rename r solver function to R_to_r

CDCgov · Feb 19, 2024 · e503a62 · e503a62
1 parent 41c1d25
commit e503a62
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Showing 4 changed files with 7 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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