Make Chains objects display only information and not statistical eval

Project.toml

@@ -8,6 +8,7 @@ version = "6.0.7"
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
+DataAPI = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d"
@@ -29,6 +30,7 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 [compat]
 AbstractMCMC = "0.4, 0.5, 1.0, 2.0, 3.0, 4, 5"
 AxisArrays = "0.4.4"
+DataAPI = "1.16.0"
 Dates = "<0.0.1, 1"
 Distributions = "0.21, 0.22, 0.23, 0.24, 0.25"
 IteratorInterfaceExtensions = "0.1.1, 1"

src/MCMCChains.jl

@@ -8,6 +8,7 @@ using Distributions
 using RecipesBase
 using Dates
 using KernelDensity: kde, pdf
+import DataAPI
 import StatsBase: autocov, counts, sem, AbstractWeights,
     autocor, describe, quantile, sample, summarystats, cov
 

src/chains.jl

@@ -347,13 +347,7 @@ end
 
 function Base.show(io::IO, mime::MIME"text/plain", chains::Chains)
     print(io, "Chains ", chains, ":\n\n", header(chains))
-
-    # Show summary stats.
-    summaries = describe(chains)
-    for summary in summaries
-        println(io)
-        show(io, mime, summary)
-    end
+    println(io, "\nUse `describe(chains)` for summary statistics and quantiles.")
 end
 
 Base.keys(c::Chains) = names(c)
@@ -889,4 +883,4 @@ function replacenames(chains::Chains, old_new::Pair...)
     )
 
     return Chains(value, chains.logevidence, namemap, chains.info)
-end
+end

src/stats.jl

@@ -171,28 +171,34 @@ function changerate(chains::AbstractArray{<:Real,3})
     changerates, mvchangerate
 end
 
-describe(c::Chains; args...) = describe(stdout, c; args...)
-
 """
     describe(io, chains[;
              q = [0.025, 0.25, 0.5, 0.75, 0.975],
              etype = :bm,
              kwargs...])
-
-Print the summary statistics and quantiles for the chain.
+Print chain metadata, summary statistics, and quantiles. Use `describe(chains)` for REPL output to `stdout`, or specify `io` for other streams (e.g., file output).
 """
-function describe(
+function DataAPI.describe(
     io::IO,
     chains::Chains;
     q = [0.025, 0.25, 0.5, 0.75, 0.975],
     etype = :bm,
     kwargs...
 )
-    dfs = vcat(summarystats(chains; etype = etype, kwargs...),
-               quantile(chains; q = q, kwargs...))
-    return dfs
+    print(io, "Chains ", chains, ":\n\n", header(chains))
+
+    summstats = summarystats(chains; etype = etype, kwargs...)
+    println(io)
+    show(io, MIME("text/plain"), summstats)
+
+    qs = quantile(chains; q = q, kwargs...)
+    println(io)
+    show(io, MIME("text/plain"), qs)
 end
 
+# Convenience method for default IO
+DataAPI.describe(chains::Chains; kwargs...) = DataAPI.describe(stdout, chains; kwargs...)
+
 function _hpd(x::AbstractVector{<:Real}; alpha::Real=0.05)
     n = length(x)
     m = max(1, ceil(Int, alpha * n))
@@ -373,4 +379,4 @@ end
 
 mean(chn::Chains, syms) = mean(chn[:, syms, :])
 # resolve method ambiguity with `mean(f, ::AbstractArray)`
-mean(chn::Chains, syms::AbstractVector) = mean(chn[:, syms, :])
+mean(chn::Chains, syms::AbstractVector) = mean(chn[:, syms, :])