From fff7e4b3206ad58b40cd1c8196b488327e52c336 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Mon, 18 Nov 2024 22:42:24 +0000
Subject: [PATCH 01/17] add model_runs as additional hierarchy

---
 pipelines/forecast_state.py |  4 ++--
 pipelines/prep_data.py      | 14 ++++++++------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/pipelines/forecast_state.py b/pipelines/forecast_state.py
index 5ba898c9..21f365b1 100644
--- a/pipelines/forecast_state.py
+++ b/pipelines/forecast_state.py
@@ -180,7 +180,7 @@ def main(
 
     model_batch_dir = Path(output_data_dir, model_batch_dir_name)
 
-    model_run_dir = Path(model_batch_dir, state)
+    model_run_dir = Path(model_batch_dir, "model_runs", state)
 
     os.makedirs(model_run_dir, exist_ok=True)
 
@@ -198,7 +198,7 @@ def main(
         first_training_date=first_training_date,
         last_training_date=last_training_date,
         param_estimates=param_estimates,
-        model_batch_dir=model_batch_dir,
+        model_run_dir=model_run_dir,
         logger=logger,
     )
     logger.info("Data preparation complete.")
diff --git a/pipelines/prep_data.py b/pipelines/prep_data.py
index b7810b76..ed815856 100644
--- a/pipelines/prep_data.py
+++ b/pipelines/prep_data.py
@@ -219,7 +219,7 @@ def process_and_save_state(
     first_training_date: datetime.date,
     last_training_date: datetime.date,
     param_estimates: pl.LazyFrame,
-    model_batch_dir: Path,
+    model_run_dir: Path,
     logger: Logger = None,
     facility_level_nssp_data: pl.LazyFrame = None,
     state_level_nssp_data: pl.LazyFrame = None,
@@ -333,13 +333,15 @@ def process_and_save_state(
         "right_truncation_offset": right_truncation_offset,
     }
 
-    state_dir = os.path.join(model_batch_dir, state_abb)
-    os.makedirs(state_dir, exist_ok=True)
+    os.makedirs(model_run_dir, exist_ok=True)
 
-    logger.info(f"Saving {state_abb} to {state_dir}")
-    data_to_save.write_csv(Path(state_dir, "data.csv"))
+    if logger is not None:
+        logger.info(f"Saving {state_abb} to {model_run_dir}")
+    data_to_save.write_csv(Path(model_run_dir, "data.csv"))
 
-    with open(Path(state_dir, "data_for_model_fit.json"), "w") as json_file:
+    with open(
+        Path(model_run_dir, "data_for_model_fit.json"), "w"
+    ) as json_file:
         json.dump(data_for_model_fit, json_file)
 
     return None

From 88e117e3de5235c2f1d966994662758b4670d12d Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 00:11:04 +0000
Subject: [PATCH 02/17] fix default tag

---
 pipelines/batch/setup_test_prod_job.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipelines/batch/setup_test_prod_job.py b/pipelines/batch/setup_test_prod_job.py
index c406c90b..987139e4 100644
--- a/pipelines/batch/setup_test_prod_job.py
+++ b/pipelines/batch/setup_test_prod_job.py
@@ -18,7 +18,7 @@
         description="Test production pipeline on small subset of locations"
     )
     parser.add_argument(
-        "tag",
+        "--tag",
         type=str,
         help="The tag name to use for the container image version",
         default=Path(Repository(os.getcwd()).head.name).stem,

From dd92acc608ae6550ab079b48f9174a217d34d0b5 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 18:04:29 +0000
Subject: [PATCH 03/17] fix path in postprocess_state_forecast.R

---
 pipelines/postprocess_state_forecast.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/pipelines/postprocess_state_forecast.R b/pipelines/postprocess_state_forecast.R
index 747cca34..69de4616 100644
--- a/pipelines/postprocess_state_forecast.R
+++ b/pipelines/postprocess_state_forecast.R
@@ -273,10 +273,15 @@ model_run_dir <- path(argv$model_run_dir)
 
 base_dir <- path_dir(model_run_dir)
 
-disease_name_raw <- base_dir |>
-  path_file() |>
+# replace this with functionality from hewr
+disease_name_raw <- model_run_dir |>
+  path_split() |>
+  pluck(1) |>
+  tail(3) |>
+  head(1) |>
   str_extract("^.+(?=_r_)")
 
+
 disease_name_nssp <- unname(disease_name_nssp_map[disease_name_raw])
 disease_name_pretty <- unname(disease_name_formatter[disease_name_raw])
 

From 776af6c3bfbf7f70611793aedfdb3fd49dd3eb14 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 18:11:41 +0000
Subject: [PATCH 04/17] remove unused base_dir definition

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

diff --git a/pipelines/postprocess_state_forecast.R b/pipelines/postprocess_state_forecast.R
index 69de4616..fc2c4567 100644
--- a/pipelines/postprocess_state_forecast.R
+++ b/pipelines/postprocess_state_forecast.R
@@ -271,8 +271,6 @@ p <- arg_parser("Generate forecast figures") |>
 argv <- parse_args(p)
 model_run_dir <- path(argv$model_run_dir)
 
-base_dir <- path_dir(model_run_dir)
-
 # replace this with functionality from hewr
 disease_name_raw <- model_run_dir |>
   path_split() |>

From 7a9306a4b466b1b9ca6bbb6b3f3d570042c79567 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 18:12:32 +0000
Subject: [PATCH 05/17] correct_path in timeseries_forecasts

---
 pipelines/timeseries_forecasts.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/pipelines/timeseries_forecasts.R b/pipelines/timeseries_forecasts.R
index 50f92290..2edfb378 100644
--- a/pipelines/timeseries_forecasts.R
+++ b/pipelines/timeseries_forecasts.R
@@ -250,10 +250,12 @@ disease_name_nssp_map <- c(
   "influenza" = "Influenza"
 )
 
-base_dir <- path_dir(model_run_dir)
-
-disease_name_raw <- base_dir |>
-  path_file() |>
+# replace this with functionality from hewr
+disease_name_raw <- model_run_dir |>
+  path_split() |>
+  pluck(1) |>
+  tail(3) |>
+  head(1) |>
   str_extract("^.+(?=_r_)")
 
 disease_name_nssp <- unname(disease_name_nssp_map[disease_name_raw])

From 915284e2886e78e3e199e53d8c8b8eb0ca7c41bc Mon Sep 17 00:00:00 2001
From: Samuel Brand <48288458+SamuelBrand1@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:44:55 +0000
Subject: [PATCH 06/17] Issue 137: unify argument patterns (#138)

---
 pipelines/build_model.py                                | 2 +-
 pipelines/fit_model.py                                  | 2 +-
 pipelines/generate_predictive.py                        | 2 +-
 pipelines/iteration_helpers/loop_fit.sh                 | 2 +-
 pipelines/iteration_helpers/loop_generate_predictive.sh | 2 +-
 pipelines/iteration_helpers/loop_postprocess.sh         | 2 +-
 pipelines/score_forecast.R                              | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/pipelines/build_model.py b/pipelines/build_model.py
index 5450cf46..148bddbd 100644
--- a/pipelines/build_model.py
+++ b/pipelines/build_model.py
@@ -48,7 +48,7 @@ def build_model_from_dir(model_dir):
         - 1
     )
 
-    priors = runpy.run_path(prior_path)
+    priors = runpy.run_path(str(prior_path))
 
     right_truncation_offset = model_data["right_truncation_offset"]
 
