From d33ffaaa98cec40655f1cb918cf126cbc133954c Mon Sep 17 00:00:00 2001
From: Phillip Alday <me@phillipalday.com>
Date: Thu, 20 Jun 2024 20:59:22 -0500
Subject: [PATCH 01/13] minor tweaks to improve type inference

---
 src/linearmixedmodel.jl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index 875b54c92..34f146b9e 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -36,8 +36,8 @@ struct LinearMixedModel{T<:AbstractFloat} <: MixedModel{T}
     sqrtwts::Vector{T}
     parmap::Vector{NTuple{3,Int}}
     dims::NamedTuple{(:n, :p, :nretrms),NTuple{3,Int}}
-    A::Vector{AbstractMatrix{T}}            # cross-product blocks
-    L::Vector{AbstractMatrix{T}}
+    A::Vector{<:AbstractMatrix{T}}            # cross-product blocks
+    L::Vector{<:AbstractMatrix{T}}
     optsum::OptSummary{T}
 end
 
@@ -408,7 +408,7 @@ function createAL(reterms::Vector{<:AbstractReMat{T}}, Xy::FeMat{T}) where {T}
             end
         end
     end
-    return A, L
+    return identity.(A), identity.(L)
 end
 
 StatsAPI.deviance(m::LinearMixedModel) = objective(m)

From 1bab6e7288bbc096e4fafc362b1e101e4940a7de Mon Sep 17 00:00:00 2001
From: Phillip Alday <me@phillipalday.com>
Date: Thu, 20 Jun 2024 21:10:40 -0500
Subject: [PATCH 02/13] remove unused kwarg

---
 src/linearmixedmodel.jl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index 34f146b9e..8c02f982a 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -432,7 +432,6 @@ end
 
 """
     fit!(m::LinearMixedModel; progress::Bool=true, REML::Bool=false,
-                              σ::Union{Real, Nothing}=nothing,
                               thin::Int=typemax(Int))
 
 Optimize the objective of a `LinearMixedModel`.  When `progress` is `true` a
@@ -446,7 +445,6 @@ function StatsAPI.fit!(
     m::LinearMixedModel{T};
     progress::Bool=true,
     REML::Bool=false,
-    σ::Union{Real,Nothing}=nothing,
     thin::Int=typemax(Int),
 ) where {T}
     optsum = m.optsum

From 2a190e31ad0ace793229589d5c70789c2dd1cc13 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 12:41:42 -0500
Subject: [PATCH 03/13] another type restriction

---
 src/linearmixedmodel.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index 8c02f982a..cd3ae8a61 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -1339,7 +1339,7 @@ function varest(m::LinearMixedModel)
     return isnothing(m.optsum.sigma) ? pwrss(m) / ssqdenom(m) : m.optsum.sigma
 end
 
-function StatsAPI.weights(m::LinearMixedModel)
+function StatsAPI.weights(m::LinearMixedModel{T}) where {T}
     rtwts = m.sqrtwts
-    return isempty(rtwts) ? ones(eltype(rtwts), nobs(m)) : abs2.(rtwts)
+    return isempty(rtwts) ? ones(T, nobs(m)) : abs2.(rtwts)
 end

From ed9f06bb6ebc55103d74c908a218528e8647329e Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 12:43:45 -0500
Subject: [PATCH 04/13] fix NEWS and version number

---
 NEWS.md      | 7 ++++++-
 Project.toml | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index ece040c1a..f4e196ce0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,10 @@
+MixedModels v4.24.2 Release Notes
+==============================
+- Add type notations in `pwrss(::LinearMixedModel)` and `logdet(::LinearMixedModel)` to enhance type inference. [#773]
+
 MixedModels v4.24.1 Release Notes
 ==============================
-Add type notations in `pwrss(::LinearMixedModel)` and `logdet(::LinearMixedModel)` to enhance type inference. [#773]
+- Re-export accidentally dropped export `lrtest`. [#769]
 
