7 +86,7 @@ test_that("epidist.epidist_latent_model Stan code has no syntax errors", { # nol
   set.seed(1)
   stancode_string <- epidist(
     data = prep_obs,
-    family = "lognormal",
+    family = lognormal(),
     seed = 1,
     silent = 2, refresh = 0,
     fn = brms::make_stancode
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index e7b602a75..ababc67de 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -40,7 +40,7 @@ test_that(".add_dpar_info works as expected for the lognormal and gamma families
 
 test_that(".make_intercepts_explicit creates a formula which is the same as if it had been explicitly created", { # nolint: line_length_linter.
   prep_obs <- as_epidist_latent_model(sim_obs)
-  epidist_family <- epidist_family(prep_obs, family = "lognormal")
+  epidist_family <- epidist_family(prep_obs, family = lognormal())
   formula <- brms:::validate_formula( # nolint
     formula = brms::bf(mu ~ 1),
     data = prep_obs,
@@ -59,7 +59,7 @@ test_that(".make_intercepts_explicit creates a formula which is the same as if i
 
 test_that(".make_intercepts_explicit does not add an intercept if the distributional parameter is set to be fixed", { # nolint: line_length_linter.
   prep_obs <- as_epidist_latent_model(sim_obs)
-  epidist_family <- epidist_family(prep_obs, family = "lognormal")
+  epidist_family <- epidist_family(prep_obs, family = lognormal())
   formula <- brms:::validate_formula( # nolint
     formula = brms::bf(mu ~ 1, sigma = 1),
     data = prep_obs,
diff --git a/vignettes/faq.Rmd b/vignettes/faq.Rmd
index 5a9a9e08f..3f8081435 100644
--- a/vignettes/faq.Rmd
+++ b/vignettes/faq.Rmd
@@ -112,12 +112,13 @@ Instead, we used [prior predictive checking](https://mc-stan.org/docs/stan-users
 For example, for the `brms::lognormal()` latent individual model, we suggest the following prior distributions for the `brms` `mu` and `sigma` intercept parameters:
 
 ```{r}
-family <- "lognormal"
+family <- lognormal()
 
 epidist_family <- epidist_family(data, family)
 epidist_formula <- epidist_formula(
   data,
-  family = epidist_family, formula = mu ~ 1
+  family = epidist_family,
+  formula = mu ~ 1
 )
 
 # NULL here means no replacing priors from the user!
@@ -140,7 +141,7 @@ set.seed(1)
 fit_ppc <- epidist(
   data = data,
   formula = mu ~ 1,
-  family = "lognormal",
+  family = lognormal(),
   sample_prior = "only",
   seed = 1
 )

From 035efeca0de5b6f3a2053fbc6d8a707c133e47a1 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 11:54:59 +0000
Subject: [PATCH 04/11] Stop with brms::bf and use bf

---
 tests/testthat/setup.R                 |  2 +-
 tests/testthat/test-formula.R          | 12 ++++++------
 tests/testthat/test-int-latent_model.R |  4 ++--
 tests/testthat/test-latent_model.R     |  2 +-
 tests/testthat/test-prior.R            |  2 +-
 tests/testthat/test-utils.R            |  6 +++---
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 0ce7a4f78..2b7abb648 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -119,7 +119,7 @@ if (not_on_cran()) {
 
   fit_sex <- epidist(
     data = prep_obs_sex,
-    formula = brms::bf(mu ~ 1 + sex, sigma ~ 1 + sex),
+    formula = bf(mu ~ 1 + sex, sigma ~ 1 + sex),
     seed = 1, silent = 2, refresh = 0,
     cores = 2, chains = 2, backend = "cmdstanr"
   )
diff --git a/tests/testthat/test-formula.R b/tests/testthat/test-formula.R
index f2ceeb9ba..759e4d291 100644
--- a/tests/testthat/test-formula.R
+++ b/tests/testthat/test-formula.R
@@ -18,7 +18,7 @@ test_that("epidist_formula with default settings produces a brmsformula with the
   )
   form_explicit <- epidist_formula(
     prep_obs,
-    family = family_lognormal, formula = brms::bf(mu ~ 1, sigma ~ 1)
+    family = family_lognormal, formula = bf(mu ~ 1, sigma ~ 1)
   )
   attr(form$pforms$sigma, ".Environment") <- NULL
   attr(form_explicit$pforms$sigma, ".Environment") <- NULL
@@ -30,7 +30,7 @@ test_that("epidist_formula with custom formulas produces a brmsformula with corr
   form_sex <- epidist_formula(
     prep_obs,
     family = family_lognormal,
-    formula = brms::bf(mu ~ 1 + sex, sigma ~ 1 + sex)
+    formula = bf(mu ~ 1 + sex, sigma ~ 1 + sex)