diff --git a/pipelines/fit_model.py b/pipelines/fit_model.py
index cdeb7250..9ecefd2a 100644
--- a/pipelines/fit_model.py
+++ b/pipelines/fit_model.py
@@ -54,7 +54,7 @@ def fit_and_save_model(
         description="Fit the hospital-only wastewater model."
     )
     parser.add_argument(
-        "--model_run_dir",
+        "model_run_dir",
         type=Path,
         help=(
             "Path to a directory containing model fitting data. "
diff --git a/pipelines/generate_predictive.py b/pipelines/generate_predictive.py
index d16e4733..5a0d82d3 100644
--- a/pipelines/generate_predictive.py
+++ b/pipelines/generate_predictive.py
@@ -53,7 +53,7 @@ def generate_and_save_predictions(
         description=("Do posterior prediction from a pyrenew-hew fit.")
     )
     parser.add_argument(
-        "model-run-dir",
+        "model_run_dir",
         type=Path,
         help=(
             "Path to a directory containing the model fitting data "
diff --git a/pipelines/iteration_helpers/loop_fit.sh b/pipelines/iteration_helpers/loop_fit.sh
index 4ff7f1cf..837d5cf0 100755
--- a/pipelines/iteration_helpers/loop_fit.sh
+++ b/pipelines/iteration_helpers/loop_fit.sh
@@ -13,5 +13,5 @@ BASE_DIR="$1"
 for SUBDIR in "$BASE_DIR"/*/; do
     # Run the Python script with the current subdirectory as the model_dir argument
     echo "$SUBDIR"
-    python fit_model.py --model_run_dir "$SUBDIR"
+    python fit_model.py "$SUBDIR"
 done
diff --git a/pipelines/iteration_helpers/loop_generate_predictive.sh b/pipelines/iteration_helpers/loop_generate_predictive.sh
index 7c0aac22..b2510d21 100755
--- a/pipelines/iteration_helpers/loop_generate_predictive.sh
+++ b/pipelines/iteration_helpers/loop_generate_predictive.sh
@@ -14,5 +14,5 @@ BASE_DIR="$1"
 for SUBDIR in "$BASE_DIR"/*/; do
     # Run the Python script with the current subdirectory as the model_dir argument
     echo "$SUBDIR"
-    python generate_predictive.py --model_dir "$SUBDIR" --n_forecast_points 28
+    python generate_predictive.py "$SUBDIR" --n-forecast-points 28
 done
diff --git a/pipelines/iteration_helpers/loop_postprocess.sh b/pipelines/iteration_helpers/loop_postprocess.sh
index 7a25d032..215d1a00 100755
--- a/pipelines/iteration_helpers/loop_postprocess.sh
+++ b/pipelines/iteration_helpers/loop_postprocess.sh
@@ -13,5 +13,5 @@ BASE_DIR="$1"
 for SUBDIR in "$BASE_DIR"/*/; do
     # Run the R script with the current subdirectory as the model_dir argument
     echo "$SUBDIR"
-    Rscript postprocess_state_forecast.R --model-run-dir "$SUBDIR"
+    Rscript postprocess_state_forecast.R "$SUBDIR"
 done
diff --git a/pipelines/score_forecast.R b/pipelines/score_forecast.R
index 9bf90e6f..62afd9a9 100644
--- a/pipelines/score_forecast.R
+++ b/pipelines/score_forecast.R
@@ -236,7 +236,7 @@ read_and_score_location <- function(model_run_dir,
 # Create a parser
 p <- arg_parser("Score a single location forecast") |>
   add_argument(
-    "model-run-dir",
+    "model_run_dir",
     help = "Directory containing the model data and output."
   )
 

From ac4d25cd55478c10b7d7b52917c356e8f0d5fb2a Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 13:13:30 -0600
Subject: [PATCH 07/17] add check to all subprocess commands (#143)

---
 pipelines/forecast_state.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/pipelines/forecast_state.py b/pipelines/forecast_state.py
index 21f365b1..f09f258f 100644
--- a/pipelines/forecast_state.py
+++ b/pipelines/forecast_state.py
@@ -29,7 +29,8 @@ def baseline_forecasts(
             f"{n_forecast_days}",
             "--n-samples",
             f"{n_samples}",
-        ]
+        ],
+        check=True,
     )
     return None
 
@@ -40,7 +41,8 @@ def convert_inferencedata_to_parquet(model_run_dir: Path) -> None:
             "Rscript",
             "pipelines/convert_inferencedata_to_parquet.R",
             f"{model_run_dir}",
-        ]
+        ],
+        check=True,
     )
     return None
 
@@ -51,7 +53,8 @@ def postprocess_forecast(model_run_dir: Path) -> None:
             "Rscript",
             "pipelines/postprocess_state_forecast.R",
             f"{model_run_dir}",
-        ]
+        ],
+        check=True,
     )
     return None
 
@@ -62,7 +65,8 @@ def score_forecast(model_run_dir: Path) -> None:
             "Rscript",
             "pipelines/score_forecast.R",
             f"{model_run_dir}",
-        ]
+        ],
+        check=True,
     )
     return None
 

From 546046314a3a1a2e0134869a602aa9b9234c10bc Mon Sep 17 00:00:00 2001
From: "Dylan H. Morris" <dylanhmorris@users.noreply.github.com>
Date: Tue, 19 Nov 2024 14:52:56 -0500
Subject: [PATCH 08/17] Organize helper functions / utilities (#141)

---
 hewr/DESCRIPTION                           |   4 +
 hewr/NAMESPACE                             |   6 +
 hewr/R/directory_utils.R                   | 127 +++++++++++++++
 hewr/R/parse_path.R                        |  63 --------
 hewr/R/to_epiweekly_quantile_table.R       | 155 ++++++++++++++++++
 hewr/man/disease_map_lower.Rd              |  18 +++
 hewr/man/get_all_model_batch_dirs.Rd       |  24 +++
 hewr/man/parse_model_batch_dir_path.Rd     |  23 +++
 hewr/man/parse_model_run_dir_path.Rd       |  22 +++
 hewr/man/to_epiweekly_quantile_table.Rd    |  24 +++
 hewr/man/to_epiweekly_quantiles.Rd         |  30 ++++
 hewr/tests/testthat.R                      |  12 ++
 hewr/tests/testthat/test_directory_utils.R | 177 +++++++++++++++++++++
 pipelines/collate_plots.py                 |  28 ++--
 pipelines/collate_score_tables.R           |  33 +---
 pipelines/create_hubverse_table.R          | 159 +++---------------
 pipelines/utils.py                         |  41 +++++
 17 files changed, 702 insertions(+), 244 deletions(-)
 create mode 100644 hewr/R/directory_utils.R
 delete mode 100644 hewr/R/parse_path.R
 create mode 100644 hewr/R/to_epiweekly_quantile_table.R
 create mode 100644 hewr/man/disease_map_lower.Rd
 create mode 100644 hewr/man/get_all_model_batch_dirs.Rd
 create mode 100644 hewr/man/parse_model_batch_dir_path.Rd
 create mode 100644 hewr/man/parse_model_run_dir_path.Rd
 create mode 100644 hewr/man/to_epiweekly_quantile_table.Rd
 create mode 100644 hewr/man/to_epiweekly_quantiles.Rd
 create mode 100644 hewr/tests/testthat.R
 create mode 100644 hewr/tests/testthat/test_directory_utils.R

