Let's say I want to create a column in a data.table, in which the value in each row is equal to the standard deviation of the values in three other cells in the same row. E.g., if I make
DT <- data.table(a = 1:4, b = c(5, 7, 9, 11), c = c(13, 16, 19, 22), d = c(25, 29, 33, 37))
DT
a b c d
1: 1 5 13 25
2: 2 7 16 29
3: 3 9 19 33
4: 4 11 22 37
and I'd like to add a column that contains the standard deviation of a, b, and d for each row, like this:
a b c d abdSD
1: 1 5 13 23 12.86
2: 2 7 16 27 14.36
3: 3 9 19 31 15.87
4: 4 11 22 35 17.39
I could of course write a for-loop or use an apply function to calculate this. Unfortunately, what I actually want to do needs to be applied to millions of rows, isn't as simple a function as calculating a standard deviation, and needs to finish within a fraction of a second, so I really need a vectorized solution. I want to write something like
DT[, abdSD := sd(c(a, b, d))]
but unfortunately that doesn't give the right answer. Is there any data.table syntax that can create a vector out of different values within the same row, and make that vector accessible to a function populating a new cell within that row? Any help would be greatly appreciated. #Arun
Depending on the size of your data, you might want to convert the data into a long format, then calculate the result as follows:
complexFunc <- function(x) sd(x)
cols <- c("a", "b", "d")
rowres <- melt(DT[, rn:=.I], id.vars="rn", variable.factor=FALSE)[,
list(abdRes=complexFunc(value[variable %chin% cols])), by=.(rn)]
DT[rowres, on=.(rn)]
or if your complex function has 3 arguments, you can do something like
DT[, abdSD := mapply(complexFunc, a, b, d)]
As #Frank mentioned, I could avoid adding a column by doing by=1:nrow(DT)
DT[, abdSD:=sd(c(a,b,d)),by=1:nrow(DT)]
output:
a b c d abdSD
1: 1 5 13 25 12.85820
2: 2 7 16 29 14.36431
3: 3 9 19 33 15.87451
4: 4 11 22 37 17.38774
if you add a row_name column, it would be ultra easy
DT$row_id<-row.names(DT)
Simply by=row_id, would get you the result you want
DT[, abdSD:=sd(c(a,b,d)),by=row_id]
Result would have:
a b c d row_id abdSD
1: 1 5 13 25 1 12.85820
2: 2 7 16 29 2 14.36431
3: 3 9 19 33 3 15.87451
4: 4 11 22 37 4 17.38774
If you want row_id removed, simply adding [,row_id:=NULL]
DT[, abdSD:=sd(c(a,b,d)),by=row_id][,row_id:=NULL]
This line would get everything you want
a b c d abdSD
1: 1 5 13 25 12.85820
2: 2 7 16 29 14.36431
3: 3 9 19 33 15.87451
4: 4 11 22 37 17.38774
You just gotta do it by row.