   )
   expect_s3_class(form_sex, "brmsformula")
   expect_identical(
@@ -48,28 +48,28 @@ test_that("epidist_formula with custom formulas errors for incorrect custom form
     epidist_formula(
       prep_obs,
       family = family_lognormal,
-      formula = brms::bf(mu ~ 1 + age, sigma ~ 1)
+      formula = bf(mu ~ 1 + age, sigma ~ 1)
     )
   )
   expect_error(
     epidist_formula(
       prep_obs,
       family = family_lognormal,
-      formula = brms::bf(mu ~ 1, sigma ~ 1 + age)
+      formula = bf(mu ~ 1, sigma ~ 1 + age)
     )
   )
   expect_error(
     epidist_formula(
       prep_obs,
       family = family_lognormal,
-      formula = brms::bf(list(), sigma ~ 1)
+      formula = bf(list(), sigma ~ 1)
     )
   )
   expect_error(
     epidist_formula(
       prep_obs,
       family = family_lognormal,
-      formula = brms::bf(mu ~ 1, shape ~ 1)
+      formula = bf(mu ~ 1, shape ~ 1)
     )
   )
 })
diff --git a/tests/testthat/test-int-latent_model.R b/tests/testthat/test-int-latent_model.R
index c7f1d9870..75fa34725 100644
--- a/tests/testthat/test-int-latent_model.R
+++ b/tests/testthat/test-int-latent_model.R
@@ -67,7 +67,7 @@ test_that("epidist.epidist_latent_model fits, the MCMC converges, and the draws
   set.seed(1)
   fit_constant <- epidist(
     data = prep_obs,
-    formula = brms::bf(mu ~ 1, sigma = 1),
+    formula = bf(mu ~ 1, sigma = 1),
     seed = 1,
     silent = 2, refresh = 0,
     cores = 2,
@@ -153,7 +153,7 @@ test_that("epidist.epidist_latent_model Stan code has no syntax errors for an al
   skip_on_cran()
   stancode_sex <- epidist(
     data = prep_obs_sex,
-    formula = brms::bf(mu ~ 1 + sex, sigma ~ 1 + sex),
+    formula = bf(mu ~ 1 + sex, sigma ~ 1 + sex),
     fn = brms::make_stancode,
     cores = 2
   )
diff --git a/tests/testthat/test-latent_model.R b/tests/testthat/test-latent_model.R
index 357008fde..9d0d6e2f8 100644
--- a/tests/testthat/test-latent_model.R
+++ b/tests/testthat/test-latent_model.R
@@ -48,7 +48,7 @@ test_that("epidist_stancode.epidist_latent_model produces valid stanvars", { # n
   epidist_family <- epidist_family(prep_obs)
   epidist_formula <- epidist_formula(
     prep_obs, epidist_family,
-    formula = brms::bf(mu ~ 1)
+    formula = bf(mu ~ 1)
   )
   stancode <- epidist_stancode(
     prep_obs,
diff --git a/tests/testthat/test-prior.R b/tests/testthat/test-prior.R
index fa77fba4e..a62fec816 100644
--- a/tests/testthat/test-prior.R
+++ b/tests/testthat/test-prior.R
@@ -1,7 +1,7 @@
 test_that("epidist_prior with default settings produces an object of the right class", { # nolint: line_length_linter.
   data <- as_epidist_latent_model(sim_obs)
   family <- brms::lognormal()
-  formula <- brms::bf(mu ~ 1, sigma ~ 1)
+  formula <- bf(mu ~ 1, sigma ~ 1)
   epidist_family <- epidist_family(data, family)
   epidist_formula <- epidist_formula(
     data = data, family = epidist_family, formula = formula
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index ababc67de..67d905560 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -42,13 +42,13 @@ test_that(".make_intercepts_explicit creates a formula which is the same as if i
   prep_obs <- as_epidist_latent_model(sim_obs)
   epidist_family <- epidist_family(prep_obs, family = lognormal())
   formula <- brms:::validate_formula( # nolint
-    formula = brms::bf(mu ~ 1),
+    formula = bf(mu ~ 1),
     data = prep_obs,
     family = epidist_family
   )
   formula <- .make_intercepts_explicit(formula)
   formula_explicit <- brms:::validate_formula( # nolint
-    formula = brms::bf(mu ~ 1, sigma ~ 1),
+    formula = bf(mu ~ 1, sigma ~ 1),
     data = prep_obs,
     family = epidist_family
   )
@@ -61,7 +61,7 @@ test_that(".make_intercepts_explicit does not add an intercept if the distributi
   prep_obs <- as_epidist_latent_model(sim_obs)
   epidist_family <- epidist_family(prep_obs, family = lognormal())
   formula <- brms:::validate_formula( # nolint
-    formula = brms::bf(mu ~ 1, sigma = 1),
+    formula = bf(mu ~ 1, sigma = 1),
     data = prep_obs,
     family = epidist_family
   )

