The overarching goal of data wrangling is to have a tidy, easy-to-use dataset.
This is the third module in the Data Wrangling I topic.
Understanding principles of “tidy” data, using relational databases, and merging datasets.
I’ll keep using the same repo / project as in data import and data manipulation, but create a new .Rmd for tidying. I’m also going to load some relevant packages, and limit the number of lines printed in a tibble.
library(tidyverse)
options(tibble.print_min = 5)pivot_longerIn data import, we used the
haven package to load the PULSE biomarkers dataset from a
.sas7bdat. Let’s reload those data and take a closer look:
pulse_df =
haven::read_sas("./data/public_pulse_data.sas7bdat") |>
janitor::clean_names()
pulse_df
## # A tibble: 1,087 × 7
## id age sex bdi_score_bl bdi_score_01m bdi_score_06m bdi_score_12m
## <dbl> <dbl> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 10003 48.0 male 7 1 2 0
## 2 10015 72.5 male 6 NA NA NA
## 3 10022 58.5 male 14 3 8 NA
## 4 10026 72.7 male 20 6 18 16
## 5 10035 60.4 male 4 0 1 2
## # ℹ 1,082 more rowsWith our new understanding of tidy data, we quickly recognize a
problem: the BDI score is spread across four columns, which correspond
to four observation times. We can fix this problem using
pivot_longer:
pulse_tidy_df =
pivot_longer(
pulse_df,
bdi_score_bl:bdi_score_12m,
names_to = "visit",
values_to = "bdi")
pulse_tidy_df
## # A tibble: 4,348 × 5
## id age sex visit bdi
## <dbl> <dbl> <chr> <chr> <dbl>
## 1 10003 48.0 male bdi_score_bl 7
## 2 10003 48.0 male bdi_score_01m 1
## 3 10003 48.0 male bdi_score_06m 2
## 4 10003 48.0 male bdi_score_12m 0
## 5 10015 72.5 male bdi_score_bl 6
## # ℹ 4,343 more rowsThis looks much better! However, now visit is an issue.
The original column names were informative but we probably don’t need to
keep the bdi_score_ prefix in each case. I’ll use an
additional option in pivot_longer to address this:
pulse_tidy_df =
pivot_longer(
pulse_df,
bdi_score_bl:bdi_score_12m,
names_to = "visit",
names_prefix = "bdi_score_",
values_to = "bdi")
pulse_tidy_df
## # A tibble: 4,348 × 5
## id age sex visit bdi
## <dbl> <dbl> <chr> <chr> <dbl>
## 1 10003 48.0 male bl 7
## 2 10003 48.0 male 01m 1
## 3 10003 48.0 male 06m 2
## 4 10003 48.0 male 12m 0
## 5 10015 72.5 male bl 6
## # ℹ 4,343 more rowsIn the preceding I’ve saved intermediate datasets to make each step
clear. While this can be a helpful crutch as you’re trying out code, it
is generally bad practice. There are also some additional
transformations needed to wrap up the data wrangling process, like
changing bl to 00m for consistency across
visits and converting visit to a factor variable. (It’s
possible that you would want visit to be a numeric variable
instead, which could be done with a different call to
mutate.)
Altogether, then, the code below will import, tidy, and transform the PULSE dataset into a usable format:
pulse_df =
haven::read_sas("./data/public_pulse_data.sas7bdat") |>
janitor::clean_names() |>
pivot_longer(
bdi_score_bl:bdi_score_12m,
names_to = "visit",
names_prefix = "bdi_score_",
values_to = "bdi") |>
mutate(
visit = replace(visit, visit == "bl", "00m"),
visit = factor(visit))
print(pulse_df, n = 12)
## # A tibble: 4,348 × 5
## id age sex visit bdi
## <dbl> <dbl> <chr> <fct> <dbl>
## 1 10003 48.0 male 00m 7
## 2 10003 48.0 male 01m 1
## 3 10003 48.0 male 06m 2
## 4 10003 48.0 male 12m 0
## 5 10015 72.5 male 00m 6
## 6 10015 72.5 male 01m NA
## 7 10015 72.5 male 06m NA
## 8 10015 72.5 male 12m NA
## 9 10022 58.5 male 00m 14
## 10 10022 58.5 male 01m 3
## 11 10022 58.5 male 06m 8
## 12 10022 58.5 male 12m NA
## # ℹ 4,336 more rowsNow we’re in pretty okay shape :-).
Learning Assessment: In the litters data,
the variables gd0_weight and gd18_weight give
the weight of the mother mouse on gestational days 0 and 18. Write a
data cleaning chain that retains only litter_number and
these columns; produces new variables gd and
weight; and makes gd a numeric variable taking
values 0 and 18 (for the last part, you might
want to use recode …). Is this version “tidy”?
