API reference

RheumaComposites

A Julia package for composite scores in Rheumatology.

AbstractComposite

Abstract type that specifies the category of composites.

It is either ContinuousComposite, BooleanComposite, or ModifiedComposite.

ContinuousComposite <: AbstractComposite

Abstract type for composites whose scores are floating point numbers.

See also score, BooleanComposite.

BooleanComposite <: AbstractComposite

Abstract type for composites only implementing a definition of remission.

See also isremission, ContinuousComposite.

ModifiedComposite <: AbstractComposite

Abstract type representing alterations to existing composites.

See also faceted, revised, threeitem.

DAS28 <: ContinuousComposite

Abstract type for DAS28 subtypes.

See also DAS28ESR, DAS28CRP.

DAS28ESR(; tjc, sjc, pga, apr[; units])

Store the component measures of the DAS28ESR.

Optionally specify the units for each component using Unitful.@u_str.

Components

• tjc 28 tender joint count
• sjc 28 swollen joint count
• pga (cm) patient's global assessment
• apr (mm/hr) active phase reactant, here ESR

Categories

• $<$ 3.2 = Remission
• $\leq$ 3.2 = Low
• $\leq$ 5.1 = Moderate
• $>$ 5.1 = High

External links

• DAS28 calculator

See also score, categorise, isremission.

DAS28CRP(; tjc, sjc, pga, apr[; units])

Store the component measures of the DAS28CRP.

Optionally specify the units for each component using Unitful.@u_str.

Components

• tjc 28 tender joint count
• sjc 28 swollen joint count
• pga (cm) patient's global assessment
• apr (mg/L) active phase reactant, here CRP

Categories

• $<$ 2.9 = Remission
• $\leq$ 2.9 = Low
• $\leq$ 4.6 = Moderate
• $>$ 4.6 = High

External links

• DAS28 calculator

See also score, categorise, isremission.

SDAI(; tjc, sjc, pga, ega, crp[; units])

Store component measures of the Simplified Disease Activity Index, or SDAI.

Optionally specify the units for each component using Unitful.@u_str.

Components

• tjc 28 tender joint count
• sjc 28 swollen joint count
• pga (cm) patient's global assessment
• ega (cm) evaluator's global assessment
• crp (mg/dL) c-reactive protein

Categories

• $\leq$ 11.0 = Remission
• $\leq$ 11.0 = Low
• $\leq$ 26.0 = Moderate
• $>$ 26.0 = High

External links

• SDAI calculator

See also score, categorise, isremission.

CDAI(; tjc, sjc, pga, ega[; units])

Store component measures of the Clinical Disease Activity Index, or CDAI.

Optionally specify the units for each component using Unitful.@u_str.

Components

• tjc 28 tender joint count
• sjc 28 swollen joint count
• pga (cm) patient's global assessment
• ega (cm) evaluator's global assessment

Categories

• $<$ 10.0 = Remission
• $\leq$ 10.0 = Low
• $\leq$ 22.0 = Moderate
• $>$ 22.0 = High

External links

• CDAI calculator

See also score, categorise, isremission.

BASDAI(; tjc, sjc, pga, jpn[; units])

Store component measures of the Bath Ankylosing Spondylitis Disease Activity Index, or BASDAI.

Optionally specify the units for each component using Unitful.@u_str.

Components

• q1 (cm) fatigue or tiredness
• q2 (cm) AS neck, back, or hip pain
• q3 (cm) pain or swelling in other joints
• q4 (cm) discomfort from tender areas
• q5 (cm) morning stiffness severity
• q6 (cm) morning stiffness duration

Categories

The only cutoff I am aware of checks if a person's BASDAI is below 4. This is currently implemented in categorise and isremission, making them effectively redundant. Feel free to open an issue on the GitHub page of this package if you know about other cutoffs.

External links

• BASDAI calculator

See also score.

DAPSA(; tjc, sjc, pga, jpn[; units])

Store component measures of the index for Disease Activity in Psoriatic Arthritis, or DAPSA.

Optionally specify the units for each component using Unitful.@u_str.

Components

• tjc 66 tender joint count
• sjc 68 swollen joint count
• pga (cm) patient's global assessment
• jpn (cm) joint pain

Categories

• $\leq$ 14.0 = Remission
• $\leq$ 14.0 = Low
• $\leq$ 28.0 = Moderate
• $>$ 28.0 = High

External links

• DAPSA calculator

See also score, categorise, isremission.

Faceted{T} <: ModifiedComposite

This type indicates a further grouping of the stored composite's components.

