added tests

Cleaning up docstrings docs lsurvresp issue jackknife for KM jackknife for AJ
alexpkeil1 · Sep 14, 2023 · cb23a04 · cb23a04
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commit cb23a04
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diff --git a/src/LSurvival.jl b/src/LSurvival.jl
@@ -37,6 +37,7 @@ import StatsBase:
     #predict, predict!,
     response,
     score,
+    var,
     vcov,
     weights
 

diff --git a/src/bootstrap.jl b/src/bootstrap.jl
@@ -1,15 +1,5 @@
-
 """
-```
-id, int, outt, data =
-LSurvival.dgm(MersenneTwister(1212), 20, 5; afun = LSurvival.int_0)
-
-d, X = data[:, 4], data[:, 1:3]
-weights = rand(length(d))
-
-# survival outcome:
-R = LSurvivalResp(int, outt, d, ID.(id))    # specification with ID only
-```
+$DOC_BOOTSTRAP_SURVRESP
 """
 function bootstrap(rng::MersenneTwister, R::T) where {T<:LSurvivalResp}
     uid = unique(R.id)
@@ -24,16 +14,9 @@ end
 bootstrap(R::T) where {T<:LSurvivalResp} = bootstrap(MersenneTwister(), R::T)
 
 
+
 """
-```
-z,x,t,d,event,weights =
-LSurvival.dgm_comprisk(MersenneTwister(1212), 300)
-enter = zeros(length(event))
-
-# survival outcome:
-R = LSurvivalCompResp(enter, t, event, weights, ID.(collect(1:length(t))))    # specification with ID only
-bootstrap(R) # note that entire observations/clusters identified by id are kept
-```
+$DOC_BOOTSTRAP_SURVCOMPRESP
 """
 function bootstrap(rng::MersenneTwister, R::T) where {T<:LSurvivalCompResp}
     uid = unique(R.id)
@@ -47,27 +30,9 @@ function bootstrap(rng::MersenneTwister, R::T) where {T<:LSurvivalCompResp}
 end
 bootstrap( R::T) where {T<:LSurvivalCompResp} = bootstrap(MersenneTwister(), R::T)
 
-"""
-```
-using LSurvival, Random
-
-id, int, outt, data =
-LSurvival.dgm(MersenneTwister(1212), 20, 5; afun = LSurvival.int_0)
-
-d, X = data[:, 4], data[:, 1:3]
-weights = rand(length(d))
-
-# survival outcome:
-R = LSurvivalResp(int, outt, d, ID.(id))    # specification with ID only
-P = PHParms(X)
-idx, R2 = bootstrap(R)
-P2 = bootstrap(idx, P)
-
-Mod = PHModel(R2, P2)
-LSurvival._fit!(Mod, start=Mod.P._B)
-
-```
 
+"""
+$DOC_BOOTSTRAP_PHPARMS
 """
 function bootstrap(idx::Vector{Int}, P::PHParms)
     P2 = PHParms(P.X[idx, :])
@@ -118,6 +83,19 @@ function bootstrap(rng::MersenneTwister, m::M;kwargs...) where{M<:KMSurv}
 end
 bootstrap(m::M;kwargs...) where{M<:KMSurv} = bootstrap(MersenneTwister(), m;kwargs...)
 
+function bootstrap(rng::MersenneTwister, m::M, iter::Int;kwargs...) where{M<:KMSurv}
+    if isnothing(m.R) 
+        throw("Model is missing response matrix, use keepy=true for original fit")
+    end
+    res = zeros(iter, 1)
+    @inbounds for i = 1:iter
+        mb = bootstrap(rng, m)
+        LSurvival._fit!(mb; kwargs...)
+        res[i, :] = mb.surv[end:end]
+    end
+    res
+end
+bootstrap(m::M, iter::Int; kwargs...) where{M<:KMSurv} = bootstrap(MersenneTwister(), m, iter::Int;kwargs...)
 
 
 
@@ -132,10 +110,6 @@ function bootstrap(rng::MersenneTwister, m::M;kwargs...) where{M<:AJSurv}
 end
 bootstrap(m::M; kwargs...) where{M<:AJSurv} = bootstrap(MersenneTwister(), m;kwargs...)
 
-
-"""
-$DOC_BOOTSTRAP_AJSURV
-"""
 function bootstrap(rng::MersenneTwister, m::M, iter::Int;kwargs...) where{M<:AJSurv}
     if isnothing(m.R)
         throw("Model is missing response matrix, use keepy=true for original fit")
@@ -150,21 +124,3 @@ function bootstrap(rng::MersenneTwister, m::M, iter::Int;kwargs...) where{M<:AJS
 end
 bootstrap(m::M, iter::Int; kwargs...) where{M<:AJSurv} = bootstrap(MersenneTwister(), m, iter::Int;kwargs...)
 
