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Refactor SummaryStats to wrap a Table (#23)
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* Add TableOperations as dependency

* Update utilities to only assume Table inputs

* Update SummaryStats to wrap a table and names

* Update SummaryStats docstring

* Update Base overloads for SummaryStats

* Update show method for SummaryStats

* Update Tables methods for SummaryStats

* Aggressively constprop `_summarize`

* Update summarize tests

* Add OrderedCollections as dependency

* Use Tables interface for equality checks

* Improve merge for many columns

* Improve show for many columns

* Don't assume columnnames of parent returns a vector

* Add more tests

* Simplify merge to always overwrite from right

* Remove row access for now

* Preserve parameter name eltype in Schema

* Update summarize tests

* Document column access of SummaryStats

* Increment minor version number
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@sethaxen
sethaxen authored Dec 23, 2023
1 parent 55e1ff2 commit 64240b9
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6 changes: 5 additions & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "PosteriorStats"
uuid = "7f36be82-ad55-44ba-a5c0-b8b5480d7aa5"
authors = ["Seth Axen <[email protected]> and contributors"]
version = "0.1.4"
version = "0.2.0"

[deps]
Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
Expand All @@ -14,13 +14,15 @@ LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0"
Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
Optim = "429524aa-4258-5aef-a3af-852621145aeb"
OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
PSIS = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04"
PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
TableOperations = "ab02a1b2-a7df-11e8-156e-fb1833f50b87"
TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"

Expand All @@ -39,6 +41,7 @@ MCMCDiagnosticTools = "0.3.4"
Markdown = "1.6"
OffsetArrays = "1"
Optim = "1"
OrderedCollections = "1"
PSIS = "0.9.1"
PrettyTables = "2.1, 2.2"
Printf = "1.6"
Expand All @@ -47,6 +50,7 @@ Random = "1.6"
Setfield = "1"
Statistics = "1.6"
StatsBase = "0.32, 0.33, 0.34"
TableOperations = "1"
TableTraits = "0.4, 1"
Tables = "1"
julia = "1.6"
Expand Down
1 change: 1 addition & 0 deletions src/PosteriorStats.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ using LogExpFunctions: LogExpFunctions
using Markdown: @doc_str
using MCMCDiagnosticTools: MCMCDiagnosticTools
using Optim: Optim
using OrderedCollections: OrderedCollections
using PrettyTables: PrettyTables
using Printf: Printf
using PSIS: PSIS, PSISResult, psis, psis!
Expand Down
151 changes: 114 additions & 37 deletions src/summarize.jl
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Original file line number Diff line number Diff line change
@@ -1,42 +1,102 @@
"""
$(SIGNATURES)
$(TYPEDEF)
A container for a column table of values computed by [`summarize`](@ref).
This object implements the Tables and TableTraits interfaces and has a custom `show` method.
This object implements the Tables and TableTraits column table interfaces. It has a custom
`show` method.
$(FIELDS)
`SummaryStats` behaves like an `OrderedDict` of columns, where the columns can be accessed
using either `Symbol`s or a 1-based integer index.
$(TYPEDFIELDS)
SummaryStats([name::String,] data[, parameter_names])
SummaryStats(data[, parameter_names]; name::String="SummaryStats")
Construct a `SummaryStats` from tabular `data` with optional stats `name` and `param_names`.
`data` must not contain a column `:parameter`, as this is reserved for the parameter names,
which are always in the first column.
"""
struct SummaryStats{D<:NamedTuple}
struct SummaryStats{D,V<:AbstractVector}
"The name of the collection of summary statistics, used as the table title in display."
name::String
"""The summary statistics for each parameter, with an optional first column `parameter`
containing the parameter names."""
"""The summary statistics for each parameter. It must implement the Tables interface."""
data::D
"Names of the parameters"
parameter_names::V
function SummaryStats(name::String, data, parameter_names::V) where {V}
coltable = Tables.columns(data)
:parameter ∈ Tables.columnnames(coltable) &&
throw(ArgumentError("Column `:parameter` is reserved for parameter names."))
length(parameter_names) == Tables.rowcount(data) || throw(
DimensionMismatch(
"length $(length(parameter_names)) of `parameter_names` does not match number of rows $(Tables.rowcount(data)) in `data`.",
),
)
return new{typeof(coltable),V}(name, coltable, parameter_names)
end
end
function SummaryStats(
data,
parameter_names::AbstractVector=Base.OneTo(Tables.rowcount(data));
name::String="SummaryStats",
)
return SummaryStats(name, data, parameter_names)
end
function SummaryStats(data::NamedTuple; name::String="SummaryStats")
n = length(first(data))
return SummaryStats(name, merge((parameter=1:n,), data))
function SummaryStats(name::String, data)
return SummaryStats(name, data, Base.OneTo(Tables.rowcount(data)))
end