BooleanRemission(; tjc, sjc, pga, crp[; units])

Store the components of the original ACR/EULAR Boolean remission.

Optionally specify the units for each component using Unitful.@u_str.

Components

• tjc 28 tender joint count
• sjc 28 swollen joint count
• pga (cm) patient's global assessment
• crp (mg/dL) C-reactive protein

See also isremission.

Revised{T} <: ModifiedComposite

This type indicates that the stored composite's threshold for remission has been revised.

See also BooleanRemission.

Partial{T}

Redefine a composite as a subset of its components.

values(x::AbstractComposite)

Return the values stored in x.

values(x::ModifiedComposite)

Return the values of the unmodified composite, i.e., x.root.values.

values(x::Partial{N,<:BooleanComposite})

Return the values kept by x.

root(x::ModifiedComposite)

Return the unmodified composite.

offsets(x::Revised{<:BooleanComposite})

Return the offsets to remission thresholds.

intercept(x::ContinuousComposite)

Return the intercept.

This function can be useful if you want to implement custom decomposition or component reweighting.

See also score, decompose.

weight(x::T) where {T}

Weight a composite score's components according to its weighting scheme.

Example

julia> DAS28CRP(tjc=2, sjc=2, pga=54u"mm", apr=19u"mg/L") |> weight
(0.7919595949289333, 0.39597979746446665, 0.756, 1.0784636184794367)

score(c::ContinuousComposite; digits=3)

Score a composite and optionally specify the rounding precision.

Examples

julia> DAS28ESR(tjc=4, sjc=2, pga=64u"mm", apr=44u"mm/hr") |> score
5.061

isremission(::Type{T}, s::Real) where {T<:ContinuousComposite}

Check whether a composite fulfils remission criteria.

Examples

julia> isremission(DAS28ESR, 3.9)
false

isremission(x::AbstractComposite)

Check whether a composite fulfils remission criteria.

Examples

julia> DAS28ESR(tjc=4, sjc=5, pga=44u"mm", apr=23u"mm/hr") |> isremission
false
julia> BooleanRemission(tjc=1, sjc=0, pga=1.4u"cm", crp=0.4u"mg/dL") |>
       revised |>
       isremission
true

decompose(x::ContinuousComposite; digits=3)

Return the proportion to which each component contributes to the composite's score.

Optionally specify the number of digits to round the results to.

See also score.

Examples

julia> SDAI(tjc=4, sjc=5, pga=1.6u"cm", ega=1.2u"cm", crp=3u"mg/dL") |> decompose
Dict{Symbol, Float64} with 5 entries:
  :tjc => 0.27
  :ega => 0.081
  :sjc => 0.338
  :pga => 0.108
  :crp => 0.203

decompose(x::Faceted{<:ContinuousComposite}; digits=3)

Return the proportion to which each facet contributes to the composite's score.

Examples

julia> root = DAS28ESR(tjc=4, sjc=5, pga=14u"mm", apr=12u"mm/hr");

julia> faceted(root, (objective=[:sjc, :apr], subjective=[:tjc, :pga])) |> decompose
Dict{Symbol, Float64} with 2 entries:
  :subjective => 0.357
  :objective  => 0.642

categorise(::Type{T}, s::Real) where {T<:ContinuousComposite}

Convert score s to a discrete value using T's thresholds.

Examples

julia> categorise(SDAI, 3.6)
"low"

categorise(x::ContinuousComposite)

Convert x to a discrete value.

Examples

julia> DAS28ESR(tjc=4, sjc=5, pga=12u"mm", apr=44u"mm/hr") |> categorise
"moderate"

categorise(x::Faceted{<:ContinuousComposite})

Convert the root composite of x to a discrete value.

faceted(root::ContinuousComposite, facets::NamedTuple)

Specify a custom grouping along which the composite can be analysed.

See also decompose.

revised(root::BooleanRemission, offset::NamedTuple)
revised(root::BooleanRemission; offset::NamedTuple=(; pga=10u"mm"))

Modify the remission thresholds of a composite.

The values passed to offset will be added to the default thresholds of root.

See also isremission.

partial(root::AbstractComposite, keep::Vector{Symbol})

Redefine a composite as a subset of its components.

Functions like score or isremission act on the subset of components.

threeitem(root::BooleanRemission)

Change the calculation of Boolean remission to exclude patient global assessment.

Alias for partial(root::BooleanRemission, [:sjc, :tjc, :crp]).

See also partial, isremission, BooleanRemission.