From b9b923c466998a1e81427a8597515ea6d90b965e Mon Sep 17 00:00:00 2001
From: RJSheppard <rjs11@ic.ac.uk>
Date: Wed, 8 May 2024 15:32:08 +0100
Subject: [PATCH] Added PCR rendering to prevalence rendering function,
 adjusting tests to rendering tests to reflect additional outputs.

---
 R/model.R                    |  4 ++--
 R/render.R                   | 19 ++++++++++++++-----
 man/run_simulation.Rd        |  4 ++--
 tests/testthat/test-render.R | 12 ++++++++++--
 4 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/R/model.R b/R/model.R
index 67f79758..ebb25bd7 100644
--- a/R/model.R
+++ b/R/model.R
@@ -29,10 +29,10 @@
 #'  * n: number of humans between an inclusive age range at this timestep. This
 #' defaults to n_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * n_detect: number of humans with an infection detectable by microscopy between an inclusive age range at this timestep. This
+#'  * n_detect_lm (or pcr): number of humans with an infection detectable by microscopy (or pcr) between an inclusive age range at this timestep. This
 #' defaults to n_detect_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-#'  * p_detect: the sum of probabilities of detection by microscopy between an
+#'  * p_detect_lm (or pcr): the sum of probabilities of detection by microscopy (or pcr) between an
 #' inclusive age range at this timestep. This
 #' defaults to p_detect_730_3650. Other age ranges can be set with
 #' prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
diff --git a/R/render.R b/R/render.R
index 60cb5b73..4f5816f3 100644
--- a/R/render.R
+++ b/R/render.R
@@ -4,8 +4,11 @@ in_age_range <- function(birth, timestep, lower, upper) {
 
 #' @title Render prevalence statistics
 #' 
-#' @description renders prevalence numerators and denominators for indivduals
-#' detected by microscopy and with severe malaria
+#' @description renders prevalence numerators and denominators for individuals
+#' detected by light microscopy and pcr, where those infected asymptomatically by
+#' P. falciparum have reduced probability of infection due to detectability
+#' immunity (reported as an integer sample: n_detect_lm, and summing over
+#' detection probabilities: p_detect_lm)
 #' 
 #' @param state human infection state
 #' @param birth variable for birth of the individual
@@ -32,7 +35,8 @@ create_prevelance_renderer <- function(
 
     clinically_detected <- state$get_index_of(c('Tr', 'D'))
     detected <- clinically_detected$copy()$or(asymptomatic_detected)
-
+    pcr_detected <- state$get_index_of(c('Tr', 'D', 'A', 'U'))
+    
     for (i in seq_along(parameters$prevalence_rendering_min_ages)) {
       lower <- parameters$prevalence_rendering_min_ages[[i]]
       upper <- parameters$prevalence_rendering_max_ages[[i]]
@@ -43,17 +47,22 @@ create_prevelance_renderer <- function(
         timestep
       ) 
       renderer$render(
-        paste0('n_detect_', lower, '_', upper),
+        paste0('n_detect_lm_', lower, '_', upper),
         in_age$copy()$and(detected)$size(),
         timestep
       )
       renderer$render(
-        paste0('p_detect_', lower, '_', upper),
+        paste0('p_detect_lm_', lower, '_', upper),
         in_age$copy()$and(clinically_detected)$size() + sum(
           prob[bitset_index(asymptomatic, in_age)]
         ),
         timestep
       )
+      renderer$render(
+        paste0('n_detect_pcr_', lower, '_', upper),
+        pcr_detected$copy()$and(in_age)$size(),
+        timestep
+      )
     }
   }
 }
diff --git a/man/run_simulation.Rd b/man/run_simulation.Rd
index 383b38f6..5861517d 100644
--- a/man/run_simulation.Rd
+++ b/man/run_simulation.Rd
@@ -45,10 +45,10 @@ the whole population)
 \item n: number of humans between an inclusive age range at this timestep. This
 defaults to n_730_3650. Other age ranges can be set with
 prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-\item n_detect: number of humans with an infection detectable by microscopy between an inclusive age range at this timestep. This
+\item n_detect_lm (or pcr): number of humans with an infection detectable by microscopy (or pcr) between an inclusive age range at this timestep. This
 defaults to n_detect_730_3650. Other age ranges can be set with
 prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
-\item p_detect: the sum of probabilities of detection by microscopy between an
+\item p_detect_lm (or pcr): the sum of probabilities of detection by microscopy (or pcr) between an
 inclusive age range at this timestep. This
 defaults to p_detect_730_3650. Other age ranges can be set with
 prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.
diff --git a/tests/testthat/test-render.R b/tests/testthat/test-render.R
index 920f09bb..cc4e9f87 100644
--- a/tests/testthat/test-render.R
+++ b/tests/testthat/test-render.R
@@ -34,7 +34,7 @@ test_that('that default rendering works', {
   mockery::expect_args(
     renderer$render_mock(),
     2,
-    'n_detect_730_3650',
+    'n_detect_lm_730_3650',
     2,
     timestep
   )
@@ -42,11 +42,19 @@ test_that('that default rendering works', {
   mockery::expect_args(
     renderer$render_mock(),
     3,
-    'p_detect_730_3650',
+    'p_detect_lm_730_3650',
     1.5,
     timestep
   )
 
+  mockery::expect_args(
+    renderer$render_mock(),
+    4,
+    'n_detect_pcr_730_3650',
+    3,
+    timestep
+  )
+  
 })
 
 test_that('that default rendering works when no one is in the age range', {