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ridgeplots for other parameters #79

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0279fcb
ridgeplots for other parameters
palday Sep 10, 2023
13be869
Merge branch 'main' of github.com:palday/MixedModelsMakie.jl into pa/…
palday Mar 22, 2024
701215f
more merge
palday Mar 22, 2024
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17 changes: 9 additions & 8 deletions src/coefplot.jl
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""
coefplot(x::Union{MixedModel,MixedModelBootstrap}; kwargs...)::Figure
coefplot!(fig::$(Indexable), x::Union{MixedModel,MixedModelBootstrap};
coefplot!(fig::$(Indexable), x::Union{MixedModel,MixedModelBootstrap};
kwargs...)
coefplot!(ax::Axis, Union{MixedModel,MixedModelBootstrap};
conf_level=0.95, vline_at_zero=true, show_intercept=true, attributes...)
Expand All @@ -13,13 +13,13 @@ Inestimable coefficients (coefficients removed by pivoting in the rank deficient

The mutating methods return the original object.

!!! note
Inestimable coefficients (coefficients removed by pivoting in the rank deficient case)
!!! note
Inestimable coefficients (coefficients removed by pivoting in the rank deficient case)
are excluded.
"""
function coefplot(x::Union{MixedModel,MixedModelBootstrap}; show_intercept=true, kwargs...)
function coefplot(x::Union{MixedModel,MixedModelBootstrap}; show_intercept=true, ptype=nothing, kwargs...)
# need to guarantee a min height of 150
fig = Figure(; size=(640, max(150, 75 * _npreds(x; show_intercept))))
fig = Figure(; size=(640, max(150, 75 * _npreds(x, ptype; show_intercept))))
coefplot!(fig, x; kwargs...)
return fig
end
Expand All @@ -36,8 +36,9 @@ function coefplot!(ax::Axis, x::Union{MixedModel,MixedModelBootstrap};
conf_level=0.95,
vline_at_zero=true,
show_intercept=true,
ptype=nothing,
attributes...)
ci = confint_table(x, conf_level; show_intercept)
ci = confint_table(x, conf_level; show_intercept, ptype)
y = nrow(ci):-1:1
xvals = ci.estimate
xlabel = @sprintf "Estimate and %g%% confidence interval" conf_level * 100
Expand All @@ -51,8 +52,8 @@ function coefplot!(ax::Axis, x::Union{MixedModel,MixedModelBootstrap};
vline_at_zero && vlines!(ax, 0; color=(:black, 0.75), linestyle=:dash)

reset_limits!(ax)
cn = _coefnames(x; show_intercept)
nticks = _npreds(x; show_intercept)
cn = _coefnames(x, ptype; show_intercept)
nticks = _npreds(x, ptype; show_intercept)
ax.yticks = (nticks:-1:1, cn)
ylims!(ax, 0, nticks + 1)
return ax
Expand Down
98 changes: 15 additions & 83 deletions src/ridge.jl
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""
ridgeplot(x::Union{MixedModel,MixedModelBootstrap}; kwargs...)::Figure
ridgeplot!(fig::$(Indexable), x::Union{MixedModel,MixedModelBootstrap};
ridgeplot!(fig::$(Indexable), x::Union{MixedModel,MixedModelBootstrap};
kwargs...)
ridgeplot!(ax::Axis, Union{MixedModel,MixedModelBootstrap};
conf_level=0.95, vline_at_zero=true, show_intercept=true, attributes...)
Expand All @@ -16,13 +16,13 @@ Setting `conf_level=missing` removes the markings for the highest density interv

The mutating methods return the original object.