diff --git a/hewr/DESCRIPTION b/hewr/DESCRIPTION
index e961c674..b8d64bc8 100644
--- a/hewr/DESCRIPTION
+++ b/hewr/DESCRIPTION
@@ -39,3 +39,7 @@ Imports:
     urca
 Remotes:
     https://github.com/cdcgov/forecasttools
+Suggests:
+    testthat (>= 3.0.0),
+    withr
+Config/testthat/edition: 3
diff --git a/hewr/NAMESPACE b/hewr/NAMESPACE
index e651b944..a8b620d1 100644
--- a/hewr/NAMESPACE
+++ b/hewr/NAMESPACE
@@ -1 +1,7 @@
 # Generated by roxygen2: do not edit by hand
+
+export(get_all_model_batch_dirs)
+export(parse_model_batch_dir_path)
+export(parse_model_run_dir_path)
+export(to_epiweekly_quantile_table)
+export(to_epiweekly_quantiles)
diff --git a/hewr/R/directory_utils.R b/hewr/R/directory_utils.R
new file mode 100644
index 00000000..b8bf8cae
--- /dev/null
+++ b/hewr/R/directory_utils.R
@@ -0,0 +1,127 @@
+#' Utilities for handling and parsing directory names
+#' based on pyrenew-hew pipeline conventions.
+
+disease_map_lower <- c(
+  "covid-19" = "COVID-19",
+  "influenza" = "Influenza"
+)
+
+#' Parse model batch directory name.
+#'
+#' Parse the name of a model batch directory
+#' (i.e. a directory representing a single
+#' report date and disease pair, but potentially
+#' with fits for multiple locations), returning
+#' a named list of quantities of interest.
+#'
+#' @param model_batch_dir_path Path to the model batch
+#' directory to parse. Will parse only the basename.
+#' @return A list of quantities: `disease`, `report_date`,
+#' `first_training_date`, and `last_training_date`.
+#' @export
+parse_model_batch_dir_path <- function(model_batch_dir_path) {
+  pattern <- "(.+)_r_(.+)_f_(.+)_t_(.+)"
+  model_batch_dir_name <- fs::path_file(model_batch_dir_path)
+  matches <- stringr::str_match(
+    model_batch_dir_name,
+    pattern
+  )
+
+  if (any(is.na(matches))) {
+    stop(
+      "Invalid format for model batch directory name; ",
+      "could not parse. Expected ",
+      "'<disease>_r_<report_date>_f_<first_training_date>_t_",
+      "<last_training_date>'."
+    )
+  }
+
+  result <- list(
+    disease = disease_map_lower[matches[2]] |> unname(),
+    # disease_map_lower
+    # is a named vector
+    # but we want disease
+    # just to be a string
+    report_date = lubridate::ymd(matches[3], quiet = TRUE),
+    first_training_date = lubridate::ymd(matches[4], quiet = TRUE),
+    last_training_date = lubridate::ymd(matches[5], quiet = TRUE)
+  )
+
+  if (any(is.na(result))) {
+    stop(
+      "Could not parse extracted disease and/or date ",
+      "values expected 'disease' to be one of 'covid-19' ",
+      "and 'influenza' and all dates to be valid dates in ",
+      "YYYY-MM-DD format. Got: ",
+      glue::glue(
+        "disease: {matches[2]}, ",
+        "report_date: {matches[3]}, ",
+        "first_training_date: {matches[4]}, ",
+        "last_training_date: {matches[5]}."
+      )
+    )
+  }
+
+  return(result)
+}
+
+#' Parse model run directory path.
+#'
+#' Parse path to a model run directory
+#' (i.e. a directory representing a run for a
+#' particular location, disease, and reference
+#' date, and extract key quantities of interest.
+#'
+#' @param model_run_dir_path Path to parse.
+#' @return A list of parsed attributes:
+#' `location`, `disease`, `report_date`,
+#' `first_training_date`, and `last_training_date`.
+#'
+#' @export
+parse_model_run_dir_path <- function(model_run_dir_path) {
+  batch_dir <- fs::path_dir(model_run_dir_path) |>
+    fs::path_file()
+  location <- fs::path_file(model_run_dir_path)
+
+  return(c(
+    location = location,
+    parse_model_batch_dir_path(batch_dir)
+  ))
+}
+
+
+#' Get forecast directories.
+#'
+#' Get all the subdirectories within a parent directory
+#' that match the pattern for a forecast run for a
+#' given disease and optionally a given report date.
+#'
+#' @param dir_of_batch_dirs Directory in which to look for
+#' "model batch" directories, each of which represents an
+#' individual forecast date / pathogen / dataset combination.
+#' @param diseases Names of the diseases to match, as a vector of strings,
+#' or a single disease as a string.
+#' @return A vector of paths to the forecast subdirectories.
+#' @export
+get_all_model_batch_dirs <- function(dir_of_batch_dirs,
+                                     diseases) {
+  # disease names are lowercase by convention
+  match_patterns <- stringr::str_c(tolower(diseases),
+    "_r",
+    collapse = "|"
+  )
+
+  dirs <- tibble::tibble(
+    dir_path = fs::dir_ls(
+      dir_of_batch_dirs,
+      type = "directory"
+    )
+  ) |>
+    dplyr::filter(stringr::str_starts(
+      fs::path_file(dir_path),
+      match_patterns
+    )) |>
+    dplyr::pull(dir_path)
+
+  return(dirs)
+}
diff --git a/hewr/R/parse_path.R b/hewr/R/parse_path.R
deleted file mode 100644
index 0629214c..00000000
--- a/hewr/R/parse_path.R
+++ /dev/null
@@ -1,63 +0,0 @@
-disease_map_lower <- list(
-  "covid-19" = "COVID-19",
-  "influenza" = "Influenza"
-)
-
-#' Parse the name of a model batch directory
-#' (i.e. a directory representing a single
-#' report date and disease pair, but potentially
-#' with fits for multiple locations), returning
-#' a named list of quantities of interest.
-#'
-#' @param model_batch_dir_name Name of the model batch
-#' directory (not the full path to it, just the directory
-#' base name) to parse.
-#' @return A list of quantities: `disease`, `report_date`,
-#' `first_training_date`, and `last_training_date`.
-#' @export
-parse_model_batch_dir <- function(model_batch_dir_name) {
-  pattern <- "(.+)_r_(.+)_f_(.+)_t_(.+)"
-
-  matches <- stringr::str_match(
-    model_batch_dir_name,
-    pattern
-  )
-
-  if (is.na(matches[1])) {
-    stop(
-      "Invalid format for model batch directory name; ",
-      "could not parse. Expected ",
-      "'<disease>_r_<report_date>_f_<first_training_date>_t_",
-      "<last_training_date>'."
-    )
-  }
-
-  return(list(
-    disease = disease_map_lower[[matches[2]]],
-    report_date = lubridate::ymd(matches[3]),
-    first_training_date = lubridate::ymd(matches[4]),
-    last_training_date = lubridate::ymd(matches[5])
-  ))
-}
-
-#' Parse path to a model run directory
-#' (i.e. a directory representing a run for a
-#' particular location, disease, and reference
-#' date, and extract key quantities of interest.
-#'
-#' @param model_run_dir_path Path to parse.
-#' @return A list of parsed attributes:
-#' `location`, `disease`, `report_date`,
-#' `first_training_date`, and `last_training_date`.
-#'
-#' @export
-parse_model_run_dir <- function(model_run_dir_path) {
-  batch_dir <- fs::path_dir(model_run_dir_path) |>
-    fs::path_file()
-  location <- fs::path_file(model_run_dir_path)
-
-  return(c(
-    list(location = location),
-    parse_model_batch_dir(batch_dir)
-  ))
-}
diff --git a/hewr/R/to_epiweekly_quantile_table.R b/hewr/R/to_epiweekly_quantile_table.R
new file mode 100644
index 00000000..9e9149f4
--- /dev/null
+++ b/hewr/R/to_epiweekly_quantile_table.R
@@ -0,0 +1,155 @@
+#' Read in daily forecast draws from a model run directory
+#' and output a set of epiweekly quantiles, as a
+#' [`tibbble`][tibble::tibble()].
+#'
+#' @param model_run_dir Path to a directory containing
+#' forecast draws to process, whose basename is the forecasted
+#' location.
+#' @param report_date Report date for which to generate epiweekly quantiles.
+#' @param max_lookback_days How many days before the report date
+#' to look back when generating epiweekly quantiles (determines how
+#' many negative epiweekly forecast horizons (i.e. nowcast/backcast)
+#' quantiles will be generated.
+#' @return A [`tibble`][tibble::tibble()] of quantiles.
+#' @export
+to_epiweekly_quantiles <- function(model_run_dir,
+                                   report_date,
+                                   max_lookback_days) {
+  message(glue::glue("Processing {model_run_dir}..."))
+  draws_path <- fs::path(model_run_dir,
+    "forecast_samples",
+    ext = "parquet"
+  )
+  location <- fs::path_file(model_run_dir)
+
+  draws <- arrow::read_parquet(draws_path) |>
+    dplyr::filter(.data$date >= lubridate::ymd(!!report_date) -
+      lubridate::days(!!max_lookback_days))
+
+  if (nrow(draws) < 1) {
+    return(NULL)
+  }
+
+  epiweekly_disease_draws <- draws |>
+    dplyr::filter(
+      disease == "Disease"
+    ) |>
+    forecasttools::daily_to_epiweekly(
+      date_col = "date",
+      value_col = ".value",
+      id_cols = ".draw",
+      weekly_value_name = "epiweekly_disease",
+      strict = TRUE
+    )
+
+  epiweekly_total_draws <- draws |>
+    dplyr::filter(.data$disease == "Other") |>
+    forecasttools::daily_to_epiweekly(
+      date_col = "date",
+      value_col = ".value",
+      id_cols = ".draw",
+      weekly_value_name = "epiweekly_total",
+      strict = TRUE
+    )
+
+  epiweekly_prop_draws <- dplyr::inner_join(
+    epiweekly_disease_draws,
+    epiweekly_total_draws,
+    by = c(
+      "epiweek",
+      "epiyear",
+      ".draw"
+    )
+  ) |>
+    dplyr::mutate(
+      "epiweekly_proportion" =
+        .data$epiweekly_disease / .data$epiweekly_total
+    )
+
+
+  epiweekly_quantiles <- epiweekly_prop_draws |>
+    forecasttools::trajectories_to_quantiles(
+      timepoint_cols = c("epiweek", "epiyear"),
+      value_col = "epiweekly_proportion"
+    ) |>
+    dplyr::mutate(
+      "location" = !!location
+    )
+
+  message(glue::glue("Done processing {model_run_dir}"))
+  return(epiweekly_quantiles)
+}
+
+#' Create an epiweekly hubverse-format forecast quantile table
+#' from a model batch directory containing forecasts
+#' for multiple locations as daily MCMC draws.
+#'
+#' @param model_batch_dir Model batch directory containing
+#' the individual location forecast directories
+#' ("model run directories") to process. Name should be in the format
+#' `{disease}_r_{reference_date}_f_{first_data_date}_t_{last_data_date}`.
+#' @param exclude Locations to exclude, if any, as a list of strings.
+#' Default `NULL` (exclude nothing).
+#'
+#' @export
+to_epiweekly_quantile_table <- function(model_batch_dir,
+                                        exclude = NULL) {
+  locations_to_process <- fs::dir_ls(model_batch_dir,
+    type = "directory"
+  )
+
+  if (!is.null(exclude)) {
+    locations_to_process <- locations_to_process[
+      !(fs::path_file(locations_to_process) %in% exclude)
+    ]
+  }
+
+  batch_params <- hewr::parse_model_batch_dir_path(
+    model_batch_dir
+  )
+  report_date <- batch_params$report_date
+  disease <- batch_params$disease
+  disease_abbr <- dplyr::case_when(
+    disease == "Influenza" ~ "flu",
+    disease == "COVID-19" ~ "covid",
+    TRUE ~ disease
+  )
+
+  report_epiweek <- lubridate::epiweek(report_date)
+  report_epiyear <- lubridate::epiyear(report_date)
+  report_epiweek_end <- forecasttools::epiweek_to_date(
+    report_epiweek,
+    report_epiyear,
+    day_of_week = 7
+  )
+
+  hubverse_table <- purrr::map(
+    locations_to_process,
+    \(x) {
+      to_epiweekly_quantiles(
+        x,
+        report_date = report_date,
+        max_lookback_days = 8
+      )
+    }
+    ## ensures we get the full -1 horizon but do not
+    ## waste time quantilizing draws that will not be
+    ## included in the final table.
+  ) |>
+    dplyr::bind_rows() |>
+    forecasttools::get_hubverse_table(
+      report_epiweek_end,
+      target_name =
+        glue::glue("wk inc {disease_abbr} prop ed visits")
+    ) |>
+    dplyr::arrange(
+      .data$target,
+      .data$output_type,
+      .data$location,
+      .data$reference_date,
+      .data$horizon,
+      .data$output_type_id
+    )
+
+  return(hubverse_table)
+}
diff --git a/hewr/man/disease_map_lower.Rd b/hewr/man/disease_map_lower.Rd
new file mode 100644
index 00000000..dbf5de27
--- /dev/null
+++ b/hewr/man/disease_map_lower.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/directory_utils.R
+\docType{data}
+\name{disease_map_lower}
+\alias{disease_map_lower}
+\title{Utilities for handling and parsing directory names
+based on pyrenew-hew pipeline conventions.}
+\format{
+An object of class \code{list} of length 2.
+}
+\usage{
+disease_map_lower
+}
+\description{
+Utilities for handling and parsing directory names
+based on pyrenew-hew pipeline conventions.
+}
+\keyword{datasets}
diff --git a/hewr/man/get_all_model_batch_dirs.Rd b/hewr/man/get_all_model_batch_dirs.Rd
new file mode 100644
index 00000000..4997d907
--- /dev/null
+++ b/hewr/man/get_all_model_batch_dirs.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/directory_utils.R
+\name{get_all_model_batch_dirs}
+\alias{get_all_model_batch_dirs}
+\title{Get forecast directories.}
+\usage{
+get_all_model_batch_dirs(dir_of_batch_dirs, diseases)
+}
+\arguments{
+\item{dir_of_batch_dirs}{Directory in which to look for
+"model batch" directories, each of which represents an
+individual forecast date / pathogen / dataset combination.}
+
+\item{diseases}{Names of the diseases to match, as a vector of strings,
+or a single disease as a string.}
+}
+\value{
+A vector of paths to the forecast subdirectories.
+}
+\description{
+Get all the subdirectories within a parent directory
+that match the pattern for a forecast run for a
+given disease and optionally a given report date.
+}
diff --git a/hewr/man/parse_model_batch_dir_path.Rd b/hewr/man/parse_model_batch_dir_path.Rd
new file mode 100644
index 00000000..a247b597
--- /dev/null
+++ b/hewr/man/parse_model_batch_dir_path.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/directory_utils.R
+\name{parse_model_batch_dir_path}
+\alias{parse_model_batch_dir_path}
+\title{Parse model batch directory name.}
+\usage{
+parse_model_batch_dir_path(model_batch_dir_path)
+}
+\arguments{
+\item{model_batch_dir_path}{Path to the model batch
+directory to parse. Will parse only the basename.}
+}
+\value{
+A list of quantities: \code{disease}, \code{report_date},
+\code{first_training_date}, and \code{last_training_date}.
+}
+\description{
+Parse the name of a model batch directory
+(i.e. a directory representing a single
+report date and disease pair, but potentially
+with fits for multiple locations), returning
+a named list of quantities of interest.
+}
diff --git a/hewr/man/parse_model_run_dir_path.Rd b/hewr/man/parse_model_run_dir_path.Rd
new file mode 100644
index 00000000..4795c6a3
--- /dev/null
+++ b/hewr/man/parse_model_run_dir_path.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/directory_utils.R
+\name{parse_model_run_dir_path}
+\alias{parse_model_run_dir_path}
+\title{Parse model run directory path.}
+\usage{
+parse_model_run_dir_path(model_run_dir_path)
+}
+\arguments{
+\item{model_run_dir_path}{Path to parse.}
+}
+\value{
+A list of parsed attributes:
+\code{location}, \code{disease}, \code{report_date},
+\code{first_training_date}, and \code{last_training_date}.
+}
+\description{
+Parse path to a model run directory
+(i.e. a directory representing a run for a
+particular location, disease, and reference
+date, and extract key quantities of interest.
+}
diff --git a/hewr/man/to_epiweekly_quantile_table.Rd b/hewr/man/to_epiweekly_quantile_table.Rd
new file mode 100644
index 00000000..56d017c1
--- /dev/null
+++ b/hewr/man/to_epiweekly_quantile_table.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/to_epiweekly_quantile_table.R
+\name{to_epiweekly_quantile_table}
+\alias{to_epiweekly_quantile_table}
+\title{Create an epiweekly hubverse-format forecast quantile table
+from a model batch directory containing forecasts
+for multiple locations as daily MCMC draws.}
+\usage{
+to_epiweekly_quantile_table(model_batch_dir, exclude = NULL)
+}
+\arguments{
+\item{model_batch_dir}{Model batch directory containing
+the individual location forecast directories
+("model run directories") to process. Name should be in the format
+\verb{\{disease\}_r_\{reference_date\}_f_\{first_data_date\}_t_\{last_data_date\}}.}
+
+\item{exclude}{Locations to exclude, if any, as a list of strings.
+Default \code{NULL} (exclude nothing).}
+}
+\description{
+Create an epiweekly hubverse-format forecast quantile table
+from a model batch directory containing forecasts
+for multiple locations as daily MCMC draws.
+}
diff --git a/hewr/man/to_epiweekly_quantiles.Rd b/hewr/man/to_epiweekly_quantiles.Rd
new file mode 100644
index 00000000..47738ad5
--- /dev/null
+++ b/hewr/man/to_epiweekly_quantiles.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/to_epiweekly_quantile_table.R
+\name{to_epiweekly_quantiles}
+\alias{to_epiweekly_quantiles}
+\title{Read in daily forecast draws from a model run directory
+and output a set of epiweekly quantiles, as a
+\code{\link[tibble:tibble]{tibbble}}.}
+\usage{
+to_epiweekly_quantiles(model_run_dir, report_date, max_lookback_days)
+}
+\arguments{
+\item{model_run_dir}{Path to a directory containing
+forecast draws to process, whose basename is the forecasted
+location.}
+
+\item{report_date}{Report date for which to generate epiweekly quantiles.}
+
+\item{max_lookback_days}{How many days before the report date
+to look back when generating epiweekly quantiles (determines how
+many negative epiweekly forecast horizons (i.e. nowcast/backcast)
+quantiles will be generated.}
+}
+\value{
+A \code{\link[tibble:tibble]{tibble}} of quantiles.
+}
+\description{
+Read in daily forecast draws from a model run directory
+and output a set of epiweekly quantiles, as a
+\code{\link[tibble:tibble]{tibbble}}.
+}
diff --git a/hewr/tests/testthat.R b/hewr/tests/testthat.R
new file mode 100644
index 00000000..588af7fd
--- /dev/null
+++ b/hewr/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(hewr)
+
+test_check("hewr")
diff --git a/hewr/tests/testthat/test_directory_utils.R b/hewr/tests/testthat/test_directory_utils.R
new file mode 100644
index 00000000..17f30e37
--- /dev/null
+++ b/hewr/tests/testthat/test_directory_utils.R
@@ -0,0 +1,177 @@
+valid_model_batch_dirs <- list(
+  list(
+    dirname = "covid-19_r_2024-02-03_f_2021-04-01_t_2024-01-23",
+    expected = list(
+      disease = "COVID-19",
+      report_date = lubridate::ymd("2024-02-03"),
+      first_training_date = lubridate::ymd("2021-04-1"),
+      last_training_date = lubridate::ymd("2024-01-23")
+    )
+  ),
+  list(
+    dirname = "influenza_r_2022-12-11_f_2021-02-05_t_2027-12-30",
+    expected = list(
+      disease = "Influenza",
+      report_date = lubridate::ymd("2022-12-11"),
+      first_training_date = lubridate::ymd("2021-02-5"),
+      last_training_date = lubridate::ymd("2027-12-30")
+    )
+  )
+)
+
+invalid_model_batch_dirs <- c(
+  "qcovid-19_r_2024-02-03_f_2021-04-01_t_2024-01-23",
+  "influenza_r_2022-12-33_f_2021-02-05_t_2027-12-30"
+)
+
+to_valid_run_dir <- function(valid_batch_dir_entry, location) {
+  x <- valid_batch_dir_entry
+  x$dirpath <- fs::path(x$dirname, location)
+  x$expected <- c(
+    location = location,
+    x$expected
+  )
+  return(x)
+}
+
+valid_model_run_dirs <- c(
+  lapply(
+    valid_model_batch_dirs, to_valid_run_dir,
+    location = "ME"
+  ),
+  lapply(
+    valid_model_batch_dirs, to_valid_run_dir,
+    location = "US"
+  )
+)
+
+
+test_that("parse_model_batch_dir_path() works as expected.", {
+  for (valid_pair in valid_model_batch_dirs) {
+    ## should work with base dirnames that are valid
+    expect_equal(
+      parse_model_batch_dir_path(valid_pair$dirname),
+      valid_pair$expected
+    )
+
+    ## should work identically with a full path rather
+    ## than just base dir
+    also_valid <- fs::path("this", "is", "a", "test", valid_pair$dirname)
+    expect_equal(
+      parse_model_batch_dir_path(also_valid),
+      valid_pair$expected
+    )
+
+    ## should error if the terminal directory is not
+    ## what is to be parsed
+    not_valid <- fs::path(valid_pair$dirname, "test")
+    expect_error(
+      {
+        parse_model_batch_dir_path(not_valid)
+      },
+      regex = "Invalid format for model batch directory name"
+    )
+  }
+
+  ## should error if entries cannot be parsed as what is expected
+
+  for (invalid_entry in invalid_model_batch_dirs) {
+    expect_error(
+      {
+        parse_model_batch_dir_path(invalid_entry)
+      },
+      regex = "Could not parse extracted disease and/or date values"
+    )
+  }
+})
+
+test_that("parse_model_run_dir_path() works as expected.", {
+  for (valid_pair in valid_model_run_dirs) {
+    expect_equal(
+      parse_model_run_dir_path(valid_pair$dirpath),
+      valid_pair$expected
+    )
+
+    ## should work identically with a longer path
+    expect_equal(
+      parse_model_run_dir_path(fs::path(
+        "this", "is", "a", "test",
+        valid_pair$dirpath
+      )),
+      valid_pair$expected
+    )
+
+    ## should fail if there is additional terminal pathing
+    expect_error(
+      {
+        parse_model_run_dir_path(fs::path(valid_pair$dirpath, "test"))
+      },
+      regex = "Invalid format for model batch directory name"
+    )
+  }
+})
+
+test_that("get_all_model_batch_dirs() returns expected output.", {
+  withr::with_tempdir({
+    ## create some directories
+    valid_covid <- c(
+      "covid-19_r_2024-02-01_f_2021-01-01_t_2024-01-31",
+      "covid-19_r"
+    )
+    valid_flu <- c(
+      "influenza_r_2022-11-12_f_2022-11-01_t_2022_11_10",
+      "influenza_r"
+    )
+    valid_dirs <- c(valid_flu, valid_covid)
+
+    invalid_dirs <- c(
+      "this_is_not_valid",
+      "covid19_r",
+      "covid-19-r",
+      "influenza-r",
+      "influnza_r",
+      "covid-19",
+      "influenza"
+    )
+
+    invalid_files <- c(
+      "covid-19_r.txt",
+      "influenza_r.txt"
+    )
+    fs::dir_create(c(valid_dirs, invalid_dirs))
+    fs::file_create(invalid_files)
+    expected_all_files <- c(
+      valid_dirs,
+      invalid_dirs,
+      invalid_files
+    )
+
+    result_all <- fs::dir_ls(".") |> fs::path_file()
+
+    result_valid <- get_all_model_batch_dirs(
+      ".",
+      c("COVID-19", "Influenza")
+    )
+
+    result_valid_alt <- get_all_model_batch_dirs(
+      ".",
+      c("Influenza", "COVID-19")
+    )
+
+    result_valid_covid <- get_all_model_batch_dirs(
+      ".",
+      "COVID-19"
+    )
+
+    result_valid_flu <- get_all_model_batch_dirs(
+      ".",
+      "Influenza"
+    )
+
+    expect_setequal(result_all, expected_all_files)
+    expect_setequal(result_valid, c(valid_flu, valid_covid))
+    expect_setequal(result_valid_alt, c(valid_flu, valid_covid))
+    expect_setequal(result_valid_covid, valid_covid)
+    expect_setequal(result_valid_flu, valid_flu)
+  })
+})
diff --git a/pipelines/collate_plots.py b/pipelines/collate_plots.py
index 3fa1e4f0..39248f15 100644
--- a/pipelines/collate_plots.py
+++ b/pipelines/collate_plots.py
@@ -208,21 +208,28 @@ def collate_from_all_subdirs(
 