The code below shows one approach to this data cleaning process:
litters_wide =
read_csv(
"./data/FAS_litters.csv",
na = c("NA", ".", "")) |>
janitor::clean_names() |>
select(litter_number, ends_with("weight")) |>
pivot_longer(
gd0_weight:gd18_weight,
names_to = "gd",
values_to = "weight") |>
mutate(
gd = case_match(
gd,
"gd0_weight" ~ 0,
"gd18_weight" ~ 18
))
## Rows: 49 Columns: 8
## ── Column specification ───────────────────────────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): Group, Litter Number
## dbl (6): GD0 weight, GD18 weight, GD of Birth, Pups born alive, Pups dead @ ...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.In one sense, this is “tidy” because I have a variable for day and a variable for weight rather that using values in my variable names. However, it’s less useful if I’m interested in computing or analyzing weight gain during pregnancy.
pivot_widerWe’ve been exclusively interested in tidying data, but we’ve admitted that sometimes untidy is better for human consumption. For that reason we’re going to take a short digression into untidying your tidy data.
The code below creates a tidy dataset that could result from an analysis. This is the correct format for additional analysis or visualization, but doesn’t facilitate quick comparisons for human readers.
analysis_result =
tibble(
group = c("treatment", "treatment", "placebo", "placebo"),
time = c("pre", "post", "pre", "post"),
mean = c(4, 8, 3.5, 4)
)
analysis_result
## # A tibble: 4 × 3
## group time mean
## <chr> <chr> <dbl>
## 1 treatment pre 4
## 2 treatment post 8
## 3 placebo pre 3.5
## 4 placebo post 4An alternative presentation of the same data might have groups in
rows, times in columns, and mean values in table cells. This is
decidedly non-tidy; to get there from here we’ll need to use
pivot_wider, which is the inverse of
pivot_longer:
pivot_wider(
analysis_result,
names_from = "time",
values_from = "mean")
## # A tibble: 2 × 3
## group pre post
## <chr> <dbl> <dbl>
## 1 treatment 4 8
## 2 placebo 3.5 4We’re pretty much there now – in some cases you might use
select to reorder columns, and (depending on your goal) use
knitr::kable() to produce a nicer table for reading.
We’ve looked at single-table non-tidy data, but non-tidiness often
stems from relevant data spread across multiple tables. In the simplest
case, these tables are basically the same and can be stacked to produce
a tidy dataset. That’s the setting in LotR_words.xlsx,
where the word counts for different races and genders in each movie in
the trilogy are spread across distinct data rectangles (these data are
based on this
example).
To produce the desired tidy dataset, we first need to read each table and do some cleaning.
fellowship_ring =
readxl::read_excel("./data/LotR_Words.xlsx", range = "B3:D6") |>
mutate(movie = "fellowship_ring")
two_towers =
readxl::read_excel("./data/LotR_Words.xlsx", range = "F3:H6") |>
mutate(movie = "two_towers")
return_king =
readxl::read_excel("./data/LotR_Words.xlsx", range = "J3:L6") |>
mutate(movie = "return_king")Here it was necessary to add a variable to each dataframe indicating the movie; that information had stored elsewhere in the original spreadsheet. As an aside, the three code snippets above are all basically the same except for the range and the movie name – later we’ll see a better way to handle cases like this by writing our own functions, but this works for now.
Once each table is ready to go, we can stack them up using
bind_rows and tidy the result:
lotr_tidy =
bind_rows(fellowship_ring, two_towers, return_king) |>
janitor::clean_names() |>
pivot_longer(
female:male,
names_to = "gender",
values_to = "words") |>
mutate(race = str_to_lower(race)) |>
select(movie, everything())
lotr_tidy
## # A tibble: 18 × 4
## movie race gender words
## <chr> <chr> <chr> <dbl>
## 1 fellowship_ring elf female 1229
## 2 fellowship_ring elf male 971
## 3 fellowship_ring hobbit female 14
## 4 fellowship_ring hobbit male 3644
## 5 fellowship_ring man female 0
## 6 fellowship_ring man male 1995
## 7 two_towers elf female 331
## 8 two_towers elf male 513
## 9 two_towers hobbit female 0
## 10 two_towers hobbit male 2463
## 11 two_towers man female 401
## 12 two_towers man male 3589
## 13 return_king elf female 183
## 14 return_king elf male 510
## 15 return_king hobbit female 2
## 16 return_king hobbit male 2673
## 17 return_king man female 268
## 18 return_king man male 2459Having the data in this form will make it easier to make comparisons across movies, aggregate within races across the trilogy, and perform other analyses.
Data can be spread across multiple related tables, in which case it is necessary to combine or join them prior to analysis. We’ll focus on the problem of combining two tables only; combining three or more is done step-by-step using the same ideas.
