Ordered Beta Regressions

Data from subjective scales often exhibit clustered responses at the extremes (e.g., zeros and ones). This makes it challenging to model with regular Beta regressions. The Ordered Beta distribution allows for the presence of zeros and ones in an convenient way.

Function

OrderedBeta(μ, ϕ, k0, k1)

julia> OrderedBeta(0.5, 1, 0.1, 0.9)
OrderedBeta{Float64}(μ=0.5, ϕ=1.0, k0=0.1, k1=0.9)

Usage

Simulate Data

Data with clustered extreme responses are common in psychology and cognitive neuroscience. Ordered Beta models are a convenient and parsimonious way of modelling such data.

The model is based on a distribution with 4 parameters, 2 of which are the parameters of the BetaPhi2 distribution (modeling data in between the extremes), and k0 and k1 delimiting fuzzy boundaries beyond which the probability of extreme values increases.

Let us start by generating data from a distribution with known parameters, and then fitting a model to recover these parameters.

using CairoMakie
using Turing
using DataFrames
using StatsFuns: logistic
using SubjectiveScalesModels

μ = 0.6
ϕ = 2.5
k0 = 0.05
k1 = 0.9

data = rand(OrderedBeta(μ, ϕ, k0, k1), 1000)
hist(data, color=:forestgreen, normalization=:pdf, bins=beta_bins(20))

Prior Specification

μ ~ Normal(0, 1)  # Logit scale
ϕ ~ Normal(0, 1)  # Log scale
k0 ~ -Gamma(3, 3)  # Logit scale
k1 ~ Gamma(3, 3)  # Logit scale

Because these 4 parameters come with their own constraints (i.e., phi $\phi$ must be positive, mu $\mu$, k0 and k1 must be between 0 and 1), it is convenient to express them on a transformed scale (in which they become unconstrained and can adopt any values).

In particular, mu $\mu$ is typically expressed on the logit scale, and phi $\phi$ is expressed on the log scale (see here for details).

Priors for the cut points require a bit more thought. They share the same constraints as mu $\mu$ (must be on the 0-1 scale), which lends itself to being expressed on the logit scale and then transformed back using the logistic function. However, additionally, we would like to ensure that k0 < k1 (i.e., the lower boundary is lower than the upper boundary). This can be achieved by setting a prior for k0 that will have an upper bound at 0 (on the logit scale, corresponding to 0.5 on the raw scale) and a prior for k1 that will have 0 as its lower bound. In other words, we force the k0 to be between 0 and 0.5 and k1 to be between 0.5 and 1, which also solves the issue of k1 being smaller than k0.

This can be achieved using the $Gamma$ and "minus" Gamma distributions (its mirrored version). We can then pick a shape of the Gamma distribution that maximizes the probability on values lower than 0.05 for k0 and higher than 0.95 for k1 (which is within the typical range in psychological science), such as $Gamma(3, 3)$ and $-Gamma(3, 3)$ (which mode is "6", i.e., ~0.998 on the raw scale).

See code

using StatsFuns: logit

k0 = -Gamma(3, 3)
k1 = Gamma(3, 3)

fig =  Figure(size = (850, 600))

ax1 = Axis(fig[1, 1],
    xlabel="Prior on the logit scale",
    ylabel="Prior on k0",
    yticksvisible=false,
    xticksvisible=false,
    yticklabelsvisible=false)

xaxis1 = range(-30, 30, 1000)
vlines!(ax1, [0], color=:red, linestyle=:dash, linewidth=1)
vlines!(ax1, logit.([0.05]), color=:black, linestyle=:dot, linewidth=1)
lines!(ax1, xaxis1, pdf.(k0, xaxis1), color=:purple, linewidth=2, label="k0 ~ -Gamma(3, 3)")
axislegend(ax1; position=:rt)