 
 def main(
-    model_base_dir: str | Path,
+    dir_of_forecast_dirs: str | Path,
     single_forecast_dir: str | Path,
     target_filenames: list[str],
-    disease: str,
+    disease: str = None,
 ) -> None:
-    if not ((model_base_dir is None) ^ (single_forecast_dir is None)):
+    if not ((dir_of_forecast_dirs is None) ^ (single_forecast_dir is None)):
         raise ValueError(
             "Must provide exactly one of "
-            "'--model-base-dir' (to process multiple "
+            "'dir_of_forecast_dirs' (to process multiple "
             "groups of forecasts) or "
-            "'--single-forecast-dir' "
+            "'single_forecast_dir' "
             "(to process a single set of forecasts"
         )
-    elif model_base_dir is not None:
-        collate_from_all_subdirs(model_base_dir, disease, target_filenames)
+    elif dir_of_forecast_dirs is not None:
+        if disease is None:
+            raise ValueError(
+                "'disease' must not be None when collating plots "
+                "from multiple forecast subdirectories"
+            )
+        collate_from_all_subdirs(
+            dir_of_forecast_dirs, disease, target_filenames
+        )
     elif single_forecast_dir is not None:
         process_dir(single_forecast_dir, target_filenames)
     return None
@@ -233,7 +240,7 @@ def main(
 )
 
