radon.Rmd

# 明尼苏达州房屋中氡含量 {#radon}


```{r, message=FALSE, warning=FALSE}
library(tidyverse)
library(tidybayes)
library(rstan)
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())
```



## 明尼苏达州房屋中氡的存在

```{r}
radon <- readr::read_rds(here::here('rawdata', "radon.rds")) 
radon
```



数据来源美国明尼苏达州85个县中房屋氡含量测量

- `log_radon`   房屋氡含量 (log scale)
- `log_uranium` 这个县放射性化学元素铀的等级 (log scale)
- `floor`       房屋楼层 (0 = basement, 1 = first floor)
- `county`      所在县 (factor)



## 任务

估计房屋中的氡含量。




### 可视化探索

```{r}
df_n_county <- radon %>% 
  group_by(county) %>%
  summarise(
    n = n()
  ) 

df_n_county 
```



统计每个县，样本量、氡含量均值、标准差、铀等级的均值、标准误
```{r}
radon_county <- radon %>%
  group_by(county) %>%
  summarise(
    log_radon_mean = mean(log_radon),
    log_radon_sd   = sd(log_radon),
    log_uranium    = mean(log_uranium),
    n              = length(county)
  ) %>%
  mutate(log_radon_se = log_radon_sd / sqrt(n))

radon_county
```



```{r fig.asp=2}
ggplot() +
  geom_boxplot(data = radon,
               mapping = aes(y = log_radon,
                             x = fct_reorder(county, log_radon, mean)),
               colour = "gray") +
  geom_point(data = radon,
             mapping = aes(y = log_radon,
                           x = fct_reorder(county, log_radon, mean)),
             colour = "gray") +
  geom_point(data = radon_county,
             mapping = aes(x = fct_reorder(county, log_radon_mean),
                           y = log_radon_mean),
             colour = "red") +
  coord_flip() +
  labs(y = "log(radon)", x = "")
```



### pooling model

这是最简单的模型，该模型假定所有的房屋的氡含量来自同一个分布， 估计整体的均值和方差

$$
\begin{aligned}[t]
y_i &\sim \operatorname{normal}(\mu, \sigma) \\
\mu &\sim \operatorname{normal}(0, 10) \\
\sigma &\sim \operatorname{exp}(1)
\end{aligned}
$$
这里我们指定 $\mu$ 和 $\sigma$ 较弱的先验信息.



```{r}
stan_program <- "
data {
  int N;
  vector[N] y;
}
parameters {
  real mu;
  real<lower=0> sigma;
}
model {
  mu ~ normal(0, 10);
  sigma ~ exponential(1);
  
  y ~ normal(mu, sigma);
}
"

stan_data <- list(
  N = nrow(radon),
  y = radon$log_radon
)

fit_pooling <- stan(model_code = stan_program, data = stan_data)
```



模型估计了均值和方差两个参数。

```{r}
summary(fit_pooling)$summary
```



### no-pooling model

每个县都有**独立**的均值和方差，又叫 *individual model*


$$
\begin{aligned}[t]
y_i &\sim \operatorname{normal}(\mu_{j[i]}, \sigma)  \\
\mu_j &\sim \operatorname{normal}(0, 10) \\
\sigma &\sim \operatorname{exp}(1)
\end{aligned}
$$
其中， $j[i]$ 表示观测$i$对应的所在县。



```{r}
stan_program <- "
data {
  int<lower=1> N;                            
  int<lower=2> J;                     
  int<lower=1, upper=J> county[N]; 
  vector[N] y; 
}
parameters {
  vector[J] mu;
  real<lower=0> sigma;
}
model {
  mu ~ normal(0, 10);
  sigma ~ exponential(1);
  
  for(i in 1:N) {
    y[i] ~ normal(mu[county[i]], sigma);
  }
}
"

stan_data <- list(
  N      = nrow(radon),
  J      = length(unique(radon$county)),
  county = as.numeric(radon$county),
  y      = radon$log_radon
)

fit_no_pooling <- stan(model_code = stan_program, data = stan_data)
```


```{r}
summary(fit_no_pooling)$summary
```


有多少县，就有多少个模型，每个模型有一个 $\mu$，参数$\sigma$是共同的。需要注意的是，每组之间彼此独立的，没有共享信息。





### partially pooled model

和 "no-pooling model" 模型一样，每个县都有自己的均值，但是，这些县彼此会分享信息，一个县获取的信息可以帮助我们估计其它县的均值。

- 模型同时考虑各个类别数据中的信息以及整个群体中的信息
- 怎么叫共享信息？参数来自同一个分布
- 怎么做到的呢？通过先验



$$
\begin{aligned}[t]
y_i &\sim \operatorname{normal}(\mu_{j[i]}, \sigma) \\
\mu_j &\sim \operatorname{normal}(\gamma, \tau) \\
\gamma &\sim \operatorname{normal}(0, 5) \\
\tau &\sim \operatorname{exp}(1)
\end{aligned}
$$

