From 63c32db95beb7fc1d3143d39bcd41cf89c2ad9f4 Mon Sep 17 00:00:00 2001
From: Phillip Alday <palday@users.noreply.github.com>
Date: Tue, 2 Mar 2021 12:24:16 +0000
Subject: [PATCH] doc hints

---
 src/Xymat.jl            | 13 ++++++++++++-
 src/linearmixedmodel.jl |  3 ++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/Xymat.jl b/src/Xymat.jl
index 71a4e3e6a..e198ae819 100644
--- a/src/Xymat.jl
+++ b/src/Xymat.jl
@@ -3,6 +3,11 @@
 
 Term with an explicit, constant matrix representation
 
+Typically, an `FeTerm` represents the model matrix for the fixed effects. 
+
+!!! note
+    `FeTerm` is not the same as [`FeMat`](@ref)!
+
 # Fields
 * `x`: full model matrix
 * `piv`: pivot `Vector{Int}` for moving linearly dependent columns to the right
@@ -79,6 +84,12 @@ isfullrank(A::FeTerm) = A.rank == length(A.piv)
 
 A matrix and a (possibly) weighted copy of itself.
 
+
+Typically, an `FeMat` represents the fixed-effects model matrix with the response (`y`) concatenated as a final column.
+
+!!! note
+    `FeMat` is not the same as [`FeTerm`](@ref).
+
 # Fields
 - `xy`: original matrix, called `xy` b/c in practice this is `hcat(fullrank(X), y)`
 - `wtxy`: (possibly) weighted copy of `xy` (shares storage with `xy` until weights are applied)
@@ -101,7 +112,7 @@ Base.eltype(::FeMat{T}) where {T} = T
 
 Base.getindex(A::FeMat, i, j) = getindex(A.xy, i, j)
 
-Base.length(A::FeMat) = length(A.wtxy)
+Base.length(A::FeMat) = length(A.xy)
 
 function *(adjA::Adjoint{T,<:FeMat{T}}, B::FeMat{T}) where {T}
     adjoint(adjA.parent.wtxy) * B.wtxy
diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index e4763f92e..56d99e9b7 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -8,7 +8,7 @@ Linear mixed-effects model representation
 * `formula`: the formula for the model
 * `reterms`: a `Vector{AbstractReMat{T}}` of random-effects terms.
 * `Xymat`: horizontal concatenation of a full-rank fixed-effects model matrix `X` and response `y` as an `FeMat{T}`
-* `feterm`: the fixed-effects model matrix as an `FeMat{T}`
+* `feterm`: the fixed-effects model matrix as an `FeTerm{T}`
 * `sqrtwts`: vector of square roots of the case weights.  Can be empty.
 * `parmap` : Vector{NTuple{3,Int}} of (block, row, column) mapping of θ to λ
 * `dims` : NamedTuple{(:n, :p, :nretrms),NTuple{3,Int}} of dimensions.  `p` is the rank of `X`, which may be smaller than `size(X, 2)`.
@@ -295,6 +295,7 @@ function pushALblock!(A, L, blk)
     push!(L, blk)
     push!(A, deepcopy(isa(blk, BlockedSparse) ? blk.cscmat : blk))
 end
+
 function createAL(reterms::Vector{AbstractReMat{T}}, Xy::FeMat{T}) where {T}
     k = length(reterms)
     vlen = kchoose2(k+1)