data.table 像 dplyr 一样按行求和、均值、最小值、最大值?

data.table row-wise sum, mean, min, max like dplyr?

还有其他关于数据表上的逐行运算符的帖子。他们是 too simple or solves a specific scenario

我的问题比较笼统。有一个使用 dplyr 的解决方案。我试过但未能找到使用 data.table 语法的等效解决方案。你能推荐一个优雅的 data.table 解决方案来重现与 dplyr 版本相同的结果吗?

编辑 1:真实数据集上建议解决方案的基准总结(10MB,73000 行,在 24 个数字列上进行的统计)。基准测试结果是主观的。但是,经过的时间始终可以重现。

| Solution By | Speed compared to dplyr     |
|-------------|-----------------------------|
| Metrics v1  |  4.3 times SLOWER (use .SD) |
| Metrics v2  |  5.6 times FASTER           |
| ExperimenteR| 15   times FASTER           |
| Arun v1     |  3   times FASTER (Map func)|
| Arun v2     |  3   times FASTER (foo func)|
| Ista        |  4.5 times FASTER           |

编辑 2:我在一天后添加了 NACount 列。这就是为什么在各种贡献者建议的解决方案中找不到此列的原因。

数据设置

library(data.table)
dt <- data.table(ProductName = c("Lettuce", "Beetroot", "Spinach", "Kale", "Carrot"),
    Country = c("CA", "FR", "FR", "CA", "CA"),
    Q1 = c(NA, 61, 40, 54, NA), Q2 = c(22,  8, NA,  5, NA),
    Q3 = c(51, NA, NA, 16, NA), Q4 = c(79, 10, 49, NA, NA))

#    ProductName Country Q1 Q2 Q3 Q4
# 1:     Lettuce      CA NA 22 51 79
# 2:    Beetroot      FR 61  8 NA 10
# 3:     Spinach      FR 40 NA NA 49
# 4:        Kale      CA 54  5 16 NA
# 5:      Carrot      CA NA NA NA NA

解决方案使用 dplyr + rowwise()

library(dplyr) ; library(magrittr)
dt %>% rowwise() %>% 
    transmute(ProductName, Country, Q1, Q2, Q3, Q4,
     AVG = mean(c(Q1, Q2, Q3, Q4), na.rm=TRUE),
     MIN = min (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
     MAX = max (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
     SUM = sum (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
     NAcnt= sum(is.na(c(Q1, Q2, Q3, Q4))))

#   ProductName Country Q1 Q2 Q3 Q4      AVG MIN  MAX SUM NAcnt
# 1     Lettuce      CA NA 22 51 79 50.66667  22   79 152     1
# 2    Beetroot      FR 61  8 NA 10 26.33333   8   61  79     1
# 3     Spinach      FR 40 NA NA 49 44.50000  40   49  89     2
# 4        Kale      CA 54  5 16 NA 25.00000   5   54  75     1
# 5      Carrot      CA NA NA NA NA      NaN Inf -Inf   0     4

错误 data.table(计算整列而不是每行)

dt[, .(ProductName, Country, Q1, Q2, Q3, Q4,
    AVG = mean(c(Q1, Q2, Q3, Q4), na.rm=TRUE),
    MIN = min (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
    MAX = max (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
    SUM = sum (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
    NAcnt= sum(is.na(c(Q1, Q2, Q3, Q4))))]

#    ProductName Country Q1 Q2 Q3 Q4      AVG MIN MAX SUM NAcnt
# 1:     Lettuce      CA NA 22 51 79 35.90909   5  79 395     9
# 2:    Beetroot      FR 61  8 NA 10 35.90909   5  79 395     9
# 3:     Spinach      FR 40 NA NA 49 35.90909   5  79 395     9
# 4:        Kale      CA 54  5 16 NA 35.90909   5  79 395     9
# 5:      Carrot      CA NA NA NA NA 35.90909   5  79 395     9

几乎是解决方案,但更复杂且缺少 Q1、Q2、Q3、Q4 输出列

dtmelt <- reshape2::melt(dt, id=c("ProductName", "Country"),
            variable.name="Quarter", value.name="Qty")

dtmelt[, .(AVG = mean(Qty, na.rm=TRUE),
    MIN = min (Qty, na.rm=TRUE),
    MAX = max (Qty, na.rm=TRUE),
    SUM = sum (Qty, na.rm=TRUE),
    NAcnt= sum(is.na(Qty))), by = list(ProductName, Country)]