 parser.add_argument(
-    "--model-base-dir",
+    "--dir-of-forecast-dirs",
     type=Path,
     help=(
         "Base directory containing subdirectories that represent "
@@ -251,7 +258,10 @@ def main(
 )
 
 parser.add_argument(
-    "disease", type=str, help="Name of the disease for which to collate plots"
+    "--disease",
+    type=str,
+    help="Name of the disease for which to collate plots.",
+    default=None,
 )
 
 parser.add_argument(
diff --git a/pipelines/collate_score_tables.R b/pipelines/collate_score_tables.R
index 70e0f9da..5c0370af 100644
--- a/pipelines/collate_score_tables.R
+++ b/pipelines/collate_score_tables.R
@@ -12,41 +12,12 @@ purrr::walk(script_packages, \(pkg) {
 })
 
 
-#' Get all the subdirectories within a parent directory
-#' that match the pattern for a forecast run for a
-#' given disease and optionally a given report date.
-#'
-#' @param parent_dir Directory in which to look for forecast subdirectories.
-#' @param diseases Names of the diseases to match, as a vector of strings,
-#' or a single disease as a string.
-#' @return A vector of paths to the forecast subdirectories.
-get_all_forecast_dirs <- function(dir_of_forecast_date_dirs,
-                                  diseases) {
-  # disease names are lowercase by convention
-  match_patterns <- str_c(tolower(diseases), "_r", collapse = "|")
-
-  dirs <- tibble::tibble(
-    dir_path = fs::dir_ls(
-      dir_of_forecast_date_dirs,
-      type = "directory"
-    )
-  ) |>
-    dplyr::filter(str_starts(
-      fs::path_file(dir_path),
-      match_patterns
-    )) |>
-    dplyr::pull(dir_path)
-
-  return(dirs)
-}
-
-
 process_loc_date_score_table <- function(model_run_dir) {
   table_path <- fs::path(model_run_dir,
     "score_table",
     ext = "rds"
   )
-  parsed <- hewr::parse_model_run_dir(model_run_dir)
+  parsed <- hewr::parse_model_run_dir_path(model_run_dir)
 
