SDeMo bugfix and QOL

SDeMo/Project.toml

@@ -1,7 +1,7 @@
 name = "SDeMo"
 uuid = "3e5feb82-bcca-434d-9cd5-c11731a21467"
 authors = ["Timothée Poisot <[email protected]>"]
-version = "0.0.5"
+version = "0.0.6"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"

SDeMo/docs/src/demo.jl

@@ -26,7 +26,7 @@ size(X)
 
 # ## Setting up the model
 
-## We will start with an initial model that uses a PCA to transform the data, and
+# We will start with an initial model that uses a PCA to transform the data, and
 # then a Naive Bayes Classifier for the classification. Note that this is the
 # partial syntax where we use the default threshold, and all the variables:
 
@@ -53,11 +53,11 @@ cv = crossvalidate(sdm, folds);
 measures = [mcc, balancedaccuracy, ppv, npv, trueskill, markedness]
 cvresult = [mean(measure.(set)) for measure in measures, set in cv]
 pretty_table(
-    hcat(string.(measures), cvresult);
-    alignment=[:l, :c, :c],
-    backend=Val(:markdown),
-    header=["Measure", "Validation", "Training"],
-    formatters=ft_printf("%5.3f", [2, 3])
+        hcat(string.(measures), cvresult);
+        alignment=[:l, :c, :c],
+        backend=Val(:markdown),
+        header=["Measure", "Validation", "Training"],
+        formatters=ft_printf("%5.3f", [2, 3])
 )
 
 # Assuming we want to get a simple idea of what the MCC is for the validation
@@ -69,6 +69,14 @@ mcc.(cv.validation)
 
 ci(cv.validation, mcc)
 
+# We can also get the same output by calling a function on a vector of `ConfusionMatrix`, *e.g.*
+
+mcc(cv.validation)
+
+# Adding the `true` argument returns a tuple with the 95% CI:
+
+mcc(cv.validation, true)
+
 # ## Variable selection
 
 # We will now select variables using forward selection, but with the added
@@ -87,11 +95,11 @@ cv2 = crossvalidate(sdm, folds)
 measures = [mcc, balancedaccuracy, ppv, npv, trueskill, markedness]
 cvresult = [mean(measure.(set)) for measure in measures, set in cv2]
 pretty_table(
-    hcat(string.(measures), cvresult);
-    alignment=[:l, :c, :c],
-    backend=Val(:markdown),
-    header=["Measure", "Validation", "Training"],
-    formatters=ft_printf("%5.3f", [2, 3])
+        hcat(string.(measures), cvresult);
+        alignment=[:l, :c, :c],
+        backend=Val(:markdown),
+        header=["Measure", "Validation", "Training"],
+        formatters=ft_printf("%5.3f", [2, 3])
 )
 
 # Quite clearly! Before thinking about the relative importance of variables, we
@@ -136,11 +144,11 @@ varimp = variableimportance(sdm, folds)
 # In relative terms, this is:
 
 pretty_table(
-    hcat(variables(sdm), varimp ./ sum(varimp));
-    alignment=[:l, :c],
-    backend=Val(:markdown),
-    header=["Variable", "Importance"],
-    formatters=(ft_printf("%5.3f", 2), ft_printf("%d", 1))
+        hcat(variables(sdm), varimp ./ sum(varimp));
+        alignment=[:l, :c],
+        backend=Val(:markdown),
+        header=["Variable", "Importance"],
+        formatters=(ft_printf("%5.3f", 2), ft_printf("%d", 1))
 )
 
 # ## Partial response curve
@@ -184,8 +192,8 @@ f = Figure()
 ax = Axis(f[1, 1])
 prx, pry = partialresponse(sdm, 1; inflated=false, threshold=false)
 for i in 1:200
-    ix, iy = partialresponse(sdm, 1; inflated=true, threshold=false)
-    lines!(ax, ix, iy, color=(:grey, 0.5))
+        ix, iy = partialresponse(sdm, 1; inflated=true, threshold=false)
+        lines!(ax, ix, iy, color=(:grey, 0.5))
 end
 lines!(ax, prx, pry, color=:black, linewidth=4)
 current_figure() #hide
@@ -279,11 +287,11 @@ cf = counterfactual(sdm, instance(sdm, inst; strict=false), target, 200.0; thres
 # is:
 