 MixedModels v4.24.0 Release Notes
 ==============================
@@ -525,4 +529,5 @@ Package dependencies
 [#755]: https://github.com/JuliaStats/MixedModels.jl/issues/755
 [#756]: https://github.com/JuliaStats/MixedModels.jl/issues/756
 [#767]: https://github.com/JuliaStats/MixedModels.jl/issues/767
+[#769]: https://github.com/JuliaStats/MixedModels.jl/issues/769
 [#773]: https://github.com/JuliaStats/MixedModels.jl/issues/773
diff --git a/Project.toml b/Project.toml
index 6d31df627..a602cbffb 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "MixedModels"
 uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 author = ["Phillip Alday <me@phillipalday.com>", "Douglas Bates <dmbates@gmail.com>", "Jose Bayoan Santiago Calderon <jbs3hp@virginia.edu>"]
-version = "4.24.1"
+version = "4.24.2"
 
 [deps]
 Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"

From 9f4a72b38a799424388f8838a81df462ae3599aa Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 12:49:40 -0500
Subject: [PATCH 05/13] Revert "remove unused kwarg"

This reverts commit 1bab6e7288bbc096e4fafc362b1e101e4940a7de.
---
 src/linearmixedmodel.jl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index cd3ae8a61..24d85fa83 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -432,6 +432,7 @@ end
 
 """
     fit!(m::LinearMixedModel; progress::Bool=true, REML::Bool=false,
+                              σ::Union{Real, Nothing}=nothing,
                               thin::Int=typemax(Int))
 
 Optimize the objective of a `LinearMixedModel`.  When `progress` is `true` a
@@ -445,6 +446,7 @@ function StatsAPI.fit!(
     m::LinearMixedModel{T};
     progress::Bool=true,
     REML::Bool=false,
+    σ::Union{Real,Nothing}=nothing,
     thin::Int=typemax(Int),
 ) where {T}
     optsum = m.optsum

From 294cd152084d7c15ff2dbe30fd9320d300e449b3 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 12:55:11 -0500
Subject: [PATCH 06/13] fixes

---
 NEWS.md                 |  4 ++++
 src/linearmixedmodel.jl | 13 +++++++------
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index f4e196ce0..ab1d3f430 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,10 @@
 MixedModels v4.24.2 Release Notes
 ==============================
 - Add type notations in `pwrss(::LinearMixedModel)` and `logdet(::LinearMixedModel)` to enhance type inference. [#773]
+- Take advantage of type parameter for `StatsAPI.weights(::LinearMixedModel{T})`. [#772]
+- Fix use of kwargs in `fit!((::LinearMixedModel)`: [#772]
+    - user-specified `σ` is actually used, defaulting to existing value
+    - `REML` defaults to model's already specified REML value.
 
 MixedModels v4.24.1 Release Notes
 ==============================
diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index 24d85fa83..3555ff90d 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -431,8 +431,8 @@ function feL(m::LinearMixedModel)
 end
 
 """
-    fit!(m::LinearMixedModel; progress::Bool=true, REML::Bool=false,
-                              σ::Union{Real, Nothing}=nothing,
+    fit!(m::LinearMixedModel; progress::Bool=true, REML::Bool=m.optsum.REML,
+                              σ::Union{Real, Nothing}=m.optsum.sigma,
                               thin::Int=typemax(Int))
 
