data.table Way - Learning Note Part 2
2015-09-25 21:01
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We resume the learning note.
Now recover it.
We create a random data.table and randomly change its value
To remove the prefix
To reorder the columns by alphabetic order.
setkey() sorts a data.table and marks it as sorted (with an attribute sorted). The sorted columns are the key. The key can be any columns in any order. The columns are sorted in ascending order always.
setkey reorders (or sorts) the rows of a data.table by the columns provided. In versions 1.9+, for integer columns… It is extremely fast, but is limited by the range of integer values being \<= 1e5.
Be aware that dtm[5] only returns the 5th row.
What if there is no such key?
It returns NA in all columns but the 2 keys.
You could also specify certain rows (
When i is a data.table, DT[i,j,by=.EACHI] evaluates j for the groups in ‘DT’ that each row in i joins to. That is, you can join (in i) and aggregate (in j) simultaneously. We call this grouping by each i.
There is no such record. How to return records without
There is no Mercedez with 7, 9 and 10 cylinders, but we allow it to roll for distance of 1. So 7 and 9 cylinders are both joined but 10 because it’s more than 1 from the prevailing observation.
Now we take a look on argument
This argument allows
This is a powerful file reading function.
library(data.table) dtm <- as.data.table(mtcars)
The set() family
Overview of set family *set()is a loopable low overhead version of
:=; * You can use
setnames()to set or change column names; *
setorder()and
setcolorder()reorder the rows, columns of a
data.table. *
setkey()set keys in a
data.table
set()
To assign the columnamto 1:
set(dtm, j = which(colnames(dtm)=='am'), value = 1) head(dtm)
## mpg cyl disp hp drat wt qsec vs am gear carb ## 1: 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 ## 2: 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 ## 3: 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 ## 4: 21.4 6 258 110 3.08 3.215 19.44 1 1 3 1 ## 5: 18.7 8 360 175 3.15 3.440 17.02 0 1 3 2 ## 6: 18.1 6 225 105 2.76 3.460 20.22 1 1 3 1
Now recover it.
set(dtm, j = which(colnames(dtm)=='am'), value = mtcars$am) head(dtm)
## mpg cyl disp hp drat wt qsec vs am gear carb ## 1: 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 ## 2: 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 ## 3: 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 ## 4: 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 ## 5: 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 ## 6: 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
We create a random data.table and randomly change its value
temp <- data.table(A = sample(1:9), B = sample(1:9), C = sample(1:9), D = sample(1:9), E = sample(1:9)) # for each row, randomly change 3 values to 10 for (i in 1:9) set(temp, i, sample(5, 3), 10) temp
## A B C D E ## 1: 5 10 6 10 10 ## 2: 10 5 2 10 10 ## 3: 10 10 1 4 10 ## 4: 10 3 4 10 10 ## 5: 10 1 10 10 9 ## 6: 7 6 10 10 10 ## 7: 6 10 10 6 10 ## 8: 8 9 10 10 10 ## 9: 9 7 10 10 10
setnames()
Still use thedata.tablewe just created. Add ‘Col_’ to the column names.
# setnames(x, old, new) setnames(temp, names(temp), paste0('Col_', names(temp))) head(temp, 3)
## Col_A Col_B Col_C Col_D Col_E ## 1: 5 10 6 10 10 ## 2: 10 5 2 10 10 ## 3: 10 10 1 4 10
To remove the prefix
Col_:
# when new is not provided, consider old as new setnames(temp, gsub('^Col_', '', names(temp))) head(temp, 3)
## A B C D E ## 1: 5 10 6 10 10 ## 2: 10 5 2 10 10 ## 3: 10 10 1 4 10
setorder() and setcolorder()
To reorder the rows:# wt in ascending order and mpg in descending order setorder(dtm, am, -mpg) # check the first 6 rows of each group dtm[, head(.SD), by = am]
## am mpg cyl disp hp drat wt qsec vs gear carb ## 1: 0 24.4 4 146.7 62 3.69 3.190 20.00 1 4 2 ## 2: 0 22.8 4 140.8 95 3.92 3.150 22.90 1 4 2 ## 3: 0 21.5 4 120.1 97 3.70 2.465 20.01 1 3 1 ## 4: 0 21.4 6 258.0 110 3.08 3.215 19.44 1 3 1 ## 5: 0 19.2 6 167.6 123 3.92 3.440 18.30 1 4 4 ## 6: 0 19.2 8 400.0 175 3.08 3.845 17.05 0 3 2 ## 7: 1 33.9 4 71.1 65 4.22 1.835 19.90 1 4 1 ## 8: 1 32.4 4 78.7 66 4.08 2.200 19.47 1 4 1 ## 9: 1 30.4 4 75.7 52 4.93 1.615 18.52 1 4 2 ## 10: 1 30.4 4 95.1 113 3.77 1.513 16.90 1 5 2 ## 11: 1 27.3 4 79.0 66 4.08 1.935 18.90 1 4 1 ## 12: 1 26.0 4 120.3 91 4.43 2.140 16.70 0 5 2
To reorder the columns by alphabetic order.
