Spatial branch for merge of main (#152)

* Adding class and methods for wwinference model fit (#58) * Starting off refactoring (expected to fail) [skip ci] * Adding new method * Fixing bug in fit_model (was exploiting scoping) * Updating docs (fixing S3 methods) * 49 output class creation (#59) * add a space * add first test of first check * add tests for all of the check/assert functions * run precommit * check bug in passing output of checkmate to cliabort * initial tests of preprocess_ww_data * add custum utils function for autoescaping brackets to pass to glue * add a bunch of tests for preprocessing wastewater data * add one more test of site lab indexing * fix bugs caught in CI * fix lab site spacing * fix spacing in name again * add test to hospital admissions preprocessing * add additional test to ensure character to indexing of sites and labs * remove bug in expected number of unique lab site indices * add tests to make sure data is daily and test to checkers * add a bunch of validation checks to the joint datasets and the user specifications * replace with new way of getting stan data * fix examples, add test, add warning * fix examples, add test, add warning * change from hosp -> count everywhere except stan and vignette/examples * add tests for pmfs * fix bugs in documentation * add padding value as a function arg * change pmf size check to a warning not an error * fix bug * make initialization function more generic * update changelog * modify to test * fix typo from merge * fix parsing of cmdstan object * change parsing of fit obj * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * some tweaks to checkers * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * fix documentation * fix typo * fix typo * change outputs from wwinference() function * fix typos, add documentation * fix bug missing stan args * exclude t columns in data join * fix vignette bug * add the ww_output documentation * document ... * fix missing comma * move documentation of params around * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * change syntax and filenames * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/wwinference.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/wwinference.R Co-authored-by: Dylan H. Morris <[email protected]> * change naming and internal checking * change syntax * move around documentation * fix check * fix tests, fix documentation * rename assert function to specify within a certain frame * add element to text * fix bug in function name * tweak to inference function * fix two bugs * adjust tests based on updated get stan data function which breaks up generation of input data * Update get_stan_data.R example * update documentation after fixing example * add example to wwinference wrapper function * attempt to move around documentation for wwinference methods * play around with the documentation of the default and the S3 method functions * export S3 method function * add back in exporting functions to get input data formatted for stan * make first argument of function have same name as class object * fix bug in how max generation time is found * update vignette to explain wwinference_fit class object vs explicit function calling, add diagnostics and show both ways * fix naming blocks adding comma when needed * dont export autoescape brackets function * fix same bug * update test and preprocessing to count at LOD values at below LOD * fix internal call to diagnostic flags function * Update R/validate.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * implement DMs suggestions * run pre-commit * export default functions * Add test-coverage.yaml from epinowcast * remove test coverage * remove example, function not exported * export default function * export both diagnostics functions * add documentation of additional arguments * Update R/validate.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/validate.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/validate.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_ww_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/validate.R Co-authored-by: Dylan H. Morris <[email protected]> * manually input some suggestions * Update tests/testthat/test_checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_checkers.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * add more checknames * run pre-commit locally * fix typo * add some very minimal tests * fix wwinference function * fix bug * fix bug * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update tests/testthat/test_preprocess_count_data.R Co-authored-by: Dylan H. Morris <[email protected]> * run pre-commit locally * fix bugs in tests * fix error in tests * move forecast date, calib time, horizon time to args to wrapper function * fix hosp only example in vignette * fix error in example * add dont run to examples * check -> expect in checkmate, confirm tests pass locally --------- Co-authored-by: Dylan H. Morris <[email protected]> Co-authored-by: George G. Vega Yon <[email protected]> * Making pre-commit happy * Reworking cross-references and print method * Removing copy of fit_model * Fixing function call * Addressing PR comments * Forgot to save some changes * Change output names (#86) * change names of outputs of wwinference wrapper function * fix a few other missed replacements * fix pre-commit * Fixing R CMD check * Pre-commit * Removing diagnostics_summary --------- Co-authored-by: George G. Vega Yon <[email protected]> * Update vignettes/wwinference.Rmd Co-authored-by: Kaitlyn Johnson <[email protected]> * Update vignettes/wwinference.Rmd Co-authored-by: Kaitlyn Johnson <[email protected]> * Adding example of summary and print in the vignette. Addressing some minor comments * fix test for expected names after changing function args * set seed in tests --------- Co-authored-by: Kaitlyn Johnson <[email protected]> Co-authored-by: Dylan H. Morris <[email protected]> Co-authored-by: kaitejohnson <[email protected]> * Addressing R CMD check notes due to tidyeval syntax (#108) * Starting to use .data and others * Removing more warnings * Think almost all issues are now solved * License warning and passing params as expected * Removing prefix * Fixing note on license and news file * Using str2lang in spread_draws * Update R/get_draws_df.R Co-authored-by: Dylan H. Morris <[email protected]> * Fixing R CMD check * fixed intercept in figures * Update R/generate_simulated_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Apply suggestions from code review by @dylanhmorris Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/get_stan_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * remove call to utils::globalVariables() * Update R/preprocessing.R * Update R/generate_simulated_data.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/preprocessing.R Co-authored-by: Dylan H. Morris <[email protected]> * Update R/get_stan_data.R Co-authored-by: Dylan H. Morris <[email protected]> --------- Co-authored-by: Dylan H. Morris <[email protected]> Co-authored-by: Kaitlyn Johnson <[email protected]> Co-authored-by: kaitejohnson <[email protected]> * update hierarchical estimate of sigma_site in `model_definition` (#120) * add a space * update hierarchical estimate of sigma_site * update prior table * run pre-commit * update comment when transforming to site level standard deviations * add to change log * Update inst/stan/wwinference.stan Co-authored-by: Dylan H. Morris <[email protected]> * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> * update notation for mode and sd of stdevs * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> * tweaks to formatting * Update model_definition.md Co-authored-by: Dylan H. Morris <[email protected]> --------- Co-authored-by: Dylan H. Morris <[email protected]> * Vignette tweaks (#141) * fix typo in indicate ww exclusions documentation * fix typos/language in vignette * Update R/preprocessing.R Co-authored-by: Chirag Kumar <[email protected]> * update docs --------- Co-authored-by: Chirag Kumar <[email protected]> * actually set seed * Set seeds in test_get_stan_data (#146) Co-authored-by: Kaitlyn Johnson <[email protected]> * Modify package to expect log scale concentration values and LODs (#122) * Tweaks to model definition (#134) * Fix check for required wastewater columns (#127) * Switch to placing prior on and inferring `i/n` at the first observed timepoint (#85) * update vignette to reflect default NULL seed in mcmcoptions (#125) * Fix NEWS.md (#126) * hot fix to readme * Update NEWS.md * run pre-commit * Update NEWS.md (#144) * run pre-commit locally * Update NEWS.md --------- Co-authored-by: George G. Vega Yon <[email protected]> * 2024-09-09 update : fixing check-package error. * 2024-09-09 update : fixing check-package error. * 2024-09-09 update : removing test_ww_model. --------- Co-authored-by: George G. Vega Yon <[email protected]> Co-authored-by: Kaitlyn Johnson <[email protected]> Co-authored-by: Dylan H. Morris <[email protected]> Co-authored-by: kaitejohnson <[email protected]> Co-authored-by: Chirag Kumar <[email protected]>
CDCgov · Sep 9, 2024 · a6d1d10 · a6d1d10
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -4,3 +4,15 @@
 ^\.github$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+
+# Misc
+^data-raw$
+^model_definition\.md$
+^scratch$
+
+# Hidden files/folders
+^\..+
+
+# Because R doesn't like having a copy of this
+# type of license in the package.
+LICENSE
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(get_draws_df,data.frame)
+S3method(get_draws_df,default)
+S3method(get_draws_df,wwinference_fit)
+S3method(get_model_diagnostic_flags,default)
+S3method(get_model_diagnostic_flags,wwinference_fit)
+S3method(print,wwinference_fit)
+S3method(summary,wwinference_fit)
 export(add_pmfs)
 export(add_time_indexing)
 export(calc_rt)
@@ -32,6 +39,7 @@ export(get_ww_data_sizes)
 export(get_ww_values)
 export(independence_corr_func)
 export(indicate_ww_exclusions)
+export(parameter_diagnostics)
 export(preprocess_count_data)
 export(preprocess_ww_data)
 export(spatial_rt_process)
@@ -58,13 +66,15 @@ importFrom(dplyr,ungroup)
 importFrom(expm,sqrtm)
 importFrom(fs,path_package)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_ribbon)
+importFrom(ggplot2,geom_step)
 importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
@@ -74,9 +84,13 @@ importFrom(ggplot2,scale_fill_discrete)
 importFrom(ggplot2,scale_x_date)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,xlab)
+importFrom(ggplot2,ylab)
 importFrom(lubridate,ymd)
 importFrom(posterior,as_draws_list)
 importFrom(posterior,subset_draws)
+importFrom(rlang,.data)
 importFrom(rlang,sym)
 importFrom(stats,dnbinom)
 importFrom(stats,dweibull)

diff --git a/NEWS.md b/NEWS.md
@@ -1,12 +1,14 @@
-# wwinference
+# wwinference 0.0.1 (dev)
 
