Add CDAI and methods (#9)

* resize logo to layout

* add cdai

* update README.md

README.md

@@ -7,6 +7,7 @@ This package implements the most common composite scores used for evaluating dis
 - DAS28ESR
 - DAS28CRP
 - SDAI
+- CDAI
 - ACR / EULAR Boolean remission
 - Revised ACR / EULAR Boolean remission
 - Three-item ACR / EULAR Boolean remission

docs/logo.jl

@@ -61,12 +61,14 @@ plt3 = add_pie!(data3, [purple, green, red])
 
 translate_all!(4.3, 3.7, plt1, plt2, plt3)
 
-#hidedecorations!(ax)
-#hidespines!(ax)
+hidedecorations!(ax)
+hidespines!(ax)
 
 colsize!(f.layout, 1, Aspect(1, 1.0))
 
+resize_to_layout!(f)
+
 f
 
 # Assuming that the active project is docs
-# CairoMakie.save(joinpath("src", "assets", "logo.svg"), f)
+CairoMakie.save(joinpath("src", "assets", "logo.svg"), f)

src/RheumaComposites.jl

@@ -19,6 +19,7 @@ export DAS28
 export DAS28ESR
 export DAS28CRP
 export SDAI
+export CDAI
 export faceted, Faceted
 export BooleanRemission
 export revised, Revised, threeitem, ThreeItem
@@ -36,6 +37,7 @@ include("types/components.jl")
 include("types/composites.jl")
 include("types/das28.jl")
 include("types/sdai.jl")
+include("types/cdai.jl")
 include("types/boolean.jl")
 include("types/modified.jl")
 include("utils/weight.jl")

src/types/cdai.jl

@@ -0,0 +1,50 @@
+"""
+    CDAI(; t28, s28, pga, ega)
+
+Store component measures of the Clinical Disease Activity Index, or CDAI.
+
+# Components
+
+- `t28` 28 tender joint count
+- `s28` 28 swollen joint count
+- `pga` patient's global assessment
+- `ega` evaluator's global assessment
+
+!!! warning "Units"
+    Currently, `pga` and `ega` must be a length (typically millimeters or centimeters).
+    See also [`Unitful.@u_str`](@extref).
+
+# External links
+
+* [CDAI calculator](https://www.mdcalc.com/calc/2177/clinical-disease-activity-index-cdai-rheumatoid-arthritis)
+
+See also [`score`](@ref), [`isremission`](@ref).
+"""
+struct CDAI <: ContinuousComposite
+    t28::Int64
+    s28::Int64
+    pga::Unitful.AbstractQuantity
+    ega::Unitful.AbstractQuantity
+    function CDAI(;
+        t28,
+        s28,
+        pga::Unitful.AbstractQuantity,
+        ega::Unitful.AbstractQuantity,
+    )
+        valid_joints.([t28, s28])
+        valid_vas.([pga, ega])
+
+        # Must convert because weights do not adjust to measurement
+        return new(
+            t28,
+            s28,
+            uconvert(units.xdai_vas, pga),
+            uconvert(units.xdai_vas, ega),
+        )
+    end
+end
+
+WeightingScheme(::Type{<:CDAI}) = IsUnweighted()
+
+"Return the evaluator's global assessment."
+ega(x::CDAI) = x.ega

src/types/sdai.jl

@@ -42,9 +42,9 @@ struct SDAI <: ContinuousComposite
         return new(
             t28,
             s28,
-            uconvert(units.sdai_vas, pga),
-            uconvert(units.sdai_vas, ega),
-            uconvert(units.sdai_crp, crp)
+            uconvert(units.xdai_vas, pga),
+            uconvert(units.xdai_vas, ega),
+            uconvert(units.xdai_crp, crp)
         )
     end
 end

src/utils/categorise.jl

@@ -49,6 +49,14 @@ function categorise(::Type{SDAI}, v)
     return out
 end
 
+function categorise(::Type{CDAI}, v)
+    out = v < 2.8 ? "Remission" :
+          v <= 10.0 ? "Low" :
+          v <= 22.0 ? "Moderate" :
+          "High"
+    return out
+end
+
 categorise(x::ContinuousComposite) = categorise(typeof(x), score(x))
 
 categorise(x::Faceted{<:ContinuousComposite}) = categorise(typeof(x.c0), score(x.c0))

src/utils/remission.jl

@@ -1,75 +1,39 @@
 """
-    isremission(x::DAS28ESR)
+    isremission(x::AbstractComposite)
 
-Check whether a DAS28ESR fulfils remission criteria (< 2.4).
+Check whether a composite fulfils remission criteria.
 