!!! note
Inestimable coefficients (coefficients removed by pivoting in the rank deficient case)
!!! note
Inestimable coefficients (coefficients removed by pivoting in the rank deficient case)
are excluded.
"""
function ridgeplot(x::MixedModelBootstrap; show_intercept=true, kwargs...)
function ridgeplot(x::MixedModelBootstrap; show_intercept=true, ptype=nothing, kwargs...)
# need to guarantee a min height of 200
fig = Figure(; size=(640, max(200, 100 * _npreds(x; show_intercept))))
fig = Figure(; size=(640, max(200, 100 * _npreds(x, ptype; show_intercept))))
return ridgeplot!(fig, x; show_intercept, kwargs...)
end

Expand All @@ -36,7 +36,7 @@ end
"""
_color(s::Symbol)
_color(p::Pair)

Extract the color part out of either a color name or a `(color, alpha)` pair.
"""
_color(s) = s
Expand All @@ -47,6 +47,7 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;
conf_level=0.95,
vline_at_zero=true,
show_intercept=true,
ptype=:β,
attributes...)
xlabel = if !ismissing(conf_level)
@sprintf "Normalized bootstrap density and %g%% confidence interval" (conf_level *
Expand All @@ -56,19 +57,22 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;
end

if !ismissing(conf_level)
coefplot!(ax, x; conf_level, vline_at_zero, show_intercept, color=:black,
attributes...)
coefplot!(ax, x; conf_level, vline_at_zero, show_intercept, ptype,
color=:black, attributes...)
end

attributes = merge((; xlabel, color=:black), attributes)
band_attributes = merge(attributes, (; color=(_color(attributes.color), 0.3)))

ax.xlabel = attributes.xlabel

df = transform!(DataFrame(x.β), :coefname => ByRow(string) => :coefname)
df = DataFrame(getproperty(boot, ptype))
rename!(c -> replace(c, "column" => "coefname"), df)
transform!(df, :coefname => ByRow(string) => :coefname)
filter!(:coefname => in(_coefnames(x; show_intercept)), df)
group = :coefname
densvar = :β
# drop trailing s
densvar = replace(string(ptype), "s" => "")
# TODO: coefplot
gdf = groupby(df, group)

dens = combine(gdf, densvar => kde => :kde)
Expand Down Expand Up @@ -96,75 +100,3 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;

return ax
end

# """
# ridgeplot!(ax::Axis, df::AbstractDataFrame, densvar::Symbol, group::Symbol; normalize=false)
# ridgeplot!(f::Union{Makie.FigureLike,Makie.GridLayout}, args...; pos=(1,1) kwargs...)
# ridgeplot(args...; kwargs...)

# Create a "ridge plot".

# A ridge plot is stacked plot of densities for a given variable (`densvar`) grouped by a different variable (`group`). Because densities can very widely in scale, it is sometimes useful to `normalize` the densities so that each density has a maximum of 1.

# The non-mutating method creates a Figure before calling the method for Figure.
# The method for Figure places the ridge plot in the grid position specified by `pos`, default is (1,1).
# """
# function ridgeplot!(ax::Axis, df::AbstractDataFrame, densvar::Symbol, group::Symbol; sort_by_group=false, vline_at_zero=true, normalize=false)
# # `normalize` makes it so that the max density is always 1
# # `normalize` works on the density not the area/mass
# gdf = groupby(df, group)
# dens = combine(gdf, densvar => kde => :kde)
# sort_by_group && sort!(dens, group)
# spacing = normalize ? 1.0 : 0.9 * maximum(dens[!, :kde]) do val
# return maximum(val.density)
# end

# nticks = length(gdf)

# for (idx, row) in enumerate(eachrow(dens))
# dd = normalize ? row.kde.density ./ maximum(row.kde.density) : row.kde.density

# offset = idx * spacing

# lower = Node(Point2f.(row.kde.x, offset))
# upper = Node(Point2f.(row.kde.x, dd .+ offset))
# band!(ax, lower, upper; color=(:black, 0.3))
# lines!(ax, upper; color=(:black, 1.0))
# end

# vline_at_zero && vlines!(ax, 0; color=(:black, 0.75), linestyle=:dash)

# ax.yticks[] = (1:spacing:(nticks*spacing), string.(dens[!, group]))
# ylims!(ax, 0, (nticks + 2) * spacing)
# ax.xlabel[] = string(densvar)
# ax.ylabel[] = string(group)

# ax
# end

# function ridgeplot!(f::Union{Makie.FigureLike,Makie.GridLayout}, args...; pos=(1,1), kwargs...)
# ridgeplot!(Axis(f[pos...]), args...; kwargs...)
# return f
# end

# """
# ridgeplot(args...; kwargs...)

# See [ridgeplot!](@ref).
# """
# ridgeplot(args...; kwargs...) = ridgeplot!(Figure(), args...; kwargs...)

# """
# ridgeplot!(Union{Figure, Axis}, bstrp::MixedModelBootstrap, args...; show_intercept=true, kwargs...)
# ridgeplot(bstrp::MixedModelBootstrap, args...; show_intercept=true, kwargs...)

