From 37eb594eeaf339f0811cd2be3c432371e537d338 Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Mon, 19 Feb 2024 17:48:28 +0000
Subject: [PATCH] rename growth_rate_to_reproductive_ratio -> r_to_R

---
 EpiAware/src/utilities.jl                              | 4 ++--
 EpiAware/test/predictive_checking/fast_approx_for_r.jl | 2 +-
 EpiAware/test/test_utilities.jl                        | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/EpiAware/src/utilities.jl b/EpiAware/src/utilities.jl
index 9388b87e1..6090a81e4 100644
--- a/EpiAware/src/utilities.jl
+++ b/EpiAware/src/utilities.jl
@@ -173,7 +173,7 @@ end
 
 
 """
-    growth_rate_to_reproductive_ratio(r, w)
+    r_to_R(r, w)
 
 Compute the reproductive ratio given exponential growth rate `r`
     and discretized generation interval `w`.
@@ -185,7 +185,7 @@ Compute the reproductive ratio given exponential growth rate `r`
 # Returns
 - The reproductive ratio.
 """
-function growth_rate_to_reproductive_ratio(r, w::AbstractVector)
+function r_to_R(r, w::AbstractVector)
     return 1 / neg_MGF(r, w::AbstractVector)
 end
 
diff --git a/EpiAware/test/predictive_checking/fast_approx_for_r.jl b/EpiAware/test/predictive_checking/fast_approx_for_r.jl
index 9374970e8..2646065ef 100644
--- a/EpiAware/test/predictive_checking/fast_approx_for_r.jl
+++ b/EpiAware/test/predictive_checking/fast_approx_for_r.jl
@@ -59,7 +59,7 @@ doubling_times = [1.0, 3.5, 7.0, 14.0]
 
 errors = mapreduce(hcat, doubling_times) do T_2
     true_r = log(2) / T_2 # 7 day doubling time
-    R0 = EpiAware.growth_rate_to_reproductive_ratio(true_r, w)
+    R0 = EpiAware.r_to_R(true_r, w)
 
     return map(idxs) do ns
         @time r = EpiAware.R_to_r(R0, w, newton_steps = ns)
diff --git a/EpiAware/test/test_utilities.jl b/EpiAware/test/test_utilities.jl
index ab66dec1c..1f36b2f2b 100644
--- a/EpiAware/test/test_utilities.jl
+++ b/EpiAware/test/test_utilities.jl
@@ -81,13 +81,13 @@ end
 
 end
 
-@testitem "Testing growth_rate_to_reproductive_ratio function" begin
+@testitem "Testing r_to_R function" begin
     #Test that zero exp growth rate imples R0 = 1
     @testset "Test case 1" begin
         r = 0
         w = ones(5) |> x -> x ./ sum(x)
         expected_ratio = 1
-        ratio = EpiAware.growth_rate_to_reproductive_ratio(r, w)
+        ratio = EpiAware.r_to_R(r, w)
         @test ratio ≈ expected_ratio atol = 1e-15
     end
 
@@ -95,7 +95,7 @@ end
     @testset "Test case 2" begin
         r = 0
         w = 1
-        @test_throws MethodError EpiAware.growth_rate_to_reproductive_ratio(r, w)
+        @test_throws MethodError EpiAware.r_to_R(r, w)
     end
 
 end