 Optimize the objective of a `LinearMixedModel`.  When `progress` is `true` a
@@ -445,8 +445,8 @@ saved in `m.optsum.fitlog`.
 function StatsAPI.fit!(
     m::LinearMixedModel{T};
     progress::Bool=true,
-    REML::Bool=false,
-    σ::Union{Real,Nothing}=nothing,
+    REML::Bool=m.optsum.REML,
+    σ::Union{Real,Nothing}=m.optsum.sigma,
     thin::Int=typemax(Int),
 ) where {T}
     optsum = m.optsum
@@ -461,6 +461,7 @@ function StatsAPI.fit!(
     end
     opt = Opt(optsum)
     optsum.REML = REML
+    optsum.sigma = σ
     prog = ProgressUnknown(; desc="Minimizing", showspeed=true)
     # start from zero for the initial call to obj before optimization
     iter = 0
@@ -1341,7 +1342,7 @@ function varest(m::LinearMixedModel)
     return isnothing(m.optsum.sigma) ? pwrss(m) / ssqdenom(m) : m.optsum.sigma
 end
 
-function StatsAPI.weights(m::LinearMixedModel{T}) where {T}
+function StatsAPI.weights(m::LinearMixedModel)
     rtwts = m.sqrtwts
-    return isempty(rtwts) ? ones(T, nobs(m)) : abs2.(rtwts)
+    return isempty(rtwts) ? ones(eltype(rtwts), nobs(m)) : abs2.(rtwts)
 end

From d22927828112b8f18155670ea0831253e6d3e387 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 13:42:22 -0500
Subject: [PATCH 07/13] simplify convenience constructors for OptSummary

---
 src/MixedModels.jl |  2 +-
 src/optsummary.jl  | 72 +++++++++++++++-------------------------------
 2 files changed, 24 insertions(+), 50 deletions(-)

diff --git a/src/MixedModels.jl b/src/MixedModels.jl
index 735b18581..231fdfcc5 100644
--- a/src/MixedModels.jl
+++ b/src/MixedModels.jl
@@ -19,7 +19,7 @@ using LinearAlgebra: ldiv!, lmul!, logdet, mul!, norm, normalize, normalize!, qr
 using LinearAlgebra: rank, rdiv!, rmul!, svd, tril!
 using Markdown: Markdown
 using MixedModelsDatasets: dataset, datasets
-using NLopt: NLopt, Opt, ftol_abs, ftol_rel, initial_step, xtol_abs, xtol_rel
+using NLopt: NLopt, Opt
 using PooledArrays: PooledArrays, PooledArray
 using PrecompileTools: PrecompileTools, @setup_workload, @compile_workload
 using ProgressMeter: ProgressMeter, Progress, ProgressUnknown, finish!, next!
diff --git a/src/optsummary.jl b/src/optsummary.jl
index e79fb4557..3f2c7b29f 100644
--- a/src/optsummary.jl
+++ b/src/optsummary.jl
@@ -31,63 +31,37 @@ The latter four fields are MixedModels functionality and not related directly to
     the future to use a different subtype of `AbstractVector` (e.g., `StaticArrays.SVector`)
     for each snapshot without being considered a breaking change.
 """
-mutable struct OptSummary{T<:AbstractFloat}
+Base.@kwdef mutable struct OptSummary{T<:AbstractFloat}
     initial::Vector{T}
     lowerbd::Vector{T}
-    finitial::T
-    ftol_rel::T
-    ftol_abs::T
-    xtol_rel::T
-    xtol_abs::Vector{T}
-    initial_step::Vector{T}
-    maxfeval::Int
-    maxtime::T
-    feval::Int
-    final::Vector{T}
-    fmin::T
-    optimizer::Symbol
-    returnvalue::Symbol
-    nAGQ::Integer           # don't really belong here but I needed a place to store them
-    REML::Bool
-    sigma::Union{T,Nothing}
-    fitlog::Vector{Tuple{Vector{T},T}} # not SVector because we would need to parameterize on size (which breaks GLMM)
+    finitial::T = T(Inf)
+    ftol_rel::T = zero(T)
+    ftol_abs::T = zero(T)
+    xtol_rel::T = zero(T)
+    xtol_abs::Vector{T} = zero(initial) .+ 1e-10
+    initial_step::Vector{T} = T[]
+    maxfeval::Int = -1
+    maxtime::T = T(-1)
+    feval::Int = -1
+    final::Vector{T} = copy(initial)
+    fmin::T = T(Inf)
+    optimizer::Symbol = :LN_BOBYQA
+    returnvalue::Symbol = :FAILURE
+    ftol_zero_abs::T = T(0.001)
+    # not SVector because we would need to parameterize on size (which breaks GLMM)
+    fitlog::Vector{Tuple{Vector{T},T}} = [(initial, T(Inf))]
+    # don't really belong here but I needed a place to store them
+    nAGQ::Integer = 1
+    REML::Bool = false
+    sigma::Union{T,Nothing} = nothing
 end
 