function _ordereddict(stats::SummaryStats)
return OrderedCollections.OrderedDict(
k => Tables.getcolumn(stats, k) for k in Tables.columnnames(stats)
)
end

# forward key interfaces from its parent
Base.parent(stats::SummaryStats) = getfield(stats, :data)
Base.keys(stats::SummaryStats) = keys(parent(stats))
Base.haskey(stats::SummaryStats, nm::Symbol) = haskey(parent(stats), nm)
Base.length(stats::SummaryStats) = length(parent(stats))
Base.getindex(stats::SummaryStats, i::Int) = getindex(parent(stats), i)
Base.getindex(stats::SummaryStats, nm::Symbol) = getindex(parent(stats), nm)
function Base.iterate(stats::SummaryStats, i::Int=firstindex(parent(stats)))
return iterate(parent(stats), i)
Base.keys(stats::SummaryStats) = map(Symbol, Tables.columnnames(stats))
Base.haskey(stats::SummaryStats, nm::Symbol) = nm ∈ keys(stats)
Base.length(stats::SummaryStats) = length(parent(stats)) + 1
Base.getindex(stats::SummaryStats, i::Union{Int,Symbol}) = Tables.getcolumn(stats, i)
function Base.iterate(stats::SummaryStats)
ncols = length(stats)
return stats.parameter_names, (2, ncols)
end
function Base.merge(stats::SummaryStats, other_stats::SummaryStats...)
return SummaryStats(stats.name, merge(parent(stats), map(parent, other_stats)...))
function Base.iterate(stats::SummaryStats, (i, ncols)::NTuple{2,Int})
i > ncols && return nothing
return Tables.getcolumn(stats, i), (i + 1, ncols)
end
function Base.isequal(stats::SummaryStats, other_stats::SummaryStats)
return isequal(parent(stats), parent(other_stats))
function Base.merge(
stats::SummaryStats{<:NamedTuple}, other_stats::SummaryStats{<:NamedTuple}...
)
isempty(other_stats) && return stats
stats_all = (stats, other_stats...)
stats_last = last(stats_all)
return SummaryStats(
stats_last.name, merge(map(parent, stats_all)...), stats_last.parameter_names
)
end
function Base.:(==)(stats::SummaryStats, other_stats::SummaryStats)
return (parent(stats) == parent(other_stats))
function Base.merge(stats::SummaryStats, other_stats::SummaryStats...)
isempty(other_stats) && return stats
stats_all = (stats, other_stats...)
data_merged = merge(map(_ordereddict, stats_all)...)
parameter_names = pop!(data_merged, :parameter)
return SummaryStats(last(stats_all).name, data_merged, parameter_names)
end
for f in (:(==), :isequal)
@eval begin
function Base.$(f)(stats::SummaryStats, other_stats::SummaryStats)
colnames1 = Tables.columnnames(stats)
colnames2 = Tables.columnnames(other_stats)
vals1 = (Tables.getcolumn(stats, k) for k in colnames1)
vals2 = (Tables.getcolumn(other_stats, k) for k in colnames2)
return all(Base.splat($f), zip(colnames1, colnames2)) &&
all(Base.splat($f), zip(vals1, vals2))
end
end
end