-This will serve as our change-log
 
-- Add functionality to fit the wastewater-informed model to an example fitting COVID-19 hospital admissions and wastewater from a few sites
-- Implemented forward simulation of spatially correlated subpopulations given a distance matrix, to be added as an option in the generate_simulated_data() function
-- 2024-07-12: Add functionality to fit the wastewater-informed model to an example fitting COVID-19 hospital admissions and wastewater from a few sites
-- 2024-07-19: Add an example in the vignette to fit the model to only the hospital admissions. Plus a few small tweaks to the vignette.
-- 2024-08-05: Add input data validation with informative error messaging
-- 2024-08-09: Add testing and additional validation of the data being passed into the model
-- 2024-08-22: Update `generate_simulated_data()` function to modularize the model components, adding additional
-forward simulation functions.
+This is the first major release, focused on providing an initial version of the package.
+Note the package is still flagged as in development, though the authors plan on using it for production work in the coming weeks.
+As it's written, the package is intended to allow users to do the following:
+
+- Provide basic functionality to fit the wastewater-informed model to an example fitting COVID-19 hospital admissions and wastewater from a few sites ([#5](https://github.com/CDCgov/ww-inference-model/issues/5))
+- Performs basic post-processing and plotting of data and modeled outputs, including calibrated, nowcasted, and forecasted count data (in the example, hospital admissions), wastewater concentrations, global R(t) estimates and subpopulation-level R(t) estimates
+- Provide an example in the vignette to fit the model to only the hospital admissions ([#24](https://github.com/CDCgov/ww-inference-model/issues/24))
+- Validate input data validation with informative error messaging ([#37](https://github.com/CDCgov/ww-inference-model/issues/37), [#54](https://github.com/CDCgov/ww-inference-model/issues/54))
+- Provide a wrapper function to generate forward simulated data with user-specified variables. It calls a number of functions to perform specific model components ([#27](https://github.com/CDCgov/ww-inference-model/issues/27))
+- Contains S3 class methods applied to the output of the main model wrapper function, the `wwinference_fit` class object ([#58](https://github.com/CDCgov/ww-inference-model/issues/58)).
+- Wastewater concentration data is expected to be in log scale ([#122](https://onetakeda.box.com/s/pju273g5khx3y3cwoae2zwv3e7vu03x3)).
diff --git a/R/checkers.R b/R/checkers.R
@@ -292,22 +292,18 @@ throw_type_error <- function(object,
 #' traceback.
 #'
 #' @return NULL, invisibly
-check_req_ww_cols_present <- function(ww_data,
-                                      conc_col_name,
-                                      lod_col_name,
-                                      add_req_col_names = c(
-                                        "date", "site",
-                                        "lab", "site_pop"
-                                      ),
-                                      call = rlang::caller_env()) {
+assert_req_ww_cols_present <- function(ww_data,
+                                       conc_col_name,
+                                       lod_col_name,
+                                       add_req_col_names = c(
+                                         "date", "site",
+                                         "lab", "site_pop"
+                                       ),
+                                       call = rlang::caller_env()) {
   column_names <- colnames(ww_data)
   expected_col_names <- c(
-    {
-      conc_col_name
-    },
-    {
-      lod_col_name
-    },
+    {{ conc_col_name }},
+    {{ lod_col_name }},
     add_req_col_names
   )
 