#    ProductName Country      AVG MIN  MAX SUM NAcnt
# 1:     Lettuce      CA 50.66667  22   79 152     1
# 2:    Beetroot      FR 26.33333   8   61  79     1
# 3:     Spinach      FR 44.50000  40   49  89     2
# 4:        Kale      CA 25.00000   5   54  75     1
# 5:      Carrot      CA      NaN Inf -Inf   0     4

您可以使用 matrixStats 包中的高效逐行函数。

library(matrixStats)
dt[, `:=`(MIN = rowMins(as.matrix(.SD), na.rm=T),
          MAX = rowMaxs(as.matrix(.SD), na.rm=T),
          AVG = rowMeans(.SD, na.rm=T),
          SUM = rowSums(.SD, na.rm=T)), .SDcols=c(Q1, Q2,Q3,Q4)]

dt
#    ProductName Country Q1 Q2 Q3 Q4 MIN  MAX      AVG SUM
# 1:     Lettuce      CA NA 22 51 79  22   79 50.66667 152
# 2:    Beetroot      FR 61  8 NA 10   8   61 26.33333  79
# 3:     Spinach      FR 40 NA 79 49  40   79 56.00000 168
# 4:        Kale      CA 54  5 16 NA   5   54 25.00000  75
# 5:      Carrot      CA NA NA NA NA Inf -Inf      NaN   0

对于具有 500000 行的数据集(使用来自 CRAN 的 data.table

dt <- rbindlist(lapply(1:100000, function(i)dt))
system.time(dt[, `:=`(MIN = rowMins(as.matrix(.SD), na.rm=T),
                      MAX = rowMaxs(as.matrix(.SD), na.rm=T),
                      AVG = rowMeans(.SD, na.rm=T),
                      SUM = rowSums(.SD, na.rm=T)), .SDcols=c("Q1", "Q2","Q3","Q4")])
#  user  system elapsed 
# 0.089   0.004   0.093

rowwise(或 by=1:nrow(dt))对于 for loop 是 "euphemism",例如

library(dplyr) ; library(magrittr)
system.time(dt %>% rowwise() %>% 
  transmute(ProductName, Country, Q1, Q2, Q3, Q4,
            MIN = min (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
            MAX = max (c(Q1, Q2, Q3, Q4), na.rm=TRUE),
            AVG = mean(c(Q1, Q2, Q3, Q4), na.rm=TRUE),
            SUM = sum (c(Q1, Q2, Q3, Q4), na.rm=TRUE)))
#   user  system elapsed 
# 80.832   0.111  80.974 

system.time(dt[, `:=`(AVG= mean(as.numeric(.SD),na.rm=TRUE),MIN = min(.SD, na.rm=TRUE),MAX = max(.SD, na.rm=TRUE),SUM = sum(.SD, na.rm=TRUE)),.SDcols=c("Q1", "Q2","Q3","Q4"),by=1:nrow(dt)] )
#    user  system elapsed 
# 141.492   0.196 141.757

With by=1:nrow(dt), 在data.table

中执行按行操作
 library(data.table)
dt[, `:=`(AVG= mean(as.numeric(.SD),na.rm=TRUE),MIN = min(.SD, na.rm=TRUE),MAX = max(.SD, na.rm=TRUE),SUM = sum(.SD, na.rm=TRUE)),.SDcols=c(Q1, Q2,Q3,Q4),by=1:nrow(dt)] 
   ProductName Country Q1 Q2 Q3 Q4      AVG MIN  MAX SUM
1:     Lettuce      CA NA 22 51 79 50.66667  22   79 152
2:    Beetroot      FR 61  8 NA 10 26.33333   8   61  79
3:     Spinach      FR 40 NA 79 49 56.00000  40   79 168
4:        Kale      CA 54  5 16 NA 25.00000   5   54  75
5:      Carrot      CA NA NA NA NA      NaN Inf -Inf   0

Warning messages:
1: In min(c(NA_real_, NA_real_, NA_real_, NA_real_), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
2: In max(c(NA_real_, NA_real_, NA_real_, NA_real_), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf

您收到警告消息,因为在第 5 行中,您正在计算最大值、总和、最小值和最大值。例如,见下文:

min(c(NA,NA,NA,NA),na.rm=TRUE)
[1] Inf
Warning message:
In min(c(NA, NA, NA, NA), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf

只是另一种方式(虽然效率不高,因为每次都会调用 na.omit(),而且还有许多内存分配):

require(data.table)
new_cols = c("MIN", "MAX", "SUM", "AVG")
dt[, (new_cols) := Map(function(x, f) f(x), 
                       list(na.omit(c(Q1,Q2,Q3,Q4))), 
                       list(min, max, sum, mean)),
   by = 1:nrow(dt)]

