From 2e84f2e41055d2e7c781f123055ef043860eca59 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 23 Mar 2020 23:07:36 +0000 Subject: [PATCH 1/5] CompatHelper: add new compat entry for "AdvancedHMC" at version "0.2" --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index 50a19c8..78e83dd 100644 --- a/Project.toml +++ b/Project.toml @@ -32,6 +32,7 @@ TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] +AdvancedHMC = "0.2" CmdStan = "^5.2, 6.0" DataFrames = "^0.19, 0.20" Distributions = "^0.21, 0.22" From d64771bb07cd5a6e84aa18301d253ed9ca38aa52 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 25 Mar 2020 09:07:30 +0000 Subject: [PATCH 2/5] CompatHelper: bump compat for "Turing" to "0.10" --- Project.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index aa6d874..7f81533 100644 --- a/Project.toml +++ b/Project.toml @@ -32,8 +32,8 @@ TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] -CSV = "^0.5" AdvancedHMC = "^0.2" +CSV = "^0.5" CmdStan = "^5.2, 6.0" DataFrames = "^0.19, 0.20" Distributions = "^0.21, 0.22, 0.23" @@ -51,7 +51,7 @@ SpecialFunctions = "^0.8, 0.9, 0.10" StatsPlots = "^0.12, 0.13, 0.14" Tracker = "^0.2" TransformVariables = "^0.3" -Turing = "^0.9" +Turing = "^0.9, 0.10" julia = "^1" [extras] From 1299a582bda737a555fb6c583e50e97bf5c9556a Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 27 Mar 2020 18:08:20 +0000 Subject: [PATCH 3/5] CompatHelper: bump compat for "CSV" to "0.6" --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index aa6d874..ede62c2 100644 --- a/Project.toml +++ b/Project.toml @@ -32,8 +32,8 @@ TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] -CSV = "^0.5" AdvancedHMC = "^0.2" +CSV = "^0.5, 0.6" CmdStan = "^5.2, 6.0" DataFrames = "^0.19, 0.20" Distributions = "^0.21, 0.22, 0.23" From 1a1be45d342ba9ed6ec400ad52b5cf3f1ca629c6 Mon Sep 17 00:00:00 2001 From: Chris Fisher Date: Wed, 15 Apr 2020 17:35:40 -0400 Subject: [PATCH 4/5] Merge branch 'master' of https://github.com/itsdfish/MCMCBenchmarks.jl --- Project.toml | 2 +- src/core_benchmarking.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index 224ad3d..c0c0a21 100644 --- a/Project.toml +++ b/Project.toml @@ -51,7 +51,7 @@ SpecialFunctions = "^0.8, 0.9, 0.10" StatsPlots = "^0.12, 0.13, 0.14" Tracker = "^0.2" TransformVariables = "^0.3" -Turing = "^0.9, 0.10" +Turing = "^0.10" julia = "^1" [extras] diff --git a/src/core_benchmarking.jl b/src/core_benchmarking.jl index 9d7cbf1..58e1b1a 100644 --- a/src/core_benchmarking.jl +++ b/src/core_benchmarking.jl @@ -226,7 +226,7 @@ function modifyConfig!(s::AHMCNUTS; Nsamples, Nadapt, delta, autodiff=:forward, s.config = Turing.NUTS(Nadapt, delta) s.Nsamples = Nsamples println("Nsamples" , Nsamples) - s.autodiff = autodiff == :reverse ? Turing.setadbackend(:reverse_diff) : Turing.setadbackend(:forward_diff) + s.autodiff = autodiff == :reverse ? Turing.setadbackend(:reverse_diff) : Turing.setadbackend(:forwarddiff) end function modifyConfig!(s::CmdStanNUTS; Nsamples, Nadapt, delta, kwargs...) From 26a33a41bad139a97cc3236fa89bfb8fbbec8130 Mon Sep 17 00:00:00 2001 From: itsdfish Date: Sat, 9 May 2020 16:45:26 -0400 Subject: [PATCH 5/5] updates for DynamicHMC, Turing and DataFrames --- Project.toml | 6 +++--- src/plotting.jl | 3 ++- test/Gaussian_Models.jl | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/Project.toml b/Project.toml index e3c433b..39c47a6 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MCMCBenchmarks" uuid = "72ce6e51-3f7f-5ebd-8e88-b86aa3e31c30" authors = ["Christopher R. Fisher, Rob J. Goedman"] -version = "0.7.1" +version = "0.7.2" [deps] AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" @@ -35,7 +35,7 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" AdvancedHMC = "^0.2" CSV = "^0.5, 0.6" CmdStan = "^5.2, 6.0" -DataFrames = "^0.19, 0.20" +DataFrames = "0.21.0" Distributions = "^0.21, 0.22, 0.23" DynamicHMC = "^2.1" FillArrays = "^0.8" @@ -51,7 +51,7 @@ SpecialFunctions = "^0.8, 0.9, 0.10" StatsPlots = "^0.12, 0.13, 0.14" Tracker = "^0.2" TransformVariables = "^0.3" -Turing = "^0.9, 0.10, 0.11" +Turing = "^0.9, 0.10, 0.11, 0.12.0" julia = "^1" [extras] diff --git a/src/plotting.jl b/src/plotting.jl index b7b56d8..db045e4 100644 --- a/src/plotting.jl +++ b/src/plotting.jl @@ -133,7 +133,8 @@ end se(x) = std(x)/sqrt(length(x)) function summarize(df, metric, grouping, func) - newDF= by(df, grouping, metric=>func) + g = groupby(df, grouping) + newDF= combine(g, metric=>func) yvar = names(newDF)[end] return newDF,yvar end diff --git a/test/Gaussian_Models.jl b/test/Gaussian_Models.jl index 3dbfa85..7c6ab91 100644 --- a/test/Gaussian_Models.jl +++ b/test/Gaussian_Models.jl @@ -62,7 +62,7 @@ function sampleDHMC(obs, N, nsamples, autodiff) results = mcmc_with_warmup(Random.GLOBAL_RNG, ∇P, nsamples; reporter = NoProgressReport()) # Undo the transformation to obtain the posterior from the chain. - posterior = transform.(trans, results.chain) + posterior = TransformVariables.transform.(trans, results.chain) return nptochain(results, posterior) end