From a2542da15e8ca996331294568e5b9e54030e21bc Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 11:58:33 +0000
Subject: [PATCH 05/11] Remove more calls to brms::lognormal that can be
 lognormal

---
 tests/testthat/test-family.R       | 2 +-
 tests/testthat/test-latent_model.R | 2 +-
 tests/testthat/test-naive_model.R  | 2 +-
 tests/testthat/test-prior.R        | 2 +-
 tests/testthat/test-utils.R        | 2 +-
 vignettes/faq.Rmd                  | 1 +
 6 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-family.R b/tests/testthat/test-family.R
index 8fb1f0f46..adeb50443 100644
--- a/tests/testthat/test-family.R
+++ b/tests/testthat/test-family.R
@@ -11,7 +11,7 @@ test_that("epidist_family gives an error when passed inappropriate family input"
 })
 
 test_that("the family argument in epidist_family passes as expected for brms and stats family objects, as well as strings", { # nolint: line_length_linter.
-  family_lognormal <- epidist_family(prep_obs, family = brms::lognormal())
+  family_lognormal <- epidist_family(prep_obs, family = lognormal())
   expect_identical(family_lognormal$name, "latent_lognormal")
   family_gamma <- epidist_family(prep_obs, family = Gamma(link = "log"))
   expect_identical(family_gamma$name, "latent_gamma")
diff --git a/tests/testthat/test-latent_model.R b/tests/testthat/test-latent_model.R
index 9d0d6e2f8..579af69fc 100644
--- a/tests/testthat/test-latent_model.R
+++ b/tests/testthat/test-latent_model.R
@@ -10,7 +10,7 @@ test_that("as_epidist_latent_model.epidist_linelist_data errors when passed inco
 })
 
 # Make this data available for other tests
-family_lognormal <- epidist_family(prep_obs, family = brms::lognormal())
+family_lognormal <- epidist_family(prep_obs, family = lognormal())
 
 test_that("is_epidist_latent_model returns TRUE for correct input", { # nolint: line_length_linter.
   expect_true(is_epidist_latent_model(prep_obs))
diff --git a/tests/testthat/test-naive_model.R b/tests/testthat/test-naive_model.R
index b63c95865..de691d49a 100644
--- a/tests/testthat/test-naive_model.R
+++ b/tests/testthat/test-naive_model.R
@@ -10,7 +10,7 @@ test_that("as_epidist_naive_model.data.frame errors when passed incorrect inputs
 })
 
 # Make this data available for other tests
-family_lognormal <- epidist_family(sim_obs, family = brms::lognormal())
+family_lognormal <- epidist_family(sim_obs, family = lognormal())
 
 test_that("is_epidist_naive_model returns TRUE for correct input", { # nolint: line_length_linter.
   expect_true(is_epidist_naive_model(prep_naive_obs))
diff --git a/tests/testthat/test-prior.R b/tests/testthat/test-prior.R
index a62fec816..aab1d08f8 100644
--- a/tests/testthat/test-prior.R
+++ b/tests/testthat/test-prior.R
@@ -1,6 +1,6 @@
 test_that("epidist_prior with default settings produces an object of the right class", { # nolint: line_length_linter.
   data <- as_epidist_latent_model(sim_obs)
-  family <- brms::lognormal()
+  family <- lognormal()
   formula <- bf(mu ~ 1, sigma ~ 1)
   epidist_family <- epidist_family(data, family)
   epidist_formula <- epidist_formula(
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 67d905560..838b34986 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -30,7 +30,7 @@ cli::test_that_cli(".replace_prior errors when passed a new prior without a matc
 })
 
 test_that(".add_dpar_info works as expected for the lognormal and gamma families", { # nolint: line_length_linter.
-  lognormal_extra <- .add_dpar_info(brms::lognormal())
+  lognormal_extra <- .add_dpar_info(lognormal())
   expect_identical(lognormal_extra$other_links, "log")
   expect_identical(lognormal_extra$other_bounds, list(list(lb = "0", ub = "")))
   gamma_extra <- .add_dpar_info(brms:::validate_family(stats::Gamma())) # nolint
diff --git a/vignettes/faq.Rmd b/vignettes/faq.Rmd
index 3f8081435..8121f0355 100644
--- a/vignettes/faq.Rmd
+++ b/vignettes/faq.Rmd
@@ -112,6 +112,7 @@ Instead, we used [prior predictive checking](https://mc-stan.org/docs/stan-users
 For example, for the `brms::lognormal()` latent individual model, we suggest the following prior distributions for the `brms` `mu` and `sigma` intercept parameters:
 
