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I want to find which values in df2 which is also present in df1, within a certain range. One value is considering both a and b in the data frames (a & b can't split up). For examples, can I find 9,1 (df1[1,1]) in df2? It doesn't have to be on the same position. Also, we can allow a diff of for example 1 for "a" and 1 for "b". For example, I want to find all values 9+-1,1+-1 in df2. "a" & "b" always go together, each row stick together. Does anyone have a suggestion of how to code this? Many many thanks!
set.seed(1)
a <- sample(10,5)
set.seed(1)
b <- sample(5,5, replace=T)
feature <- LETTERS[1:5]
df1 <- data.frame(feature,a,b)
df1
> df1
feature a b
A 9 1
B 4 4
C 7 1
D 1 2
E 2 5
set.seed(2)
a <- sample(10,5)
b <- sample(5,5, replace=T)
feature <- LETTERS[1:5]
df2 <- data.frame(feature,a,b)
df2
df2
feature a b
A 5 1
B 6 4
C 9 5
D 1 1
E 10 2
Not correct but Im imaging this can be done for a for loop somehow!
for(i in df1[,1]) {
for(j in df1[,2]){
s<- c(s,(df1[i,1] & df1[j,2]== df2[,1] & df2[,2]))# how to add certain allowed diff levels?
}
}
s
Output wanted:
feature_df1 <- LETTERS[1:5]
match <- c(1,0,0,1,0)
feature_df2 <- c("E","","","D", "")
df <- data.frame(feature_df1, match, feature_df2)
df
feature_df1 match feature_df2
A 1 E
B 0
C 0
D 1 D
E 0
I loooove data.table, which is (imo) the weapon of choice for these kind of problems..
library( data.table )
#make df1 and df2 a data.table
setDT(df1, key = "feature"); setDT(df2)
#now perform a join operation on each row of df1,
# creating an on-the-fly subset of df2
df1[ df1, c( "match", "feature_df2") := {
val = df2[ a %between% c( i.a - 1, i.a + 1) & b %between% c(i.b - 1, i.b + 1 ), ]
unique_val = sort( unique( val$feature ) )
num_val = length( unique_val )
list( num_val, paste0( unique_val, collapse = ";" ) )
}, by = .EACHI ][]
# feature a b match feature_df2
# 1: A 9 1 1 E
# 2: B 4 4 0
# 3: C 7 1 0
# 4: D 1 2 1 D
# 5: E 2 5 0
One way to go about this in Base R would be to split the data.frames() into a list of rows then calculate the absolute difference of row vectors to then evaluate how large the absolute difference is and if said difference is larger than a given value.
Code
# Find the absolute difference of all row vectors
listdif <- lapply(l1, function(x){
lapply(l2, function(y){
abs(x - y)
})
})
# Then flatten the list to a list of data.frames
listdifflat <- lapply(listdif, function(x){
do.call(rbind, x)
})
# Finally see if a pair of numbers is within our threshhold or not
m1 <- 2
m2 <- 3
listfin <- Map(function(x){
x[1] > m1 | x[2] > m2
},
listdifflat)
head(listfin, 1)
[[1]]
V1
[1,] TRUE
[2,] FALSE
[3,] TRUE
[4,] TRUE
[5,] TRUE
[6,] TRUE
[7,] TRUE
[8,] TRUE
[9,] TRUE
[10,] TRUE
Data
df1 <- read.table(text = "
4 1
7 5
1 5
2 10
13 6
19 10
11 7
17 9
14 5
3 5")
df2 <- read.table(text = "
15 1
6 3
19 6
8 2
1 3
13 7
16 8
12 7
9 1
2 6")
# convert df to list of row vectors
l1<- lapply(1:nrow(df1), function(x){
df1[x, ]
})
l2 <- lapply(1:nrow(df2), function(x){
df2[x, ]
})
I try to obtain percentages grouping values regarding one variable.
