Question

我需要使用一个函数，我在R中实现了。这是我的代码：

IS_IV <- function(name,SR){  ## SR is in Hz
data <- get(name)
SR <- SR
n <- nrow(data)
p <- 60*60*24*SR  ## no. of data points per day
l <- 60*60*SR   ## no. of data points per hour
mean_all <- mean(data[1:n,])
## -----------------------------
## IS numerator calculation
for (h in 1:p){
x <- ((mean(data[h:(l+h-1),]))-mean_all)^2
if (h == 1){
  result_ISnum <- x
} else {
  result_ISnum <- rbind (result_ISnum, x)
}
}
ISnum <- sum(result_ISnum)
ISnumerator <- n*ISnum
## -----------------------------
## IS denominator calculation
  for (i in 1:n){
    y <- ((data[i,]-mean_all)^2)
    if (i == 1){
    result_ISdenom <- y
  } else {
    result_ISdenom <- rbind (result_ISdenom, y)
  }
}
ISdenom <- sum(result_ISdenom)  
## -----------------------------
ISdenominator <- p*ISdenom
## -----------------------------
## IS calculation
IS <- ISnumerator/ISdenominator
## -----------------------------

## -----------------------------
## IV numerator calculation
  for (k in 2:n){
    x <- ((data[i,]-data[(i-1),])^2)
    if (k == 1){
      result_IVnum <- x
    } else {
      result_IVnum <- rbind (result_IVnum, x)
    }
  }
  IVnum <- sum(result_IVnum)
  IVnumerator <- n*IVnum
## -----------------------------
## IV denominator calculation
IVdenominator <- (n-1)*ISdenom ## uses ISdenom as only the multiplier is different
## -----------------------------
## IV calculation
IV <- IVnumerator/IVdenominator

result <- c(IS, IV)
colnames(result) <- c("Interday Stability (IS)", "Intraday Variability (IV)")
return(result)
}

显然，这个过程如此缓慢的原因在于ISdenominator的计算，因为它必须循环遍历每个数据点（可能高达800,000甚至更多）。

现在的问题是，我是否只需要忍受这一点，寻找最快的电脑，或者你是否有机会，加快整个过程。

非常感谢！

Answer 1

你的功能有一些问题我纠正了它们。

IS_IV <- function(name,SR){  ## SR is in Hz
  data <- name
  SR <- SR
  n <- nrow(data)
  p <- 60*60*24*SR  ## no. of data points per day
  l <- 60*60*SR   ## no. of data points per hour
  mean_all <- mean(data[1:n,])
  ## -----------------------------
  ## IS numerator calculation
  for (h in 1:p){
    x <- ((mean(data[h:(l+h-1),]))-mean_all)^2
    if (h == 1){
      result_ISnum <- x
    } else {
      result_ISnum <- rbind (result_ISnum, x)
    }
  }

  ISnum <- sum(result_ISnum)
  ISnumerator <- n*ISnum
  ## -----------------------------
  ## IS denominator calculation
  for (i in 1:n){
    y <- ((data[i,]-mean_all)^2)
    if (i == 1){
      result_ISdenom <- y
    } else {
      result_ISdenom <- rbind (result_ISdenom, y)
    }
  }

  ISdenom <- sum(result_ISdenom)  
  ## -----------------------------
  ISdenominator <- p*ISdenom
  ## -----------------------------
  ## IS calculation
  IS <- ISnumerator/ISdenominator
  ## -----------------------------

  ## -----------------------------
  ## IV numerator calculation
  for (k in 2:n){
    x <- ((data[k,]-data[(k-1),])^2)
    if (k == 2){
      result_IVnum <- x
    } else {
      result_IVnum <- rbind (result_IVnum, x)
    }
  }

  IVnum <- sum(result_IVnum)
  IVnumerator <- n*IVnum
  ## -----------------------------
  ## IV denominator calculation
  IVdenominator <- (n-1)*ISdenom ## uses ISdenom as only the multiplier is different
  ## -----------------------------
  ## IV calculation
  IV <- IVnumerator/IVdenominator

  result <- c(IS, IV)
  names(result) <- c("Interday Stability (IS)", "Intraday Variability (IV)")
  return(result)
}

我纠正了以上功能。

IS_IV_vck<-function(name,SR){
  data <- name
  SR <- SR
  n <- nrow(data)
  p <- 60*60*24*SR  ## no. of data points per day
  l <- 60*60*SR   ## no. of data points per hour
  mean_all <- mean(data[1:n,])
  ## -----------------------------
  ## IS numerator calculation
  result_ISnum<- matrix(sapply(1:p,FUN = function(x) ((mean(data[x:(l+x-1),]))-mean_all)^2),ncol = 1)
  ISnum <- sum(result_ISnum)
  ISnumerator <- n*ISnum
  ## -----------------------------
  ## IS denominator calculation
  result_ISdenom <- (data-mean_all)^2
  ISdenom <- sum(result_ISdenom)  
  ## -----------------------------
  ISdenominator <- p*ISdenom
  ## -----------------------------
  ## IS calculation
  IS <- ISnumerator/ISdenominator
  ## -----------------------------

  ## -----------------------------
  ## IV numerator calculation
  result_IVnum <- diff(data)^2
  IVnum <- sum(result_IVnum)
  IVnumerator <- n*IVnum
  ## -----------------------------
  ## IV denominator calculation
  IVdenominator <- (n-1)*ISdenom ## uses ISdenom as only the multiplier is different
  ## -----------------------------
  ## IV calculation
  IV <- IVnumerator/IVdenominator

  result <- c(IS, IV)
  names(result) <- c("Interday Stability (IS)", "Intraday Variability (IV)")
  return(result)
}

set.seed(123)
data<-matrix(rnorm(50000,5,2),ncol = 2)

> microbenchmark(IS_IV(data,.1),IS_IV_vck(data,.1),times = 3)
Unit: milliseconds
                 expr        min         lq       mean     median         uq          max neval
 IS_IV(data, 0.1)     20182.1790 20191.8787 20246.1370 20201.5784 20278.1160 20354.6535     3
 IS_IV_vck(data, 0.1)   167.3961   169.2664   170.8591   171.1366   172.5905   174.0444     3

res1<-IS_IV(data,.1)
res2<-IS_IV_vck(data,.1)
> identical(res1,res2)
[1] TRUE

R：加速循环功能的想法？

1 个答案: