diff --git a/Project.toml b/Project.toml new file mode 100644 index 0000000..7362a9f --- /dev/null +++ b/Project.toml @@ -0,0 +1,20 @@ +name = "BIGUQ" +uuid = "7f9c7709-75fb-5397-acba-f980073965f6" +version = "0.6.0" + +[deps] +AffineInvariantMCMC = "a0f608ac-68d0-5108-ad9a-0cdca73324f3" +BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" +RobustPmap = "27aeedcb-f738-516b-a0b8-3211cf1146e5" + +[compat] +julia = "≥ 1.0.0" + +[extras] +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[targets] +test = ["Test"] \ No newline at end of file diff --git a/REQUIRE b/REQUIRE index 49b2692..ba496a4 100644 --- a/REQUIRE +++ b/REQUIRE @@ -1,8 +1,7 @@ -julia 0.6 1.0 +julia 1.0 RobustPmap AffineInvariantMCMC DataFrames ForwardDiff BlackBoxOptim -Klara 0.8.6 Distributions diff --git a/src/BIGOED.jl b/src/BIGOED.jl index fb4f02d..2be6e82 100644 --- a/src/BIGOED.jl +++ b/src/BIGOED.jl @@ -96,22 +96,22 @@ function generateproposedobs(bigoed::BigOED, proposedindex::Int, numobsrealizati return retval end #mcmcmodel = Klara.model(loglikelihood, init=bigoed.nominalparams) - mcmcparams = Klara.BasicContMuvParameter(:p, logtarget=loglikelihood) - mcmcmodel = Klara.likelihood_model(mcmcparams, false) + # mcmcparams = Klara.BasicContMuvParameter(:p, logtarget=loglikelihood) + # mcmcmodel = Klara.likelihood_model(mcmcparams, false) #= if Base.isbindingresolved(Klara, :RAM) mcmcsampler = Klara.RAM(fill(1e-1, length(bigoed.nominalparams)), 0.3) else warn("Robust Adaptive Metropolis (RAM) method is not available") =# - mcmcsampler = Klara.MH(fill(1e-1, length(bigoed.nominalparams))) + # mcmcsampler = Klara.MH(fill(1e-1, length(bigoed.nominalparams))) #end - mcmcrange = Klara.BasicMCRange(nsteps=thinning * numobsrealizations + burnin, burnin=burnin, thinning=thinning) + # mcmcrange = Klara.BasicMCRange(nsteps=thinning * numobsrealizations + burnin, burnin=burnin, thinning=thinning) mcmcparams0 = Dict(:p=>bigoed.nominalparams) outopts = Dict{Symbol, Any}(:monitor=>[:value, :logtarget, :loglikelihood], :diagnostics=>[:accept]) - job = Klara.BasicMCJob(mcmcmodel, mcmcsampler, mcmcrange, mcmcparams0, outopts=outopts, tuner=Klara.VanillaMCTuner()) - Klara.run(job) - mcmcchain = Klara.output(job) + # job = Klara.BasicMCJob(mcmcmodel, mcmcsampler, mcmcrange, mcmcparams0, outopts=outopts, tuner=Klara.VanillaMCTuner()) + # Klara.run(job) + # mcmcchain = Klara.output(job) #use the mcmc samples to generate realizations of the proposed obs proposedlocations = bigoed.proposedlocations[proposedindex] proposedtimes = bigoed.proposedtimes[proposedindex] diff --git a/src/BIGUQ.jl b/src/BIGUQ.jl index a02cac4..e4d3c26 100644 --- a/src/BIGUQ.jl +++ b/src/BIGUQ.jl @@ -32,7 +32,6 @@ LA-CC-15-080; Copyright Number Assigned: C16008 module BIGUQ import DataFrames -import Klara import ForwardDiff import BlackBoxOptim import Distributions diff --git a/test/runtests.jl b/test/runtests.jl index 7659afd..d6b86d0 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,5 +1,5 @@ -using Base.Test +import Test -@assert(1 == 1) +@Test.test 1 == 1 :passed \ No newline at end of file