 function OptSummary(
     initial::Vector{T},
     lowerbd::Vector{T},
-    optimizer::Symbol;
-    ftol_rel::T=zero(T),
-    ftol_abs::T=zero(T),
-    xtol_rel::T=zero(T),
-    xtol_abs::Vector{T}=zero(initial) .+ 1e-10,
-    initial_step::Vector{T}=T[],
-    maxfeval=-1,
-    maxtime=T(-1),
+    optimizer::Symbol=:LN_BOBYQA; kwargs...
 ) where {T<:AbstractFloat}
-    fitlog = [(initial, T(Inf))]
-
-    return OptSummary(
-        initial,
-        lowerbd,
-        T(Inf),
-        ftol_rel,
-        ftol_abs,
-        xtol_rel,
-        xtol_abs,
-        initial_step,
-        maxfeval,
-        maxtime,
-        -1,
-        copy(initial),
-        T(Inf),
-        optimizer,
-        :FAILURE,
-        1,
-        false,
-        nothing,
-        fitlog,
-    )
+    return OptSummary( ; initial, lowerbd, optimizer, kwargs...)
 end
 
 """

From f47fb4a2b292213c49d14f65e86ec43f14539008 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 14:54:02 -0500
Subject: [PATCH 08/13] fix use of type parameters in defaults

---
 NEWS.md           |  1 +
 src/optsummary.jl | 29 ++++++++++++++++-------------
 2 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index ab1d3f430..186d8d556 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -5,6 +5,7 @@ MixedModels v4.24.2 Release Notes
 - Fix use of kwargs in `fit!((::LinearMixedModel)`: [#772]
     - user-specified `σ` is actually used, defaulting to existing value
     - `REML` defaults to model's already specified REML value.
+- Clean up code of keyword convenience constructor for `OptSummary`. [#772]
 
 MixedModels v4.24.1 Release Notes
 ==============================
diff --git a/src/optsummary.jl b/src/optsummary.jl
index 3f2c7b29f..dc3c7bfe8 100644
--- a/src/optsummary.jl
+++ b/src/optsummary.jl
@@ -34,34 +34,37 @@ The latter four fields are MixedModels functionality and not related directly to
 Base.@kwdef mutable struct OptSummary{T<:AbstractFloat}
     initial::Vector{T}
     lowerbd::Vector{T}
-    finitial::T = T(Inf)
-    ftol_rel::T = zero(T)
-    ftol_abs::T = zero(T)
-    xtol_rel::T = zero(T)
+    # the @kwdef macro isn't quite smart enough for us to use the type parameter
+    # for the default values, but we can fake it
+    finitial::T = Inf * one(eltype(initial))
+    ftol_rel::T = zero(eltype(initial))
+    ftol_abs::T = zero(eltype(initial))
+    xtol_rel::T = zero(eltype(initial))
     xtol_abs::Vector{T} = zero(initial) .+ 1e-10
-    initial_step::Vector{T} = T[]
+    initial_step::Vector{T} = empty(initial)
     maxfeval::Int = -1
-    maxtime::T = T(-1)
+    maxtime::T = -one(eltype(initial))
     feval::Int = -1
     final::Vector{T} = copy(initial)
-    fmin::T = T(Inf)
+    fmin::T = Inf * one(eltype(initial))
     optimizer::Symbol = :LN_BOBYQA
     returnvalue::Symbol = :FAILURE
-    ftol_zero_abs::T = T(0.001)
+    ftol_zero_abs::T = one(eltype(initial)) / 1000
     # not SVector because we would need to parameterize on size (which breaks GLMM)
-    fitlog::Vector{Tuple{Vector{T},T}} = [(initial, T(Inf))]
+    fitlog::Vector{Tuple{Vector{T},T}} = [(initial, fmin)]
     # don't really belong here but I needed a place to store them
-    nAGQ::Integer = 1
+    nAGQ::Int = 1
     REML::Bool = false
     sigma::Union{T,Nothing} = nothing
 end
 