ax2 = Axis(fig[1, 2],
    xlabel="Prior after logistic transformation",
    yticksvisible=false,
    xticksvisible=false,
    yticklabelsvisible=false)
vlines!(ax2, [0.05], color=:black, linestyle=:dot, linewidth=1)
lines!(ax2, logistic.(xaxis1), pdf.(k0, xaxis1), color=:purple, linewidth=2, label="k0")

ax3 = Axis(fig[2, 1],
    xlabel="Prior on the logit scale",
    ylabel="Prior on k1",
    yticksvisible=false,
    xticksvisible=false,
    yticklabelsvisible=false)
vlines!(ax3, [0], color=:red, linestyle=:dash, linewidth=1)
vlines!(ax3, logit.([0.95]), color=:black, linestyle=:dot, linewidth=1)
lines!(ax3, xaxis1, pdf.(k1, xaxis1), color=:green, linewidth=2, label="k1 ~ Gamma(3, 3)")
axislegend(ax3; position=:rt)

ax4 = Axis(fig[2, 2],
    xlabel="Prior after logistic transformation",
    yticksvisible=false,
    xticksvisible=false,
    yticklabelsvisible=false)
vlines!(ax4, [0.95], color=:black, linestyle=:dot, linewidth=1)
lines!(ax4, logistic.(xaxis1), pdf.(k1, xaxis1), color=:green, linewidth=2, label="k1")

fig[0, :] = Label(fig, "Priors for Cut Points in Ordered Beta Regressions", fontsize=20, color=:black, font=:bold)
fig;

Bayesian Model with Turing

The parameters (and their priors) are expressed on the transformed scale, and then transformed using logistic() or exp() functions before being used in the model.

@model function model_ordbeta(y)
    # Priors
    μ ~ Normal(0, 1)
    ϕ ~ Normal(0, 1)
    k0 ~ -Gamma(3, 3)
    k1 ~ Gamma(3, 3)

    # Inference
    for i in 1:length(y)
        y[i] ~ OrderedBeta(logistic(μ), exp(ϕ), logistic(k0), logistic(k1))
    end
end

posteriors = sample(model_ordbeta(data), NUTS(), 1000);

Chains MCMC chain (1000×16×1 Array{Float64, 3}):

Iterations        = 501:1:1500
Number of chains  = 1
Samples per chain = 1000
Wall duration     = 7.1 seconds
Compute duration  = 7.1 seconds
parameters        = μ, ϕ, k0, k1
internals         = lp, n_steps, is_accept, acceptance_rate, log_density, hamiltonian_energy, hamiltonian_energy_error, max_hamiltonian_energy_error, tree_depth, numerical_error, step_size, nom_step_size

Summary Statistics
  parameters      mean       std      mcse    ess_bulk   ess_tail      rhat    ⋯
      Symbol   Float64   Float64   Float64     Float64    Float64   Float64    ⋯

           μ    0.3869    0.0282    0.0009    891.1001   803.7116    1.0029    ⋯
           ϕ    0.9453    0.0450    0.0011   1737.5728   875.0756    0.9992    ⋯
          k0   -3.3067    0.1992    0.0056   1240.6242   738.0123    0.9995    ⋯
          k1    2.0367    0.0922    0.0029   1013.4645   813.3185    0.9991    ⋯
                                                                1 column omitted

Quantiles
  parameters      2.5%     25.0%     50.0%     75.0%     97.5% 
      Symbol   Float64   Float64   Float64   Float64   Float64 

           μ    0.3302    0.3681    0.3871    0.4054    0.4411
           ϕ    0.8559    0.9128    0.9467    0.9783    1.0292
          k0   -3.7050   -3.4335   -3.3025   -3.1654   -2.9473
          k1    1.8607    1.9739    2.0359    2.0977    2.2256

means = DataFrame(mean(posteriors))

table = DataFrame(
    Parameter = means.parameters,
    PosteriorMean = means.mean,
    Estimate = [logistic(means.mean[1]), exp(means.mean[2]), logistic(means.mean[3]), logistic(means.mean[4])],
    TrueValue = [0.6, 2.5, 0.05, 0.9]
)