data.frame does it by row on default, data.table does it by column on default I think. It's a bit tricky
Hope this helps
I think you should try matrixStats package
library(matrixStats)
#sample data
dt <- data.table(a = 1:4, b = c(5, 7, 9, 11), c = c(13, 16, 19, 22), d = c(25, 29, 33, 37))
dt[, `:=`(abdSD = rowSds(as.matrix(.SD), na.rm=T)), .SDcols=c('a','b','d')]
dt
Output is:
a b c d abdSD
1: 1 5 13 25 12.85820
2: 2 7 16 29 14.36431
3: 3 9 19 33 15.87451
4: 4 11 22 37 17.38774
Not an answer, but just trying to show the difference between using apply and the solution provided by Prem above :
I have blown up the sample data to 40,000 rows to show solid time differences :
library(matrixStats)
#sample data
dt <- data.table(a = 1:40000, b = rep(c(5, 7, 9, 11),10000), c = rep(c(13, 16, 19, 22),10000), d = rep(c(25, 29, 33, 37),10000))
df <- data.frame(a = 1:40000, b = rep(c(5, 7, 9, 11),10000), c = rep(c(13, 16, 19, 22),10000), d = rep(c(25, 29, 33, 37),10000))
t0 = Sys.time()
dt[, `:=`(abdSD = rowSds(as.matrix(.SD), na.rm=T)), .SDcols=c('a','b','d')]
print(paste("Time taken for data table operation = ",Sys.time() - t0))
# [1] "Time taken for data table operation = 0.117115020751953"
t0 = Sys.time()
df$abdSD <- apply(df[,c("a","b","d")],1, function(x){sd(x)})
print(paste("Time taken for apply opertaion = ",Sys.time() - t0))
# [1] "Time taken for apply opertaion = 2.93488311767578"
Using DT and matrixStats clearly wins the race
It's not hard to vectorize the sd for this situation:
vecSD = function(x) {
n = ncol(x)
sqrt((n/(n-1)) * (Reduce(`+`, x*x)/n - (Reduce(`+`, x)/n)^2))
}
DT[, vecSD(.SD), .SDcols = c('a', 'b', 'd')]
#[1] 12.85820 14.36431 15.87451 17.38774
Related
For example : I have frame with 4 columns and I want divide columns A and B by C, but I want unchanged column ID
A B C ID
4 8 23 1
5 12 325 2
6 23 56 3
73 234 21 4
23 23 213 5
The result which i expect is
A B C ID
0,173913043 0,347826087 1 1
0,015384615 0,036923077 1 2
0,107142857 0,410714286 1 3
3,476190476 11,14285714 1 4
0,107981221 0,107981221 1 5
or without the column C, doesn't matter
So, I have the code which give me only columns A and B without the column 'ID'
columns_to_divide <- c(1,2)
results <- results[,columns_to_divide ]/results[,3]
We can use mutate, which creates or alters the values in a column. across says to alter columns A and B, and then we can define a function to divide both of these columns by C.
library(dplyr)
dat %>% mutate(across(c(A, B), function(x) x/C))
A B C ID
1: 0.17391304 0.34782609 23 1
2: 0.01538462 0.03692308 325 2
3: 0.10714286 0.41071429 56 3
4: 3.47619048 11.14285714 21 4
5: 0.10798122 0.10798122 213 5
div = c("A", "B")
div_by = "C"
DF[div] <- DF[div] / DF[[div_by]]
# A B C
# 1 0.17391304 0.34782609 23
# 2 0.01538462 0.03692308 325
# 3 0.10714286 0.41071429 56
# 4 3.47619048 11.14285714 21
# 5 0.10798122 0.10798122 213
Data
DF data.frame(
A = c(4, 5, 6, 73, 23), B = c(8, 12, 23, 234, 23), C = c(23, 325, 56, 21, 213)
)
Create Columns
A <- c(4, 5, 6, 73, 23)
B <- c(8, 12, 23, 234, 23)
C <- c(23, 325, 56, 21, 213)
ID <- c(1, 2, 3, 4, 5)
Add to data frame
df = data.frame(A, B, C, ID)
divide by and print
df$A <- df$A / df$C
df$B <- df$B / df$C
df$C <- df$C / df$C
print(df)
I have a large dataframe. I want to remove the observation if any column contains NA.
For example,
A B C
1 23 NA 2
2 NA 12 10
3 6 27 18
4 18 22 NA
the only observation remaining should be the third observation in the above dataframe.
How can I remove the observation if any column contains NA?
Is this what you mean?
test <- data.frame(A = c(23, NA, 6, 18),
B = c(NA, 12, 27, 22),
C = c(2, 10, 18, NA))
na.omit(test)
A B C
3 6 27 18
We can use complete.cases
subset(test, complete.cases(test))
A bit more verbose way...
