在R中输出多个图形（用于动画）

Question

为了更好地理解贝叶斯更新，我一直在使用来自Bayesian生物学家的代码。由于我需要学会创建动画图形，所以我认为创建一个更新的动画图形会是一个有趣的练习。然而，这比我预期的要困难得多。受Rob Hyndman关于此问题的博客的启发，我尝试创建以下内容：

library(animation)
setwd("~/Dropbox/PriorUpdating") #set working directory

## Simulate Bayesian Binomial updating

sim_bayes<-function(p=0.5,N=10,y_lim=15,prior_a=1,prior_b=1)
{
   print(paste("The prior expectation of p is ",prior_a/(prior_a+prior_b)))
   success<-0
   curve(dbeta(x,prior_a,prior_b),xlim=c(0,1),ylim=c(0,y_lim),xlab='p',ylab='Posterior Density',lty=2)
   legend('topright',legend=c('Prior','Updated Posteriors','Final Posterior'),lty=c(2,1,1),col=c('black','black','red'))

  for(i in 1:N)
     {

        if(runif(1,0,1)<=p) success<-success+1 #this is where we see if there is a "success"

      curve(dbeta(x,success+prior_a,(i-success)+prior_b),add=TRUE) #plot updated
      }
curve(dbeta(x,success+prior_a,(i-success)+prior_b),add=TRUE,col='red',lwd=1.5) #plot final posterior
}

oopt = ani.options(interval = 0)
saveMovie(sim_bayes(p=0.6,N=90,prior_a=1,prior_b=1),interval=0.1,width=580,height=400)
ani.options(oopt)

然而，这只生成了最终的图表。因此，我想尝试输出所有图表的PDF文件。

library(animation)
setwd("~/Dropbox/PriorUpdating") #set working directory

## Simulate Bayesian Binomial updating

sim_bayes<-function(p=0.5,N=10,y_lim=15,prior_a=1,prior_b=1)
{
  print(paste("The prior expectation of p is ",prior_a/(prior_a+prior_b)))
  success<-0



  curve(dbeta(x,prior_a,prior_b),xlim=c(0,1),ylim=c(0,y_lim),xlab='p',ylab='Posterior Density',lty=2)
  legend('topright',legend=c('Prior','Updated Posteriors','Final Posterior'),lty=c(2,1,1),col=c('black','black','red'))



  for(i in 1:N)
  {
    pdf(paste("posterior",i,".pdf",sep=""),height=4,width=6.5)

    if(runif(1,0,1)<=p) success<-success+1 #this is where we see if there is a "success"

    curve(dbeta(x,success+prior_a,(i-success)+prior_b),add=TRUE) #plot updated

    #print(paste(success,"successes and ",i-success," failures"))
    dev.off()
  }
  pdf(paste("posterior_final",".pdf",sep=""),height=4,width=6.5)
  curve(dbeta(x,success+prior_a,(i-success)+prior_b),add=TRUE,col='red',lwd=1.5) #plot final posterior
  dev.off()
}

然而，这给我带来了以下错误。

Error in plot.xy(xy.coords(x, y), type = type, ...) : 
  plot.new has not been called yet

我尝试在某些位置插入plot.new()，但我认为这会与图的加性特性冲突。

有人有什么想法，如何使这两种方法都正常工作？虽然这对我来说是一个玩具示例，但我需要绘制一些更有趣的动画，而理解如何动画化图表将是有用/必要的。

感谢任何帮助！

- MatthewK

Answer 1

就像MatthewK所说，您已经将调用pdf的位置放错了。不过，以下代码应该可以让您开始运行：

sim_bayes <- function(p=0.5, N=10, y_lim=15, prior_a=1, prior_b=1) {
    success <- 0
    for (i in 1:N) {
        pdf(paste("posterior",i,".pdf",sep=""), height=4, width=6.5)

        if (runif(1,0,1) <= p)
            success<-success + 1

        # Start a new plot.
        curve(dbeta(x,prior_a,prior_b), lty=2,
              xlim=c(0,1), ylim=c(0,y_lim), xlab='p', ylab='Posterior Density')
        # Update plot.
        curve(dbeta(x,success+prior_a, (i-success) + prior_b), add=TRUE)

        legend('topright',
               legend=c('Prior','Updated Posteriors','Final Posterior'),
               lty=c(2,1,1), col=c('black','black','red'))

        dev.off()
    }
}

# `x` had no visible binding in your implementation, so I took the following
# from the `dbeta` documentation example.
x <- seq(0, 1, length=21)
sim_bayes()

- fotNelton

Answer 2

您只在此处制作一个图。如果使用add=TRUE，则会添加到当前图而不是创建新图。因此，删除它应该可以解决问题：

sim_bayes<-function(p=0.5,N=10,y_lim=15,prior_a=1,prior_b=1)
{
   print(paste("The prior expectation of p is ",prior_a/(prior_a+prior_b)))
   success<-0
   curve(dbeta(x,prior_a,prior_b),xlim=c(0,1),ylim=c(0,y_lim),xlab='p',ylab='Posterior Density',lty=2)
   legend('topright',legend=c('Prior','Updated Posteriors','Final Posterior'),lty=c(2,1,1),col=c('black','black','red'))

  for(i in 1:N)
     {

        if(runif(1,0,1)<=p) success<-success+1 #this is where we see if there is a "success"

      curve(dbeta(x,success+prior_a,(i-success)+prior_b)) #plot updated
      }
curve(dbeta(x,success+prior_a,(i-success)+prior_b),col='red',lwd=1.5) #plot final posterior
}

测试：

sim_bayes(p=0.6,N=90,prior_a=1,prior_b=1)

提供多个图表。

- Sacha Epskamp