贝叶斯地理统计模型R-INLA-2

Jamesjin63

发布于 2022-10-25 14:47:35

5870

发布于 2022-10-25 14:47:35

文章被收录于专栏：EpiHub

Validation

上一期我们介绍了，如何利用100空间位置，来估计研究区域内的降雨量。但是并没有做模型的validation 虽然我们已经将数据集分成test与train两个部分；接下来我们将介绍如何测试模型的好坏及与glm模型对比。

validation

首先我们将367个点绘制出来，看一下效果。

image.png

然后根据前述的SPDE函数，将367个空间效应给提取出来然后整合放在stack.train里面，提示这里的y为NA但是X变量还是来源于train数据里面

# plot train
dim(train)
# train plot
ggplot() + 
  geom_point(data=train, aes(y = lat, x = lon,size=rainfall))

# Mesh and SPDE and stack
A.train=inla.spde.make.A(Mesh,loc=train_loc)
## 5.2 train stack
Xm <- model.matrix(~ -1 + altitude, data = train)
X=data.frame(altitude=Xm[,1])
N=nrow(train)
N
stack.train=inla.stack(tag="train",
                       data=list(y=NA),
                       A = list(1,1,A.train),
                       effects= list(
                         Intercept = rep(1, N),
                         X = X,
                         w = s.index))
# join stack
stack_fit=inla.stack(stack.test,stack.train)

## 7. fit model
formula = y ~ -1+Intercept+altitude+f(w, model = spde)

fit=inla(formula = formula,
         data = inla.stack.data(stack_fit,spde=spde),
         family = "gaussian",
         control.compute = list(dic = TRUE,waic = TRUE),
         control.predictor = list(A = inla.stack.A(stack_fit),compute=TRUE)
)

接下来就是拟合INLA模型了，formula跟前面介绍的一样，写好formula以后带入fit model；这里inla里面的stack就使用了train与test结合的stack

# join stack
stack_fit=inla.stack(stack.test,stack.train)

## 7. fit model
formula = y ~ -1+Intercept+altitude+f(w, model = spde)

fit_train=inla(formula = formula,
         data = inla.stack.data(stack_fit,spde=spde),
         family = "gaussian",
         control.compute = list(dic = TRUE,waic = TRUE),
         control.predictor = list(A = inla.stack.A(stack_fit),compute=TRUE)
)

> round(fit_train$summary.fixed, 4)
            mean      sd 0.025quant 0.5quant 0.975quant   mode   kld
Intercept 0.0032 31.6144   -62.0665   0.0023    62.0211 0.0032 0e+00
altitude  0.0129  0.0173    -0.0211   0.0130     0.0467 0.0130 1e-04

predict

## prediction 367 sites
index.train=inla.stack.index(stack_fit,"train")$data
post_mean_train=fit$summary.linear.predictor[index.train,"mean"]
post_sd_train=fit$summary.linear.predictor[index.train,"sd"]

pred_df=tibble(obs=train$rainfall,
               pre=post_mean_train)

ggplot(data=pred_df, aes(x = obs, y = pre)) + 
  geom_point()+
  geom_smooth()+
   labs(title="INLA-prediction") 

cor.test(pred_df$obs,pred_df$pre)

367个位置的拟合值与实际值的相关系数为0.84，认为该INLA模型预测效果较好。

image.png

glm

同样我们利用glm一般线形模型来拟合降雨量与海拔高度之间的关系，并对367个点进行预测。

## GLM

fit_glm=glm(rainfall~altitude,data=test)
summary(fit_glm)

# predict
newdata=train %>% mutate(rainfall=NA)

pre_glm=predict(fit_glm,newdata)

pred_df2=tibble(obs=train$rainfall,
               pre=as.numeric(pre_glm))

ggplot(data=pred_df2, aes(x = obs, y = pre)) + 
  geom_point()+
  geom_smooth()+
  labs(title="GLM-prediction") 

cor.test(pred_df2$obs,pred_df2$pre)

可以看到，glm模型预测的结果很不理想。相关系数为0.198