For this I used sapply to obtain the percentage of each column regarding another one, but I dont know how to group these values by type (another variable)
x <- data.frame("A" = c(0,0,1,1,1,1,1), "B" = c(0,1,0,1,0,1,1), "C" = c(1,0,1,1,0,0,1),
"type" = c("x","x","x","y","y","y","x"), "yes" = c(0,0,1,1,0,1,1))
x
A B C type yes
1 0 0 1 x 0
2 0 1 0 x 0
3 1 0 1 x 1
4 1 1 1 y 1
5 1 0 0 y 0
6 1 1 0 y 1
7 1 1 1 x 1
I need to obtaing the next value (percentage): A==1&yes==1/A==1, and for this I use the next code:
result <- as.data.frame(sapply(x[,1:3],
function(i) (sum(i & x$yes)/sum(i))*100))
result
sapply(x[, 1:3], function(i) (sum(i & x$yes)/sum(i)) * 100)
A 80
B 75
C 75
Now I need to obtain the same math operation but taking into account the varible "type". It means, obtaing the same percentage but discriminating it by type. So, my expected table was:
type sapply(x[, 1:3], function(i) (sum(i & x$yes)/sum(i)) * 100)
A x 40
A y 40
B x 25
B y 50
C x 50
C y 25
In the example it's possible to observe that, by letters, the percentage sum is the same value that the obtained in the first result, just here is discriminated by type.
thanks a lot.
You can do the following using data.table:
Code
setDT(df)
cols = c('A', 'B', 'C')
mat = df[yes == 1, lapply(.SD, function(x){
100 * sum(x)/df[, lapply(.SD, sum), .SDcols = cols][[substitute(x)]]
# Here, the numerator is sum(x | yes == 1) for x == columns A, B, C
# If we look at the denominator, it equals sum(x) for x == columns A, B, C
# The reason why we need to apply substitute(x) is because df[, lapply(.SD, sum)]
# generates a list of column sums, i.e. list(A = sum(A), B = sum(B), ...).
# Hence, for each x in the column names we must subset the list above using [[substitute(x)]]
# Ultimately, the operation equals sum(x | yes == 1)/sum(x) for A, B, C.
}), .(type), .SDcols = cols]
# '.(type)' simply means that we apply this for each type group,
# i.e. once for x and once for y, for each ABC column.
# The dot is just shorthand for 'list()'.
# .SDcols assigns the subset that I want to apply my lapply statement onto.
Result
> mat
type A B C
1: x 40 25 50
2: y 40 50 25
Long format (your example)
> melt(mat)
type variable value
1: x A 40
2: y A 40
3: x B 25
4: y B 50
5: x C 50
6: y C 25
Data
df <- data.frame("A" = c(0,0,1,1,1,1,1), "B" = c(0,1,0,1,0,1,1), "C" = c(1,0,1,1,0,0,1),
"type" = c("x","x","x","y","y","y","x"), "yes" = c(0,0,1,1,0,1,1))
I have data set
ID <- c(1,1,2,2,2,2,3,3,3,3,3,4,4,4)
Eval <- c("A","A","B","B","A","A","A","A","B","B","A","A","A","B")
med <- c("c","d","k","k","h","h","c","d","h","h","h","c","h","k")
df <- data.frame(ID,Eval,med)
> df
ID Eval med
1 1 A c
2 1 A d
3 2 B k
4 2 B k
5 2 A h
6 2 A h
7 3 A c
8 3 A d
9 3 B h
10 3 B h
11 3 A h
12 4 A c
13 4 A h
14 4 B k
I try to create variable x and y, group by ID and Eval. For each ID, if Eval = A, and med = "h" or "k", I set x = 1, other wise x = 0, if Eval = B and med = "h" or "k", I set y = 1, other wise y = 0. I use the way I don't like it, I got answer but it seem like not that great
df <- data.table(df)
setDT(df)[, count := uniqueN(med) , by = .(ID,Eval)]
setDT(df)[Eval == "A", x:= ifelse(count == 1 & med %in% c("k","h"),1,0), by=ID]
setDT(df)[Eval == "B", y:= ifelse(count == 1 & med %in% c("k","h"),1,0), by=ID]
ID Eval med count x y
1: 1 A c 2 0 NA
2: 1 A d 2 0 NA
3: 2 B k 1 NA 1
4: 2 B k 1 NA 1
5: 2 A h 1 1 NA
6: 2 A h 1 1 NA
7: 3 A c 3 0 NA
8: 3 A d 3 0 NA
9: 3 B h 1 NA 1
10: 3 B h 1 NA 1
11: 3 A h 3 0 NA
12: 4 A c 2 0 NA
13: 4 A h 2 0 NA
14: 4 B k 1 NA 1
Then I need to collapse the row to get unique ID, I don't know how to collapse rows, any idea?