# Convenience methods that call `DataFrame(bstrp.β)` and pass that onto the primary `ridgeplot[!]` methods.
# By default, the intercept is shown, but this can be disabled.
# """
# function ridgeplot!(axis::Axis, bstrp::MixedModelBootstrap, args...;
# show_intercept=true, normalize=true, kwargs...)

# df = DataFrame(bstrp.β)
# show_intercept || filter!(:coefname => !=(Symbol("(Intercept)")), df)
# ridgeplot!(axis, df, :β, :coefname, args...; sort_by_group=false, normalize, kwargs...)
# end
31 changes: 20 additions & 11 deletions src/utilities.jl
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
function _coefnames(x; show_intercept=true)
function _coefnames(x::MixedModel, ptype::Nothing=nothing; show_intercept=true)
cn = fixefnames(x)
return show_intercept ? cn : filter!(!=("(Intercept)"), cn)
end

function _coefnames(x::MixedModelBootstrap; show_intercept=true)
cn = [string(k) for (k, v) in pairs(first(x.fits).β) if !isequal(v, -0.0)]
function _coefnames(x::MixedModelBootstrap, ptype; show_intercept=true)
ptype = something(ptype, :β)
nt = getproperty(first(x.fits), ptype)
cn = [string(k) for (k, v) in pairs(nt) if !isequal(v, -0.0)]
return show_intercept ? cn : filter!(!=("(Intercept)"), cn)
end

Expand All @@ -30,7 +32,8 @@ The returned table has the following columns:
This function is internal and may be removed in a future release
without being considered a breaking change.
"""
function confint_table(x::MixedModel, level=0.95; show_intercept=true)
function confint_table(x::MixedModel, level=0.95; ptype=nothing, show_intercept=true)
isnothing(ptype) || throw(ArgumentError("`ptype` not supported for MixedModel"))
# taking from the lower tail
semultiple = zquantile((1 - level) / 2)
se = stderror(x)
Expand All @@ -45,17 +48,23 @@ function confint_table(x::MixedModel, level=0.95; show_intercept=true)
return filter!(:coefname => in(_coefnames(x; show_intercept)), df)
end

function confint_table(x::MixedModelBootstrap, level=0.95; show_intercept=true)
df = transform!(select!(DataFrame(x.β), Not(:iter)),
:coefname => ByRow(string) => :coefname)
function confint_table(x::MixedModelBootstrap, level=0.95; ptype=:β, show_intercept=true)
ptype = something(ptype, :β)
ptype in (:β, :σs) || throw(ArgumentError("ptype $(ptype) not supported"))
df = DataFrame(getproperty(x, ptype))
rename!(c -> replace(c, "column" => "coefname"), df)
transform!(select!(df, Not(:iter)),
:coefname => ByRow(string) => :coefname)
ci(x) = shortestcovint(x, level)
# drop trailing s
var = replace(string(ptype), "s" => "")
df = combine(groupby(df, :coefname),
:β => mean => :estimate,
:β => NamedTuple{(:lower, :upper)} ∘ ci => [:lower, :upper])
return filter!(:coefname => in(_coefnames(x; show_intercept)), df)
var => mean => :estimate,
var => NamedTuple{(:lower, :upper)} ∘ ci => [:lower, :upper])
return filter!(:coefname => in(_coefnames(x, ptype; show_intercept)), df)
end

_npreds(x; show_intercept=true) = length(_coefnames(x; show_intercept))
_npreds(args...; kwargs...) = length(_coefnames(args...; kwargs...))

"""
ppoints(n::Integer)
Expand Down