rename growth_rate_to_reproductive_ratio -> r_to_R

CDCgov · Feb 19, 2024 · 37eb594 · 37eb594
1 parent 6e7a93f
commit 37eb594
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git 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
@@ -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
@@ -81,21 +81,21 @@ 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
 
     #Test MethodError when w is not a vector
     @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