 ```{r}
+# Note that we export lognormal() as part of epidist hence no need for brms::
 family <- lognormal()
 
 epidist_family <- epidist_family(data, family)

From 6685e2545d39e872a8790a0bfb6693682f6a3938 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 11:59:30 +0000
Subject: [PATCH 06/11] We are also exporting stats::Gamma

---
 tests/testthat/setup.R                 | 2 +-
 tests/testthat/test-int-latent_model.R | 4 ++--
 tests/testthat/test-utils.R            | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 2b7abb648..1d638f3a9 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -112,7 +112,7 @@ if (not_on_cran()) {
   )
 
   fit_gamma <- epidist(
-    data = prep_obs_gamma, family = stats::Gamma(link = "log"),
+    data = prep_obs_gamma, family = Gamma(link = "log"),
     seed = 1, chains = 2, cores = 2, silent = 2, refresh = 0,
     backend = "cmdstanr"
   )
diff --git a/tests/testthat/test-int-latent_model.R b/tests/testthat/test-int-latent_model.R
index 75fa34725..e0d7db070 100644
--- a/tests/testthat/test-int-latent_model.R
+++ b/tests/testthat/test-int-latent_model.R
@@ -29,7 +29,7 @@ test_that("epidist.epidist_latent_model samples from the prior according to marg
     cores = 2
   )
   pred <- predict_delay_parameters(prior_samples)
-  family <- brms::lognormal()
+  family <- lognormal()
   epidist_family <- epidist_family(data = prep_obs, family = family)
   epidist_formula <- epidist_formula(
     data = prep_obs,
@@ -111,7 +111,7 @@ test_that("epidist.epidist_latent_model Stan code has no syntax errors and compi
   skip_on_cran()
   stancode_gamma <- epidist(
     data = prep_obs_gamma,
-    family = stats::Gamma(link = "log"),
+    family = Gamma(link = "log"),
     formula = mu ~ 1,
     cores = 2,
     fn = brms::make_stancode
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 838b34986..f0012d6ed 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -33,7 +33,7 @@ test_that(".add_dpar_info works as expected for the lognormal and gamma families
   lognormal_extra <- .add_dpar_info(lognormal())
   expect_identical(lognormal_extra$other_links, "log")
   expect_identical(lognormal_extra$other_bounds, list(list(lb = "0", ub = "")))
-  gamma_extra <- .add_dpar_info(brms:::validate_family(stats::Gamma())) # nolint
+  gamma_extra <- .add_dpar_info(brms:::validate_family(Gamma())) # nolint
   expect_null(gamma_extra$other_links)
   expect_identical(gamma_extra$other_bounds, list(list(lb = "0", ub = "")))
 })

From bc9c953a6802311f620a77c7f506117c25ca63da Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 12:00:18 +0000
Subject: [PATCH 07/11] Another one