#### custom tabular show methods
Expand All @@ -49,15 +109,15 @@ function Base.show(io::IO, mime::MIME"text/html", stats::SummaryStats; kwargs...
end

function _show(io::IO, mime::MIME, stats::SummaryStats; kwargs...)
data = NamedTuple{eachindex(stats)[2:end]}(parent(stats))
data = parent(stats)
rhat_formatter = _prettytables_rhat_formatter(data)
extra_formatters = rhat_formatter === nothing ? () : (rhat_formatter,)
return _show_prettytable(
io,
mime,
data;
title=stats.name,
row_labels=parent(stats).parameter,
row_labels=Tables.getcolumn(stats, :parameter),
extra_formatters,
kwargs...,
)
Expand All @@ -68,12 +128,29 @@ end
Tables.istable(::Type{<:SummaryStats}) = true
Tables.columnaccess(::Type{<:SummaryStats}) = true
Tables.columns(s::SummaryStats) = s
Tables.columnnames(s::SummaryStats) = Tables.columnnames(parent(s))
Tables.getcolumn(s::SummaryStats, i::Int) = Tables.getcolumn(parent(s), i)
Tables.getcolumn(s::SummaryStats, nm::Symbol) = Tables.getcolumn(parent(s), nm)
Tables.rowaccess(::Type{<:SummaryStats}) = true
Tables.rows(s::SummaryStats) = Tables.rows(parent(s))
Tables.schema(s::SummaryStats) = Tables.schema(parent(s))
function Tables.columnnames(s::SummaryStats)
data_cols = Tables.columnnames(parent(s))
data_cols isa Tuple && return (:parameter, data_cols...)
return collect(Iterators.flatten(((:parameter,), data_cols)))
end
function Tables.getcolumn(stats::SummaryStats, i::Int)
i == 1 && return stats.parameter_names
return Tables.getcolumn(parent(stats), i - 1)
end
function Tables.getcolumn(stats::SummaryStats, nm::Symbol)
nm === :parameter && return stats.parameter_names
return Tables.getcolumn(parent(stats), nm)
end
function Tables.schema(s::SummaryStats)
data_schema = Tables.schema(parent(s))
data_schema === nothing && return nothing
T = eltype(s.parameter_names)
if data_schema isa Tables.Schema{Nothing,Nothing}
return Tables.Schema([:parameter; data_schema.names], [T; data_schema.types])
else
return Tables.Schema((:parameter, data_schema.names...), (T, data_schema.types...))
end
end

IteratorInterfaceExtensions.isiterable(::SummaryStats) = true
function IteratorInterfaceExtensions.getiterator(s::SummaryStats)
Expand Down Expand Up @@ -194,8 +271,7 @@ Compute the summary statistics in `stats_funs` on each param in `data`, with siz
fnames = map(first, names_and_funs)
_check_function_names(fnames)
funs = map(last, names_and_funs)
nt = merge((; parameter=var_names), _summarize(data, funs, fnames)...)
return SummaryStats(name, nt)
return SummaryStats(name, _summarize(data, funs, fnames), var_names)
end

function _check_function_names(fnames)
Expand Down Expand Up @@ -295,14 +371,15 @@ function _prob_interval_to_strings(interval_type, prob; digits=2)
end
end

function _summarize(data::AbstractArray{<:Any,3}, funs, fun_names)
return map(fun_names, funs) do fname, f
# aggressive constprop allows summarize to be type-inferrable when called by
# another function

@constprop :aggressive function _summarize(data::AbstractArray{<:Any,3}, funs, fun_names)
return merge(map(fun_names, funs) do fname, f
return _map_over_params(fname, f, data)
end
end...)
end

