From 2d0b379c12995f0538065cd5062c9bc2ac5355b8 Mon Sep 17 00:00:00 2001
From: Adam Howes <xwg3@cdc.gov>
Date: Fri, 13 Sep 2024 15:49:37 +0100
Subject: [PATCH] Issue #320: Rename delay central (#325)

* Rename delay_central as delay

* Run document
---
 R/globals.R                             | 2 +-
 R/latent_individual.R                   | 8 ++++----
 tests/testthat/test-latent_individual.R | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/globals.R b/R/globals.R
index ace04826a..d7a6f93b9 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -15,7 +15,7 @@ utils::globalVariables(c(
   "stime_upr", # <as_latent_individual.data.frame>
   "woverlap", # <as_latent_individual.data.frame>
   "swindow", # <as_latent_individual.data.frame>
-  "delay_central", # <as_latent_individual.data.frame>
+  "delay", # <as_latent_individual.data.frame>
   "row_id", # <as_latent_individual.data.frame>
   "woverlap", # <epidist_stancode.epidist_latent_individual>
   "row_id", # <epidist_stancode.epidist_latent_individual>
diff --git a/R/latent_individual.R b/R/latent_individual.R
index 134e59321..d065c4fbd 100644
--- a/R/latent_individual.R
+++ b/R/latent_individual.R
@@ -56,7 +56,7 @@ as_latent_individual.data.frame <- function(data) {
   )]
   data[, woverlap := as.numeric(stime_lwr < ptime_upr)]
   data[, swindow := stime_upr - stime_lwr]
-  data[, delay_central := stime_lwr - ptime_lwr]
+  data[, delay := stime_lwr - ptime_lwr]
   data[, row_id := seq_len(.N)]
   if (nrow(data) > 1) {
     data <- data[, id := as.factor(id)]
@@ -86,7 +86,7 @@ epidist_validate.epidist_latent_individual <- function(data) {
     must.include = c("case", "ptime_lwr", "ptime_upr",
                      "stime_lwr", "stime_upr", "obs_at",
                      "id", "obs_t", "pwindow", "woverlap",
-                     "swindow", "delay_central", "row_id")
+                     "swindow", "delay", "row_id")
   )
   if (nrow(data) > 1) {
     checkmate::assert_factor(data$id)
@@ -95,7 +95,7 @@ epidist_validate.epidist_latent_individual <- function(data) {
   checkmate::assert_numeric(data$pwindow, lower = 0)
   checkmate::assert_numeric(data$woverlap, lower = 0)
   checkmate::assert_numeric(data$swindow, lower = 0)
-  checkmate::assert_numeric(data$delay_central, lower = 0)
+  checkmate::assert_numeric(data$delay, lower = 0)
   checkmate::assert_integer(data$row_id, lower = 0)
 }
 
@@ -157,7 +157,7 @@ epidist_formula.epidist_latent_individual <- function(data, family, formula,
   formula <- brms:::validate_formula(formula, data = data, family = family)
 
   formula <- stats::update(
-    formula, delay_central | vreal(obs_t, pwindow, swindow) ~ .
+    formula, delay | vreal(obs_t, pwindow, swindow) ~ .
   )
 
   # Using this here for checking purposes
diff --git a/tests/testthat/test-latent_individual.R b/tests/testthat/test-latent_individual.R
index f6ac673fb..5f7a55da6 100644
--- a/tests/testthat/test-latent_individual.R
+++ b/tests/testthat/test-latent_individual.R
@@ -84,7 +84,7 @@ test_that("epidist_formula.epidist_latent_individual with default settings produ
   expect_s3_class(form, "brmsformula")
   expect_equal(
     as_string_formula(form$formula),
-    "delay_central | vreal(obs_t, pwindow, swindow) ~ 1"
+    "delay | vreal(obs_t, pwindow, swindow) ~ 1"
   )
   expect_equal(
     as_string_formula(form$pforms$sigma),
@@ -102,7 +102,7 @@ test_that("epidist_formula.epidist_latent_individual with custom formulas produc
   expect_s3_class(form_sex, "brmsformula")
   expect_equal(
     as_string_formula(form_sex$formula),
-    "delay_central | vreal(obs_t, pwindow, swindow) ~ sex"
+    "delay | vreal(obs_t, pwindow, swindow) ~ sex"
   )
   expect_equal(
     as_string_formula(form_sex$pforms$sigma),