每个县的氡含量均值$\mu_j$都服从均值为 $\gamma$、标准差为 $\tau$ 的正态分布。但先验分布中的参数
$\gamma$ 和 $\tau$ 都各自有自己的先验分布，即**参数的参数**， 通常称之为**超参数**，这就是多层模型中"层"的来历，$\mu_j$ 是第一层参数，$\gamma$ 是第二层参数。

- $\gamma$ 和 $\tau$ 的先验称为 **超先验分布**。
- **超参数**是多层模型的标志。


```{r}
stan_program <- "
data {
  int<lower=1> N;                            
  int<lower=2> J;                     
  int<lower=1, upper=J> county[N]; 
  vector[N] y; 
}
parameters {
  vector[J] mu;
  real mu_a;
  real<lower=0> sigma_y;
  real<lower=0> sigma_a;
}
model {
  mu_a ~ normal(0, 5);
  sigma_a ~ exponential(1);
  sigma_y ~ exponential(1);
  
  mu ~ normal(mu_a, sigma_a);
  
  for(i in 1:N) {
    y[i] ~ normal(mu[county[i]], sigma_y);
  }
}
"

stan_data <- list(
  N      = nrow(radon),
  J      = length(unique(radon$county)),
  county = as.numeric(radon$county),
  y      = radon$log_radon
)

fit_partial_pooling <- stan(model_code = stan_program, data = stan_data)
```


```{r}
summary(fit_partial_pooling)$summary
```



### 小结


```{r, out.width = '85%', echo = FALSE}
knitr::include_graphics(here::here("images", "hirerachical.jpg"))
```



```{r}
overall_mean <- broom.mixed::tidyMCMC(fit_pooling) %>% 
  filter(term == "mu") %>% 
  pull(estimate)



df_no_pooling <- fit_no_pooling %>% 
  tidybayes::gather_draws(mu[i]) %>%
  tidybayes::mean_hdi() %>% 
  ungroup() %>% 
  mutate(
    type = "no_pooling"
  ) %>% 
  select(type, .value) %>% 
  bind_cols(df_n_county)



df_partial_pooling <- fit_partial_pooling %>% 
  tidybayes::gather_draws(mu[i]) %>%
  tidybayes::mean_hdi() %>% 
  ungroup() %>% 
  mutate(
    type = "partial_pooling"
  ) %>% 
  select(type, .value) %>% 
  bind_cols(df_n_county)


bind_rows(df_no_pooling, df_partial_pooling) %>% 
  ggplot(
    aes(x = n, y = .value, color = type)
  ) +
  geom_point(size = 3) +
  geom_hline(yintercept = overall_mean) +
  scale_x_log10()
```


- 层级模型可以实现不同分组之间的信息交换
- 分组的均值向整体的均值靠拢（收缩）
- 分组的样本量越小，收缩效应越明显


用我们四川火锅记住他们。

```{r, out.width = '85%', echo = FALSE}
knitr::include_graphics(here::here("images", "pooling.jpg"))
```



## 增加预测变量

### 增加楼层floor作为预测变量


$$
\begin{aligned}
y_i &\sim  N(\mu_i, \sigma^2) \\
\mu_i &= \alpha_{j[i]} + \beta~\mathtt{floor}_i  \\
\alpha_j &\sim \operatorname{normal}(\gamma, \tau)  \\
\beta &\sim \operatorname{normal}(0, 2.5)\\
\gamma &\sim \operatorname{normal}(0, 10) \\
\tau &\sim \operatorname{exp}(1) \\
\end{aligned}
$$
不同的县有不同的截距，但有共同的$\beta$，因此被称为**变化的截距**。





```{r}
stan_program <- "
data {
  int<lower=1> N;                            
  int<lower=2> J;                     
  int<lower=1, upper=J> county[N]; 
  vector[N] x; 
  vector[N] y; 
}
parameters {
  vector[J] alpha;
  real beta;
  real gamma;
  real<lower=0> sigma_y;
  real<lower=0> sigma_a;
}
model {
  vector[N] mu;
  for(i in 1:N) {
    mu[i] = alpha[county[i]] + beta * x[i];
  }
  
  for(i in 1:N) {
    y[i] ~ normal(mu[i], sigma_y);
  }
  
  alpha ~ normal(gamma, sigma_a);
  gamma ~ normal(0, 10);
  beta ~ normal(0, 2.5);
  sigma_a ~ exponential(1);
  sigma_y ~ exponential(1);

}
"

stan_data <- list(
  N      = nrow(radon),
  J      = length(unique(radon$county)),
  county = as.numeric(radon$county),
  x      = radon$floor,
  y      = radon$log_radon
)

fit_intercept_partial <- stan(model_code = stan_program, data = stan_data)
```



```{r}
summary(fit_intercept_partial)$summary
```



