CODEWITHSUNDEEP
rdplyrstringrrecode
Atanas Janackovski
Atanas Janackovski

Reputation: 368

How to recode numerous factor variables in a tidy manner

I have numerous variables that are essentially factors that I would like to recode as integers.

A number of variables are a string with the first character being a digit which corresponds with the integer e.g. 2 = I have considered suicide in the past week, but not made any plans. should be 2. Other variables are yes or no and should be 1 or 0 respectively. Others, have numerous levels based on a number of strings:

none = 0
one = 1
two = 2
three = 3
four or more = 4

Similarly:

ptsd = 0
depression = 1
generalised anxiety = 2
no diagnosis warranted = 3

And:

Female = 0
Male = 1
Other = 2

Some of the values in the cells are NA and need to remain as NA. I have tried tried the following code without trying to change all variables (to start simple):

vars1 <- vars(pastpsyc, pastmed, hxsuicide)
vars2 <- vars(siss, mssi_1)

df_rc <- df %>%
    ## this works
    mutate_at(vars1, ~ (case_when(
        . == "yes" ~ 1,
        . == "no" ~ 0
    ))) %>%
    ## this does not
    mutate_at(vars2, ~as.integer(str_extract(vars2, "[0-9]"))) %>%
    ## nor does this
    mutate_at(diag1, ~ (case_when(
        . == "ptsd" ~ 0,
        . == "depression" ~ 1,
        . == "generalised anxiety" ~ 2,
        . == "no diagnosis warranted" ~ 3
    )))

But this fails and I am totally stumped on how to recode the other variables.

How can I change the different strings to the format I need (preferably in a tidy way)? Below is a minimally reproducible dataset.

structure(list(siss = c("2 = I have considered suicide in the past week, but not made any plans.",
"1 = I have had vague thoughts of suicide in the past week.",
"2 = I have considered suicide in the past week, but not made any plans.",
"1 = I have had vague thoughts of suicide in the past week.",
"3 = I have made plans to suicide in the past week, but I haven’t intended to act on these plans."
), mssi_1 = c("1. Weak - unsure about whether he/she wants to die, seldom thinks about death, or intensity seems low.",
"1. Weak - unsure about whether he/she wants to die, seldom thinks about death, or intensity seems low.",
"1. Weak - unsure about whether he/she wants to die, seldom thinks about death, or intensity seems low.",
"1. Weak - unsure about whether he/she wants to die, seldom thinks about death, or intensity seems low.",
"2. Moderate - current desire to die, may be preoccupied with ideas about death, or intensity seems greater than a rating of 1."
), diag1 = c("ptsd", NA, "depression", "generalised anxiety",
"no diagnosis warranted"), pastpsyc = c("yes", NA, "no", NA,
"yes"), pastmed = c("no", "yes", NA, "no", "no"), hxsuicide = c("yes",
NA, "yes", "yes", "yes"), suicide_attempts = c("none", NA, "one",
"two", "four or more"), sex = c("Male", "Other", NA, "Female",
NA)), class = c("spec_tbl_df", "tbl_df", "tbl", "data.frame"), row.names = c(NA,
-5L), spec = structure(list(cols = list(siss = structure(list(), class = c("collector_character",
"collector")), mssi_1 = structure(list(), class = c("collector_character",
"collector")), diag1 = structure(list(), class = c("collector_character",
"collector")), pastpsyc = structure(list(), class = c("collector_character",
"collector")), pastmed = structure(list(), class = c("collector_character",
"collector")), hxsuicide = structure(list(), class = c("collector_character",
"collector")), suicide_attempts = structure(list(), class = c("collector_character",
"collector")), sex = structure(list(), class = c("collector_character",
"collector"))), default = structure(list(), class = c("collector_guess",
"collector")), skip = 1), class = "col_spec"))

Upvotes: 1

Views: 55

Answers (1)

Ben
Ben

Reputation: 30474

This works with very minor changes.

  • You want a dot (.) instead of vars2 in str_extract
  • You want vars(diag1) or "diag1" (or just use mutate) to change that single column

Hope this is helpful.

df %>%
  ## this works
  mutate_at(vars1, ~ (case_when(
    . == "yes" ~ 1,
    . == "no" ~ 0
  ))) %>%
  ## this does not
  mutate_at(vars2, ~as.integer(str_extract(., "[0-9]"))) %>%
  ## nor does this
  mutate_at(vars(diag1), ~ (case_when(
    . == "ptsd" ~ 0,
    . == "depression" ~ 1,
    . == "generalised anxiety" ~ 2,
    . == "no diagnosis warranted" ~ 3
  )))

If you want to use mutate instead of mutate_at:

mutate(diag1 = case_when(
  diag1 == "ptsd" ~ 0,
  diag1 == "depression" ~ 1,
  diag1 == "generalised anxiety" ~ 2,
  diag1 == "no diagnosis warranted" ~ 3
))

Upvotes: 2

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