Filter rows based on variables “beginning with” strings specified by vector

Question

I\'m trying to filter a patient database based on specific ICD9 (diagnosis) codes. I would like to use a vector indicating the first 3 strings of the ICD9 codes.

The exa

Answer 1

This looks close to what you're looking for, but requires a bit more manipulation:

library(dplyr)
library(stringr)
library(tidyr)

obs2 <- observations %>%
  gather(vars, value, -patient) %>%
  filter(str_sub(value, 1, 3) %in% dx)

# A tibble: 2 × 3
  patient  vars value
    <chr> <chr> <chr>
1       a  var1  8661
2       b  var2  8674

Answer 2

You can make a regex pattern from the interest vector and apply it to each column of your data frame except for the patient id, use rowSums to check if there is any var in a row match the pattern:

library(dplyr)
pattern = paste("^(", paste0(dx, collapse = "|"), ")", sep = "")

pattern
# [1] "^(866|867)"

filter(observations, rowSums(sapply(observations[-1], grepl, pattern = pattern)) != 0)

# A tibble: 2 × 4
#  patient  var1  var2  var3
#    <chr> <chr> <chr> <chr>
#1       a  8661  8651  2430
#2       b   865  8674  3456

Another option is to use Reduce with lapply:

filter(observations, Reduce("|", lapply(observations[-1], grepl, pattern = pattern)))

# A tibble: 2 × 4
#  patient  var1  var2  var3
#    <chr> <chr> <chr> <chr>
#1       a  8661  8651  2430
#2       b   865  8674  3456

---

This approach works when you have more then two patterns and different patterns have different character length, for instance, if you have dx as dx<-c("866","867", "9089"):

dx<-c("866","867", "9089")
pattern = paste("^(", paste0(dx, collapse = "|"), ")", sep = "")

pattern
# [1] "^(866|867|9089)"

filter(observations, Reduce("|", lapply(observations[-1], grepl, pattern = pattern)))

# A tibble: 3 × 4
#  patient  var1  var2  var3
#    <chr> <chr> <chr> <chr>
#1       a  8661  8651  2430
#2       b   865  8674  3456
#3       c  8651  2866  9089

---

Check this and this stack answer for more about multiple or conditions in regex.

Answer 3

You can use apply and ldply

library(plyr)
filtered_obs <- apply(observations, 1, function(x) if(sum(substr(x,1,3) %in% dx)>0){x})
filtered_obs <- plyr::ldply(filtered_obs,rbind)

If you have variable number of characters then this should work-

filtered_obs <- lapply(dx, function(y)
                 {
                  plyr::ldply(apply(observations, 1, function(x) 
                   {
                    if(sum(substr(x,1,nchar(y)) %in% y)>0){x}
                   }), rbind)
                 })

filtered_obs <- unique(plyr::ldply(filtered_obs,rbind))