### 截距中增加预测因子

相当于在第二层参数中增加预测因子

$$
\begin{aligned}
y_i &\sim  N(\mu_i, ~\sigma) \\
\mu_i &= \alpha_{j[i]} + \beta~\mathtt{floor}_i  \\
\alpha_j &\sim \operatorname{normal}(\gamma_0 + \gamma_1~u_j, ~\tau)  \\
\beta &\sim \operatorname{normal}(0, 1)\\
\gamma_0 &\sim  \operatorname{normal}(0, 2.5)\\
\gamma_1 &\sim  \operatorname{normal}(0, 2.5)\\
\tau &\sim \operatorname{exp}(1) \\
\end{aligned}
$$


```{r, warning=FALSE, message=FALSE}
stan_program <- "
data {
  int<lower=0> N;
  vector[N] y;             
  int<lower=0, upper=1> x[N];             
  int<lower=2> J;                     
  int<lower=1, upper=J> county[N]; 
  vector[J] u; 
}
parameters {
  vector[J] alpha;
  real beta;
  real gamma0;
  real gamma1;
  real<lower=0> sigma_a;
  real<lower=0> sigma_y;
}
model {
  vector[N] mu;

  for(i in 1:N) {
    mu[i] = alpha[county[i]] + x[i] * beta;
  }
  
  for(j in 1:J) {
    alpha[j] ~ normal(gamma0 + gamma1 * u[j], sigma_a);
  }
  
  y ~ normal(mu, sigma_y);

  beta ~ normal(0, 1);
  gamma0 ~ normal(0, 2.5);
  gamma1 ~ normal(0, 2.5);
  sigma_a ~ exponential(1);
  sigma_y ~ exponential(1);

}


"

stan_data <- list(
  N      = nrow(radon),
  J      = length(unique(radon$county)),
  county = as.numeric(radon$county),
  x      = radon$floor,
  y      = radon$log_radon,
  u      = unique(radon$log_uranium)
)



fit_intercept_partial_2 <- stan(model_code = stan_program, data = stan_data)
```




```{r}
summary(fit_intercept_partial_2, c("beta", "gamma0", "gamma1", "sigma_y", "sigma_a"))$summary
```



```{r}
fit_intercept_partial_2 %>% 
  tidybayes::gather_draws(alpha[i]) %>%
  tidybayes::mean_hdi() %>%
  bind_cols(
    radon %>% distinct(log_uranium)
  ) %>%
  
  ggplot(aes(x = log_uranium, y = .value)) +
  geom_point() +
  geom_pointrange(aes(ymin = .lower, ymax = .upper))

```




### 变化的截距和斜率

之前模型假定，不管哪个县，所有的房屋一楼和二楼的氡含量的差别是一样的（beta系数是不变的），现在，我们将模型进一步扩展，假定一楼和二楼的氡含量的差别**不是固定不变的，而是随县变化的**，也就说不同县的房屋，一二楼氡含量差别是不同的。


写出变化的截距和斜率模型的数学表达式

$$
\begin{aligned}[t]
y_i &\sim \operatorname{Normal}(\mu_i, \sigma_y) \\
\mu_i &= \alpha_{j[i]} + \beta_{j[i]}~\mathtt{floor}_i  \\
  \begin{bmatrix}
  \alpha_j \\
  \beta_j
  \end{bmatrix}
& \sim
\operatorname{MVNormal}
\left(
  \begin{bmatrix}
  \gamma_0^{\alpha} + \gamma_1^{\alpha} ~ u_j \\
  \gamma_0^{\beta} + \gamma_1^{\beta} ~ u_j \\
  \end{bmatrix}, ~\mathbf S 
\right) \\
\mathbf S     & = \begin{bmatrix} \sigma_\alpha & 0 \\ 0 & \sigma_\beta \end{bmatrix} \mathbf R \begin{bmatrix} \sigma_\alpha & 0 \\ 0 & \sigma_\beta \end{bmatrix} \\
& = \begin{bmatrix} \sigma_\alpha & 0 \\ 0 & \sigma_\beta \end{bmatrix} \begin{bmatrix} 1 & \rho \\ \rho & 1 \end{bmatrix} \begin{bmatrix} \sigma_\alpha & 0 \\ 0 & \sigma_\beta \end{bmatrix} \\
\gamma_a      & \sim \operatorname{Normal}(0, 4) \\
\gamma_b     & \sim \operatorname{Normal}(0, 4) \\
\sigma        & \sim \operatorname{Exponential}(1) \\
\sigma_\alpha & \sim \operatorname{Exponential}(1) \\
\sigma_\beta  & \sim \operatorname{Exponential}(1) \\
\mathbf R     & \sim \operatorname{LKJcorr}(2)
\end{aligned} 
$$





- 模型表达式中 $\alpha_j$ 和 $\beta_j$ 不是直接给先验，而是给的层级先验。

- $\alpha_j$ 和 $\beta_j$ 也可能存在关联，常见的有，多元正态分布（Multivariate Gaussian Distribution）


$$
\begin{aligned}[t]
\begin{bmatrix}
\alpha_j \\
\beta_j
\end{bmatrix} &\sim
\operatorname{MVNormal}\left(\begin{bmatrix}\gamma_{\alpha} \\ \gamma_{\beta} \end{bmatrix}, \mathbf S\right) \\
\end{aligned}
$$

### 协方差矩阵(covariance matrix) 

`MASS::mvrnorm(n, mu, Sigma)`产生多元高斯分布的随机数，每组随机变量高度相关。
比如，人的身高服从正态分布，人的体重也服从正态分布，同时身高和体重又存在强烈的关联。


- `n`: 随机样本的大小
- `mu`: 多元高斯分布的均值向量
- `Sigma`: 协方差矩阵，主要这里是大写的S (Sigma)，提醒我们它是一个矩阵，不是一个数值

```{r}
a       <- 3.5
b       <- -1
sigma_a <- 1
sigma_b <- 0.5
rho     <- -0.7
mu      <- c(a, b)
cov_ab  <- sigma_a * sigma_b * rho 
sigma   <- matrix(c(sigma_a^2, cov_ab, 
                    cov_ab, sigma_b^2), ncol = 2)
sigma
```





```{r}
d <- MASS::mvrnorm(1000, mu = mu, Sigma = sigma) %>%
  data.frame() %>%
  set_names("group_a", "group_b")
head(d)
```




```{r}
d %>%
  ggplot(aes(x = group_a)) +
  geom_density(
    color = "transparent",
    fill = "dodgerblue3",
    alpha = 1 / 2
  ) +
  stat_function(
    fun = dnorm,
    args = list(mean = 3.5, sd = 1),
    linetype = 2
  )
```


```{r}
d %>%
  ggplot(aes(x = group_b)) +
  geom_density(
    color = "transparent",
    fill = "dodgerblue3",
    alpha = 1 / 2
  ) +
  stat_function(
    fun = dnorm,
    args = list(mean = -1, sd = 0.5),
    linetype = 2
  )
```


```{r}
d %>%
  ggplot(aes(x = group_a, y = group_b)) +
  geom_point() +
  stat_ellipse(type = "norm", level = 0.95)
```



### 回到模型

在stan中要给协方差矩阵指定一个先验，[Priors for Covariances](https://mc-stan.org/docs/2_26/stan-users-guide/multivariate-hierarchical-priors-section.html)



```{r, warning=FALSE, message=FALSE}
stan_program <- "
data {
  int<lower=0> N;
  vector[N] y;             
  int<lower=0, upper=1> x[N];             
  int<lower=2> J;                     
  int<lower=1, upper=J> county[N]; 
  vector[J] u; 
}
parameters {
  vector[J] alpha;
  vector[J] beta;
  vector[2] gamma_a;
  vector[2] gamma_b;
  
  real<lower=0> sigma;
  vector<lower=0>[2] tau;
  corr_matrix[2] Rho;
}
transformed parameters {
  vector[2] YY[J];

  for (j in 1:J) {
    YY[j] = [alpha[j], beta[j]]';
  }
}
model {
  vector[N] mu;
  vector[2] MU[J];
  
  sigma ~ exponential(1);
  tau ~ exponential(1);
  Rho ~ lkj_corr(2);
  gamma_a ~ normal(0, 2);
  gamma_b ~ normal(0, 2);
  
  for(i in 1:N) {
    mu[i] = alpha[county[i]] + beta[county[i]] * x[i];  
  }
  
  for(j in 1:J) {
    MU[j, 1] = gamma_a[1] + gamma_a[2] * u[j];
    MU[j, 2] = gamma_b[1] + gamma_b[2] * u[j];
  }
 

  target += multi_normal_lpdf(YY | MU, quad_form_diag(Rho, tau));
  
  y ~ normal(mu, sigma); 
}
"


stan_data <- list(
  N      = nrow(radon),
  J      = length(unique(radon$county)),
  county = as.numeric(radon$county),
  x      = radon$floor,
  y      = radon$log_radon,
  u      = unique(radon$log_uranium)
)


fit_slope_partial <- stan(model_code = stan_program, data = stan_data)
```


```{r}
summary(fit_slope_partial, c("alpha"))$summary
summary(fit_slope_partial, c("beta"))$summary
summary(fit_slope_partial, c("sigma"))$summary
summary(fit_slope_partial, c("gamma_a", "gamma_b"))$summary
```




```{r}
rstan::traceplot(fit_slope_partial, pars = c("sigma"))
```