@@ -317,10 +313,11 @@ check_req_ww_cols_present <- function(ww_data,
   )
   if (!isTRUE(name_check_result)) {
     cli::cli_abort(
-      message = c(
-        "Required columns are missing from the wastewater data. ",
-        autoescape_brackets(name_check_result)
-      ),
+      message =
+        c(
+          "Required columns are missing from the wastewater data. ",
+          autoescape_brackets(name_check_result)
+        ),
       class = "wwinference_input_data_error",
       call = call
     )
@@ -582,10 +579,10 @@ assert_equivalent_indexing <- function(first_data,
                                        call = rlang::caller_env(),
                                        add_err_msg = "") {
   first_index <- first_data |>
-    dplyr::distinct(date, t)
+    dplyr::distinct(.data$date, .data$t)
   second_index <- second_data |>
-    dplyr::distinct(date, t) |>
-    dplyr::rename(second_t = t)
+    dplyr::distinct(.data$date, .data$t) |>
+    dplyr::rename("second_t" = "t")
 
 
   test_df <- first_index |>

diff --git a/R/compile_model.R b/R/compile_model.R
@@ -5,7 +5,7 @@
 #' This function reads in and optionally compiles a Stan model.
 #' It is written to search the installed package `stan` directory
 #' for additional source files to include. Within each stan file,
-#' use #include {path to your file with the `stan` directory}.stan
+#' use `#include {path to your file with the stan directory}.stan`
 #'
 #'
 #' @details The code for this function has been adapted

diff --git a/R/data.R b/R/data.R
@@ -1,12 +1,13 @@
 #' Example wastewater dataset with site correlations from exp. corr. func.
 #'
 #' A dataset containing the simulated wastewater concentrations
-#' (labeled here as `genome_copies_per_ml`) by sample collection date (`date`),
-#' the site where the sample was collected (`site`) and the lab where the
-#' samples were processed (`lab`). Additional columns that are required
-#' attributes needed for the model are the limit of detection for that lab on
-#' each day (labeled here as `lod`) and the population size of the wastewater
-#' catchment area represented by the wastewater concentrations in each `site`.
+#' (labeled here as `log_genome_copies_per_ml`) by sample collection date
+#' (`date`), the site where the sample was collected (`site`) and the lab
+#' where the samples were processed (`lab`). Additional columns that are
+#' required attributes needed for the model are the limit of detection for
+#' that lab on each day (labeled here as `log_lod`) and the population size of
+#' the wastewater catchment area represented by the wastewater concentrations
+#' in each `site`.
 #'
 #' This data is generated via the default values in the
 #'  `generate_simulated_data()` function. They represent the bare minumum
@@ -22,13 +23,13 @@
 #'   YYYY-MM-DD}
 #'   \item{site}{The wastewater treatment plant where the sample was collected}
 #'   \item{lab}{The lab where the sample was processed}
-#'   \item{genome_copies_per_ml}{The wastewater concentration measured on the
-#'   date specified, collected in the site specified, and processed in the lab
-#'   specified. The default parameters assume that this quantity is reported
-#'   as the genome copies per mL, on a natural scale.}
-#'   \item{lod}{The limit of detection in the site and lab on a particular day
-#'   of the quantification device (e.g. PCR). This is also by default reported
-#'   in terms of the genome copies per mL.}
+#'   \item{log_genome_copies_per_ml}{The natural log of the wastewater
+#'   concentration measured on the date specified, collected in the site
+#'   specified, and processed in the lab specified. The package expects
+#'   this quantity in units of log estimated genome copies per mL.}
+#'   \item{log_lod}{The log of the limit of detection in the site and lab on a
+#'   particular day of the quantification device (e.g. PCR).  This should be in
+#'    units of log estimated genome copies per mL.}
 #'   \item{site_pop}{The population size of the wastewater catchment area
 #'   represented by the site variable}
 #'   }

diff --git a/R/delay_distribs.R b/R/delay_distribs.R
@@ -1,4 +1,4 @@
-#' Simulate daily double censored PMF. From {epinowcast}:
+#' Simulate daily double censored PMF. From epinowcast:
 #' https://package.epinowcast.org/dev/reference/simulate_double_censored_pmf.html #nolint
 #'
 #' This function simulates the probability mass function of a  daily

diff --git a/R/figures.R b/R/figures.R
@@ -33,21 +33,23 @@ get_plot_forecasted_counts <- function(draws,
   sampled_draws <- sample(1:max(draws$draw), n_draws_to_plot)
 
   draws_to_plot <- draws |> dplyr::filter(
-    name == "pred_counts",
-    draw %in% !!sampled_draws
+    .data$name == "predicted counts",
+    .data$draw %in% !!sampled_draws
   )
 