setcolorder(dtm, sort(names(dtm))) head(dtm)
## am carb cyl disp drat gear hp mpg qsec vs wt ## 1: 0 2 4 146.7 3.69 4 62 24.4 20.00 1 3.190 ## 2: 0 2 4 140.8 3.92 4 95 22.8 22.90 1 3.150 ## 3: 0 1 4 120.1 3.70 3 97 21.5 20.01 1 2.465 ## 4: 0 1 6 258.0 3.08 3 110 21.4 19.44 1 3.215 ## 5: 0 4 6 167.6 3.92 4 123 19.2 18.30 1 3.440 ## 6: 0 2 8 400.0 3.08 3 175 19.2 17.05 0 3.845
setkey()
set character column as key
To make thedata.tablea database table. According to the document:
setkey() sorts a data.table and marks it as sorted (with an attribute sorted). The sorted columns are the key. The key can be any columns in any order. The columns are sorted in ascending order always.
setkey reorders (or sorts) the rows of a data.table by the columns provided. In versions 1.9+, for integer columns… It is extremely fast, but is limited by the range of integer values being \<= 1e5.
dti <- as.data.table(iris) # Set Species as key setkey(dti, Species) # Query by Species == 'setosa' head(dti['setosa'])
## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## 1: 5.1 3.5 1.4 0.2 setosa ## 2: 4.9 3.0 1.4 0.2 setosa ## 3: 4.7 3.2 1.3 0.2 setosa ## 4: 4.6 3.1 1.5 0.2 setosa ## 5: 5.0 3.6 1.4 0.2 setosa ## 6: 5.4 3.9 1.7 0.4 setosa
# Select 'setosa' and 'versicolor' in the same time dti[c('setosa', 'versicolor')][, head(.SD, 3), by = Species]
## Species Sepal.Length Sepal.Width Petal.Length Petal.Width ## 1: setosa 5.1 3.5 1.4 0.2 ## 2: setosa 4.9 3.0 1.4 0.2 ## 3: setosa 4.7 3.2 1.3 0.2 ## 4: versicolor 7.0 3.2 4.7 1.4 ## 5: versicolor 6.4 3.2 4.5 1.5 ## 6: versicolor 6.9 3.1 4.9 1.5
set numeric column as key
dtm <- data.table(model = rownames(mtcars), mtcars) # Set gear as key setkey(dtm, gear) # Select records with gear == 5 dtm[J(5)]
## model mpg cyl disp hp drat wt qsec vs am gear carb ## 1: Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.7 0 1 5 2 ## 2: Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.9 1 1 5 2 ## 3: Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.5 0 1 5 4 ## 4: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.5 0 1 5 6 ## 5: Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.6 0 1 5 8
# or dtm[.(5)]
## model mpg cyl disp hp drat wt qsec vs am gear carb ## 1: Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.7 0 1 5 2 ## 2: Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.9 1 1 5 2 ## 3: Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.5 0 1 5 4 ## 4: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.5 0 1 5 6 ## 5: Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.6 0 1 5 8
Be aware that dtm[5] only returns the 5th row.
set multiple columns as keys
# add a column: brand dtm[, brand:=sapply(.SD[,model], function(x) strsplit(x, ' ')[[1]][1])] setkey(dtm, brand, cyl) dtm[.('Merc', 8)]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: Merc 450SE 16.4 8 275.8 180 3.07 4.07 17.4 0 0 3 3 Merc ## 2: Merc 450SL 17.3 8 275.8 180 3.07 3.73 17.6 0 0 3 3 Merc ## 3: Merc 450SLC 15.2 8 275.8 180 3.07 3.78 18.0 0 0 3 3 Merc
What if there is no such key?
dtm[.('Renault', 8)]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: NA NA 8 NA NA NA NA NA NA NA NA NA Renault
It returns NA in all columns but the 2 keys.
select groups
By default, subsettingdata.tablereturns all the records, it is related to argument
multof which the default value is
all. You can also specify ‘first’ or ‘last’.
# Introduce argument mult dti[c('setosa', 'versicolor'), mult = 'first']
## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## 1: 5.1 3.5 1.4 0.2 setosa ## 2: 7.0 3.2 4.7 1.4 versicolor
dti[c('setosa', 'versicolor'), mult = 'last']
## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## 1: 5.0 3.3 1.4 0.2 setosa ## 2: 5.7 2.8 4.1 1.3 versicolor
You could also specify certain rows (
i). To display each i, you need to specify
by = .EACHI.