 pretty_table(
-    hcat(variables(sdm), instance(sdm, inst), cf[variables(sdm)]);
-    alignment=[:l, :c, :c],
-    backend=Val(:markdown),
-    header=["Variable", "Obs.", "Counterf."],
-    formatters=(ft_printf("%4.1f", [2, 3]), ft_printf("%d", 1))
+        hcat(variables(sdm), instance(sdm, inst), cf[variables(sdm)]);
+        alignment=[:l, :c, :c],
+        backend=Val(:markdown),
+        header=["Variable", "Obs.", "Counterf."],
+        formatters=(ft_printf("%4.1f", [2, 3]), ft_printf("%d", 1))
 )
 
 # We can check the prediction that would be made on the counterfactual:

SDeMo/src/crossvalidation/crossvalidation.jl

@@ -68,17 +68,15 @@ function montecarlo(y, X; n = 100, kwargs...)
     return [holdout(y, X; kwargs...) for _ in 1:n]
 end
 
-
 @testitem "We can do montecarlo validation" begin
     X, y = SDeMo.__demodata()
     model = SDM(MultivariateTransform{PCA}, NaiveBayes, X, y)
-    folds = montecarlo(model; n=10)
+    folds = montecarlo(model; n = 10)
     cv = crossvalidate(model, folds)
     @test eltype(cv.validation) <: ConfusionMatrix
     @test length(cv.training) == 10
 end
 
-
 """
     kfold(y, X; k = 10, permute = true)
 
@@ -113,32 +111,39 @@ function kfold(y, X; k = 10, permute = true)
     return folds
 end
 
-
 @testitem "We can do kfold validation" begin
     X, y = SDeMo.__demodata()
     model = SDM(MultivariateTransform{PCA}, NaiveBayes, X, y)
-    folds = kfold(model; k=12)
+    folds = kfold(model; k = 12)
     cv = crossvalidate(model, folds)
     @test eltype(cv.validation) <: ConfusionMatrix
     @test length(cv.training) == 12
 end
 
-
 for op in (:leaveoneout, :holdout, :montecarlo, :kfold)
-    eval(quote
-        """
-            $($op)(sdm::SDM)
-
-        Version of `$($op)` using the instances and labels of an SDM.
-        """
-        $op(sdm::SDM, args...; kwargs...) = $op(labels(sdm), features(sdm), args...; kwargs...)
-    end)
+    eval(
+        quote
+            """
+                $($op)(sdm::SDM)
+
+            Version of `$($op)` using the instances and labels of an SDM.
+            """
+            $op(sdm::SDM, args...; kwargs...) =
+                $op(labels(sdm), features(sdm), args...; kwargs...)
+            """
+                $($op)(sdm::Bagging)
+
+            Version of `$($op)` using the instances and labels of a bagged SDM. In this case, the instances of the model used as a reference to build the bagged model are used.
+            """
+            $op(sdm::Bagging, args...; kwargs...) = $op(sdm.model, args...; kwargs...)
+        end,
+    )
 end
 
 @testitem "We can split data in an SDM" begin
     X, y = SDeMo.__demodata()
     sdm = SDM(MultivariateTransform{PCA}(), BIOCLIM(), 0.01, X, y, 1:size(X, 1))
-    folds = montecarlo(sdm; n=10)
+    folds = montecarlo(sdm; n = 10)
     @test length(folds) == 10
 end
 
@@ -153,27 +158,39 @@ This method returns two vectors of `ConfusionMatrix`, with the confusion matrix
 for each set of validation data first, and the confusion matrix for the training
 data second.
 """
-function crossvalidate(sdm, folds; thr = nothing, kwargs...)
+function crossvalidate(sdm::T, folds; thr = nothing, kwargs...) where {T <: AbstractSDM}
     Cv = zeros(ConfusionMatrix, length(folds))
     Ct = zeros(ConfusionMatrix, length(folds))
     models = [deepcopy(sdm) for _ in Base.OneTo(Threads.nthreads())]
     Threads.@threads for i in eachindex(folds)
         trn, val = folds[i]
         train!(models[Threads.threadid()]; training = trn, kwargs...)
         pred = predict(models[Threads.threadid()], features(sdm)[:, val]; threshold = false)
-        ontrn = predict(models[Threads.threadid()], features(sdm)[:, trn]; threshold = false)
+        ontrn =
+            predict(models[Threads.threadid()], features(sdm)[:, trn]; threshold = false)
         thr = isnothing(thr) ? threshold(sdm) : thr
         Cv[i] = ConfusionMatrix(pred, labels(sdm)[val], thr)
         Ct[i] = ConfusionMatrix(ontrn, labels(sdm)[trn], thr)
     end
     return (validation = Cv, training = Ct)
 end
 