 function OptSummary(
     initial::Vector{T},
-    lowerbd::Vector{T},
+    lowerbd::Vector{S},
     optimizer::Symbol=:LN_BOBYQA; kwargs...
-) where {T<:AbstractFloat}
-    return OptSummary( ; initial, lowerbd, optimizer, kwargs...)
+) where {T<:AbstractFloat, S<:AbstractFloat}
+    TS = promote_type(T, S)
+    return OptSummary{TS}( ; initial, lowerbd, optimizer, kwargs...)
 end
 
 """

From 822be0f6d6499f257614245604b309d098037111 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 14:56:28 -0500
Subject: [PATCH 09/13] NEWS

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 186d8d556..8e218aeef 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -535,4 +535,5 @@ Package dependencies
 [#756]: https://github.com/JuliaStats/MixedModels.jl/issues/756
 [#767]: https://github.com/JuliaStats/MixedModels.jl/issues/767
 [#769]: https://github.com/JuliaStats/MixedModels.jl/issues/769
+[#772]: https://github.com/JuliaStats/MixedModels.jl/issues/772
 [#773]: https://github.com/JuliaStats/MixedModels.jl/issues/773

From de68714bd7eda5a78ad2ea6008d6a3056860b05f Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 15:04:56 -0500
Subject: [PATCH 10/13] tweaks

---
 src/linearmixedmodel.jl | 2 +-
 src/optsummary.jl       | 9 +++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index 3555ff90d..2b1951570 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -175,7 +175,7 @@ function LinearMixedModel(
     A, L = createAL(reterms, Xy)
     lbd = foldl(vcat, lowerbd(c) for c in reterms)
     θ = foldl(vcat, getθ(c) for c in reterms)
-    optsum = OptSummary(θ, lbd, :LN_BOBYQA; ftol_rel=T(1.0e-12), ftol_abs=T(1.0e-8))
+    optsum = OptSummary(θ, lbd)
     optsum.sigma = isnothing(σ) ? nothing : T(σ)
     fill!(optsum.xtol_abs, 1.0e-10)
     return LinearMixedModel(
diff --git a/src/optsummary.jl b/src/optsummary.jl
index dc3c7bfe8..6f5065350 100644
--- a/src/optsummary.jl
+++ b/src/optsummary.jl
@@ -19,12 +19,13 @@ Summary of an `NLopt` optimization
 * `feval`: the number of function evaluations
 * `optimizer`: the name of the optimizer used, as a `Symbol`
 * `returnvalue`: the return value, as a `Symbol`
+* `ftol_zero_abs`: the tolerance for change in the objective for setting a near zero parameter to zero
+* `fitlog`: A vector of tuples of parameter and objectives values from steps in the optimization
 * `nAGQ`: number of adaptive Gauss-Hermite quadrature points in deviance evaluation for GLMMs
 * `REML`: use the REML criterion for LMM fits
 * `sigma`: a priori value for the residual standard deviation for LMM
-* `fitlog`: A vector of tuples of parameter and objectives values from steps in the optimization
 
-The latter four fields are MixedModels functionality and not related directly to the `NLopt` package or algorithms.
+The last three fields are MixedModels functionality and not related directly to the `NLopt` package or algorithms.
 