# aggressive constprop allows summarize to be type-inferrable when called by
# another function
@constprop :aggressive function _map_over_params(fname, f, data)
vals = _map_paramslices(f, data)
return _namedtuple_of_vals(f, fname, vals)
Expand Down
41 changes: 24 additions & 17 deletions src/utils.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -257,13 +257,15 @@ function ft_printf_sigdigits_matching_se(
end

function _prettytables_rhat_formatter(data)
cols = findall(x -> x === :rhat, keys(data))
cols = findall(x -> x === :rhat, Tables.columnnames(data))
isempty(cols) && return nothing
return PrettyTables.ft_printf("%.2f", cols)
end

function _prettytables_integer_formatter(data)
cols = findall(v -> eltype(v) <: Integer, values(data))
sch = Tables.schema(data)
sch === nothing && return nothing
cols = findall(t -> t <: Integer, sch.types)
isempty(cols) && return nothing
return PrettyTables.ft_printf("%d", cols)
end
Expand All @@ -272,20 +274,24 @@ end
# see https://ronisbr.github.io/PrettyTables.jl/stable/man/formatters/
function _default_prettytables_formatters(data; sigdigits_se=2, sigdigits_default=3)
formatters = []
for (i, k) in enumerate(keys(data))
col_names = Tables.columnnames(data)
for (i, k) in enumerate(col_names)
for mcse_key in (Symbol("mcse_$k"), Symbol("$(k)_mcse"))
if haskey(data, mcse_key)
push!(formatters, ft_printf_sigdigits_matching_se(data[mcse_key], [i]))
push!(
formatters,
ft_printf_sigdigits_matching_se(Tables.getcolumn(data, mcse_key), [i]),
)
continue
end
end
end
mcse_cols = findall(keys(data)) do k
mcse_cols = findall(col_names) do k
s = string(k)
return startswith(s, "mcse_") || endswith(s, "_mcse")
end
isempty(mcse_cols) || push!(formatters, ft_printf_sigdigits(sigdigits_se, mcse_cols))
ess_cols = findall(_is_ess_label, keys(data))
ess_cols = findall(_is_ess_label, col_names)
isempty(ess_cols) || push!(formatters, PrettyTables.ft_printf("%d", ess_cols))
ft_integer = _prettytables_integer_formatter(data)
ft_integer === nothing || push!(formatters, ft_integer)
Expand All @@ -300,12 +306,10 @@ function _show_prettytable(
extra_formatters...,
_default_prettytables_formatters(data; sigdigits_se, sigdigits_default)...,
)
alignment = fill(:r, length(data))
for (i, v) in enumerate(values(data))
if !(eltype(v) <: Real)
alignment[i] = :l
end
end
col_names = Tables.columnnames(data)
alignment = [
eltype(Tables.getcolumn(data, col_name)) <: Real ? :r : :l for col_name in col_names
]
kwargs_new = merge(
(
show_subheader=false,
Expand All @@ -331,13 +335,16 @@ function _show_prettytable(
newline_at_end=false,
kwargs...,
)
alignment_anchor_regex = Dict{Int,Vector{Regex}}(
i => [r"\.", r"e", r"^NaN$", r"Inf$"] for (i, (k, v)) in enumerate(pairs(data)) if
(eltype(v) <: Real && !(eltype(v) <: Integer) && !_is_ess_label(k))
)
alignment_anchor_regex = Dict{Int,Vector{Regex}}()
for (i, k) in enumerate(Tables.columnnames(data))
v = Tables.getcolumn(data, k)
if eltype(v) <: Real && !(eltype(v) <: Integer) && !_is_ess_label(k)
alignment_anchor_regex[i] = [r"\.", r"e", r"^NaN$", r"Inf$"]
end
end
alignment_anchor_fallback = :r
alignment_anchor_fallback_override = Dict(
i => :r for (i, k) in enumerate(keys(data)) if _is_ess_label(k)
i => :r for (i, k) in enumerate(Tables.columnnames(data)) if _is_ess_label(k)
)
return _show_prettytable(
io,
Expand Down
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Registration pull request created: JuliaRegistries/General/97674

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## Breaking changes

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