-
-
-"""
-$DOC_BOOTSTRAP_KMSURV
-"""
-function bootstrap(rng::MersenneTwister, m::M, iter::Int;kwargs...) where{M<:KMSurv}
-    if isnothing(m.R) 
-        throw("Model is missing response matrix, use keepy=true for original fit")
-    end
-    res = zeros(iter, 1)
-    @inbounds for i = 1:iter
-        mb = bootstrap(rng, m)
-        LSurvival._fit!(mb; kwargs...)
-        res[i, :] = mb.surv[end:end]
-    end
-    res
-end
-bootstrap(m::M, iter::Int; kwargs...) where{M<:KMSurv} = bootstrap(MersenneTwister(), m, iter::Int;kwargs...)
diff --git a/src/coxmodel.jl b/src/coxmodel.jl
@@ -68,9 +68,6 @@ mutable struct PHModel{G<:LSurvivalResp,L<:AbstractLSurvivalParms} <: AbstractPH
     RL::Union{Nothing,Vector{Matrix{Float64}}}        # residual matrix    
 end
 
-"""
-$DOC_PHMODEL 
-"""
 function PHModel(
     R::Union{Nothing,G},
     P::L,
@@ -87,9 +84,6 @@ function PHModel(
     return PHModel(R, P, formula, ties, fit, bh, nothing)
 end
 
-"""
-$DOC_PHMODEL 
-"""
 function PHModel(
     R::Union{Nothing,G},
     P::L,
@@ -100,9 +94,6 @@ function PHModel(
     return PHModel(R, P, formula, ties, fit, zeros(Float64, length(R.eventtimes), 6))
 end
 
-"""
-$DOC_PHMODEL 
-"""
 function PHModel(
     R::Union{Nothing,G},
     P::L,
@@ -112,9 +103,6 @@ function PHModel(
     return PHModel(R, P, formula, ties, false)
 end
 
-"""
-$DOC_PHMODEL  
-"""
 function PHModel(
     R::Union{Nothing,G},
     P::L,
@@ -123,9 +111,6 @@ function PHModel(
     return PHModel(R, P, nothing, ties, false)
 end
 
-"""
-$DOC_PHMODEL    
-"""
 function PHModel(
     R::Union{Nothing,G},
     P::L,
@@ -134,9 +119,6 @@ function PHModel(
     return PHModel(R, P, formula, "efron", false)
 end
 
-"""
-$DOC_PHMODEL    
-"""
 function PHModel(R::Union{Nothing,G}, P::L) where {G<:LSurvivalResp,L<:AbstractLSurvivalParms}
     return PHModel(R, P, "efron")
 end
@@ -155,9 +137,6 @@ mutable struct PHSurv{G<:Array{T} where {T<:PHModel}} <: AbstractNPSurv
     fit::Bool
 end
 
-"""
-$DOC_PHSURV
-"""
 function PHSurv(fitlist::Array{T}, eventtypes) where {T<:PHModel}
     bhlist = [ft.bh for ft in fitlist]
     bhlist = [hcat(bh, fill(eventtypes[i], size(bh, 1))) for (i, bh) in enumerate(bhlist)]
@@ -171,9 +150,6 @@ function PHSurv(fitlist::Array{T}, eventtypes) where {T<:PHModel}
     PHSurv(fitlist, eventtypes, times, surv, risk, bh[:, 1], event, false)
 end
 
-"""
-$DOC_PHSURV
-"""
 function PHSurv(fitlist::Array{T}) where {T<:PHModel}
     eventtypes = collect(eachindex(fitlist))
     PHSurv(fitlist, eventtypes)
@@ -827,7 +803,7 @@ end
 """
 $DOC_FIT_PHSURV   
 """
-function fit(::Type{M}, fitlist::Vector{<:T}, ; fitargs...) where {M<:PHSurv,T<:PHModel}
+function fit(::Type{M}, fitlist::Vector{T}, ; fitargs...) where {M<:PHSurv,T<:PHModel}
 
     res = M(fitlist)
 
@@ -837,7 +813,7 @@ end
 """
 $DOC_FIT_PHSURV
 """
-risk_from_coxphmodels(fitlist::Array{T}, args...; kwargs...) where {T<:PHModel} =
+risk_from_coxphmodels(fitlist::Vector{T}, args...; kwargs...) where {T<:PHModel} =
     fit(PHSurv, fitlist, args...; kwargs...)
 
 

diff --git a/src/data_generators.jl b/src/data_generators.jl
@@ -20,7 +20,7 @@ end
 """
 $DOC_DGM
 """
-function dgm(rng, n, maxT; afun = int_0, yfun = yprob, lfun = lprob)
+function dgm(rng::MersenneTwister, n::Int, maxT::Int; afun = int_0, yfun = yprob, lfun = lprob)
     V = rand(rng, n)
     LAY = Array{Float64,2}(undef, n * maxT, 4)
     keep = ones(Bool, n * maxT)
@@ -43,13 +43,13 @@ function dgm(rng, n, maxT; afun = int_0, yfun = yprob, lfun = lprob)
     end
     id[findall(keep)], time[findall(keep)] .- 1, time[findall(keep)], LAY[findall(keep), :]
 end
-dgm(n, maxT; kwargs...) = dgm(MersenneTwister(), n, maxT; kwargs...)
+dgm(n::Int, maxT::Int; kwargs...) = dgm(MersenneTwister(), n::Int, maxT::Int; kwargs...)
 
 
 """
 $DOC_DGM_COMPRISK
 """
-function dgm_comprisk(rng, n)
+function dgm_comprisk(rng::MersenneTwister, n::Int)
     z = rand(rng, n) .* 5
     x = rand(rng, n) .* 5
     dt1 = Weibull.(fill(0.75, n), inv.(exp.(-x .- z)))
@@ -72,4 +72,4 @@ function dgm_comprisk(rng, n)
     event,
     round.(weights, digits = 4)
 end
-dgm_comprisk(n) = dgm_comprisk(MersenneTwister(), n)
+dgm_comprisk(n) = dgm_comprisk(MersenneTwister(), n)