The output
ID x y
1 0 0
2 1 1
3 0 1
4 0 1
We create the 'x' and 'y' variables grouped by 'ID' without the NA elements directly coercing the logical vector to binary (as.integer)
df[, x := as.integer(Eval == "A" & count ==1 & med %in% c("h", "k")) , by = ID]
and similarly for 'y'
df[, y := as.integer(Eval == "B" & count ==1 & med %in% c("h", "k")) , by = ID]
and summarise it, using any after grouping by "ID"
df[, lapply(.SD, function(x) as.integer(any(x))) , ID, .SDcols = x:y]
# ID x y
#1: 1 0 0
#2: 2 1 1
#3: 3 0 1
#4: 4 0 1
If we need a compact approach, instead of assinging (:=), we summarise the output grouped by "ID", "Eval" based on the conditions and then grouped by 'ID', we check if there is any TRUE values in 'x' and 'y' by looping over the columns described in the .SDcols.
setDT(df)[, if(any(uniqueN(med)==1 & med %in% c("h", "k"))) {
.(x= Eval=="A", y= Eval == "B") } else .(x=FALSE, y=FALSE),
by = .(ID, Eval)][, lapply(.SD, any) , by = ID, .SDcols = x:y]
# ID x y
#1: 1 FALSE FALSE
#2: 2 TRUE TRUE
#3: 3 FALSE TRUE
#4: 4 FALSE TRUE
If needed, we can convert to binary similar to the approach showed in the first solution.
The OP's goal...
"I try to create variable x and y, group by ID and Eval. For each ID, if Eval = A, and med = "h" or "k", I set x = 1, other wise x = 0, if Eval = B and med = "h" or "k", I set y = 1, other wise y = 0. [...] Then I need to collapse the row to get unique ID"
can be simplified to...
For each ID and Eval, flag if all med values are h or all med values are k.
setDT(df) # only do this once
df[, all(med=="k") | all(med=="h"), by=.(ID,Eval)][, dcast(.SD, ID ~ Eval, fun=any)]
ID A B
1: 1 FALSE FALSE
2: 2 TRUE TRUE
3: 3 FALSE TRUE
4: 4 FALSE TRUE
To see what dcast is doing, read ?dcast and try running just the first part on its own, df[, all(med=="k") | all(med=="h"), by=.(ID,Eval)].
The change to use x and y instead of A and B is straightforward but ill-advised (since unnecessary renaming can be confusing and lead to extra work when there are new Eval values); and ditto the change for 1/0 instead of TRUE/FALSE (since the values captured are actually boolean).
Here is my dplyr solution since I find it more readable than data.table.
library(dplyr)
df %>%
group_by(ID, Eval) %>%
mutate(
count = length(unique(med)),
x = ifelse(Eval == "A" &
count == 1 & med %in% c("h", "k"), 1, 0),
y = ifelse(Eval == "B" &
count == 1 & med %in% c("h", "k"), 1, 0)
) %>%
group_by(ID) %>%
summarise(x1 = max(unique(x)),
y1 = max(unique(y)))
A one liner solution for collapsing the rows of your result :
df[,lapply(.SD,function(i) {ifelse(1 %in% i,ifelse(!0 %in% i,1,0),0)}),.SDcols=x:y,by=ID]
ID x y
1: 1 0 0
2: 2 1 1
3: 3 0 1
4: 4 0 1
I would like to add a counter column in a data frame based on a set of identical rows. To do this, I used the package data.table. In my case, the comparison between rows need doing from the combination of columns "z" AND ("x" OR "y").