   if (!(fs::file_exists(table_path))) {
     warning(glue::glue(
@@ -137,7 +108,7 @@ collate_scores_for_date <- function(model_run_dir,
 collate_all_score_tables <- function(model_base_dir,
                                      disease,
                                      score_file_save_path = NULL) {
-  date_dirs_to_process <- get_all_forecast_dirs(
+  date_dirs_to_process <- hewr::get_all_model_batch_dirs(
     model_base_dir,
     diseases = disease
   )
diff --git a/pipelines/create_hubverse_table.R b/pipelines/create_hubverse_table.R
index a706cd66..db724c39 100644
--- a/pipelines/create_hubverse_table.R
+++ b/pipelines/create_hubverse_table.R
@@ -1,144 +1,21 @@
-draws_to_quantiles <- function(forecast_dir,
-                               report_date,
-                               max_lookback_days) {
-  message(glue::glue("Processing {forecast_dir}..."))
-  draws_path <- fs::path(forecast_dir,
-    "forecast_samples",
-    ext = "parquet"
-  )
-  location <- fs::path_file(forecast_dir)
-
-  draws <- arrow::read_parquet(draws_path) |>
-    dplyr::filter(date >= lubridate::ymd(report_date) -
-      lubridate::days(max_lookback_days))
-
-  if (nrow(draws) < 1) {
-    return(NULL)
-  }
-
-  epiweekly_disease_draws <- draws |>
-    dplyr::filter(
-      disease == "Disease"
-    ) |>
-    forecasttools::daily_to_epiweekly(
-      date_col = "date",
-      value_col = ".value",
-      id_cols = ".draw",
-      weekly_value_name = "epiweekly_disease",
-      strict = TRUE
-    )
-
-  epiweekly_total_draws <- draws |>
-    dplyr::filter(disease == "Other") |>
-    forecasttools::daily_to_epiweekly(
-      date_col = "date",
-      value_col = ".value",
-      id_cols = ".draw",
-      weekly_value_name = "epiweekly_total",
-      strict = TRUE
-    )
-
-  epiweekly_prop_draws <- dplyr::inner_join(
-    epiweekly_disease_draws,
-    epiweekly_total_draws,
-    by = c(
-      "epiweek",
-      "epiyear",
-      ".draw"
-    )
-  ) |>
-    dplyr::mutate(
-      epiweekly_proportion =
-        epiweekly_disease / epiweekly_total
-    )
-
-
-  epiweekly_quantiles <- epiweekly_prop_draws |>
-    forecasttools::trajectories_to_quantiles(
-      timepoint_cols = c("epiweek", "epiyear"),
-      value_col = "epiweekly_proportion"
-    ) |>
-    dplyr::mutate(
-      location = !!location
-    )
-
-  message(glue::glue("Done processing {forecast_dir}"))
-  return(epiweekly_quantiles)
-}
-
-create_hubverse_table <- function(model_run_dir,
-                                  exclude = NULL) {
-  locations_to_process <- fs::dir_ls(model_run_dir,
-    type = "directory"
-  )
-
-  if (!is.null(exclude)) {
-    locations_to_process <- locations_to_process[
-      !(fs::path_file(locations_to_process) %in% exclude)
-    ]
-  }
-
-  report_date <- stringr::str_match(
-    model_run_dir,
-    "r_(([0-9]|-)+)_f"
-  )[2]
-
-  report_epiweek <- lubridate::epiweek(report_date)
-  report_epiyear <- lubridate::epiyear(report_date)
-  report_epiweek_end <- forecasttools::epiweek_to_date(
-    report_epiweek,
-    report_epiyear,
-    day_of_week = 7
-  )
-
-  disease <- dplyr::case_when(
-    stringr::str_starts(
-      fs::path_file(model_run_dir),
-      "covid-19"
-    ) ~ "covid",
-    stringr::str_starts(
-      fs::path_file(model_run_dir),
-      "influenza"
-    ) ~ "flu",
-    TRUE ~ NA
-  )
-
-  hubverse_table <- purrr::map(
-    locations_to_process,
-    \(x) {
-      draws_to_quantiles(
-        x,
-        report_date = report_date,
-        max_lookback_days = 8
-      )
-    }
-    ## ensures we get the full -1 horizon but do not
-    ## waste time quantilizing draws that will not be
-    ## included in the final table.
-  ) |>
-    dplyr::bind_rows() |>
-    forecasttools::get_hubverse_table(
-      report_epiweek_end,
-      target_name =
-        glue::glue("wk inc {disease} prop ed visits")
-    ) |>
-    dplyr::arrange(
-      target,
-      output_type,
-      location,
-      reference_date,
-      horizon,
-      output_type_id
-    )
-
-  return(hubverse_table)
-}
-
-
-main <- function(model_run_dir,
+#!/usr/bin/env Rscript
+
+
+#' Create a hubverse table from model output, using
+#' utilities from `hewr`.
+#'
+#' @param model_batch_dir Model batch directory from which
+#' to create a hubverse table
+#' @param output_path path to save the table as a tsv
+#' @param exclude Locations to exclude, as a vector of strings.
+#' @return Nothing, saving the table as a side effect.
+main <- function(model_batch_dir,
                  output_path,
                  exclude = NULL) {
-  create_hubverse_table(model_run_dir, exclude = exclude) |>
+  hewr::to_epiweekly_quantile_table(
+    model_batch_dir,
+    exclude = exclude
+  ) |>
     readr::write_tsv(output_path)
 }
 
@@ -147,7 +24,7 @@ p <- argparser::arg_parser(
   "Create a hubverse table from location specific forecast draws."
 ) |>
   argparser::add_argument(
-    "model_run_dir",
+    "model_batch_dir",
     help = paste0(
       "Directory containing subdirectories that represent ",
       "individual forecast locations, with a directory name ",
@@ -166,7 +43,7 @@ p <- argparser::arg_parser(
 argv <- argparser::parse_args(p)
 
 main(
-  argv$model_run_dir,
+  argv$model_batch_dir,
   argv$output_path,
   stringr::str_split_1(argv$exclude, " ")
 )
diff --git a/pipelines/utils.py b/pipelines/utils.py
index 9a15a777..c18215cc 100644
--- a/pipelines/utils.py
+++ b/pipelines/utils.py
@@ -5,9 +5,12 @@
 
 import datetime
 import os
+import re
 from collections.abc import MutableSequence
 from pathlib import Path
 
+disease_map_lower_ = {"influenza": "Influenza", "covid-19": "COVID-19"}
+
 
 def ensure_listlike(x):
     """
@@ -36,6 +39,44 @@ def ensure_listlike(x):
     return x if isinstance(x, MutableSequence) else [x]
 
 
+def parse_model_batch_dir_name(model_batch_dir_name):
+    """
+    Parse the name of a model batch directory,
+    returning a dictionary of parsed values.
+
+    Parameters
+    ----------
+    model_batch_dir_name
+       Model batch directory name to parse.
+
+    Returns
+    -------
+    dict
+       A dictionary with keys 'disease', 'report_date',
+       'first_training_date', and 'last_training_date'.
+    """
+    regex_match = re.match(r"(.+)_r_(.+)_f_(.+)_t_(.+)", model_batch_dir_name)
+    if regex_match:
+        disease, report_date, first_training_date, last_training_date = (
+            regex_match.groups()
+        )
+    else:
+        raise ValueError(
+            "Invalid model batch directory name format: "
+            f"{model_batch_dir_name}"
+        )
+    return dict(
+        disease=disease_map_lower_[disease],
+        report_date=datetime.strptime(report_date, "%Y-%m-%d").date(),
+        first_training_date=datetime.strptime(
+            first_training_date, "%Y-%m-%d"
+        ).date(),
+        last_training_date=datetime.strptime(
+            last_training_date, "%Y-%m-%d"
+        ).date(),
+    )
+
+
 def get_all_forecast_dirs(
     parent_dir: Path | str,
     diseases: str | list[str],

From 9634b33f5283f5709bd5c1d4d1fc5e96b92b1f35 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 20:43:37 +0000
Subject: [PATCH 09/17] provide missing namespace

---
 pipelines/timeseries_forecasts.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pipelines/timeseries_forecasts.R b/pipelines/timeseries_forecasts.R
index 2edfb378..9e915054 100644
--- a/pipelines/timeseries_forecasts.R
+++ b/pipelines/timeseries_forecasts.R
@@ -252,11 +252,11 @@ disease_name_nssp_map <- c(
 
 # replace this with functionality from hewr
 disease_name_raw <- model_run_dir |>
-  path_split() |>
-  pluck(1) |>
+  fs::path_split() |>
+  purrr::pluck(1) |>
   tail(3) |>
   head(1) |>
-  str_extract("^.+(?=_r_)")
+  stringr::str_extract("^.+(?=_r_)")
 
 disease_name_nssp <- unname(disease_name_nssp_map[disease_name_raw])
 

From eae81c4d741f9fdbbcef5c11d134cd256df980c8 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 15:04:17 -0600
Subject: [PATCH 10/17] merge main into model_runs_2 (#146)

* Issue 137: unify argument patterns (#138)

* add check to all subprocess commands (#143)

* Organize helper functions / utilities (#141)

---------

Co-authored-by: Samuel Brand <48288458+SamuelBrand1@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

From 877ff117b959dd4ccc1b7007d48fe39a2e57d9e2 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 21:14:19 +0000
Subject: [PATCH 11/17] load required packages

---
 pipelines/timeseries_forecasts.R | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/pipelines/timeseries_forecasts.R b/pipelines/timeseries_forecasts.R
index 9e915054..7d9319b2 100644
--- a/pipelines/timeseries_forecasts.R
+++ b/pipelines/timeseries_forecasts.R
@@ -11,11 +11,14 @@ script_packages <- c(
   "arrow",
   "glue",
   "epipredict",
-  "epiprocess"
+  "epiprocess",
+  "purrr",
+  "rlang",
+  "glue"
 )
 
 ## load in packages without messages
-purrr::walk(script_packages, \(pkg) {
+walk(script_packages, \(pkg) {
   suppressPackageStartupMessages(
     library(pkg, character.only = TRUE)
   )
@@ -29,12 +32,12 @@ to_prop_forecast <- function(forecast_disease_count,
                              other_count_col =
                                "other_ed_visits",
                              output_col = "prop_disease_ed_visits") {
-  result <- dplyr::inner_join(
+  result <- inner_join(
     forecast_disease_count,
     forecast_other_count,
     by = c(".draw", "date")
   ) |>
-    dplyr::mutate(
+    mutate(
       !!output_col :=
         .data[[disease_count_col]] /
           (.data[[disease_count_col]] +
@@ -68,9 +71,9 @@ fit_and_forecast <- function(data,
                              n_samples = 2000,
                              target_col = "ed_visits",
                              output_col = "other_ed_visits") {
-  forecast_horizon <- glue::glue("{n_forecast_days} days")
-  target_sym <- rlang::sym(target_col)
-  output_sym <- rlang::sym(output_col)
+  forecast_horizon <- glue("{n_forecast_days} days")
+  target_sym <- sym(target_col)
+  output_sym <- sym(output_col)
 
   max_visits <- data |>
     pull(!!target_sym) |>
@@ -200,7 +203,7 @@ main <- function(model_run_dir, n_forecast_days = 28, n_samples = 2000) {
     aheads = 1:n_forecast_days
   )
 