---
 tests/testthat/test-formula.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-formula.R b/tests/testthat/test-formula.R
index 759e4d291..c93f8f829 100644
--- a/tests/testthat/test-formula.R
+++ b/tests/testthat/test-formula.R
@@ -1,6 +1,6 @@
 prep_obs_gamma <- as_epidist_latent_model(sim_obs_gamma)
 
-family_lognormal <- epidist_family(prep_obs, family = brms::lognormal())
+family_lognormal <- epidist_family(prep_obs, family = lognormal())
 
 test_that("epidist_formula with default settings produces a brmsformula with the correct intercept only formula", { # nolint: line_length_linter.
   form <- epidist_formula(

From 2fe98c7ce01044276bd3494eaf7590577c94cfc2 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Sat, 16 Nov 2024 12:01:32 +0000
Subject: [PATCH 08/11] Document

---
 man/dot-add_dpar_info.Rd              |  5 +++--
 man/epidist.Rd                        |  5 +++--
 man/epidist.default.Rd                |  7 ++++---
 man/epidist_family.Rd                 |  7 ++++---
 man/epidist_family_prior.Rd           |  5 +++--
 man/epidist_family_prior.default.Rd   |  5 +++--
 man/epidist_family_prior.lognormal.Rd |  5 +++--
 man/epidist_family_reparam.Rd         |  5 +++--
 man/epidist_family_reparam.default.Rd |  5 +++--
 man/epidist_family_reparam.gamma.Rd   |  5 +++--
 man/reexports.Rd                      | 21 +++++++++++++++++++++
 11 files changed, 53 insertions(+), 22 deletions(-)
 create mode 100644 man/reexports.Rd

diff --git a/man/dot-add_dpar_info.Rd b/man/dot-add_dpar_info.Rd
index 444cbbc75..ac4460d66 100644
--- a/man/dot-add_dpar_info.Rd
+++ b/man/dot-add_dpar_info.Rd
@@ -10,8 +10,9 @@
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 }
 \description{
 Includes additional information (link functions and parameter bound) about
diff --git a/man/epidist.Rd b/man/epidist.Rd
index f6663d66c..a9a4ab7c0 100644
--- a/man/epidist.Rd
+++ b/man/epidist.Rd
@@ -18,8 +18,9 @@ parameters.}
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{prior}{One or more \code{brmsprior} objects created by \code{\link[brms:set_prior]{brms::set_prior()}}
 or related functions. These priors are passed to \code{\link[=epidist_prior]{epidist_prior()}} in the
diff --git a/man/epidist.default.Rd b/man/epidist.default.Rd
index 18353ca08..3de4f4b8f 100644
--- a/man/epidist.default.Rd
+++ b/man/epidist.default.Rd
@@ -7,7 +7,7 @@
 \method{epidist}{default}(
   data,
   formula = mu ~ 1,
-  family = "lognormal",
+  family = lognormal(),
   prior = NULL,
   fn = brms::brm,
   ...
@@ -25,8 +25,9 @@ parameters.}
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{prior}{One or more \code{brmsprior} objects created by \code{\link[brms:set_prior]{brms::set_prior()}}
 or related functions. These priors are passed to \code{\link[=epidist_prior]{epidist_prior()}} in the
diff --git a/man/epidist_family.Rd b/man/epidist_family.Rd
index bb4bdc615..ba7960fc7 100644
--- a/man/epidist_family.Rd
+++ b/man/epidist_family.Rd
@@ -4,7 +4,7 @@
 \alias{epidist_family}
 \title{Define \code{epidist} family}
 \usage{
-epidist_family(data, family = "lognormal", ...)
+epidist_family(data, family = lognormal(), ...)
 }
 \arguments{
 \item{data}{A \code{data.frame} containing line list data.}
@@ -12,8 +12,9 @@ epidist_family(data, family = "lognormal", ...)
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{...}{Additional arguments passed to \code{fn} method.}
 }
diff --git a/man/epidist_family_prior.Rd b/man/epidist_family_prior.Rd
index 82ce122dd..48344ce2b 100644
--- a/man/epidist_family_prior.Rd
+++ b/man/epidist_family_prior.Rd
@@ -10,8 +10,9 @@ epidist_family_prior(family, ...)
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{...}{Additional arguments passed to \code{fn} method.}
 }
diff --git a/man/epidist_family_prior.default.Rd b/man/epidist_family_prior.default.Rd
index eb2677626..3139ac0a4 100644
--- a/man/epidist_family_prior.default.Rd
+++ b/man/epidist_family_prior.default.Rd
@@ -10,8 +10,9 @@
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{formula}{An object of class \link[stats:formula]{stats::formula} or \link[brms:brmsformula]{brms::brmsformula}
 (or one that can be coerced to those classes). A symbolic description of the
diff --git a/man/epidist_family_prior.lognormal.Rd b/man/epidist_family_prior.lognormal.Rd
index 2708ba9ff..2830dd82e 100644
--- a/man/epidist_family_prior.lognormal.Rd
+++ b/man/epidist_family_prior.lognormal.Rd
@@ -10,8 +10,9 @@
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{formula}{An object of class \link[stats:formula]{stats::formula} or \link[brms:brmsformula]{brms::brmsformula}
 (or one that can be coerced to those classes). A symbolic description of the
diff --git a/man/epidist_family_reparam.Rd b/man/epidist_family_reparam.Rd
index 27ecba0a4..13a39547b 100644
--- a/man/epidist_family_reparam.Rd
+++ b/man/epidist_family_reparam.Rd
@@ -10,8 +10,9 @@ epidist_family_reparam(family, ...)
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{...}{Additional arguments passed to \code{fn} method.}
 }
diff --git a/man/epidist_family_reparam.default.Rd b/man/epidist_family_reparam.default.Rd
index 4fc4531de..8ab4d39ce 100644
--- a/man/epidist_family_reparam.default.Rd
+++ b/man/epidist_family_reparam.default.Rd
@@ -10,8 +10,9 @@
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{...}{Additional arguments passed to \code{fn} method.}
 }
diff --git a/man/epidist_family_reparam.gamma.Rd b/man/epidist_family_reparam.gamma.Rd
index 70acfa454..090cae603 100644
--- a/man/epidist_family_reparam.gamma.Rd
+++ b/man/epidist_family_reparam.gamma.Rd
@@ -10,8 +10,9 @@
 \item{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 \code{\link[=brmsfamily]{brmsfamily()}}.}
+If not specified, default links are used. For details of all supported
+families see \code{\link[=brmsfamily]{brmsfamily()}}. Commonly used, such as \code{\link[=lognormal]{lognormal()}}, are also
+reexported as part of \code{epidist}.}
 