I tested:
DF[ , Index := .GRP, by = c("x","y","z") ]
but the result is the combination of "z" AND "x" AND "y".
How can I have the combination of "z" AND ("x" OR "y") ?
Here is a data example:
DF = data.frame(x=c("a","a","a","b","c","d","e","f","f"), y=c(1,3,2,8,8,4,4,6,0), z=c("M","M","M","F","F","M","M","F","F"))
DF <- data.table(DF)
I would like to have this output:
> DF
x y z Index
1: a 1 M 1
2: a 3 M 1
3: a 2 M 1
4: b 8 F 2
5: c 8 F 2
6: d 4 M 3
7: e 4 M 3
8: f 6 F 4
9: f 0 F 4
The new group starts if the value for z is changing or the values both for x and y are changing.
Try this example.
require(data.table)
DF <- data.table(x = c("a","a","a","b","c","d","e","f","f"),
y = c(1,3,2,8,8,4,4,6,0),
z=c("M","M","M","F","F","M","M","F","F"))
# The functions to compare if value is not equal with the previous value
is.not.eq.with.lag <- function(x) c(T, tail(x, -1) != head(x, -1))
DF[, x1 := is.not.eq.with.lag(x)]
DF[, y1 := is.not.eq.with.lag(y)]
DF[, z1 := is.not.eq.with.lag(z)]
DF
DF[, Index := cumsum(z1 | (x1 & y1))]
DF
I know a lot of people warn against a for loop in R, but in this instance I think it is a very direct way of approaching the problem. Plus, the result isn't growing in size so performance issues aren't a large issue. The for loop approach would be:
dt$grp <- rep(NA,nrow(dt))
for (i in 1:nrow(dt)){
if (i == 1){
dt$grp[i] = 1
}
else {
if(dt$z[i-1] == dt$z[i] & (dt$x[i-1] == dt$x[i] | dt$y[i-1] == dt$y[i])){
dt$grp[i] = dt$grp[i-1]
}else{
dt$grp[i] = dt$grp[i-1] + 1
}
}
}
Trying this on OPs original problem, the result is:
DF = data.frame(x=c("a","a","a","b","c","d","e","f","f"), y=c(1,3,2,8,8,4,4,6,0), z=c("M","M","M","F","F","M","M","F","F"))
dt <- data.table(DF)
dt$grp <- rep(NA,nrow(dt))
for (i in 1:nrow(dt)){
if (i == 1){
dt$grp[i] = 1
}
else {
if(dt$z[i-1] == dt$z[i] & (dt$x[i-1] == dt$x[i] | dt$y[i-1] == dt$y[i])){
dt$grp[i] = dt$grp[i-1]
}else{
dt$grp[i] = dt$grp[i-1] + 1
}
}
}
dt
x y z grp
1: a 1 M 1
2: a 3 M 1
3: a 2 M 1
4: b 8 F 2
5: c 8 F 2
6: d 4 M 3
7: e 4 M 3
8: f 6 F 4
9: f 0 F 4
Trying this on the data.table in #Frank's comment, gives the expected result as well:
dt<-data.table(x = c("b", "a", "a"), y = c(1, 1, 2), z = c("F", "F", "F"))
dt$grp <- rep(NA,nrow(dt))
for (i in 1:nrow(dt)){
if (i == 1){
dt$grp[i] = 1
}
else {
if(dt$z[i-1] == dt$z[i] & (dt$x[i-1] == dt$x[i] | dt$y[i-1] == dt$y[i])){
dt$grp[i] = dt$grp[i-1]
}else{
dt$grp[i] = dt$grp[i-1] + 1
}
}
}
dt
x y z grp
1: b 1 F 1
2: a 1 F 1
3: a 2 F 1
EDITED TO ADD: This solution is in some ways a more verbose version of the one advocated by djhurio above. I think it shows what is happening a bit more so I'll leave it.