Validation against R Implementation

R Output

Let's start by making some toy data (the data itself doesn't matter, as we are only interested in getting the same results) and fit an Ordered Beta model using the ordbetareg package.

library(ordbetareg)

data <- iris 
data$y  <- data$Petal.Width - min(data$Petal.Width)
data$y <- data$y / max(data$y)
data$x <- data$Petal.Length / max(data$Petal.Length)
# Inflate zeros and ones
data <- rbind(data, data[(data$y==0) | (data$y == 1), ])
data <- rbind(data, data[(data$y==0) | (data$y == 1), ])

ordbetareg(formula=y ~ x, data=data)

 Family: ord_beta_reg 
  Links: mu = identity; phi = identity; cutzero = identity; cutone = identity 
Formula: y ~ x 
   Data: data (Number of observations: 174) 
  Draws: 4 chains, each with iter = 2000; warmup = 1000; thin = 1;
         total post-warmup draws = 4000

Regression Coefficients:
          Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept    -3.82      0.14    -4.09    -3.55 1.00     2701     2494
x             6.42      0.21     6.00     6.83 1.00     2999     2808

Further Distributional Parameters:
        Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
phi        22.33      2.56    17.61    27.69 1.00     4220     3026
cutzero    -3.41      0.27    -3.95    -2.88 1.00     3202     3248
cutone      1.87      0.06     1.75     2.00 1.00     3323     3298

Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS
and Tail_ESS are effective sample size measures, and Rhat is the potential
scale reduction factor on split chains (at convergence, Rhat = 1).

Julia Implementation

Let us now do the same thing in Julia and Turing.

using RDatasets
using CairoMakie
using Turing
using StatsFuns: logistic
using SubjectiveScalesModels


data = dataset("datasets", "iris")
data.y = data.PetalWidth .- minimum(data.PetalWidth)
data.y = data.y ./ maximum(data.y)
data.x = data.PetalLength ./ maximum(data.PetalLength)

# Inflate zeros and ones
data = vcat(data, data[(data.y .== 0) .| (data.y .== 1), :])
data = vcat(data, data[(data.y .== 0) .| (data.y .== 1), :])

println("N-zero: ", sum(data.y .== 0) ,  ", N-one: ", sum(data.y .== 1))

N-zero: 20, N-one: 12

@model function model_ordbeta(y, x)
    μ_intercept ~ Normal(0, 3)
    μ_x ~ Normal(0, 3)

    ϕ ~ Normal(0, 3)
    cutzero ~ Normal(-3, 3)
    cutone ~ Normal(3, 3)

    for i in 1:length(y)
        μ = μ_intercept + μ_x * x[i]
        y[i] ~ OrderedBeta(logistic(μ), exp(ϕ), logistic(cutzero), logistic(cutone))
    end
end


fit = model_ordbeta(data.y, data.x)
posteriors = sample(fit, NUTS(), 1000)

# Mean posterior
mean(posteriors)

Mean
   parameters      mean 
       Symbol   Float64 

  μ_intercept   -3.8198
          μ_x    6.4144
            ϕ    2.4086
      cutzero   -3.4668
       cutone    3.2012

The parameters for mu μ are very similar, and that of phi ϕ is different (but that is expected as a different parametrization is used). The values for the cut points k0 and k1 (after the transformation specified above) are also very similar.

# Make predictions
pred = predict(model_ordbeta([missing for _ in 1:length(data.y)], data.x), posteriors)
pred = Array(pred)

fig = hist(data.y, color=:forestgreen, normalization=:pdf, bins=beta_bins(20))
for i in 1:size(pred, 1) # Iterate over each draw
    # density!(pred[i, :], color=(:black, 0), strokecolor=(:crimson, 0.05), strokewidth=1)
    hist!(pred[i, :], color=(:crimson, 0.01), normalization=:pdf, bins=beta_bins(20))
end
fig

Conclusion: it seems like the Julia version is working as expected as compared to the original R implementation.