When i is a data.table, DT[i,j,by=.EACHI] evaluates j for the groups in ‘DT’ that each row in i joins to. That is, you can join (in i) and aggregate (in j) simultaneously. We call this grouping by each i.
dti[c('setosa', 'versicolor'), .SD[c(1, .N)], by = .EACHI]
## Species Sepal.Length Sepal.Width Petal.Length Petal.Width ## 1: setosa 5.1 3.5 1.4 0.2 ## 2: setosa 5.0 3.3 1.4 0.2 ## 3: versicolor 7.0 3.2 4.7 1.4 ## 4: versicolor 5.7 2.8 4.1 1.3
dti[c('setosa', 'versicolor'), {print(.SD[3:5]); .SD[c(1, .N)]}, by = .EACHI]
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1: 4.7 3.2 1.3 0.2
## 2: 4.6 3.1 1.5 0.2
## 3: 5.0 3.6 1.4 0.2
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1: 6.9 3.1 4.9 1.5
## 2: 5.5 2.3 4.0 1.3
## 3: 6.5 2.8 4.6 1.5
## Species Sepal.Length Sepal.Width Petal.Length Petal.Width ## 1: setosa 5.1 3.5 1.4 0.2 ## 2: setosa 5.0 3.3 1.4 0.2 ## 3: versicolor 7.0 3.2 4.7 1.4 ## 4: versicolor 5.7 2.8 4.1 1.3
Rolling joins
Let’s check the records of brand ‘Merc’ and 7 cylinders.dtm[.('Merc', 5)]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: NA NA 5 NA NA NA NA NA NA NA NA NA Merc
There is no such record. How to return records without
NA? Use argument
roll.
roll = TRUE: i’s row matches to all but the last x join column, and its value in the last i join column falls in a gap (including after the last observation in x for that group), then the prevailing value in x is rolled forward.
dtm[.(c('Merc', 'Toyota'), 5), roll = TRUE]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: Merc 230 22.8 5 140.8 95 3.92 3.150 22.9 1 0 4 2 Merc ## 2: Toyota Corolla 33.9 5 71.1 65 4.22 1.835 19.9 1 1 4 1 Toyota
roll = 'nearest': the nearest value is joined to.
# compare the commands below dtm[.(c('Merc', 'Toyota'), 3), roll = TRUE]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: NA NA 3 NA NA NA NA NA NA NA NA NA Merc ## 2: NA NA 3 NA NA NA NA NA NA NA NA NA Toyota
dtm[.(c('Merc', 'Toyota'), 3), roll = 'nearest']
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: Merc 240D 24.4 3 146.7 62 3.69 3.190 20.00 1 0 4 2 Merc ## 2: Toyota Corona 21.5 3 120.1 97 3.70 2.465 20.01 1 0 3 1 Toyota
rollcan also be a finite number.
# compare the commands below dtm[.('Merc', 6:10)]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: Merc 280 19.2 6 167.6 123 3.92 3.44 18.3 1 0 4 4 Merc ## 2: Merc 280C 17.8 6 167.6 123 3.92 3.44 18.9 1 0 4 4 Merc ## 3: NA NA 7 NA NA NA NA NA NA NA NA NA Merc ## 4: Merc 450SE 16.4 8 275.8 180 3.07 4.07 17.4 0 0 3 3 Merc ## 5: Merc 450SL 17.3 8 275.8 180 3.07 3.73 17.6 0 0 3 3 Merc ## 6: Merc 450SLC 15.2 8 275.8 180 3.07 3.78 18.0 0 0 3 3 Merc ## 7: NA NA 9 NA NA NA NA NA NA NA NA NA Merc ## 8: NA NA 10 NA NA NA NA NA NA NA NA NA Merc
dtm[.('Merc', 6:10), roll = 1]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: Merc 280 19.2 6 167.6 123 3.92 3.44 18.3 1 0 4 4 Merc ## 2: Merc 280C 17.8 6 167.6 123 3.92 3.44 18.9 1 0 4 4 Merc ## 3: Merc 280C 17.8 7 167.6 123 3.92 3.44 18.9 1 0 4 4 Merc ## 4: Merc 450SE 16.4 8 275.8 180 3.07 4.07 17.4 0 0 3 3 Merc ## 5: Merc 450SL 17.3 8 275.8 180 3.07 3.73 17.6 0 0 3 3 Merc ## 6: Merc 450SLC 15.2 8 275.8 180 3.07 3.78 18.0 0 0 3 3 Merc ## 7: Merc 450SLC 15.2 9 275.8 180 3.07 3.78 18.0 0 0 3 3 Merc ## 8: NA NA 10 NA NA NA NA NA NA NA NA NA Merc
There is no Mercedez with 7, 9 and 10 cylinders, but we allow it to roll for distance of 1. So 7 and 9 cylinders are both joined but 10 because it’s more than 1 from the prevailing observation.