I think this is a task easier to do if it is broken down a little bit. The below code creates TWO indices at first, one for changes in x (nested in z) and one for changes in y (nested in z). We then find the first row from each of these indices. Taking the cumulative sum of the case where both FIRST.x and FIRST.y is true should give your desired index.
library(data.table)
dt_example <- data.table(x = c("a","a","a","b","c","d","e","f","f"),
y = c(1,3,2,8,8,4,4,6,0),
z = c("M","M","M","F","F","M","M","F","F"))
dt_example[,Index_x := .GRP,by = c("z","x")]
dt_example[,Index_y := .GRP,by = c("z","y")]
dt_example[,FIRST.x := !duplicated(Index_x)]
dt_example[,FIRST.y := !duplicated(Index_y)]
dt_example[,Index := cumsum(FIRST.x & FIRST.y)]
dt_example
x y z Index_x Index_y FIRST.x FIRST.y Index
1: a 1 M 1 1 TRUE TRUE 1
2: a 3 M 1 2 FALSE TRUE 1
3: a 2 M 1 3 FALSE TRUE 1
4: b 8 F 2 4 TRUE TRUE 2
5: c 8 F 3 4 TRUE FALSE 2
6: d 4 M 4 5 TRUE TRUE 3
7: e 4 M 5 5 TRUE FALSE 3
8: f 6 F 6 6 TRUE TRUE 4
9: f 0 F 6 7 FALSE TRUE 4
This approach looks for changes in x & z | y & z. The extra columns are left in the data.table to show the calculations.
DF[, c("Ix", "Iy", "Iz", "dx", "dy", "min.change", "Index") :=
#Create index of values based on consecutive order
list(ix <- rleid(x), iy <- rleid(y), iz <- rleid(z),
#Determine if combinations of x+z OR y+z change
ix1 <- c(0, diff(rleid(ix+iz))),
iy1 <- c(0, diff(rleid(iy+iz))),
#Either combination is constant (no change)?
change <- pmin(ix1, iy1),
#New index based on change
cumsum(change) + 1
)]
x y z Ix Iy Iz dx dy min.change Index
1: a 1 M 1 1 1 0 0 0 1
2: a 3 M 1 2 1 0 1 0 1
3: a 2 M 1 3 1 0 1 0 1
4: b 8 F 2 4 2 1 1 1 2
5: c 8 F 3 4 2 1 0 0 2
6: d 4 M 4 5 3 1 1 1 3
7: e 4 M 5 5 3 1 0 0 3
8: f 6 F 6 6 4 1 1 1 4
9: f 0 F 6 7 4 0 1 0 4
I have an array of data that can be modelled roughly as follows:
x=data.frame(c(2,2,2),c(3,4,6),c(3,4,6), c("x/-","x/x","-/x"))
names(x)=c("A","B","C","D")
I wish to change the values of B to (C + 1) if only the first character in D is -.
I have tried using the following and iterating over the rows:
if(substring(x$D, 1,1) == "-")
{
x$B <- x$C + 1
}
However this method does not seem to work. Is there a way to do this using sapply?
Thanks,
Matt
You can use ifelse and within
within(x, B <- ifelse(substr(D, 1, 1) == "-", C + 1, B))
# A B C D
# 1 2 3 3 x/-
# 2 2 4 4 x/x
# 3 2 7 6 -/x
Or instead of substr, you could use grepl
within(x, B <- ifelse(grepl("^[-]", D), C + 1, B))
# A B C D
# 1 2 3 3 x/-
# 2 2 4 4 x/x
# 3 2 7 6 -/x
data.table solution.
require(data.table)
x <- data.table(c(2,2,2), c(3,4,6), c(3,4,6), c("x/-","x/x","-/x"))
setnames(x, c("A","B","C","D"))
x[grepl("^[-]", D), B := C + 1]