Updated Documentation

src/HMC.jl

@@ -2,76 +2,6 @@
 HAMILTONIAN MONTE CARLO TYPE INSTANTIATION
 
 Approximate Bayesian Inference via Hamiltonian Monte Carlo.
-
-**Examples:**
-```julia
-using DataFrames
-using Distributions
-using Gadfly
-using StochMCMC
-Gadfly.push_theme(:dark)
-
-srand(123);
-
-# Define data parameters
-w0 = -.3; w1 = -.5; stdev = 5.; a =  1 / stdev
-
-# Generate Hypothetical Data
-n = 200;
-x = rand(Uniform(-1, 1), n);
-A = [ones(length(x)) x];
-B = [w0; w1];
-f = A * B;
-y = f + rand(Normal(0, a), n);
-
-my_df = DataFrame(Independent = round(x, 4), Dependent = round(y, 4));
-
-"""
-The log prior function is given by the following codes:
-"""
-function logprior(theta::Array{Float64}; mu::Array{Float64} = zero_vec, s::Array{Float64} = eye_mat)
-  w0_prior = log(pdf(Normal(mu[1, 1], s[1, 1]), theta[1]))
-  w1_prior = log(pdf(Normal(mu[2, 1], s[2, 2]), theta[2]))
-   w_prior = [w0_prior w1_prior]
-
-  return w_prior |> sum
-end
-
-"""
-The log likelihood function is given by the following codes:
-"""
-function loglike(theta::Array{Float64}; alpha::Float64 = a, x::Array{Float64} = x, y::Array{Float64} = y)
-  yhat = theta[1] + theta[2] * x
-
-  likhood = Float64[]
-  for i in 1:length(yhat)
-    push!(likhood, log(pdf(Normal(yhat[i], alpha), y[i])))
-  end
-
-  return likhood |> sum
-end
-
-"""
-The log posterior function is given by the following codes:
-"""
-function logpost(theta::Array{Float64})
-  loglike(theta, alpha = a, x = x, y = y) + logprior(theta, mu = zero_vec, s = eye_mat)
-end
-
-U(theta::Array{Float64}) = - logpost(theta);
-K(p::Array{Float64}; Σ = eye(length(p))) = (p' * inv(Σ) * p) / 2;
-function dU(theta::Array{Float64}; alpha::Float64 = a, b::Float64 = eye_mat[1, 1])
-  [-alpha * sum(y - (theta[1] + theta[2] * x));
-   -alpha * sum((y - (theta[1] + theta[2] * x)) .* x)] + b * theta
-end
-dK(p::AbstractArray{Float64}; Σ::Array{Float64} = eye(length(p))) = inv(Σ) * p;
-
-srand(123);
-HMC_object = HMC(U, K, dU, dK, zeros(2), 2);
-chain2 = mcmc(HMC_object, leapfrog_params = Dict([:ɛ => .09, :τ => 20]), r = 10000);
-```
-
-
 """
 immutable HMC
   U       ::Function