[r] Set NA to 0 in R

A solution using mutate_all from dplyr in case you want to add that to your dplyr pipeline:

library(dplyr)
df %>%
  mutate_all(funs(ifelse(is.na(.), 0, .)))

Result:

   A B C
1  0 0 0
2  1 0 0
3  2 0 2
4  3 0 5
5  0 0 2
6  0 0 1
7  1 0 1
8  2 0 5
9  3 0 2
10 0 0 4
11 0 0 3
12 1 0 5
13 2 0 5
14 3 0 0
15 0 0 1

If in any case you only want to replace the NA's in numeric columns, which I assume it might be the case in modeling, you can use mutate_if:

library(dplyr)
df %>%
  mutate_if(is.numeric, funs(ifelse(is.na(.), 0, .)))

or in base R:

replace(is.na(df), 0)

Result:

   A    B C
1  0    0 0
2  1 <NA> 0
3  2    0 2
4  3 <NA> 5
5  0    0 2
6  0 <NA> 1
7  1    0 1
8  2 <NA> 5
9  3    0 2
10 0 <NA> 4
11 0    0 3
12 1 <NA> 5
13 2    0 5
14 3 <NA> 0
15 0    0 1

Update

with dplyr 1.0.0, across is introduced:

library(dplyr)
# Replace `NA` for all columns
df %>%
  mutate(across(everything(), ~ ifelse(is.na(.), 0, .)))

# Replace `NA` for numeric columns
df %>%
  mutate(across(where(is.numeric), ~ ifelse(is.na(.), 0, .)))

Data:

set.seed(123)
df <- data.frame(A=rep(c(0:3, NA), 3), 
                 B=rep(c("0", NA), length.out = 15), 
                 C=sample(c(0:5, NA), 15, replace = TRUE))