From 3d6909c06eae0eb60aa575372dfea94a861d3d11 Mon Sep 17 00:00:00 2001
From: RJSheppard <rjs11@ic.ac.uk>
Date: Thu, 11 Jul 2024 09:28:45 +0100
Subject: [PATCH] Adjusted spacing formatting in recovery rates function and
 make ifelse statement explicit for vivax in rendering.

---
 R/disease_progression.R | 16 +++++++++++-----
 R/render.R              |  2 +-
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/R/disease_progression.R b/R/disease_progression.R
index 82326776..d922e502 100644
--- a/R/disease_progression.R
+++ b/R/disease_progression.R
@@ -14,11 +14,17 @@ create_recovery_rates_process <- function(
     recovery_rates <- variables$recovery_rates$get_values()
     if (parameters$parasite == "vivax"){
       # p.v subpatent recovery is immunity-dependent
-      recovery_rates[variables$state$get_index_of("U")$to_vector()] <-
-        1/anti_parasite_immunity(
-          parameters$dpcr_min, parameters$dpcr_max, parameters$apcr50, parameters$kpcr,
-          variables$iaa$get_values(index = variables$state$get_index_of("U")),
-          variables$iam$get_values(index = variables$state$get_index_of("U"))
+      
+      U_index <- variables$state$get_index_of("U")
+      
+      recovery_rates[U_index$to_vector()] <-
+        1 / anti_parasite_immunity(
+          min = parameters$dpcr_min,
+          max = parameters$dpcr_max,
+          a50 = parameters$apcr50,
+          k = parameters$kpcr,
+          iaa = variables$iaa$get_values(index = U_index),
+          iam =variables$iam$get_values(index = U_index)
         )
     }
     recovery_outcome$set_rates(recovery_rates)
diff --git a/R/render.R b/R/render.R
index 68d551ad..b219cdb9 100644
--- a/R/render.R
+++ b/R/render.R
@@ -35,7 +35,7 @@ create_prevelance_renderer <- function(
         parameters
       )
       asymptomatic_detected <- bitset_at(asymptomatic, bernoulli_multi_p(prob))
-    } else {
+    } else if (parameters$parasite == "vivax") {
       asymptomatic_detected <- asymptomatic
     }