-  to_save <- tibble::tribble(
+  to_save <- tribble(
     ~basename, ~value,
     "other_ed_visits_forecast", forecast_other,
     "baseline_ts_count_ed_visits_forecast", baseline_ts_count,
@@ -208,13 +211,13 @@ main <- function(model_run_dir, n_forecast_days = 28, n_samples = 2000) {
     "baseline_cdc_count_ed_visits_forecast", baseline_cdc_count,
     "baseline_cdc_prop_ed_visits_forecast", baseline_cdc_prop
   ) |>
-    dplyr::mutate(save_path = path(
+    mutate(save_path = path(
       !!model_run_dir, basename,
       ext = "parquet"
     ))
 
 
-  purrr::walk2(
+  walk2(
     to_save$value,
     to_save$save_path,
     write_parquet
@@ -252,11 +255,11 @@ disease_name_nssp_map <- c(
 
 # replace this with functionality from hewr
 disease_name_raw <- model_run_dir |>
-  fs::path_split() |>
-  purrr::pluck(1) |>
+  path_split() |>
+  pluck(1) |>
   tail(3) |>
   head(1) |>
-  stringr::str_extract("^.+(?=_r_)")
+  str_extract("^.+(?=_r_)")
 
 disease_name_nssp <- unname(disease_name_nssp_map[disease_name_raw])
 

From 980ad06936b0b127d022eda7a2199a1f7f87e744 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Tue, 19 Nov 2024 22:27:21 +0000
Subject: [PATCH 12/17] more namespace fixes

---
 pipelines/timeseries_forecasts.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipelines/timeseries_forecasts.R b/pipelines/timeseries_forecasts.R
index 7d9319b2..4cc59a72 100644
--- a/pipelines/timeseries_forecasts.R
+++ b/pipelines/timeseries_forecasts.R
@@ -18,7 +18,7 @@ script_packages <- c(
 )
 
 ## load in packages without messages
-walk(script_packages, \(pkg) {
+purrr::walk(script_packages, \(pkg) {
   suppressPackageStartupMessages(
     library(pkg, character.only = TRUE)
   )

From 3f8139b920dbba75c425e6851be835b47d22f050 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Wed, 20 Nov 2024 18:51:53 +0000
Subject: [PATCH 13/17] use hewr functionality

---
 hewr/R/directory_utils.R                   |  5 ++++-
 hewr/tests/testthat/test_directory_utils.R |  2 +-
 pipelines/postprocess_state_forecast.R     | 21 +++++----------------
 pipelines/timeseries_forecasts.R           | 13 +++----------
 4 files changed, 13 insertions(+), 28 deletions(-)

diff --git a/hewr/R/directory_utils.R b/hewr/R/directory_utils.R
index ba1e6549..d31b8fa0 100644
--- a/hewr/R/directory_utils.R
+++ b/hewr/R/directory_utils.R
@@ -79,8 +79,11 @@ parse_model_batch_dir_path <- function(model_batch_dir_path) {
 #'
 #' @export
 parse_model_run_dir_path <- function(model_run_dir_path) {
-  batch_dir <- fs::path_dir(model_run_dir_path) |>
+  batch_dir <- model_run_dir_path |>
+    fs::path_dir() |>
+    fs::path_dir() |>
     fs::path_file()
+
   location <- fs::path_file(model_run_dir_path)
 
   return(c(
diff --git a/hewr/tests/testthat/test_directory_utils.R b/hewr/tests/testthat/test_directory_utils.R
index 17f30e37..5ae9c1fa 100644
--- a/hewr/tests/testthat/test_directory_utils.R
+++ b/hewr/tests/testthat/test_directory_utils.R
@@ -26,7 +26,7 @@ invalid_model_batch_dirs <- c(
 
 to_valid_run_dir <- function(valid_batch_dir_entry, location) {
   x <- valid_batch_dir_entry
-  x$dirpath <- fs::path(x$dirname, location)
+  x$dirpath <- fs::path(x$dirname, "model_runs", location)
   x$expected <- c(
     location = location,
     x$expected
diff --git a/pipelines/postprocess_state_forecast.R b/pipelines/postprocess_state_forecast.R
index fc2c4567..2e023322 100644
--- a/pipelines/postprocess_state_forecast.R
+++ b/pipelines/postprocess_state_forecast.R
@@ -13,7 +13,8 @@ script_packages <- c(
   "tidyr",
   "readr",
   "here",
-  "forcats"
+  "forcats",
+  "hewr"
 )
 
 ## load in packages without messages
@@ -255,12 +256,6 @@ postprocess_state_forecast <- function(model_run_dir) {
 
 theme_set(theme_minimal_grid())
 
-disease_name_formatter <- c("covid-19" = "COVID-19", "influenza" = "Flu")
-disease_name_nssp_map <- c(
-  "covid-19" = "COVID-19",
-  "influenza" = "Influenza"
-)
-
 # Create a parser
 p <- arg_parser("Generate forecast figures") |>
   add_argument(
@@ -271,16 +266,10 @@ p <- arg_parser("Generate forecast figures") |>
 argv <- parse_args(p)
 model_run_dir <- path(argv$model_run_dir)
 
-# replace this with functionality from hewr
-disease_name_raw <- model_run_dir |>
-  path_split() |>
-  pluck(1) |>
-  tail(3) |>
-  head(1) |>
-  str_extract("^.+(?=_r_)")
 
+disease_name_nssp <- parse_model_run_dir_path(model_run_dir)$disease
 
-disease_name_nssp <- unname(disease_name_nssp_map[disease_name_raw])
-disease_name_pretty <- unname(disease_name_formatter[disease_name_raw])
+disease_name_formatter <- c("COVID-19" = "COVID-19", "Influenza" = "Flu")
+disease_name_pretty <- unname(disease_name_formatter[disease_name_nssp])
 
 postprocess_state_forecast(model_run_dir)
diff --git a/pipelines/timeseries_forecasts.R b/pipelines/timeseries_forecasts.R
index 4cc59a72..8c8e1c0a 100644
--- a/pipelines/timeseries_forecasts.R
+++ b/pipelines/timeseries_forecasts.R
@@ -14,7 +14,8 @@ script_packages <- c(
   "epiprocess",
   "purrr",
   "rlang",
-  "glue"
+  "glue",
+  "hewr"
 )
 
 ## load in packages without messages
@@ -253,14 +254,6 @@ disease_name_nssp_map <- c(
   "influenza" = "Influenza"
 )
 
-# replace this with functionality from hewr
-disease_name_raw <- model_run_dir |>
-  path_split() |>
-  pluck(1) |>
-  tail(3) |>
-  head(1) |>
-  str_extract("^.+(?=_r_)")
-
-disease_name_nssp <- unname(disease_name_nssp_map[disease_name_raw])
+disease_name_nssp <- parse_model_run_dir_path(model_run_dir)$disease
 
 main(model_run_dir, n_forecast_days, n_samples)

From 26cf4aeca1bc715891c306579edbc5aee4c88675 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Wed, 20 Nov 2024 19:29:57 +0000
Subject: [PATCH 14/17] first collate plots changes

---
 pipelines/collate_plots.py | 50 ++++++++++++++++++++++++++++++--------
 1 file changed, 40 insertions(+), 10 deletions(-)

diff --git a/pipelines/collate_plots.py b/pipelines/collate_plots.py
index 39248f15..174927e5 100644
--- a/pipelines/collate_plots.py
+++ b/pipelines/collate_plots.py
@@ -39,6 +39,7 @@ def merge_pdfs_and_save(
 def merge_pdfs_from_subdirs(
     base_dir: str | Path,
     file_name: str,
+    save_dir: str | Path = None,
     output_file_name: str = None,
     subdirs_only: list[str] = None,
     subdir_pattern="*",
@@ -59,6 +60,11 @@ def merge_pdfs_from_subdirs(
        Name of the files to merge. Must be an
        exact match.
 
+    save_dir
+       Directory in which to save the merged PDF.
+       If ``None``, use ``base_dir``.
+       Default ``None``.
+
     output_file_name
        Name for the merged PDF file, which will be
        saved within ``base_dir``. If ``None``,
@@ -84,6 +90,10 @@ def merge_pdfs_from_subdirs(
     -------
     None
     """
+
+    if save_dir is None:
+        save_dir = base_dir
+
     subdirs = [
         f.name for f in Path(base_dir).glob(subdir_pattern) if f.is_dir()
     ]
@@ -101,14 +111,15 @@ def merge_pdfs_from_subdirs(
         output_file_name = file_name
 
     if len(to_merge) > 0:
-        merge_pdfs_and_save(to_merge, Path(base_dir, output_file_name))
+        merge_pdfs_and_save(to_merge, Path(save_dir, output_file_name))
 
     return None
 
 
 def process_dir(
-    dir_path: Path | str,
+    base_dir: Path | str,
     target_filenames: str | list[str],
+    save_dir: Path | str = None,
     file_prefix: str = "",
     subdirs_only: list[str] = None,
 ) -> None:
@@ -119,14 +130,17 @@ def process_dir(
 
     Parameters
     ----------
-    dir_path
-        Path to the base directory, in which the merged
-        PDFs will be saved.
+    base_dir
+        Path to the base directory in which to look
 
     target_filenames
         One or more PDFs filenames to look for in the
         subdirectories and merge.
 
