3. Priors

In bage: Bayesian Estimation and Forecasting of Age-Specific Rates

knitr::opts_chunk$set(
  collapse = TRUE,
  echo = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 1.5
)

Set-up

suppressPackageStartupMessages({
  library(bage)
  library(poputils)
  library(ggplot2)
  library(dplyr)
})  

plot_exch <- function(draws) {
  ggplot(draws, aes(x = element, y = value)) +
    facet_wrap(vars(draw), nrow = 1) +
    geom_hline(yintercept = 0, col = "grey") +
    geom_point(col = "darkblue", size = 0.7) +
    scale_x_continuous(n.breaks = max(draws$element)) +
    xlab("Unit") +
    ylab("") +
    theme(text = element_text(size = 8))
}          

plot_cor_one <- function(draws) {
  ggplot(draws, aes(x = along, y = value)) +
    facet_wrap(vars(draw), nrow = 1) +
    geom_hline(yintercept = 0, col = "grey") +
    geom_line(col = "darkblue") +
    xlab("Unit") +
    ylab("") +
    theme(text = element_text(size = 8))
}          

plot_cor_many <- function(draws) {
  ggplot(draws, aes(x = along, y = value)) +
    facet_grid(vars(by), vars(draw)) +
    geom_hline(yintercept = 0, col = "grey") +
    geom_line(col = "darkblue") +
    xlab("Unit") +
    ylab("") +
    theme(text = element_text(size = 8))
}          

plot_svd_one <- function(draws) {
  ggplot(draws, aes(x = age_mid(age), y = value, color = sexgender)) +
    facet_wrap(vars(draw), nrow = 1) +
    geom_line() +
    scale_color_manual(values = c("darkgreen", "darkorange")) +
    xlab("Age") +
    ylab("") +
    theme(text = element_text(size = 8),
          legend.position = "top",
          legend.title = element_blank())
}

plot_svd_many <- function(draws) {
  draws |>
    mutate(element = paste("Unit", element)) |>
    ggplot(aes(x = age_mid(age), y = value, color = sexgender)) +
    facet_grid(vars(element), vars(draw)) +
    geom_line() +
    scale_color_manual(values = c("darkgreen", "darkorange")) +
    xlab("Age") +
    ylab("") +
    theme(text = element_text(size = 8),
          legend.position = "top",
          legend.title = element_blank())
}

Exchangeable Units

Fixed Normal NFix()

Model

\begin{equation} \beta_j \sim \text{N}(0, \mathtt{sd}^2) \end{equation}

All defaults

sd = 1

set.seed(0)

NFix() |>
  generate(n_element = 10, n_draw = 8) |>
  plot_exch()

Reduce sd

sd = 0.01

set.seed(0)

NFix(sd = 0.01) |>
  generate(n_element = 10, n_draw = 8) |>
  plot_exch()

Normal N()

Model

\begin{align} \beta_j & \sim \text{N}(0, \tau^2) \ \tau & \sim \text{N}^+(0, \mathtt{s}) \end{align}

All defaults

s = 1

set.seed(0)

N() |>
  generate(n_element = 10, n_draw = 8) |>
  plot_exch()

Reduce s

s = 0.01

set.seed(0)

N(s = 0.01) |>
  generate(n_element = 10, n_draw = 8) |>
  plot_exch()

Units Correlated With Neighbours

Random Walk RW()

Model

\begin{align} \beta_1 & \sim \text{N}(0, \mathtt{sd}^2) \ \beta_j & \sim \text{N}(\beta_{j-1}, \tau^2), \quad j = 2, \cdots, J \ \tau & \sim \text{N}^+(0, \mathtt{s}^2) \end{align}

All defaults

s = 1, sd = 1

set.seed(0)

RW() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s

s = 0.01, sd = 1

set.seed(0)

RW(s = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s and sd

s = 0.01, sd = 0

set.seed(0)

RW(s = 0.01, sd = 0) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Second-Order Random Walk RW2()