#    ProductName Country Q1 Q2 Q3 Q4 MIN  MAX SUM      AVG
# 1:     Lettuce      CA NA 22 51 79  22   79 152 50.66667
# 2:    Beetroot      FR 61  8 NA 10   8   61  79 26.33333
# 3:     Spinach      FR 40 NA 79 49  40   79 168 56.00000
# 4:        Kale      CA 54  5 16 NA   5   54  75 25.00000
# 5:      Carrot      CA NA NA NA NA Inf -Inf   0      NaN

但正如我提到的,一旦 colwise()rowwise() 实施,这将变得更加简单。这种情况下的语法可能类似于:

dt[, rowwise(.SD, list(MIN=min, MAX=max, SUM=sum, AVG=mean), na.rm=TRUE), by = 1:nrow(dt)]
# `by = ` is really not necessary in this case.

对于这种情况甚至更直接:

rowwise(dt, list(...), na.rm=TRUE)

编辑:

另一个变体:

myNACount <- function(x, ...) length(attributes(x)$na.action)
foo <- function(x, ...) {
    funs = c(min, max, mean, sum, myNACount)
    lapply(funs, function(f) f(x, ...))
}

dt[, (new_cols) := foo(na.omit(c(Q1, Q2, Q3, Q4)), na.rm=TRUE), by=1:nrow(dt)]
#    ProductName Country Q1 Q2 Q3 Q4 MIN  MAX      SUM AVG NAs
# 1:     Lettuce      CA NA 22 51 79  22   79 50.66667 152   1
# 2:    Beetroot      FR 61  8 NA 10   8   61 26.33333  79   1
# 3:     Spinach      FR 40 NA NA 49  40   49 44.50000  89   2
# 4:        Kale      CA 54  5 16 NA   5   54 25.00000  75   1
# 5:      Carrot      CA NA NA NA NA Inf -Inf      NaN   0   4

apply函数可用于执行逐行计算。单独定义函数使事情更清晰:

dstats <- function(x){
    c(mean(x,na.rm=TRUE),
      min(x, na.rm=TRUE),
      max(x, na.rm=TRUE),
      sum(x, na.rm=TRUE))
}

该函数现在可以应用于 data.table 的行。

(dt[,
   c("AVG", "MIN", "MAX", "SUM") := data.frame(t(apply(.SD, 1, dstats))),
   .SDcols=c("Q1", "Q2","Q3","Q4"),
])

请注意,使用 [.data.table 执行此操作的唯一优势是它允许使用 := 通过引用快速添加。

这比 matrixStats 解决方案更慢但更灵活,并且比@ExperimenteR 的 dplyr 解决方案更快,计时为 36 秒(我对其他方法的计时与那些相似在@ExperimenteR 的回答中)。

希望其他人在遇到同样的问题时能有所帮助。

第一种方法:结合碱基 R

dt[,`:=`(MIN = apply(dt[, Q1:Q4], 1, FUN = min, na.rm=TRUE),
       MAX = apply(dt[, Q1:Q4], 1, FUN = max, na.rm = TRUE),
       AVG = rowMeans(dt[, Q1:Q4], na.rm = TRUE),
       SUM = rowSums(dt[, Q1:Q4], na.rm = TRUE))][]
# ProductName Country Q1 Q2 Q3 Q4 MIN  MAX      AVG SUM
# 1:     Lettuce      CA NA 22 51 79  22   79 50.66667 152
# 2:    Beetroot      FR 61  8 NA 10   8   61 26.33333  79
# 3:     Spinach      FR 40 NA NA 49  40   49 44.50000  89
# 4:        Kale      CA 54  5 16 NA   5   54 25.00000  75
# 5:      Carrot      CA NA NA NA NA Inf -Inf      NaN   0

第二种方法:基于@ExperimenteR的想法,使用matrixStats包

dt1 <- dt[,`:=`(MIN = rowMins(as.matrix(dt[, Q1:Q4]), na.rm=TRUE),
                MAX = rowMaxs(as.matrix(dt[, Q1:Q4]), na.rm = TRUE),
                AVG = rowMeans(dt[, Q1:Q4], na.rm = TRUE),
                SUM = rowSums(dt[, Q1:Q4], na.rm = TRUE))][]
# ProductName Country Q1 Q2 Q3 Q4 MIN  MAX      AVG SUM
# 1:     Lettuce      CA NA 22 51 79  22   79 50.66667 152
# 2:    Beetroot      FR 61  8 NA 10   8   61 26.33333  79
# 3:     Spinach      FR 40 NA NA 49  40   49 44.50000  89
# 4:        Kale      CA 54  5 16 NA   5   54 25.00000  75
# 5:      Carrot      CA NA NA NA NA Inf -Inf      NaN   0