Bayesian Age-Period-Cohort Modeling

Volker Schmid

2024-11-07

Source: vignettes/largevignettes/modeling.Rmd

Data example

BAMP includes a data example.

data(apc)
plot(cases[,1],type="l",ylim=range(cases), ylab="cases", xlab="year", main="cases per age group")
for (i in 2:8)lines(cases[,i], col=i)

APC model with random walk first order prior 

model1 <- bamp(cases, population, age="rw1", period="rw1", cohort="rw1",
              periods_per_agegroup = 5)
## 
## Automatic check procedure removed 1 Markov chain. Please check for convergence using checkConvergence() and maybe change your model settings (maybe add overdispersion).

bamp() automatically performs a check for MCMC convergence using Gelman and Rubin’s convergence diagnostic. We can manually check the convergence again:

## [1] TRUE

Now we have a look at the model results. This includes estimates of smoothing parameters and deviance and DIC:

print(model1)
## 
##  Model:
## age (rw1)  - period (rw1)  - cohort (rw1) model
## Deviance:     231.33
## pD:            36.82
## DIC:          268.16
## 
## 
##  Hyper parameters:                 5%           50%          95%         
## age                              0.352        0.911        1.914
## period                          66.500      196.313      619.346
## cohort                          35.126       59.319       98.755
## 
## 
## Markov Chains convergence checked succesfully using Gelman's R (potential scale reduction factor).

We can plot the main APC effects using point-wise quantiles:

plot(model1)

More quantiles are possible:

plot(model1, quantiles = c(0.025,0.1,0.5,0.9,0.975))

APC model with random walk second order prior 

model2 <- bamp(cases, population, age="rw2", period="rw2", cohort="rw2",
              periods_per_agegroup = 5,
              mcmc.options=list("number_of_iterations"=200000, "burn_in"=100000, "step"=50, "tuning"=500),
              hyperpar=list("age"=c(1,.5), "period"=c(1,0.05), "cohort"=c(1,0.05)))
## 
## Automatic check procedure removed 1 Markov chain. Please check for convergence using checkConvergence() and maybe change your model settings (maybe add overdispersion).
## Warning: MCMC chains did not converge!
## Warning: MCMC chains did not converge!
## [1] FALSE
print(model2)
## 
## WARNING! Markov Chains have apparently not converged! DO NOT TRUST THIS MODEL!
## 
##  Model:
## age (rw2)  - period (rw2)  - cohort (rw2) model
## Deviance:     233.94
## pD:            36.77
## DIC:          270.71
## 
## 
##  Hyper parameters:                 5%           50%          95%         
## age                              1.001        2.918        6.610
## period                          16.395       41.703       91.754
## cohort                          23.690       44.558       81.006
plot(model2)

model3<-bamp(cases, population, age="rw1", period=" ", cohort="rw2",
              periods_per_agegroup = 5)
## [1] TRUE
print(model3)
## 
##  Model:
## age (rw1) cohort (rw2) model
## Deviance:     276.78
## pD:            30.24
## DIC:          307.02
## 
## 
##  Hyper parameters:                 5%           50%          95%         
## age                              0.285        0.711        1.476
## cohort                          37.991       74.151      140.697
## 
## 
## Markov Chains convergence checked succesfully using Gelman's R (potential scale reduction factor).
plot(model3)

(model4<-bamp(cases, population, age="rw1", period="rw1", cohort="rw1",
             cohort_covariate = cov_c, periods_per_agegroup = 5))
## 
##  Model:
## age (rw1)  - period (rw1)  - cohort (rw1) model
## Deviance:     231.21
## pD:            36.79
## DIC:          268.00
## 
## 
##  Hyper parameters:                 5%           50%          95%         
## age                              0.363        0.915        1.977
## period                          66.572      196.755      597.112
## cohort                          35.011       59.305       96.936
## 
## 
## Markov Chains convergence checked succesfully using Gelman's R (potential scale reduction factor).
plot(model4)

(model5<-bamp(cases, population, age="rw1", period="rw1", cohort="rw1",
             period_covariate = cov_p, periods_per_agegroup = 5))
## 
##  Model:
## age (rw1)  - period (rw1)  - cohort (rw1) model
## Deviance:     231.33
## pD:            36.98
## DIC:          268.32
## 
## 
##  Hyper parameters:                 5%           50%          95%         
## age                              0.350        0.924        1.941
## period                          64.539      197.622      631.998
## cohort                          33.974       59.102       97.111
## 
## 
## Markov Chains convergence checked succesfully using Gelman's R (potential scale reduction factor).
plot(model5)