From cade3d051cc37bdced3fb3eef29c91afefed8d32 Mon Sep 17 00:00:00 2001
From: Adam Howes <xwg3@cdc.gov>
Date: Fri, 4 Oct 2024 13:38:34 +0100
Subject: [PATCH] Issue #359: Fix to `filter_obs_by_obs_time` function (#360)

* Fix to filter_obs_by_obs_time function

* Strange bug fix: reordering the columns makes a difference. Needs issue to fix

* Remove "censored_obs_time" and "censored" columns and include "obs_time" as a column

* Lint code
---
 R/observe.R            | 5 ++---
 tests/testthat/setup.R | 6 ++++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/observe.R b/R/observe.R
index 59c751c92..96088313c 100644
--- a/R/observe.R
+++ b/R/observe.R
@@ -44,9 +44,8 @@ observe_process <- function(linelist) {
 filter_obs_by_obs_time <- function(linelist, obs_time) {
   linelist |>
     mutate(
-      obs_time = obs_time - .data$ptime,
-      censored_obs_time = .data$obs_time - .data$ptime_lwr,
-      censored = "interval"
+      obs_time = obs_time,
+      relative_obs_time = .data$obs_time - .data$ptime,
     ) |>
     filter(.data$stime_upr <= .data$obs_time)
 }
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index c3d6abed2..9ccab8c56 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -52,14 +52,16 @@ sim_obs_sex_m <- dplyr::filter(sim_obs_sex, sex == 0) |>
     dist = rlnorm,
     meanlog = meanlog_m,
     sdlog = sdlog_m
-  )
+  ) |>
+  dplyr::select(case, ptime, delay, stime, sex)
 
 sim_obs_sex_f <- dplyr::filter(sim_obs_sex, sex == 1) |>
   simulate_secondary(
     dist = rlnorm,
     meanlog = meanlog_f,
     sdlog = sdlog_f
-  )
+  ) |>
+  dplyr::select(case, ptime, delay, stime, sex)
 
 sim_obs_sex <- dplyr::bind_rows(sim_obs_sex_m, sim_obs_sex_f) |>
   observe_process() |>