My data has many columns and subjects, but to illustrate it simpler, lets say I have 7 subjects with 3 variables/columns called x1, x2 and x3 (values range from 1 to 3 and NAs). In the analysis that I want it is important I actually call the columns I want to use (since I cannot just use the whole dataframe in my analysis because there are more variables/columns there)
>data <- data.frame(‘id’=c(1,2,3,4,5,6,7), ‘x1’=c(1,2,2,NA,3,3,1), ‘x2’=c(NA,3,1,NA,2,3,2), ‘x3’=c(NA,2,NA,NA,3,NA,1)
id x1 x2 x3
1 1 NA NA
2 2 3 2
3 2 1 NA
4 NA NA NA
5 3 2 NA
6 3 3 NA
7 1 2 1
The class of x1 x2 and x3 are numeric. Out of that, I want to create a variable/column called ‘x4’ that: - gives me the lowest number of row x1, x2 and x3.
-If there is an NA in a row of x1,x2,x3, the NA shall be ignored.
-If they are however ALL NAs, I would want the outcome to be NA. (NOT Inf, which is what it does with my code now)
-If there are two lowest numbers that are the same, just display any one of those two. So like this:
>data <- data.frame(‘id’=c(1,2,3,4,5,6,7), ‘x1’=c(1,2,2,NA,3,3,1), ‘x2’=c(NA,3,1,NA,2,3,2), ‘x3’=c(NA,2,NA,NA,3,NA,1), ‘x4’=c(1,2,1,NA,2,3,1)
id x1 x2 x3 x4
1 1 NA NA 1
2 2 3 2 2
3 2 1 NA 1
4 NA NA NA NA
5 3 2 NA 2
6 3 3 NA 3
7 1 2 1 1
I managed to find a very similar question, and I can mostly make it work: min for each row with dataframe in R
data$x4 <- apply(data[, c("x1","x2","x3")],1, FUN=min, na.rm = TRUE)
the problem I have now is that in case of all NAs (so id number 4), my outcome is not NA, but it is 'Inf'.
Question 1:How can I make it so it becomes an NA instead of Inf? I can of course do that afterwards like this:
is.na(data$x4) <- sapply(data$x4, is.infinite)
But I wonder if there is a nice way to do that already with/inside the previous code?
Also, rather then using sapply and the inside FUNction min, I would also like to try to make it work with code in a way like below: Question 2: is using this other code below possible?
data$x4 <- min(data[, c("x1","x2","x3")],1 , na.rm = TRUE)
for this x4 gets the outcome '1' everytime. I guess it just shows the lowest number (1) of the whole column? I dont understand why. I am already using ',1' but doesnt help.
I hope somebody can help me(r and stackoverflow newbie) out, thanks!
You are looking for pmin function which returns the (regular or parallel) minima of the input values. Below are two approaches using pmin:
df$minIget <- do.call(pmin, c(df[,-1], na.rm = TRUE)) # Approch1: using do.call
df %>% rowwise() %>% mutate(minIget = pmin(x1, x2,x3,na.rm = T))# Approch2: using tidyverse.
output:
A tibble: 7 x 5
# Rowwise:
id x1 x2 x3 minIget
<dbl> <dbl> <dbl> <dbl> <dbl>
1 1 1 NA NA 1
2 2 2 3 2 2
3 3 2 1 NA 1
4 4 NA NA NA NA
5 5 3 2 3 2
6 6 3 3 NA 3
7 7 1 2 1 1