#Your df
x=matrix(c(23 ,NA,2,NA,12,10,6,27,18,18,22,NA),4,3,byrow = T)
x1=as.data.frame(x)
#actual solution
x2=rep(0,nrow(x1))
for (i in 1:nrow(x1)) x2[i]=!any(is.na(x1[i,]))
x1=x1[which(x2!=0),]
I have 1000+ datasets with the exact same dimensions and the same column a that I need to load from the web (using jsonlite) and then merge. I can choose the data.frame names but not change the data itself. I could do it all manually but there might be a more efficient way to do this. Let me show what I mean with this example of three datasets.
cola <- c(1, 2, 3, 4)
x0001 <- c(10, 11, 12, 13)
x0002 <- c(20, 22, 25, 29)
x0003 <- c(30, 31, 33, 38)
df0001 <- data.frame(cola, x0001)
colnames(df0001) <- c("A","B")
df0002 <- data.frame(cola, x0002)
colnames(df0002) <- c("A","B")
df0003 <- data.frame(cola, x0003)
colnames(df0003) <- c("A","B")
# data.frame names do not matter to me
alldata <- Reduce(function(x,y) merge(x=x, y=y, by="A"), list(df0001, df0002, df0003))
colnames(alldata) <- c("A", "df0001", "df0002", "df0003")
The merging to alldata and the colnames() function below would be veery long if I do it manually by listing all 1000+ variables. Maybe there is a better way, perhaps with a loop?
If the objects are all loaded in memory, you can load all the objects into a list with the mget and ls(pattern = ...) functions.
dfs <- mget(ls(pattern = "df[0-9]+"))
dfs
#$df0001
# A B
#1 1 10
#2 2 11
#3 3 12
#4 4 13
#
#...
#
#$df0003
# A B
#1 1 30
#2 2 31
#3 3 33
#4 4 38
If the data.frames always have the same columns, in the same order, you can use do.call:
cbind(dfs[[1]],do.call(cbind,lapply(dfs[-1],`[`,,-1)))
# A B df0002 df0003
#1 1 10 20 30
#2 2 11 22 31
#3 3 12 25 33
#4 4 13 29 38
Otherwise, you can use Reduce:
Reduce(function(x,y) merge(x,y,by = "A"), dfs)
# A B.x B.y B
#1 1 10 20 30
#2 2 11 22 31
#3 3 12 25 33
#4 4 13 29 38
The drawback of Reduce is it results in significant memory allocation.
I would like to find the overlapping part of multiple ranges which are given rowise in a data.table object.
An example would be:
t <- data.table(a = c(3,4,5), b = c(13,12,19))
So we have the ranges:
3 - 13,
4 - 12,
5 - 19
Hence the overlapping range would be:
5 - 12
In case of an additional range 19 - 22 the overlap should return NA - NA or 0 - 0 since there is no overlap.
I found solutions for similar problems like spatstat.utils:: intersect.ranges(). However this works only on two vectors and is hard to implement in a data.table
DT[,.(o.l = function()[1], o.r = function()[2], by=.()]
manner which I would really like to do if possible,..
As output for this example I would like to have:
t <- data.table(a = c(3,4,5), b = c(13,12,19), o.l = c(5,5,5), o.r = c(12,12,12))
Here's a one-line example:
library(data.table)
dt = data.table(a = c(3,4,5), b = c(13,12,19))
dt[, c("o.l", "o.r") := as.list(range(Reduce(intersect, mapply(seq, a, b, 1))))]
dt
# a b o.l o.r
# 1: 3 13 5 12
# 2: 4 12 5 12
# 3: 5 19 5 12
Where the core of the problem is
dt = data.table(a = c(3,4,5), b = c(13,12,19))
dt[, Reduce(intersect, mapply(seq, a, b, 1))]
# [1] 5 6 7 8 9 10 11 12
Borrowing idea from David Aurenburg answer in How to flatten / merge overlapping time periods, here is another possible approach:
DT[, g := c(0L, cumsum(shift(a, -1L) >= cummax(b))[-.N])][,
c("ol", "or") := .(max(a), min(b)), g]
data:
DT <- data.table(a = c(3,4,5,19,20,24), b = c(13,12,19,22,23,25))
output:
a b g ol or
1: 3 13 0 5 12
2: 4 12 0 5 12
3: 5 19 0 5 12
4: 19 22 1 20 22
5: 20 23 1 20 22
6: 24 25 2 24 25
I have a dataframe like this:
V1 = paste0("AB", seq(1:48))
V2 = seq(1:48)
test = data.frame(name = V1, value = V2)
I want to calculate the means of the value-column and specific rows.
