4 min read

Some notes on data cleaning

Maëlle Salmon has a new post up where she looks at a data set on guest hosts on a popular Swedish radio show. In the post Maëlle specifically asks for constructive criticism on her code, so here are some thoughts.

Original approach

Maëlle starts by manually downloading an xlsx file and converting it to a csv, which she then reads with readr::read_csv.

# all summer guests
sommargaester <- readr::read_csv("data/p1sommar.csv", col_names = FALSE, 
                                 locale = readr::locale(encoding = "latin1"))

To deal with the fact that the names are of the form “Last name, First name”, she then defines a function to split the names, creates a new data frame with those names, and then left joins that data frame to the original one.

# get their names
sommargaester_names <- unique(sommargaester$X1)

# for putting names in the right order for later queries
transform_name <- function(name){
  paste(stringr::str_split(name, ",",
                           simplify = TRUE)[2],
        stringr::str_split(name, ",",
                           simplify = TRUE)[1])

pretty_sommargaester_names <- purrr::map_chr(sommargaester_names, transform_name)
sommargaester_names <- tibble::tibble(name = pretty_sommargaester_names,
                                      X1 = sommargaester_names)
sommargaester <- dplyr::left_join(sommargaester, sommargaester_names,
                                  by = "X1")

sommargaester <- dplyr::select(sommargaester, - X1)

She then gathers the dates into a single date variable and generates a rep variable by grouping on name.

# transform the date
sommargaester <- tidyr::gather(sommargaester, "rep", "date", X2:X7)
sommargaester <- dplyr::group_by(sommargaester, name)
sommargaester <- dplyr::mutate(sommargaester, rep = 1:n())
sommargaester <- dplyr::ungroup(sommargaester)

Finally, she filters out a bunch of unwanted dates, and converts date to a proper format.

sommargaester <- dplyr::filter(sommargaester, !is.na(date))
# remove winter
sommargaester <- dplyr::filter(sommargaester, !stringr::str_detect(date, "V"))
# remove repeat episodes
sommargaester <- dplyr::filter(sommargaester, !stringr::str_detect(date, "R"))

# transform the date to a format with a non ambiguous year
sommargaester <- dplyr::mutate(sommargaester, date = as.numeric(date))
sommargaester <- dplyr::mutate(sommargaester, date = ifelse(date > 180000, paste0("19", date),
                                                            ifelse(date < 100000,
                                                                   paste0("200", date),
                                                                   paste0("20", date))))
sommargaester <- dplyr::mutate(sommargaester, pretty_date = lubridate::ymd(date))

Alternative approach

Here are some thoughts on how one could’ve done this cleaning in bit differently.

To make the process more reproducible we want to avoid having to download and convert the xlsx file manually. So we define a helper function that takes a url as input, creates a temporary file, downloads the url, reads it in as a data frame, and finally unlinks the temporary file.


read_xlsx <- function(url) {
  tmp <- tempfile(fileext = ".xlsx")
  download.file(url, tmp, mode = "wb")
  readxl::read_xlsx(tmp, col_names = FALSE)

A less-than-optimal pattern I often see is when people have a data frame from which they derived a second data frame with some additional meta data, which they then merge back into the original data frame. This can almost always be avoided. I think one should always strive towards keeping all data relevant to a data frame within that same data frame (this is also why I think people should use list-columns more often).

To avoid having to make a second data frame with names, we use tidyr::separate to generate two new variable (last and first) which we then paste together into name.

Given how the original data set was structured, the names of the date columns (“X__2" etc) actually contains the information for the rep variable, so we can just drop the “X__" part and coerce it to a numeric variable. This avoids having to group and ungroup on name.

Instead of doing two separate filter calls with str_detect we can use a regular expression.

To avoid a lot of the issues with cleaning the dates, we can exploit the fact that characters have an order defined on them (e.g. “a” < “b”). So we can simply check if the date is greater than “570000” to get all years from 1957-1999 and then add the “19” prefix to those and “20” to the rest. We then use ’lubridate::ymdto convert to aDate` format.

Finally, we drop an aberrant observation (a date was miscoded and it’s not clear what the correct date would be) and select only the variables we need.

sommargaester <- 
         "Files/2071/b5aebbfa-cee4-4733-96f5-10fe96edfa91.xlsx") %>% 
  read_xlsx() %>% 
  separate(X__1, c("last", "first"), ",") %>% 
  mutate(name = paste(first, last)) %>%
  gather(rep, date, starts_with("X")) %>% 
  mutate(rep = as.numeric(str_replace(rep, "X__", ""))) %>% 
  filter(!str_detect(date, "[VR]")) %>% 
  mutate(date = if_else(date >= "570000", 
                        paste0("19", date), 
                        paste0("20", date)),
         date = ymd(date)) %>% 
  filter(!is.na(date)) %>% 
  select(name, rep, date)
## # A tibble: 6 × 3
##                         name   rep       date
##                        <chr> <dbl>     <date>
## 1             Lars-Eric Aaro     2 2011-07-14
## 2            Magdi Abdelhadi     2 2007-08-09
## 3 Sherihan 'Cherrie' Abdulle     2 2017-07-06
## 4                Anton Abele     2 2013-07-25
## 5              Folke Abenius     2 1980-06-27
## 6     Kjell-Albin Abrahamson     2 1988-08-09

With these few tricks, we’ve reduced the cleaning section from 2040 to 871 characters, for a reduction of about 60%, without reducing its readability.