There are four major ways join dataframes x and
y:
x and
yxyx or
yLeft joins are the most common, because they add data from a smaller
table y into a larger table x without removing
anything from x.
As an example, consider the data tables in FAS_pups.csv
and FAS_litters.csv, which are related through the
Litter Number variable. The former contains data unique to
each pup, and the latter contains data unique to each litter. We can
combine these using a left join of litter data into pup data; doing so
retains data on each pup and adds data in new columns.
(While revisiting this example, take a look at the group
variable in the litters dataset: this encodes both dose and day of
treatment! We’ll fix that bit of untidiness as part of the processing
pipeline. I’m also going to address a pet peeve of mine, which is coding
sex as an ambiguous numeric variable.)
pup_df =
read_csv(
"./data/FAS_pups.csv",
na = c("NA", "", ".")) |>
janitor::clean_names() |>
mutate(
sex =
case_match(
sex,
1 ~ "male",
2 ~ "female"),
sex = as.factor(sex))
## Rows: 313 Columns: 6
## ── Column specification ───────────────────────────────────────────────────────────────────────────────
## Delimiter: ","
## chr (1): Litter Number
## dbl (5): Sex, PD ears, PD eyes, PD pivot, PD walk
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
litter_df =
read_csv(
"./data/FAS_litters.csv",
na = c("NA", ".", "")) |>
janitor::clean_names() |>
separate(group, into = c("dose", "day_of_tx"), sep = 3) |>
relocate(litter_number) |>
mutate(
wt_gain = gd18_weight - gd0_weight,
dose = str_to_lower(dose))
## Rows: 49 Columns: 8
## ── Column specification ───────────────────────────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): Group, Litter Number
## dbl (6): GD0 weight, GD18 weight, GD of Birth, Pups born alive, Pups dead @ ...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
fas_df =
left_join(pup_df, litter_df, by = "litter_number")
fas_df
## # A tibble: 313 × 15
## litter_number sex pd_ears pd_eyes pd_pivot pd_walk dose day_of_tx
## <chr> <fct> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
## 1 #85 male 4 13 7 11 con 7
## 2 #85 male 4 13 7 12 con 7
## 3 #1/2/95/2 male 5 13 7 9 con 7
## 4 #1/2/95/2 male 5 13 8 10 con 7
## 5 #5/5/3/83/3-3 male 5 13 8 10 con 7
## # ℹ 308 more rows
## # ℹ 7 more variables: gd0_weight <dbl>, gd18_weight <dbl>, gd_of_birth <dbl>,
## # pups_born_alive <dbl>, pups_dead_birth <dbl>, pups_survive <dbl>,
## # wt_gain <dbl>We made the key explicit in the join. By default, the
*_join functions in dplyr will try to
determine the key(s) based on variable names in the datasets you want to
join. This is often but not always sufficient, and an extra step to make
the key clear will help you and others reading your code.
Note that joining is not particularly amenable to the
|> operator because it is fundamentally non-linear: two
separate datasets are coming together, rather than a single dataset
being processed in a step-by-step fashion.
As a final point, the *_join functions are very much
related to SQL syntax, but emphasize operations common to data
analysis.
Learning Assessment: The datasets in this zip file contain de-identified responses to surveys included in past years of this course. Both contain a unique student identifier; the first has responses to a question about operating systems, and the second has responses to questions about degree program and git experience. Write a code chunk that imports and cleans both datasets, and then joins them.
I put both datasets in the data directory in my repo /
project. The code below imports both datasets, cleans up variable names,
and joins the datasets using left_join,
inner_join, and anti_join.
surv_os =
read_csv("data/surv_os.csv") |>
janitor::clean_names() |>
rename(id = what_is_your_uni, os = what_operating_system_do_you_use)
surv_pr_git =
read_csv("data/surv_program_git.csv") |>
janitor::clean_names() |>
rename(
id = what_is_your_uni,
prog = what_is_your_degree_program,
git_exp = which_most_accurately_describes_your_experience_with_git)
left_join(surv_os, surv_pr_git)
inner_join(surv_os, surv_pr_git)
anti_join(surv_os, surv_pr_git)
anti_join(surv_pr_git, surv_os)Both left_join and inner_join give warnings
about “many-to-many” relationships. These indicate that the matching
variable is not unique, and the warnings should be investigated. In the
code below we look into the warning that “Row 7 of x
matches multiple rows in y.”
surv_os |> slice(7)
surv_pr_git |> filter(id == "student_15")surv_pr_git gave the
id value student_15 – probably someone filled
in the survey more than once. Adjudicating and correcting these issues
can be an important step in data cleaning!
For a while, folks were using gather and
spread instead of pivot_longer and
pivot_wider. The new functions were updated for good
reasons; gather and spread will still
exist, but they’re going to be less common over time and you may never
see them.
The code that I produced working examples in lecture is here.