Now we take a look on argument
rollends. This argument is actually a vector of two logical values (a single logical is recycled).
# compare the commands below setkey(dtm, am, carb) dtm[.(1, (-1):8)]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: NA NA NA NA NA NA NA NA NA 1 NA -1 NA ## 2: NA NA NA NA NA NA NA NA NA 1 NA 0 NA ## 3: Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 Datsun ## 4: Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 Fiat ## 5: Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 Fiat ## 6: Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 Toyota ## 7: Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 Honda ## 8: Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 Lotus ## 9: Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 Porsche ## 10: Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 Volvo ## 11: NA NA NA NA NA NA NA NA NA 1 NA 3 NA ## 12: Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 Ford ## 13: Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 Mazda ## 14: Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 Mazda ## 15: NA NA NA NA NA NA NA NA NA 1 NA 5 NA ## 16: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 Ferrari ## 17: NA NA NA NA NA NA NA NA NA 1 NA 7 NA ## 18: Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 Maserati
dtm[.(1, (-1):8), roll = TRUE]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: NA NA NA NA NA NA NA NA NA 1 NA -1 NA ## 2: NA NA NA NA NA NA NA NA NA 1 NA 0 NA ## 3: Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 Datsun ## 4: Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 Fiat ## 5: Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 Fiat ## 6: Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 Toyota ## 7: Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 Honda ## 8: Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 Lotus ## 9: Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 Porsche ## 10: Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 Volvo ## 11: Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 3 Volvo ## 12: Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 Ford ## 13: Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 Mazda ## 14: Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 Mazda ## 15: Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 5 Mazda ## 16: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 Ferrari ## 17: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 7 Ferrari ## 18: Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 Maserati
dtm[.(1, (-1):8), roll = TRUE, rollends = TRUE]
## model mpg cyl disp hp drat wt qsec vs am gear carb brand ## 1: Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 -1 Datsun ## 2: Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 0 Datsun ## 3: Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 Datsun ## 4: Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 Fiat ## 5: Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 Fiat ## 6: Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 Toyota ## 7: Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 Honda ## 8: Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 Lotus ## 9: Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 Porsche ## 10: Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 Volvo ## 11: Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 3 Volvo ## 12: Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 Ford ## 13: Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 Mazda ## 14: Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 Mazda ## 15: Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 5 Mazda ## 16: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 Ferrari ## 17: Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 7 Ferrari ## 18: Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 Maserati
This argument allows
NArecords to look forward to the nearest‘matching’ records
Other data.table functions
fread() fast read
Borrow the example fromdata.tabledocument:
n=1e6 DT = data.table( a=sample(1:1000,n,replace=TRUE), b=sample(1:1000,n,replace=TRUE), c=rnorm(n), d=sample(c("foo","bar","baz","qux","quux"),n,replace=TRUE), e=rnorm(n), f=sample(1:1000,n,replace=TRUE) ) DT[2,b:=NA_integer_] DT[4,c:=NA_real_] DT[3,d:=NA_character_] DT[5,d:=""] DT[2,e:=+Inf] DT[3,e:=-Inf] write.table(DT,"test.csv",sep=",",row.names=FALSE,quote=FALSE) cat("File size (MB):", round(file.info("test.csv")$size/1024^2),"\n")
## File size (MB): 50
system.time(DF1 <-read.csv("test.csv",stringsAsFactors=FALSE))
## user system elapsed ## 21.556 0.196 21.760
# first time in fresh R session system.time(DF1 <- read.csv("test.csv",stringsAsFactors=FALSE))
## user system elapsed ## 11.728 0.144 11.873
# immediate repeat is faster, varies system.time(DF2 <- read.table("test.csv",header=TRUE,sep=",",quote="", stringsAsFactors=FALSE,comment.char="",nrows=n, colClasses=c("integer","integer","numeric", "character","numeric","integer")))
## user system elapsed ## 7.324 0.040 7.369
require(data.table) system.time(DT <- fread("test.csv"))
## user system elapsed ## 1.988 0.008 1.993
This is a powerful file reading function.
others
Enter the commandlibrary(help = data.table)and you could see many other small functions, like
frank,
foverlaps, etc. All of them are aiming at speeding up the available functions with similar effect in
baseor other packages. You could take a look on them when necessary.
Reference
Data Analysis in R, the data.table Way.相关文章推荐
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