fixed issues caused by renaming. In favor of #7 and JuliaLang/METADAT…

…A.jl#17212

src/plot.jl

@@ -3,7 +3,7 @@ using StatPlots
 import Plots.plot
 #################### Posterior Plot Recipies ####################
 
-@recipe function plot(c::Chain.AbstractChains, ptypes::Vector{Symbol}; 
+@recipe function plot(c::MCMCChain.AbstractChains, ptypes::Vector{Symbol}; 
                       maxlag = round(Int, 10 * log10(length(c.range))),
   barbounds = (0, Inf))
 
@@ -26,11 +26,11 @@ import Plots.plot
           subplot := indices[i, j]
           title := c.names[i]
           labels := map(k -> "Chain $k", 1:nchains)
-          Chain.cummean(c.value[:, i, :])
+          MCMCChain.cummean(c.value[:, i, :])
         end
       end
     elseif ptype == :autocor
-      ac = Chain.autocor(c, lags=collect(lags))
+      ac = MCMCChain.autocor(c, lags=collect(lags))
       for i in 1:nvars
         @series begin
           seriestype := :line
@@ -43,7 +43,7 @@ import Plots.plot
         end
       end
     elseif ptype == :mixeddensity
-      discrete = Chain.indiscretesupport(c, barbounds)
+      discrete = MCMCChain.indiscretesupport(c, barbounds)
       for i in 1:nvars
         @series begin
           seriestype := discrete[i] ? :histogram : :density
@@ -71,11 +71,11 @@ import Plots.plot
   end
 end
 
-plot(c::Chain.AbstractChains, ptype::Symbol; args...) = plot(c, [ptype]; args...)
+plot(c::MCMCChain.AbstractChains, ptype::Symbol; args...) = plot(c, [ptype]; args...)
 
-meanplot(c::Chain.AbstractChains; args...) = plot(c, [:mean]; args...)
-autocorplot(c::Chain.AbstractChains; args...) = plot(c, [:autocor]; args...)
-histogramplot(c::Chain.AbstractChains; args...) = plot(c, [:histogram]; args...)
-densityplot(c::Chain.AbstractChains; args...) = plot(c, [:density]; args...)
-mixeddensityplot(c::Chain.AbstractChains; args...) = plot(c, [:mixeddensity]; args...)
-traceplot(c::Chain.AbstractChains; args...) = plot(c, [:trace]; args...)
+meanplot(c::MCMCChain.AbstractChains; args...) = plot(c, [:mean]; args...)
+autocorplot(c::MCMCChain.AbstractChains; args...) = plot(c, [:autocor]; args...)
+histogramplot(c::MCMCChain.AbstractChains; args...) = plot(c, [:histogram]; args...)
+densityplot(c::MCMCChain.AbstractChains; args...) = plot(c, [:density]; args...)
+mixeddensityplot(c::MCMCChain.AbstractChains; args...) = plot(c, [:mixeddensity]; args...)
+traceplot(c::MCMCChain.AbstractChains; args...) = plot(c, [:trace]; args...)

test/diagnostic_tests.jl

@@ -20,11 +20,11 @@ chn = Chains(val, start = 1, thin = 2)
   @test last(chn) == 999
   @test size(chn) == (999, 4, 2)
   @test keys(chn) == ["Param1", "Param2", "Param3", "Param4"]
-  @test isa(chn[:,1,:], Chain.AbstractChains)
+  @test isa(chn[:,1,:], MCMCChain.AbstractChains)
   @test length(vec(chn[:,1,:].value)) == n_chain * n_iter
   @test all(chn[:,1,1].value .== val[:,1,1])
   @test all(chn[:,1,2].value .== val[:,1,2])
-  @test all(Chain.indiscretesupport(chn) .== [false, false, false, true])
+  @test all(MCMCChain.indiscretesupport(chn) .== [false, false, false, true])
 end
 
 @testset "function tests" begin
@@ -35,15 +35,15 @@ end
   # - 
 
   # the following tests only check if the function calls work!
-  @test Chain.diag_all(rand(100, 2), :weiss, 1, 1, 1) != nothing
-  @test Chain.diag_all(rand(100, 2), :hangartner, 1, 1, 1) != nothing
-  @test Chain.diag_all(rand(100, 2), :billingsley, 1, 1, 1) != nothing
-
-  @test isa(discretediag(chn[:,4,:]), Chain.ChainSummary)
-  @test isa(gelmandiag(chn[:,1,:]), Chain.ChainSummary)
-  @test isa(gewekediag(chn[:,1,:]), Chain.ChainSummary)
-  @test isa(heideldiag(chn[:,1,:]), Chain.ChainSummary)
-  @test isa(rafterydiag(chn[:,1,:]), Chain.ChainSummary)
+  @test MCMCChain.diag_all(rand(100, 2), :weiss, 1, 1, 1) != nothing
+  @test MCMCChain.diag_all(rand(100, 2), :hangartner, 1, 1, 1) != nothing
+  @test MCMCChain.diag_all(rand(100, 2), :billingsley, 1, 1, 1) != nothing
+
+  @test isa(discretediag(chn[:,4,:]), MCMCChain.ChainSummary)
+  @test isa(gelmandiag(chn[:,1,:]), MCMCChain.ChainSummary)
+  @test isa(gewekediag(chn[:,1,:]), MCMCChain.ChainSummary)
+  @test isa(heideldiag(chn[:,1,:]), MCMCChain.ChainSummary)
+  @test isa(rafterydiag(chn[:,1,:]), MCMCChain.ChainSummary)
 
 
 end