From e503a62a5e1e835a8b142e44a5747cc4400b7f4e Mon Sep 17 00:00:00 2001
From: Samuel Brand <sam055@mac.com>
Date: Mon, 19 Feb 2024 12:37:09 +0000
Subject: [PATCH] rename `r` solver function to `R_to_r`

---
 EpiAware/src/EpiAware.jl                            |  2 +-
 EpiAware/src/epimodel.jl                            |  2 +-
 EpiAware/src/utilities.jl                           | 13 ++++---------
 .../test/predictive_checking/fast_approx_for_r.jl   |  2 +-
 4 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/EpiAware/src/EpiAware.jl b/EpiAware/src/EpiAware.jl
index c8f754194..360c8118e 100644
--- a/EpiAware/src/EpiAware.jl
+++ b/EpiAware/src/EpiAware.jl
@@ -38,7 +38,7 @@ export scan,
     default_rw_priors,
     neg_MGF,
     dneg_MGF_dr,
-    fast_R_to_r_approx
+    R_to_r
 
 # Exported types
 export EpiData, Renewal, ExpGrowthRate, DirectInfections, AbstractEpiModel
diff --git a/EpiAware/src/epimodel.jl b/EpiAware/src/epimodel.jl
index 2b1cc8e77..052d9f6f4 100644
--- a/EpiAware/src/epimodel.jl
+++ b/EpiAware/src/epimodel.jl
@@ -80,7 +80,7 @@ function (epimodel::Renewal)(_Rt, latent_process_aux)
     I₀ = epimodel.data.transformation(latent_process_aux.init)
     Rt = epimodel.data.transformation.(_Rt)
 
-    r_approx = fast_R_to_r_approx(Rt[1], epimodel)
+    r_approx = R_to_r(Rt[1], epimodel)
     init = I₀ * [exp(-r_approx * t) for t = 0:(epimodel.data.len_gen_int-1)]
 
     function generate_infs(recent_incidence, Rt)
diff --git a/EpiAware/src/utilities.jl b/EpiAware/src/utilities.jl
index 641bbd485..9388b87e1 100644
--- a/EpiAware/src/utilities.jl
+++ b/EpiAware/src/utilities.jl
@@ -131,7 +131,7 @@ function dneg_MGF_dr(r, w::AbstractVector)
 end
 
 """
-    fast_R_to_r_approx(R₀, w::Vector{T}; newton_steps = 2, Δd = 1.0)
+    R_to_r(R₀, w::Vector{T}; newton_steps = 2, Δd = 1.0)
 
 This function computes an approximation to the exponential growth rate `r`
 given the reproductive ratio `R₀` and the discretized generation interval `w` with
@@ -156,12 +156,7 @@ The two step approximation is based on:
 Returns:
 - The approximate value of `r`.
 """
-function fast_R_to_r_approx(
-    R₀,
-    w::Vector{T};
-    newton_steps = 2,
-    Δd = 1.0,
-) where {T<:AbstractFloat}
+function R_to_r(R₀, w::Vector{T}; newton_steps = 2, Δd = 1.0) where {T<:AbstractFloat}
     mean_gen_time = dot(w, 1:length(w)) * Δd
     # Small r approximation as initial guess
     r_approx = (R₀ - 1) / (R₀ * mean_gen_time)
@@ -172,8 +167,8 @@ function fast_R_to_r_approx(
     return r_approx
 end
 
-function fast_R_to_r_approx(R₀, epimodel::AbstractEpiModel; newton_steps = 2, Δd = 1.0)
-    fast_R_to_r_approx(R₀, epimodel.data.gen_int; newton_steps = newton_steps, Δd = Δd)
+function R_to_r(R₀, epimodel::AbstractEpiModel; newton_steps = 2, Δd = 1.0)
+    R_to_r(R₀, epimodel.data.gen_int; newton_steps = newton_steps, Δd = Δd)
 end
 
 
diff --git a/EpiAware/test/predictive_checking/fast_approx_for_r.jl b/EpiAware/test/predictive_checking/fast_approx_for_r.jl
index 7235ee44c..f0c314a88 100644
--- a/EpiAware/test/predictive_checking/fast_approx_for_r.jl
+++ b/EpiAware/test/predictive_checking/fast_approx_for_r.jl
@@ -55,7 +55,7 @@ errors = mapreduce(hcat, doubling_times) do T_2
     R0 = growth_rate_to_reproductive_ratio(true_r, w)
 
     return map(idxs) do ns
-        @time r = fast_R_to_r_approx(R0, w, newton_steps = ns)
+        @time r = R_to_r(R0, w, newton_steps = ns)
         abs(r - true_r) + jitter
     end
 end