   p <- ggplot(draws_to_plot) +
-    geom_line(aes(x = date, y = pred_value, group = draw),
+    geom_line(
+      aes(x = .data$date, y = .data$pred_value, group = .data$draw),
       color = "red4", alpha = 0.1, linewidth = 0.2
     ) +
     geom_point(
       data = count_data_eval,
-      aes(x = date, y = .data[[count_data_eval_col_name]]),
+      aes(x = .data$date, y = .data[[count_data_eval_col_name]]),
       shape = 21, color = "black", fill = "white"
     ) +
-    geom_point(aes(x = date, y = observed_value)) +
-    geom_vline(aes(xintercept = lubridate::ymd(forecast_date)),
+    geom_point(aes(x = .data$date, y = .data$observed_value)) +
+    geom_vline(
+      xintercept = lubridate::ymd(forecast_date),
       linetype = "dashed"
     ) +
     xlab("") +
@@ -95,8 +97,8 @@ get_plot_ww_conc <- function(draws,
 
   draws_to_plot <- draws |>
     dplyr::filter(
-      name == "pred_ww",
-      draw %in% !!sampled_draws
+      .data$name == "predicted wastewater",
+      .data$draw %in% !!sampled_draws
     ) |>
     dplyr::mutate(
       site_lab_name = glue::glue("{subpop}, Lab: {lab}")
@@ -105,22 +107,23 @@ get_plot_ww_conc <- function(draws,
   p <- ggplot(draws_to_plot) +
     geom_line(
       aes(
-        x = date, y = log(pred_value),
-        color = subpop,
-        group = draw
+        x = .data$date, y = .data$pred_value,
+        color = .data$subpop,
+        group = .data$draw
       ),
       alpha = 0.1, linewidth = 0.2,
       show.legend = FALSE
     ) +
-    geom_point(aes(x = date, y = log(observed_value)),
+    geom_point(aes(x = .data$date, y = .data$observed_value),
       color = "black", show.legend = FALSE
     ) +
     facet_wrap(~site_lab_name, scales = "free") +
-    geom_vline(aes(xintercept = lubridate::ymd(forecast_date)),
+    geom_vline(
+      xintercept = lubridate::ymd(forecast_date),
       linetype = "dashed"
     ) +
     xlab("") +
-    ylab("Log(Genome copies/mL)") +
+    ylab("Log genome copies/mL") +
     ggtitle("Lab-site level wastewater concentration") +
     scale_x_date(
       date_breaks = "2 weeks",
@@ -163,17 +166,18 @@ get_plot_global_rt <- function(draws,
   sampled_draws <- sample(1:max(draws$draw), n_draws_to_plot)
 
   draws_to_plot <- draws |> dplyr::filter(
-    name == "global R(t)",
-    draw %in% !!sampled_draws
+    .data$name == "global R(t)",
+    .data$draw %in% !!sampled_draws
   )
 
   # R(t) timeseries
   p <- ggplot(draws_to_plot) +
-    ggplot2::geom_step(
-      aes(x = date, y = pred_value, group = draw),
+    geom_step(
+      aes(x = .data$date, y = .data$pred_value, group = .data$draw),
       color = "blue4", alpha = 0.1, linewidth = 0.2
     ) +
-    geom_vline(aes(xintercept = lubridate::ymd(forecast_date)),
+    geom_vline(
+      xintercept = lubridate::ymd(forecast_date),
       linetype = "dashed"
     ) +
     geom_hline(aes(yintercept = 1), linetype = "dashed") +
@@ -221,20 +225,21 @@ get_plot_subpop_rt <- function(draws,
   sampled_draws <- sample(1:max(draws$draw), n_draws_to_plot)
 
   draws_to_plot <- draws |> dplyr::filter(
-    name == "subpop R(t)",
-    draw %in% !!sampled_draws
+    .data$name == "subpopulation R(t)",
+    .data$draw %in% !!sampled_draws
   )
 
   p <- ggplot(draws_to_plot) +
-    ggplot2::geom_step(
+    geom_step(
       aes(
-        x = date, y = pred_value, group = draw,
-        color = subpop
+        x = .data$date, y = .data$pred_value, group = .data$draw,
+        color = .data$subpop
       ),
       alpha = 0.1, linewidth = 0.2,
       show.legend = FALSE
     ) +
-    geom_vline(aes(xintercept = lubridate::ymd(forecast_date)),
+    geom_vline(
+      xintercept = lubridate::ymd(forecast_date),
       linetype = "dashed",
       show.legend = FALSE
     ) +