 !!! note
     The internal storage of the parameter values within `fitlog` may change in
@@ -37,8 +38,8 @@ Base.@kwdef mutable struct OptSummary{T<:AbstractFloat}
     # the @kwdef macro isn't quite smart enough for us to use the type parameter
     # for the default values, but we can fake it
     finitial::T = Inf * one(eltype(initial))
-    ftol_rel::T = zero(eltype(initial))
-    ftol_abs::T = zero(eltype(initial))
+    ftol_rel::T = eltype(initial)(1.0e-12)
+    ftol_abs::T = eltype(initial)(1.0e-8)
     xtol_rel::T = zero(eltype(initial))
     xtol_abs::Vector{T} = zero(initial) .+ 1e-10
     initial_step::Vector{T} = empty(initial)

From 60cbed73b69cba4d3dcf17e87adee77f05b8a404 Mon Sep 17 00:00:00 2001
From: Phillip Alday <palday@users.noreply.github.com>
Date: Mon, 24 Jun 2024 15:05:26 -0500
Subject: [PATCH 11/13] JuliaFormatter

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 src/optsummary.jl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/optsummary.jl b/src/optsummary.jl
index dc3c7bfe8..74ab05e89 100644
--- a/src/optsummary.jl
+++ b/src/optsummary.jl
@@ -61,10 +61,10 @@ end
 function OptSummary(
     initial::Vector{T},
     lowerbd::Vector{S},
-    optimizer::Symbol=:LN_BOBYQA; kwargs...
-) where {T<:AbstractFloat, S<:AbstractFloat}
+    optimizer::Symbol=:LN_BOBYQA; kwargs...,
+) where {T<:AbstractFloat,S<:AbstractFloat}
     TS = promote_type(T, S)
-    return OptSummary{TS}( ; initial, lowerbd, optimizer, kwargs...)
+    return OptSummary{TS}(; initial, lowerbd, optimizer, kwargs...)
 end
 
 """

From 63264fe024a3b00245c39a5675b2679b64321ba9 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 15:15:37 -0500
Subject: [PATCH 12/13] abstract near-zero checks into configurable params

---
 NEWS.md                            | 1 +
 src/generalizedlinearmixedmodel.jl | 4 ++--
 src/linearmixedmodel.jl            | 4 ++--
 src/optsummary.jl                  | 4 +++-
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 8e218aeef..964886040 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,6 +6,7 @@ MixedModels v4.24.2 Release Notes
     - user-specified `σ` is actually used, defaulting to existing value
     - `REML` defaults to model's already specified REML value.
 - Clean up code of keyword convenience constructor for `OptSummary`. [#772]
+- Refactor thresholding parameters for forcing near-zero parameter values into `OptSummary`. [#772]
 
