Nicer describeblocks output (#299)

* Nicer describeblocks output

* Replace describeblocks by BlockDescription

Co-authored-by: Phillip Alday <[email protected]>

Author: dmbates

src/MixedModels.jl

@@ -35,6 +35,7 @@ export @formula,
        Bernoulli,
        Binomial,
        Block,
+       BlockDescription,
        BlockedSparse,
        DummyCoding,
        EffectsCoding,
@@ -150,5 +151,6 @@ include("linalg/logdet.jl")
 include("linalg.jl")
 include("simulate.jl")
 include("bootstrap.jl")
+include("blockdescription.jl")
 
 end # module

src/blockdescription.jl

@@ -0,0 +1,63 @@
+"""
+    BlockDescription
+
+Description of blocks of `A` and `L` in a [`LinearMixedModel`](@ref)
+
+## Fields
+* `blknms`: Vector{String} of block names
+* `blkrows`: Vector{Int} of the number of rows in each block
+* `ALtypes`: Matrix{String} of datatypes for blocks in `A` and `L`.
+
+When a block in `L` is the same type as the corresponding block in `A`, it is
+described with a single name, such as `Dense`.  When the types differ the entry
+in `ALtypes` is of the form `Diag/Dense`, as determined by a `shorttype` method.
+"""
+struct BlockDescription
+    blknms::Vector{String}
+    blkrows::Vector{Int}
+    ALtypes::Matrix{String}
+end
+function BlockDescription(m::LinearMixedModel)
+    A = m.A
+    L = m.L
+    blknms = push!(string.([fnames(m)...]), "fixed")
+    k = length(blknms)
+    ALtypes = fill("", k, k)
+    Ltypes = fill(Nothing, k, k)
+    for i in 1:k, j in 1:i
+        ALtypes[i, j] = shorttype(A[Block(i,j)], L[Block(i,j)])
+    end
+    BlockDescription(
+        blknms,
+        [size(A[Block(i, 1)], 1) for i in 1:k],
+        ALtypes,
+     )
+end
+
+BlockDescription(m::GeneralizedLinearMixedModel) = BlockDescription(m.LMM)
+
+shorttype(::UniformBlockDiagonal,::UniformBlockDiagonal) = "BlkDiag"
+shorttype(::UniformBlockDiagonal,::Matrix) = "BlkDiag/Dense"
+shorttype(::SparseMatrixCSC,::BlockedSparse) = "Sparse"
+shorttype(::Diagonal,::Diagonal) = "Diagonal"
+shorttype(::Diagonal,::Matrix) = "Diag/Dense"
+shorttype(::Matrix,::Matrix) = "Dense"
+shorttype(::SparseMatrixCSC,::SparseMatrixCSC) = "Sparse"
+
+function Base.show(io::IO, ::MIME"text/plain", b::BlockDescription)
+    rowwidth = max(maximum(ndigits, b.blkrows) + 1, 5)
+    colwidth = max(maximum(textwidth, b.blknms) + 1, 14)
+    print(io, rpad("rows:", rowwidth))
+    println(io, cpad.(b.blknms, colwidth)...)
+    for (i, r) in enumerate(b.blkrows)
+        print(io, lpad(string(r, ':'), rowwidth))
+        for j in 1:i
+            print(io, cpad(b.ALtypes[i, j], colwidth))
+        end
+        println(io)
+    end
+end
+Base.show(io::IO, b::BlockDescription) = show(io, MIME"text/plain"(), b)
+
+@deprecate describeblocks(io, m) show(io, BlockDescription(m))
+@deprecate describeblocks(m) show(stdout, BlockDescription(m))

src/linearmixedmodel.jl

@@ -251,32 +251,6 @@ function createAL(allterms::Vector{Union{ReMat{T},FeMat{T}}}) where {T}
     A, L
 end
 
-"""
-    describeblocks(io::IO, m::MixedModel)
-    describeblocks(m::MixedModel)
-
-Describe the types and sizes of the blocks in the lower triangle of `m.A` and `m.L`.
-"""
-function describeblocks(io::IO, m::LinearMixedModel)
-    A = m.A
-    L = m.L
-    for i = 1:length(m.allterms), j = 1:i
-        Aij = A[Block(i,j)]
-        println(
-            io,
-            i,
-            ",",
-            j,
-            ": ",
-            typeof(Aij),
-            " ",
-            size(Aij),
-            " ",
-            typeof(L[Block(i, j)]),
-        )
-    end
-end
-describeblocks(m::MixedModel) = describeblocks(stdout, m)
 
 StatsBase.deviance(m::MixedModel) = objective(m)
 

test/pirls.jl

@@ -37,6 +37,7 @@ using Test
     #@test isapprox(sum(abs2, gm1.u[1]), 48.4747, atol=0.1)
     #@test isapprox(sum(gm1.resp.devresid), 2237.349, atol=0.1)
     show(IOBuffer(), gm1)
+    show(IOBuffer(), BlockDescription(gm0))
 end
 
 @testset "cbpp" begin

test/pls.jl

@@ -10,6 +10,35 @@ using Tables
 using Test
 
 const LMM = LinearMixedModel
+const forms = Dict(
+    :dyestuff => [@formula(yield ~ 1 + (1|batch))],
+    :dyestuff2 => [@formula(yield ~ 1 + (1|batch))],
+    :d3 => [@formula(y ~ 1 + u + (1+u|g) + (1+u|h) + (1+u|i))],
+    :insteval => [
+        @formula(y ~ 1 + service + (1|s) + (1|d) + (1|dept)),
+        @formula(y ~ 1 + service*dept + (1|s) + (1|d)),
+    ],
+    :kb07 => [
+        @formula(rt_trunc ~ 1+spkr+prec+load+(1|subj)+(1|item)),
+        @formula(rt_trunc ~ 1+spkr*prec*load+(1|subj)+(1+prec|item)),
+        @formula(rt_trunc ~ 1+spkr*prec*load+(1+spkr+prec+load|subj)+(1+spkr+prec+load|item)),
+    ],
+    :ml1m => [@formula(Y ~ 1 + (1|G) + (1|H))],
+    :pastes => [
+        @formula(strength ~ 1 + (1|sample)),
+        @formula(strength ~ 1 + (1|sample) + (1|batch)),
+    ],
+    :penicillin => [@formula(diameter ~ 1 + (1|plate) + (1|sample))],
+    :sleepstudy => [
+        @formula(reaction ~ 1 + days + (1|subj)),
+        @formula(reaction ~ 1 + days + zerocorr(1+days|subj)),
+        @formula(reaction ~ 1 + days + (1+days|subj)),
+    ],
+)
+
+#=         # replace all the model fits by
+fits = Dict(k => fit.(MixedModel, forms[k], Ref(MixedModels.dataset[k])) for k in keys(forms))
+=#
 
 @testset "Dyestuff" begin
     ds = MixedModels.dataset(:dyestuff)
@@ -25,7 +54,13 @@ const LMM = LinearMixedModel
     @test_logs (:warn, "Model has not been fit") show(fm1)
 
     @test objective(updateL!(setθ!(fm1, [0.713]))) ≈ 327.34216280955366
-    MixedModels.describeblocks(IOBuffer(), fm1)
+    @test_deprecated MixedModels.describeblocks(IOBuffer(), fm1)
+    
+    io = IOBuffer()
+    show(io, BlockDescription(fm1))
+    @test countlines(seekstart(io)) == 3
+    output = String(take!(io))
+    @test startswith(output, "rows:")
 
     fit!(fm1);
     @test :θ in propertynames(fm1)