replacing values of a string variable in stringr

1
votes

Many values of my data frame are written differently although they were referring to the same value. I should change some of the column values to make them similar. I used stringr package str_replace_all, but it didn't work very well. It is not doing what I wanted it. Here is my reproducible data and the code.

    df <- data.frame(
  stringsAsFactors = FALSE,
              Var1 = c("16-pathway","16a-OH E1",
                       "16a-OHE1","16OHE","17-b-estradiol","17-OH-progesterone",
                       "17-OH-progesterone/ androstenedione ratio",
                       "17b-HSD (rs2830A)","17b-HSD (rs592389 G)","17b-HSD (rs615492 G)",
                       "17b-HSD (rs615942 G)","17b estradiol",
                       "17OH-progesterone","2-hydroxy (OH) E1","2-OHE-1","2-OHE-2",
                       "2-pathway","2:16 OHE ratio","2:16 pathway ratio","2:16a-OH E1",
                       "2:16OHE","2OHE","Adiponectin","androstenedione",
                       "Androstenedione","androstenedione  (A)"),
              Freq = c(2L,1L,4L,8L,1L,6L,6L,2L,
                       2L,1L,1L,1L,5L,1L,4L,4L,2L,4L,2L,1L,8L,8L,
                       8L,1L,62L,1L)
  )

library(stringr)
df$new_var1 <- str_replace_all(df$Var1,
                                  c(#16OHE1
                                    "16a-OH E1" = "16-OHE1", 
                                    "16a-OHE1" = "16-OHE1", 
                                    "16OHE" = "16-OHE1",
                                    
                                    #17Beta estradiol
                                    "17-b-estradiol" = "17-b-estradiol",
                                    "17b estradiol"= "17-b-estradiol",
                                    #Andreostenedione

                                    "androstenedione" = "Androstenedione",
                                    "Androstenedione" = "Androstenedione",
                                    "androstenedione  (A)" = "Androstenedione",

                                    #2-OHE-1
                                    "2-OHE-1" = "2-OHE-1",
                                    "2-hydroxy (OH) E1" = "2-OHE-1")
)

Now, if you compare Var1 and new_var1, it didn't work to change "2-hydroxy (OH) E1" to "2-OHE-1" and "Androstenedione (A)" to "Androstenedione". See screenshots below. enter image description here

enter image description here

2
rstringr
By default most (or all?) of the stringr functions use regex, so you need to escape special characters like brackets, parentheses, and hyphens. If you don't want to use regex, the docs explain how to use fixed patterns: "Match a fixed string (i.e. by comparing only bytes), using fixed(). This is fast, but approximate. Generally, for matching human text, you'll want coll() which respects character matching rules for the specified locale." - camille

2 Answers

0
votes

In str_replace_all you need to escape the ( and ) by using "double " in front. Try the below it works. :)

df$new_var1 <- str_replace_all(df$Var1,
                               c(#16OHE1
                                 "16a-OH E1" = "16-OHE1", 
                                 "16a-OHE1" = "16-OHE1", 
                                 "16OHE" = "16-OHE1",
                                 "17-b-estradiol" = "17-b-estradiol",
                                 "17b estradiol"= "17-b-estradiol",
                                 "androstenedione" = "Androstenedione",
                                 "Androstenedione" = "Androstenedione",
                                 "androstenedione  \\(A\\)" = "Androstenedione",
                                 "2-OHE-1" = "2-OHE-1",
                                 "2-hydroxy \\(OH\\) E1" = "2-OHE-1"))
0
votes

There are two things you need to change in your code to obtain the desired output. The first one is the one @Emax mentioned: escaping parentheses with double backslashes (\\( and \\)). Additionally, you need to pay attention to the order of the replacements, as certain replacements might affect the outcome of following replacements. That is the reason in your OP "androstenedione \\(A\\)" do not get replaced by "Androstenedione", because the replacement "androstenedione" = "Androstenedione" is happening before "androstenedione \\(A\\)" = "Androstenedione". A simple solution to get the desired output would be to first replace the most specific cases (e.g., "androstenedione \\(A\\)"), before the more general ones (e.g., "androstenedione").

library(stringr)
df$new_var1 <- str_replace_all(df$Var1,
                               c(#16OHE1
                                 "16a-OH E1" = "16-OHE1", 
                                 "16a-OHE1" = "16-OHE1", 
                                 "16OHE" = "16-OHE1",
                                 #17Beta estradiol
                                 "17-b-estradiol" = "17-b-estradiol",
                                 "17b estradiol"= "17-b-estradiol",
                                 #Andreostenedione
                                 "androstenedione  \\(A\\)" = "Androstenedione",
                                 "androstenedione" = "Androstenedione",
                                 "Androstenedione" = "Androstenedione",
                                 #2-OHE-1
                                 "2-OHE-1" = "2-OHE-1",
                                 "2-hydroxy \\(OH\\) E1" = "2-OHE-1")
)