 \item{...}{Additional arguments passed to \code{fn} method.}
 }
diff --git a/man/reexports.Rd b/man/reexports.Rd
new file mode 100644
index 000000000..afd1c9f79
--- /dev/null
+++ b/man/reexports.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reexports.R
+\docType{import}
+\name{reexports}
+\alias{reexports}
+\alias{lognormal}
+\alias{weibull}
+\alias{Gamma}
+\alias{bf}
+\title{Objects exported from other packages}
+\keyword{internal}
+\description{
+These objects are imported from other packages. Follow the links
+below to see their documentation.
+
+\describe{
+  \item{brms}{\code{\link[brms:brmsformula]{bf}}, \code{\link[brms:brmsfamily]{lognormal}}, \code{\link[brms:brmsfamily]{weibull}}}
+
+  \item{stats}{\code{\link[stats:family]{Gamma}}}
+}}
+

From 7d278a1ef50a9e1fb698c3c13c53532c30c114c1 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Mon, 18 Nov 2024 10:55:13 +0000
Subject: [PATCH 09/11] Use predictions in test of sex effect

---
 tests/testthat/test-int-latent_model.R | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-int-latent_model.R b/tests/testthat/test-int-latent_model.R
index e0d7db070..93b74179f 100644
--- a/tests/testthat/test-int-latent_model.R
+++ b/tests/testthat/test-int-latent_model.R
@@ -167,9 +167,21 @@ test_that("epidist.epidist_latent_model recovers a sex effect", { # nolint: line
   # Note: this test is stochastic. See note at the top of this script
   skip_on_cran()
   set.seed(1)
-  draws <- posterior::as_draws_df(fit_sex$fit)
-  expect_equal(mean(draws$b_sex), -0.73, tolerance = 0.2)
-  expect_equal(mean(draws$b_sigma_sex), 0.43, tolerance = 0.2)
+  sex_effect <- predict_delay_parameters(fit_sex) |>
+    left_join(
+      mutate(sim_obs_sex, index = row_number()) |>
+        select(index, sex),
+      by = "index"
+    ) |>
+    group_by(sex) |>
+    summarise(
+      mu = mean(mu),
+      sigma = mean(sigma)
+    )
+  expect_equal(sex_effect$mu[1], meanlog_m, tolerance = 0.1)
+  expect_equal(sex_effect$sigma[1], sdlog_m, tolerance = 0.1)
+  expect_equal(sex_effect$mu[2], meanlog_f, tolerance = 0.1)
+  expect_equal(sex_effect$sigma[2], sdlog_f, tolerance = 0.1)
   expect_s3_class(fit_sex, "brmsfit")
   expect_s3_class(fit_sex, "epidist_fit")
   expect_convergence(fit_sex)