 # Examples
 
 ```jldoctest
 julia> DAS28ESR(t28=4, s28=5, pga=44u"mm", apr=23u"mm/hr") |> isremission
 false
-```
-
-    isremission(x::DAS28CRP)
-
-Check whether a DAS28CRP fulfils remission criteria (< 2.6).
-
-# Examples
-
-```jldoctest
-julia> DAS28CRP(t28=0, s28=1, pga=12u"mm", apr=9u"mg/L") |> isremission
-true
-```
-
-    isremission(x::SDAI)
-
-Check whether an SDAI fulfils remission criteria (<= 3.3).
-
-# Examples
-
-```jldoctest
-julia> SDAI(t28=0, s28=0, pga=12u"mm", ega=8u"mm", crp=4u"mg/L") |> isremission
-true
-```
-
-    isremission(x::BooleanRemission)
-
-Check whether a BooleanRemission fulfils remission criteria (all T28, S28, PGA, CRP <= 1), where PGA is measured in cm and CRP measured in mg/dL.
-
-See also [`revised`](@ref), [`threeitem`](@ref).
-
-# Examples
-
-```jldoctest
-julia> BooleanRemission(t28=1, s28=0, pga=14u"mm", crp=0.4u"mg/dl") |>
-       isremission
-false
 julia> BooleanRemission(t28=1, s28=0, pga=14u"mm", crp=0.4u"mg/dl") |>
        revised |>
        isremission
 true
-julia> BooleanRemission(t28=1, s28=0, pga=14u"mm", crp=0.4u"mg/dl") |>
-       threeitem |>
-       isremission
-true
 ```
 """
-isremission(x::DAS28ESR) = score(x) < 2.6
-isremission(x::DAS28CRP) = score(x) < 2.4
+isremission(::Type{DAS28ESR}, x) = score(x) < 2.6
+isremission(::Type{DAS28CRP}, x) = score(x) < 2.4
 
-isremission(x::SDAI) = score(x) <= 3.3
+isremission(::Type{SDAI}, x) = score(x) <= 3.3
+isremission(::Type{CDAI}, x) = score(x) <= 2.8
 
-isremission(x::PGA) = x.value <= 10.0u"mm"
-isremission(x::SJC28) = x.value == 0
+isremission(::Type{PGA}, x) = x.value <= 10.0u"mm"
+isremission(::Type{SJC28}, x) = x.value == 0
 
-function isremission(x::BooleanRemission)
+function isremission(::Type{BooleanRemission}, x)
     return t28(x) <= 1 && s28(x) <= 1 && pga(x) <= 10.0u"mm" && crp(x) <= 1.0u"mg/dL"
 end
 
-function isremission(x::Revised{<:BooleanRemission})
+function isremission(::Type{<:Revised{<:BooleanRemission}}, x)
     return t28(x) <= 1 && s28(x) <= 1 && pga(x) <= 20.0u"mm" && crp(x) <= 1.0u"mg/dL"
 end
 
-function isremission(x::ThreeItem{<:BooleanRemission})
+function isremission(::Type{<:ThreeItem{<:BooleanRemission}}, x)
     return t28(x) <= 1 && s28(x) <= 1 && crp(x) <= 1.0u"mg/dL"
 end
+
+isremission(x::AbstractComposite) = isremission(typeof(x), x)
+isremission(x::AbstractComponent) = isremission(typeof(x), x)

src/utils/units.jl

@@ -2,8 +2,9 @@ units = (
     das28_vas=u"mm",
     das28_crp=u"mg/L",
     das28_esr=u"mm/hr",
-    sdai_vas=u"cm",
-    sdai_crp=u"mg/dL",
+    # xdai is for both c- and sdai
+    xdai_vas=u"cm",
+    xdai_crp=u"mg/dL",
     brem_vas=u"mm",
     brem_crp=u"mg/dL",
 )

test/runtests.jl

@@ -14,6 +14,10 @@ end
     include("types/sdai.jl")
 end
 
+@testset "CDAI" begin
+    include("types/cdai.jl")
+end
+
 @testset "Boolean" begin
     include("types/boolean.jl")
 end

test/types/cdai.jl

@@ -0,0 +1,40 @@
+# Dummy CDAIs for testing
+cdai = CDAI(t28=1, s28=0, pga=1u"cm", ega=0u"cm")
+cdai_ref = 2.0
+
+# Intercept
+i_cdai = RheumaComposites.intercept(cdai)
+
+# Test if different unit scales lead to same results
+cdai_u1 = CDAI(t28=0, s28=1, pga=10u"mm", ega=10u"mm")
+cdai_u2 = CDAI(t28=0, s28=1, pga=1u"cm", ega=1u"cm")
+
+@testset "Construct CDAI" begin
+    @test cdai isa AbstractComposite
+    @test cdai isa ContinuousComposite
+    @test cdai isa CDAI
+    @test t28(cdai) isa Real
+    @test s28(cdai) isa Real
+    @test pga(cdai) isa Unitful.AbstractQuantity
+    @test ega(cdai) isa Unitful.AbstractQuantity
+end
+
+@testset "Score CDAI" begin
+    @test i_cdai == 0.0
+    @test score(cdai) isa Float64
+    @test score(cdai) ≈ i_cdai + sum(weight(cdai)) atol = 1e-3
+    @test score(cdai) ≈ cdai_ref atol = 1e-2
+    @test score(cdai_u1) ≈ score(cdai_u2) atol = 1e-3
+end
+
+@testset "CDAI Remission" begin
+    @test isremission(cdai)
+    @test !isremission(CDAI(t28=3, s28=4, pga=4u"cm", ega=4u"cm"))
+end
+
+@testset "Categorise CDAI" begin
+    @test categorise(cdai) == "Remission"
+    @test categorise.(CDAI, [2.79, 2.81]) == ["Remission", "Low"]
+    @test categorise.(CDAI, [9.99, 10.01]) == ["Low", "Moderate"]
+    @test categorise.(CDAI, [21.99, 22.01]) == ["Moderate", "High"]
+end