 MixedModels v4.24.1 Release Notes
 ==============================
diff --git a/src/generalizedlinearmixedmodel.jl b/src/generalizedlinearmixedmodel.jl
index 3e2125499..cfc06a778 100644
--- a/src/generalizedlinearmixedmodel.jl
+++ b/src/generalizedlinearmixedmodel.jl
@@ -309,13 +309,13 @@ function StatsAPI.fit!(
     ## check if very small parameter values bounded below by zero can be set to zero
     xmin_ = copy(xmin)
     for i in eachindex(xmin_)
-        if iszero(optsum.lowerbd[i]) && zero(T) < xmin_[i] < T(0.001)
+        if iszero(optsum.lowerbd[i]) && zero(T) < xmin_[i] < optsum.xtol_zero_abs
             xmin_[i] = zero(T)
         end
     end
     loglength = length(fitlog)
     if xmin ≠ xmin_
-        if (zeroobj = obj(xmin_, T[])) ≤ (fmin + 1.e-5)
+        if (zeroobj = obj(xmin_, T[])) ≤ (fmin + optsum.ftol_zero_abs)
             fmin = zeroobj
             copyto!(xmin, xmin_)
         elseif length(fitlog) > loglength
diff --git a/src/linearmixedmodel.jl b/src/linearmixedmodel.jl
index 2b1951570..14f297835 100644
--- a/src/linearmixedmodel.jl
+++ b/src/linearmixedmodel.jl
@@ -512,13 +512,13 @@ function StatsAPI.fit!(
     xmin_ = copy(xmin)
     lb = optsum.lowerbd
     for i in eachindex(xmin_)
-        if iszero(lb[i]) && zero(T) < xmin_[i] < T(0.001)
+        if iszero(lb[i]) && zero(T) < xmin_[i] < optsum.xtol_zero_abs
             xmin_[i] = zero(T)
         end
     end
     loglength = length(fitlog)
     if xmin ≠ xmin_
-        if (zeroobj = obj(xmin_, T[])) ≤ (fmin + 1.e-5)
+        if (zeroobj = obj(xmin_, T[])) ≤ (fmin + optsum.ftol_zero_abs)
             fmin = zeroobj
             copyto!(xmin, xmin_)
         elseif length(fitlog) > loglength
diff --git a/src/optsummary.jl b/src/optsummary.jl
index 89a2b5f89..2ee69144c 100644
--- a/src/optsummary.jl
+++ b/src/optsummary.jl
@@ -19,6 +19,7 @@ Summary of an `NLopt` optimization
 * `feval`: the number of function evaluations
 * `optimizer`: the name of the optimizer used, as a `Symbol`
 * `returnvalue`: the return value, as a `Symbol`
+* `xtol_zero_abs`: the tolerance for a near zero parameter to be considered practically zero
 * `ftol_zero_abs`: the tolerance for change in the objective for setting a near zero parameter to zero
 * `fitlog`: A vector of tuples of parameter and objectives values from steps in the optimization
 * `nAGQ`: number of adaptive Gauss-Hermite quadrature points in deviance evaluation for GLMMs
@@ -50,7 +51,8 @@ Base.@kwdef mutable struct OptSummary{T<:AbstractFloat}
     fmin::T = Inf * one(eltype(initial))
     optimizer::Symbol = :LN_BOBYQA
     returnvalue::Symbol = :FAILURE
-    ftol_zero_abs::T = one(eltype(initial)) / 1000
+    xtol_zero_abs::T = eltype(initial)(0.001)
+    ftol_zero_abs::T = eltype(initial)(1.e-5)
     # not SVector because we would need to parameterize on size (which breaks GLMM)
     fitlog::Vector{Tuple{Vector{T},T}} = [(initial, fmin)]
     # don't really belong here but I needed a place to store them

From 33211b6ba23119d2254c33c3ac7a98edfdc6b988 Mon Sep 17 00:00:00 2001
From: Phillip Alday <phillip.alday@beacon.bio>
Date: Mon, 24 Jun 2024 15:17:53 -0500
Subject: [PATCH 13/13] technically we've added a feature....

---
 NEWS.md      | 2 +-
 Project.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 964886040..728e40fd7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-MixedModels v4.24.2 Release Notes
+MixedModels v4.25 Release Notes
 ==============================
 - Add type notations in `pwrss(::LinearMixedModel)` and `logdet(::LinearMixedModel)` to enhance type inference. [#773]
 - Take advantage of type parameter for `StatsAPI.weights(::LinearMixedModel{T})`. [#772]
diff --git a/Project.toml b/Project.toml
index a602cbffb..9e02e7138 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "MixedModels"
 uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 author = ["Phillip Alday <me@phillipalday.com>", "Douglas Bates <dmbates@gmail.com>", "Jose Bayoan Santiago Calderon <jbs3hp@virginia.edu>"]
-version = "4.24.2"
+version = "4.25.0"
 
 [deps]
 Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"