The pattern of the rows is pretty complicated:
Rows of MeanA1: 1, 5, 9
Rows of MeanA2: 2, 6, 10
Rows of MeanA3: 3, 7, 11
Rows of MeanA4: 4, 8, 12
Rows of MeanB1: 13, 17, 21
Rows of MeanB2: 14, 18, 22
Rows of MeanB3: 15, 19, 23
Rows of MeanB4: 16, 20, 24
Rows of MeanC1: 25, 29, 33
Rows of MeanC2: 26, 30, 34
Rows of MeanC3: 27, 31, 35
Rows of MeanC4: 28, 32, 36
Rows of MeanD1: 37, 41, 45
Rows of MeanD2: 38, 42, 46
Rows of MeanD3: 39, 43, 47
Rows of MeanD4: 40, 44, 48
As you see its starting at 4 different points (1, 13, 25, 37) then always +4 and for the following 4 means its just stepping 1 more row down.
I would like to have an output of all these means in one list.
Any ideas? NOTE: In this example the mean is of course always the middle number, but my real df is different.
Not quite sure about the output format you require, but the following codes can calculate what you want anyhow.
calc_mean1 <- function(x) mean(test$value[seq(x, by = 4, length.out = 3)])
calc_mean2 <- function(x){sapply(x:(x+3), calc_mean1)}
output <- lapply(seq(1, 37, 12), calc_mean2)
names(output) <- paste0('Mean', LETTERS[seq_along(output)]) # remove this line if more than 26 groups.
output
## $MeanA
## [1] 5 6 7 8
## $MeanB
## [1] 17 18 19 20
## $MeanC
## [1] 29 30 31 32
## $MeanD
## [1] 41 42 43 44
An idea via base R is to create a grouping variable for every 4 rows, split the data every 12 rows (nrow(test) / 4) and aggregate to find the mean, i.e.
test$new = rep(1:4, nrow(test)%/%4)
lapply(split(test, rep(1:4, each = nrow(test) %/% 4)), function(i)
aggregate(value ~ new, i, mean))
# $`1`
# new value
# 1 1 5
# 2 2 6
# 3 3 7
# 4 4 8
# $`2`
# new value
# 1 1 17
# 2 2 18
# 3 3 19
# 4 4 20
# $`3`
# new value
# 1 1 29
# 2 2 30
# 3 3 31
# 4 4 32
# $`4`
# new value
# 1 1 41
# 2 2 42
# 3 3 43
# 4 4 44
And yet another way.
fun <- function(DF, col, step = 4){
run <- nrow(DF)/step^2
res <- lapply(seq_len(step), function(inc){
inx <- seq_len(run*step) + (inc - 1)*run*step
dftmp <- DF[inx, ]
tapply(dftmp[[col]], rep(seq_len(step), run), mean, na.rm = TRUE)
})
names(res) <- sprintf("Mean%s", LETTERS[seq_len(step)])
res
}
fun(test, 2, 4)
#$MeanA
#1 2 3 4
#5 6 7 8
#
#$MeanB
# 1 2 3 4
#17 18 19 20
#
#$MeanC
# 1 2 3 4
#29 30 31 32
#
#$MeanD
# 1 2 3 4
#41 42 43 44
Since you said you wanted a long list of the means, I assumed it could also be a vector where you just have all these values. You would get that like this:
V1 = paste0("AB", seq(1:48))
V2 = seq(1:48)
test = data.frame(name = V1, value = V2)
meanVector <- NULL
for (i in 1:(nrow(test)-8)) {
x <- c(test$value[i], test$value[i+4], test$value[i+8])
m <- mean(x)
meanVector <- c(meanVector, m)
}