Model

\begin{align} \beta_1 & \sim \text{N}(0, \mathtt{sd}^2) \ \beta_2 & \sim \text{N}(\beta_1, \mathtt{sd_slope}^2) \ \beta_j & \sim \text{N}(2\beta_{j-1} - \beta_{j-2}, \tau^2), \quad j = 3, \cdots, J \ \tau & \sim \text{N}^+(0, \mathtt{s}^2) \end{align}

All defaults

s = 1, sd = 1, sd_slope = 1

set.seed(0)

RW2() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s

s = 0.01, sd = 1, sd_slope = 1

set.seed(0)

RW2(s = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s and sd_slope

s = 0.01, sd = 1, sd_slope = 0.01

set.seed(0)

RW2(s = 0.01, sd_slope = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s, sd, and sd_slope

s = 0.01, sd = 0, sd_slope = 0.01

set.seed(0)

RW2(s = 0.01, sd = 0, sd_slope = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Autoregressive AR()

Model

\begin{equation} \beta_j \sim \text{N}\left(\phi_1 \beta_{j-1} + \cdots + \phi_{\mathtt{n_coef}} \beta_{j-\mathtt{n_coef}}, \omega^2\right) \end{equation} TMB derives a value of $\omega$ that gives each $\beta_j$ variance $\tau^2$. The prior for $\tau$ is \begin{equation} \tau \sim \text{N}^+(0, \mathtt{s}^2). \end{equation} The prior for each $\phi_k$ is \begin{equation} \frac{\phi_k + 1}{2} \sim \text{Beta}(\mathtt{shape1}, \mathtt{shape2}). \end{equation}

All defaults

n_coef = 2, s = 1

set.seed(0)

AR() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Increase n_coef

set.seed(0)

AR(n_coef = 3) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s

set.seed(0)

AR(s = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Specify 'along' and 'by' dimensions

set.seed(0)

AR() |>
  generate(n_along = 20, n_by = 3, n_draw = 8) |>
  plot_cor_many()

Specify 'along' and 'by' dimensions, set con = "by"

set.seed(0)

AR(con = "by") |>
  generate(n_along = 20, n_by = 3, n_draw = 8) |>
  plot_cor_many()

First-Order Autoregressive AR1()

Model

\begin{equation} \beta_j \sim \text{N}\left(\phi \beta_{j-1}, \omega^2\right) \end{equation} TMB derives a value of $\omega$ that gives each $\beta_j$ variance $\tau^2$. The prior for $\tau$ is \begin{equation} \tau \sim \text{N}^+(0, \mathtt{s}^2). \end{equation} The prior for $\phi$ is \begin{equation} \frac{\phi - \mathtt{min}}{\mathtt{max} - \mathtt{min}} \sim \text{Beta}(\mathtt{shape1}, \mathtt{shape2}). \end{equation}

All defaults

s = 1, min = 0.8, max = 0.98

set.seed(0)

AR1() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s

set.seed(0)

AR1(s = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s and modify min, max

set.seed(0)

AR1(s = 0.01, min = -1, max = 1) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Random Walk with Seasonal Effects RW_Seas()

Model

\begin{align} \beta_j & = \alpha_j + \lambda_j \ \alpha_1 & \sim \text{N}(0, \mathtt{sd}^2) \ \alpha_j & \sim \text{N}(\alpha_{j-1}, \tau^2), \quad j = 2, \cdots, J \ \tau & \sim \text{N}^+\left(0, \mathtt{s}^2\right) \ \lambda_j & \sim \text{N}(0, \mathtt{sd_seas}^2), \quad j = 1, \cdots, \mathtt{n_seas} - 1 \ \lambda_j & = -\sum_{s=1}^{j-1} \lambda_{j-s}, \quad j = \mathtt{n_seas},\; 2 \mathtt{n_seas}, \cdots \ \lambda_j & \sim \text{N}(\lambda_{j-\mathtt{n_seas}}, \omega^2), \quad \text{otherwise} \ \omega & \sim \text{N}^+\left(0, \mathtt{s_seas}^2\right) \end{align}

All defaults

s = 1, sd = 1, s_seas = 0, sd_seas = 1

set.seed(0)

RW_Seas(n_seas = 4) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s, sd

s = 0.01, sd = 0, s_seas = 0, sd_seas = 1

set.seed(0)