+    save_dir
+        Directory in which to save the merged PDFs.
+        If ``None``, use ``dir_path``. Default ``None``.
+
     file_prefix
         Prefix to append to the names in `target_filenames`
         when naming the merged files.
@@ -136,17 +150,24 @@ def process_dir(
         named subdirectories. If ``None``, look in all
         subdirectories of ``base_dir``. Default ``None``.
     """
+    if save_dir is None:
+        save_dir = base_dir
+
     for file_name in ensure_listlike(target_filenames):
         merge_pdfs_from_subdirs(
-            dir_path,
+            base_dir,
             file_name,
+            save_dir,
             output_file_name=file_prefix + file_name,
             subdirs_only=subdirs_only,
         )
 
 
 def collate_from_all_subdirs(
-    model_base_dir: str | Path, disease: str, target_filenames: str | list[str]
+    model_base_dir: str | Path,
+    disease: str,
+    target_filenames: str | list[str],
+    save_dir: str | Path = None,
 ) -> None:
     """
     Collate target plots for a given disease
@@ -156,8 +177,7 @@ def collate_from_all_subdirs(
     ----------
     model_base_dir
         Path to the base directory in whose subdirectories
-        the script will look for PDFs to merge and in which
-        the merged PDFs will be saved.
+        the script will look for PDFs to merge.
 
     disease
         Name of the target disease. Merged PDFs will be named
@@ -167,10 +187,17 @@ def collate_from_all_subdirs(
         One or more PDFs filenames to look for in the
         subdirectories and merge.
 
+    save_dir
+        Directory in which to save the merged PDFs.
+        If ``None``, use ``model_base_dir``. Default ``None``.
+
     Returns
     -------
     None
     """
+    if save_dir is None:
+        save_dir = model_base_dir
+
     logging.basicConfig(level=logging.INFO)
     logger = logging.getLogger(__name__)
 
@@ -188,6 +215,7 @@ def collate_from_all_subdirs(
         process_dir(
             dir_path=Path(model_base_dir, f_dir),
             target_filenames=target_filenames,
+            save_dir=save_dir,
         )
     logger.info("Done collating across locations by date.")
 
@@ -197,11 +225,13 @@ def collate_from_all_subdirs(
     # for multiple diseases.
     logger.info("Collating plots from forecast date directories...")
     process_dir(
-        dir_path=model_base_dir,
+        base_dir=model_base_dir,
         target_filenames=target_filenames,
+        save_dir=save_dir,
         file_prefix=f"{disease}_",
         subdirs_only=forecast_dirs,
     )
+
     logger.info("Done collating plots from forecast date directories.")
 
     return None

From 51e43d7193b4ae8901d20f010af7a5a2dfc6adae Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Wed, 20 Nov 2024 19:33:41 +0000
Subject: [PATCH 15/17] use parent dir for saving by default

---
 pipelines/collate_plots.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/pipelines/collate_plots.py b/pipelines/collate_plots.py
index 174927e5..1f1c25a0 100644
--- a/pipelines/collate_plots.py
+++ b/pipelines/collate_plots.py
@@ -62,7 +62,7 @@ def merge_pdfs_from_subdirs(
 
     save_dir
        Directory in which to save the merged PDF.
-       If ``None``, use ``base_dir``.
+       If ``None``, use the parent directory of ``base_dir``.
        Default ``None``.
 
     output_file_name
@@ -92,7 +92,7 @@ def merge_pdfs_from_subdirs(
     """
 
     if save_dir is None:
-        save_dir = base_dir
+        save_dir = Path(base_dir).parent
 
     subdirs = [
         f.name for f in Path(base_dir).glob(subdir_pattern) if f.is_dir()
@@ -139,7 +139,7 @@ def process_dir(
 
     save_dir
         Directory in which to save the merged PDFs.
-        If ``None``, use ``dir_path``. Default ``None``.
+        If ``None``, use the parent directory of ``base_dir``. Default ``None``.
 
     file_prefix
         Prefix to append to the names in `target_filenames`
@@ -151,7 +151,7 @@ def process_dir(
         subdirectories of ``base_dir``. Default ``None``.
     """
     if save_dir is None:
-        save_dir = base_dir
+        save_dir = Path(base_dir).parent
 
     for file_name in ensure_listlike(target_filenames):
         merge_pdfs_from_subdirs(
@@ -189,14 +189,14 @@ def collate_from_all_subdirs(
 
     save_dir
         Directory in which to save the merged PDFs.
-        If ``None``, use ``model_base_dir``. Default ``None``.
+        If ``None``, use the parent directory of ``model_base_dir``. Default ``None``.
 
     Returns
     -------
     None
     """
     if save_dir is None:
-        save_dir = model_base_dir
+        save_dir = Path(model_base_dir).parent
 
     logging.basicConfig(level=logging.INFO)
     logger = logging.getLogger(__name__)
@@ -213,7 +213,7 @@ def collate_from_all_subdirs(
     for f_dir in forecast_dirs:
         logger.info(f"Collating plots from {f_dir}")
         process_dir(
-            dir_path=Path(model_base_dir, f_dir),
+            base_dir=Path(model_base_dir, f_dir),
             target_filenames=target_filenames,
             save_dir=save_dir,
         )

From 2afe9c0608ea276f82651da1b5bc2c8d90c7731d Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Wed, 20 Nov 2024 19:49:07 +0000
Subject: [PATCH 16/17] put figures in figures dir

---
 pipelines/collate_plots.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/pipelines/collate_plots.py b/pipelines/collate_plots.py
index 1f1c25a0..8e4b39bf 100644
--- a/pipelines/collate_plots.py
+++ b/pipelines/collate_plots.py
@@ -62,7 +62,7 @@ def merge_pdfs_from_subdirs(
 
     save_dir
        Directory in which to save the merged PDF.
-       If ``None``, use the parent directory of ``base_dir``.
+       If ``None``, use a "figures" directory in the parent directory of ``base_dir``.
        Default ``None``.
 
     output_file_name
@@ -92,7 +92,10 @@ def merge_pdfs_from_subdirs(
     """
 
     if save_dir is None:
-        save_dir = Path(base_dir).parent
+        save_dir = Path(base_dir).parent / "figures"
+
+    if not os.path.exists(save_dir):
+        os.makedirs(save_dir)
 
     subdirs = [
         f.name for f in Path(base_dir).glob(subdir_pattern) if f.is_dir()
@@ -139,7 +142,7 @@ def process_dir(
 
     save_dir
         Directory in which to save the merged PDFs.
-        If ``None``, use the parent directory of ``base_dir``. Default ``None``.
+        If ``None``, use a "figures" directory in the parent directory of ``base_dir``. Default ``None``.
 
     file_prefix
         Prefix to append to the names in `target_filenames`
@@ -151,7 +154,7 @@ def process_dir(
         subdirectories of ``base_dir``. Default ``None``.
     """
     if save_dir is None:
-        save_dir = Path(base_dir).parent
+        save_dir = Path(base_dir).parent / "figures"
 
     for file_name in ensure_listlike(target_filenames):
         merge_pdfs_from_subdirs(
@@ -189,14 +192,14 @@ def collate_from_all_subdirs(
 
     save_dir
         Directory in which to save the merged PDFs.
-        If ``None``, use the parent directory of ``model_base_dir``. Default ``None``.
+        If ``None``, use a "figures" directory in the parent directory of ``model_base_dir``. Default ``None``.
 
     Returns
     -------
     None
     """
     if save_dir is None:
-        save_dir = Path(model_base_dir).parent
+        save_dir = Path(model_base_dir).parent / "figures"
 
     logging.basicConfig(level=logging.INFO)
     logger = logging.getLogger(__name__)

From a23945bc70b60e45db72e255e41ae1fcf9493307 Mon Sep 17 00:00:00 2001
From: Damon Bayer <xum8@cdc.gov>
Date: Wed, 20 Nov 2024 19:54:21 +0000
Subject: [PATCH 17/17] update score tables collation

---
 pipelines/collate_score_tables.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipelines/collate_score_tables.R b/pipelines/collate_score_tables.R
index 5c0370af..9a6aaf3c 100644
--- a/pipelines/collate_score_tables.R
+++ b/pipelines/collate_score_tables.R
@@ -83,7 +83,7 @@ collate_scores_for_date <- function(model_run_dir,
                                     score_file_ext = "rds",
                                     save = FALSE) {
   message(glue::glue("Processing scores from {model_run_dir}..."))
-  locations_to_process <- fs::dir_ls(model_run_dir,
+  locations_to_process <- fs::dir_ls(model_run_dir, "model_runs",
     type = "directory"
   )
   date_score_table <- purrr::map(