From bb12c41ec4753b9c718dd0abbb6609f54e0d5b84 Mon Sep 17 00:00:00 2001
From: Zachary Susswein <utb2@cdc.gov>
Date: Sat, 31 Aug 2024 14:11:32 +0000
Subject: [PATCH] Add parameter skipping

---
 R/parameters.R                   |  2 +
 tests/testthat/test-parameters.R | 65 +++++++++++++++++++++++++++++++-
 2 files changed, 66 insertions(+), 1 deletion(-)

diff --git a/R/parameters.R b/R/parameters.R
index 2aef6ca8..2671f74f 100644
--- a/R/parameters.R
+++ b/R/parameters.R
@@ -23,6 +23,7 @@ read_parameters <- function(
     cli::cli_alert_warning(
       "No delay interval path specified. Using a delay of 0 days"
     )
+    delay_interval <- NA
   }
 
   if (path_is_specified(right_truncation_path)) {
@@ -37,6 +38,7 @@ read_parameters <- function(
     cli::cli_alert_warning(
       "No right truncation path specified. Not adjusting for right truncation."
     )
+    right_truncation <- NA
   }
 
   parameters <- list(
diff --git a/tests/testthat/test-parameters.R b/tests/testthat/test-parameters.R
index 00b07ab4..650c4abf 100644
--- a/tests/testthat/test-parameters.R
+++ b/tests/testthat/test-parameters.R
@@ -44,7 +44,70 @@ test_that("Can read all params on happy path", {
   })
 
 
-  expect_equal(actual, c(rep(list(c(0.8, 0.2)), 3)))
+  expect_equal(
+    actual,
+    list(
+      generation_interval = expected,
+      delay_interval = expected,
+      right_truncation = expected
+    )
+  )
+})
+
+test_that("Can skip params on happy path", {
+  expected <- c(0.8, 0.2)
+  start_date <- as.Date("2023-01-01")
+  disease <- "COVID-19"
+
+  withr::with_tempdir({
+    write_sample_parameters_file(
+      value = expected,
+      parameter = "generation_interval",
+      path = "generation_interval.parquet",
+      disease = disease,
+      state = NA,
+      start_date = start_date,
+      end_date = NA
+    )
+    write_sample_parameters_file(
+      value = expected,
+      parameter = "delay",
+      path = "delay_interval.parquet",
+      disease = disease,
+      state = NA,
+      start_date = start_date,
+      end_date = NA
+    )
+    write_sample_parameters_file(
+      value = expected,
+      parameter = "right_truncation",
+      path = "right_truncation.parquet",
+      disease = disease,
+      state = "test",
+      start_date = start_date,
+      end_date = NA
+    )
+
+
+    actual <- read_parameters(
+      generation_interval_path = "generation_interval.parquet",
+      delay_interval_path = NULL,
+      right_truncation_path = NULL,
+      disease = "COVID-19",
+      as_of_date = start_date + 1,
+      state = "test"
+    )
+  })
+
+
+  expect_equal(
+    actual,
+    list(
+      generation_interval = expected,
+      delay_interval = NA,
+      right_truncation = NA
+    )
+  )
 })
 
 test_that("Can read right-truncation on happy path", {