RW_Seas(n_seas = 4, s = 0.01, sd = 0) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Increase s_seas

s = 0.01, sd = 0, s_seas = 1, sd_seas = 1

set.seed(0)

RW_Seas(n_seas = 4, s = 0.01, sd = 0, s_seas = 1) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce sd_seas

s = 0.01, sd = 0, s_seas = 1, s_seas = 0, sd_seas = 0.01

set.seed(0)

RW_Seas(n_seas = 4, s = 0.01, sd = 0, sd_seas = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Second-Order Random Walk with Seasonal Effects RW2_Seas()

Model

\begin{align} \beta_j & = \alpha_j + \lambda_j \ \alpha_1 & \sim \text{N}(0, \mathtt{sd}^2) \ \alpha_2 & \sim \text{N}(\alpha_1, \mathtt{sd_slope}^2) \ \alpha_j & \sim \text{N}(2\alpha_{j-1} - \alpha_{j-2}, \tau^2), \quad j = 3, \cdots, J \ \tau & \sim \text{N}^+\left(0, \mathtt{s}^2\right) \ \lambda_j & \sim \text{N}(0, \mathtt{sd_seas}^2), \quad j = 1, \cdots, \mathtt{n_seas} - 1 \ \lambda_j & = -\sum_{s=1}^{j-1} \lambda_{j-s}, \quad j = \mathtt{n_seas},\; 2 \mathtt{n_seas}, \cdots \ \lambda_j & \sim \text{N}(\lambda_{j-\mathtt{n_seas}}, \omega^2), \quad \text{otherwise} \ \omega & \sim \text{N}^+\left(0, \mathtt{s_seas}^2\right) \end{align}

All defaults

s = 1, sd = 1, sd_slope = 1, s_seas = 0, sd_seas = 1

set.seed(0)

RW2_Seas(n_seas = 4) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s, sd, sd_slope, sd_seas

s = 0.01, sd = 0, sd_slope = 0.01, s_seas = 0, sd_seas = 0.01

set.seed(0)

RW2_Seas(n_seas = 4, s = 0.01, sd = 0, sd_slope = 0.01, sd_seas = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Linear Lin()

Model

\begin{align} \beta_j & = \alpha_j + \epsilon_j \ \alpha_j & = \left(j - \frac{J + 1}{2}\right) \eta \ \eta & \sim \text{N}\left(\mathtt{mean_slope}, \mathtt{sd_slope}^2 \right) \ \epsilon & \sim \text{N}(0, \tau^2) \ \tau & \sim \text{N}^+\left(0, \mathtt{s}^2\right) \end{align}

All defaults

s = 1, mean_slope = 0, sd_slope = 1

set.seed(0)

Lin() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s

s = 0, mean_slope = 0, sd_slope = 1

set.seed(0)

Lin(s = 0) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Modify mean_slope, sd_slope

s = 1, mean_slope = 0.2, sd_slope = 0.1

set.seed(0)

Lin(mean_slope = 0.2, sd_slope = 0.1) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Specify 'along' and 'by' dimensions

set.seed(0)

Lin() |>
  generate(n_along = 20, n_by = 3, n_draw = 8) |>
  plot_cor_many()

Specify 'along' and 'by' dimensions, set con = "by"

set.seed(0)

Lin(con = "by") |>
  generate(n_along = 20, n_by = 3, n_draw = 8) |>
  plot_cor_many()

Linear with AR Errors Lin_AR()

Model

\begin{align} \beta_j & = \alpha_j + \epsilon_j \ \alpha_j & = \left(j - \frac{J + 1}{2}\right) \eta \ \eta & \sim \text{N}\left(\mathtt{mean_slope}, \mathtt{sd_slope}^2 \right) \ \epsilon_j & \sim \text{N}\left(\phi_1 \epsilon_{j-1} + \cdots + \phi_{\mathtt{n_coef}} \epsilon_{j-\mathtt{n_coef}}, \omega^2\right) \tau & \sim \text{N}^+\left(0, \mathtt{s}^2\right) \ \frac{\phi_k + 1}{2} & \sim \text{Beta}(\mathtt{shape1}, \mathtt{shape2}) \end{align}