From 32ec9a6e504a288947badf5d836fc9bec05a94ad Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Mon, 18 Nov 2024 11:06:07 +0000
Subject: [PATCH 10/11] Can do this without predict_delay_pars

---
 tests/testthat/test-int-latent_model.R | 27 ++++++++++++--------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/tests/testthat/test-int-latent_model.R b/tests/testthat/test-int-latent_model.R
index 93b74179f..e4cd0109a 100644
--- a/tests/testthat/test-int-latent_model.R
+++ b/tests/testthat/test-int-latent_model.R
@@ -167,21 +167,18 @@ test_that("epidist.epidist_latent_model recovers a sex effect", { # nolint: line
   # Note: this test is stochastic. See note at the top of this script
   skip_on_cran()
   set.seed(1)
-  sex_effect <- predict_delay_parameters(fit_sex) |>
-    left_join(
-      mutate(sim_obs_sex, index = row_number()) |>
-        select(index, sex),
-      by = "index"
-    ) |>
-    group_by(sex) |>
-    summarise(
-      mu = mean(mu),
-      sigma = mean(sigma)
-    )
-  expect_equal(sex_effect$mu[1], meanlog_m, tolerance = 0.1)
-  expect_equal(sex_effect$sigma[1], sdlog_m, tolerance = 0.1)
-  expect_equal(sex_effect$mu[2], meanlog_f, tolerance = 0.1)
-  expect_equal(sex_effect$sigma[2], sdlog_f, tolerance = 0.1)
+  draws <- posterior::as_draws_df(fit_sex$fit)
+  expect_equal(mean(draws$b_Intercept), meanlog_m, tolerance = 0.1)
+  expect_equal(
+    mean(draws$b_Intercept + draws$b_sex), meanlog_f,
+    tolerance = 0.1
+  )
+  expect_equal(mean(exp(draws$b_sigma_Intercept)), sdlog_m, tolerance = 0.1)
+  expect_equal(
+    mean(exp(draws$b_sigma_Intercept + draws$b_sigma_sex)),
+    sdlog_f,
+    tolerance = 0.1
+  )
   expect_s3_class(fit_sex, "brmsfit")
   expect_s3_class(fit_sex, "epidist_fit")
   expect_convergence(fit_sex)

From 9c96cb5dc1584763fefd0d56a01f59aa16f7b549 Mon Sep 17 00:00:00 2001
From: athowes <xwg3@cdc.gov>
Date: Mon, 18 Nov 2024 11:48:11 +0000
Subject: [PATCH 11/11] Change to link function here

---
 tests/testthat/test-int-latent_model.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-int-latent_model.R b/tests/testthat/test-int-latent_model.R
index e4cd0109a..5f8cc3842 100644
--- a/tests/testthat/test-int-latent_model.R
+++ b/tests/testthat/test-int-latent_model.R
@@ -45,7 +45,7 @@ test_that("epidist.epidist_latent_model samples from the prior according to marg
   param1 <- extract_normal_parameters_brms(epidist_prior[1, ])
   param2 <- extract_normal_parameters_brms(epidist_prior[2, ])
   samples1 <- rnorm(1000, mean = param1$mean, sd = param1$sd)
-  samples2 <- rnorm(1000, mean = param2$mean, sd = param2$sd)
+  samples2 <- exp(rnorm(1000, mean = param2$mean, sd = param2$sd))
   # suppressWarnings here used to prevent warnings about ties
   ks1 <- suppressWarnings(stats::ks.test(pred$mu, samples1))
   ks2 <- suppressWarnings(stats::ks.test(pred$sigma, samples2))