-@testitem "We can crossvalidate an SDM" begin
+@testitem "We can cross-validate an SDM" begin
     X, y = SDeMo.__demodata()
-    sdm = SDM(MultivariateTransform{PCA}(), BIOCLIM(), 0.5, X, y, [1,2,12])
+    sdm = SDM(MultivariateTransform{PCA}(), BIOCLIM(), 0.5, X, y, [1, 2, 12])
     train!(sdm)
-    cv = crossvalidate(sdm, kfold(sdm; k=15))
+    cv = crossvalidate(sdm, kfold(sdm; k = 15))
+    @test eltype(cv.validation) <: ConfusionMatrix
+    @test eltype(cv.training) <: ConfusionMatrix
+end
+
+@testitem "We can cross-validate an ensemble model using the consensus keyword" begin
+    using Statistics
+    X, y = SDeMo.__demodata()
+    sdm = SDM(MultivariateTransform{PCA}(), NaiveBayes(), 0.5, X, y, [1, 2, 12])
+    ens = Bagging(sdm, 10)
+    train!(ens)
+    cv = crossvalidate(ens, kfold(ens; k = 15); consensus = median)
     @test eltype(cv.validation) <: ConfusionMatrix
     @test eltype(cv.training) <: ConfusionMatrix
-end
+end

SDeMo/src/crossvalidation/validation.jl

@@ -229,4 +229,53 @@ specificity(M::ConfusionMatrix) = tnr(M)
 
 Alias for `ppv`, the positive predictive value
 """
-precision(M::ConfusionMatrix) = ppv(M)
+precision(M::ConfusionMatrix) = ppv(M)
+
+for op in (
+    :tpr,
+    :tnr,
+    :fpr,
+    :fnr,
+    :ppv,
+    :npv,
+    :fdir,
+    :fomr,
+    :plr,
+    :nlr,
+    :accuracy,
+    :balancedaccuracy,
+    :f1,
+    :fscore,
+    :trueskill,
+    :markedness,
+    :dor,
+    :κ,
+    :mcc,
+    :specificity,
+    :sensitivity,
+    :recall,
+    :precision,
+)
+    eval(
+        quote
+            """
+                $($op)(C::Vector{ConfusionMatrix}, full::Bool=false)
+
+            Version of `$($op)` using a vector of confusion matrices. Returns the mean, and when the second argument is `true`, returns a tuple where the second argument is the CI.
+            """
+            function $op(
+                C::Vector{ConfusionMatrix},
+                full::Bool = false,
+                args...;
+                kwargs...,
+            )
+                m = $op.(C, args...; kwargs...)
+                if full
+                    return (mean(m), ci(C, $op))
+                else
+                    return mean(m)
+                end
+            end
+        end,
+    )
+end

SDeMo/src/ensembles/pipeline.jl

@@ -17,10 +17,13 @@ Trains all the model in an ensemble model - the keyword arguments are passed to
 includes the transformers.
 """
 function train!(ensemble::Bagging; kwargs...)
+    # The ensemble model can be given a consensus argument, in which can we drop it for
+    # training as it's relevant for prediction only
+    trainargs = filter(kw -> kw.first != :consensus, kwargs)
     Threads.@threads for m in eachindex(ensemble.models)
-        train!(ensemble.models[m]; training = ensemble.bags[m][1], kwargs...)
+        train!(ensemble.models[m]; training = ensemble.bags[m][1], trainargs...)
     end
-    train!(ensemble.model; kwargs...)
+    train!(ensemble.model; trainargs...)
     return ensemble
 end