All defaults

n_coef = 2, s = 1, mean_slope = 0, sd_slope = 1

set.seed(0)

Lin_AR() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s, sd_slope

s = 0.1, mean_slope = 0, sd_slope = 0.01

set.seed(0)

Lin_AR(s = 0.1, sd_slope = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Linear with AR1 Errors Lin_AR1()

Model

\begin{align} \beta_j & = \alpha_j + \epsilon_j \ \alpha_j & = \left(j - \frac{J + 1}{2}\right) \eta \ \eta & \sim \text{N}\left(\mathtt{mean_slope}, \mathtt{sd_slope}^2 \right) \ \epsilon_j & \sim \text{N}\left(\phi \epsilon_{j-1}, \omega^2\right) \tau & \sim \text{N}^+\left(0, \mathtt{s}^2\right) \ \frac{\phi - \mathtt{min}}{\mathtt{max} - \mathtt{min}} \sim \text{Beta}(\mathtt{shape1}, \mathtt{shape2}) \end{align}

All defaults

s = 1, min = 0.8, max = 0.98, mean_slope = 0, sd_slope = 1

set.seed(0)

Lin_AR1() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Modify min, max

s = 1, min = -1, max = 1, mean_slope = 0, sd_slope = 1

set.seed(0)

Lin_AR1(min = -1, max = 1) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s, sd_slope

s = 0.1, min = 0.8, max = 0.98, mean_slope = 0, sd_slope = 0.02

set.seed(0)

Lin_AR1(s = 0.1, sd_slope = 0.02) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Penalised Spline Sp()

Model

\begin{align} \pmb{\beta} & = \bm{X} \pmb{\alpha} \ \alpha_1 & \sim \text{N}(0, \mathtt{sd}^2) \ \alpha_2 & \sim \text{N}(\alpha_1, \mathtt{sd_slope}^2) \ \alpha_j & \sim \text{N}(2\alpha_{j-1} - \alpha_{j-2}, \tau^2), \quad j = 3, \cdots, J \ \tau & \sim \text{N}^+\left(0, \mathtt{s}^2\right) \ \end{align}

All defaults

n_comp = NULL, s = 1, sd = 1, sd_slope = 1

set.seed(0)

Sp() |>
  generate(n_draw = 8) |>
  plot_cor_one()

Specify n_comp

n_comp = 15, s = 1, sd = 1, sd_slope = 1

set.seed(0)

Sp(n_comp = 5) |>
  generate(n_draw = 8) |>
  plot_cor_one()

Reduce s, sd, sd_slope

n_comp = NULL, s = 0.01, sd = 0.01, sd_slope = 0.01

set.seed(0)

Sp(s = 0.01, sd = 0.01, sd_slope = 0.01) |>
  generate(n_draw = 8) |>
  plot_cor_one()

SVD-Based Priors

Exchangeable SVD()

Model

\begin{equation} \pmb{\beta} = \pmb{F} \pmb{\alpha} + \pmb{g} \end{equation}

All defaults

n_comp = NULL, indep = TRUE

set.seed(0)

SVD(HMD) |>
  generate(n_draw = 8) |>
  plot_svd_one()

Increase n_comp

n_comp = 5, indep = TRUE

SVD(HMD, n_comp = 5) |>
  generate(n_draw = 8) |>
  plot_svd_one()

Set indep to FALSE

SVD(HMD, indep = FALSE) |>
  generate(n_draw = 8) |>
  plot_svd_one()

Multiple units

SVD(HMD, indep = FALSE) |>
  generate(n_draw = 8, n_element = 3) |>
  plot_svd_many()

Dynamic SVD Prior: SVD_AR()

SVD_AR(HMD, indep = FALSE, s = 0.1) |>
  generate(n_draw = 6, n_along = 5) |>
    ggplot(aes(x = age_mid(age), 
                      y = value, 
                      color = sexgender)) +
      facet_grid(vars(draw), vars(along)) +
      geom_line() +
      scale_color_manual(values = c("darkgreen", "darkorange")) +
      xlab("Age") +
      ylab("") +
      theme(text = element_text(size = 8),
            legend.position = "top",
            legend.title = element_blank())

bage documentation built on April 3, 2025, 8:53 p.m.