# Comparison with dplyr Tabulation

#### Gabriel Becker and Adrian Waddell

#### 2024-09-20

tabulation_dplyr.R

## Introduction

In this vignette, we would like to discuss the similarities and differences between `dplyr` and `rtable`.

Much of the `rtables` framework focuses on tabulation/summarizing of data and then the visualization of the table. In this vignette, we focus on summarizing data using `dplyr` and contrast it to `rtables`. We won’t pay attention to the table visualization/markup and just derive the cell content.

Using `dplyr` to summarize data and `gt` to visualize the table is a good way if the tabulation is of a certain nature or complexity. However, there are tables such as the table created in the `introduction` vignette that take some effort to create with `dplyr`. Part of the effort is due to fact that when using `dplyr` the table data is stored in `data.frame`s or `tibble`s which is not the most natural way to represent a table as we will show in this vignette.

If you know a more elegant way of deriving the table content with `dplyr` please let us know and we will update the vignette.

    library(rtables)
    library(dplyr)

tabulation_dplyr.R

Here is the table and data used in the `introduction` vignette:

    n <- 400

    set.seed(1)

    df <- tibble(
      arm = factor(sample(c("Arm A", "Arm B"), n, replace = TRUE), levels = c("Arm A", "Arm B")),
      country = factor(sample(c("CAN", "USA"), n, replace = TRUE, prob = c(.55, .45)), levels = c("CAN", "USA")),
      gender = factor(sample(c("Female", "Male"), n, replace = TRUE), levels = c("Female", "Male")),
      handed = factor(sample(c("Left", "Right"), n, prob = c(.6, .4), replace = TRUE), levels = c("Left", "Right")),
      age = rchisq(n, 30) + 10
    ) %>% mutate(
      weight = 35 * rnorm(n, sd = .5) + ifelse(gender == "Female", 140, 180)
    )

    lyt <- basic_table(show_colcounts = TRUE) %>%
      split_cols_by("arm") %>%
      split_cols_by("gender") %>%
      split_rows_by("country") %>%
      summarize_row_groups() %>%
      split_rows_by("handed") %>%
      summarize_row_groups() %>%
      analyze("age", afun = mean, format = "xx.x")

    tbl <- build_table(lyt, df)
    tbl
    #                     Arm A                     Arm B
    #              Female        Male        Female        Male
    #              (N=96)      (N=105)       (N=92)      (N=107)
    # ————————————————————————————————————————————————————————————
    # CAN        45 (46.9%)   64 (61.0%)   46 (50.0%)   62 (57.9%)
    #   Left     32 (33.3%)   42 (40.0%)   26 (28.3%)   37 (34.6%)
    #     mean      38.9         40.4         40.3         37.7
    #   Right    13 (13.5%)   22 (21.0%)   20 (21.7%)   25 (23.4%)
    #     mean      36.6         40.2         40.2         40.6
    # USA        51 (53.1%)   41 (39.0%)   46 (50.0%)   45 (42.1%)
    #   Left     34 (35.4%)   19 (18.1%)   25 (27.2%)   25 (23.4%)
    #     mean      40.4         39.7         39.2         40.1
    #   Right    17 (17.7%)   22 (21.0%)   21 (22.8%)   20 (18.7%)
    #     mean      36.9         39.8         38.5         39.0

tabulation_dplyr.R

## Getting Started

We will start by deriving the first data cell on row 3 (note, row 1 and 2 have content cells, see the `introduction` vignette). Cell 3,1 contains the mean age for left handed & female Canadians in “Arm A”:

    mean(df$age[df$country == "CAN" & df$arm == "Arm A" & df$gender == "Female" & df$handed == "Left"])
    # [1] 38.86979

tabulation_dplyr.R

or with `dplyr`:

    df %>%
      filter(country == "CAN", arm == "Arm A", gender == "Female", handed == "Left") %>%
      summarise(mean_age = mean(age))
    # # A tibble: 1 × 1
    #   mean_age
    #      <dbl>
    # 1     38.9

tabulation_dplyr.R

Further, `dplyr` gives us other verbs to easily get the average age of left handed Canadians for each group defined by the 4 columns:

    df %>%
      group_by(arm, gender) %>%
      filter(country == "CAN", handed == "Left") %>%
      summarise(mean_age = mean(age))
    # `summarise()` has grouped output by 'arm'. You can override using the `.groups`
    # argument.
    # # A tibble: 4 × 3
    # # Groups:   arm [2]
    #   arm   gender mean_age
    #   <fct> <fct>     <dbl>
    # 1 Arm A Female     38.9
    # 2 Arm A Male       40.4
    # 3 Arm B Female     40.3
    # 4 Arm B Male       37.7

tabulation_dplyr.R

We can further get to all the average age cell values with:

    average_age <- df %>%
      group_by(arm, gender, country, handed) %>%
      summarise(mean_age = mean(age))
    # `summarise()` has grouped output by 'arm', 'gender', 'country'. You can
    # override using the `.groups` argument.

    average_age
    # # A tibble: 16 × 5
    # # Groups:   arm, gender, country [8]
    #    arm   gender country handed mean_age
    #    <fct> <fct>  <fct>   <fct>     <dbl>
    #  1 Arm A Female CAN     Left       38.9
    #  2 Arm A Female CAN     Right      36.6
    #  3 Arm A Female USA     Left       40.4
    #  4 Arm A Female USA     Right      36.9
    #  5 Arm A Male   CAN     Left       40.4
    #  6 Arm A Male   CAN     Right      40.2
    #  7 Arm A Male   USA     Left       39.7
    #  8 Arm A Male   USA     Right      39.8
    #  9 Arm B Female CAN     Left       40.3
    # 10 Arm B Female CAN     Right      40.2
    # 11 Arm B Female USA     Left       39.2
    # 12 Arm B Female USA     Right      38.5
    # 13 Arm B Male   CAN     Left       37.7
    # 14 Arm B Male   CAN     Right      40.6
    # 15 Arm B Male   USA     Left       40.1
    # 16 Arm B Male   USA     Right      39.0

tabulation_dplyr.R

In `rtable` syntax, we need the following code to get to the same content:

    lyt <- basic_table() %>%
      split_cols_by("arm") %>%
      split_cols_by("gender") %>%
      split_rows_by("country") %>%
      split_rows_by("handed") %>%
      analyze("age", afun = mean, format = "xx.x")

    tbl <- build_table(lyt, df)
    tbl
    #                Arm A           Arm B
    #            Female   Male   Female   Male
    # ————————————————————————————————————————
    # CAN
    #   Left
    #     mean    38.9    40.4    40.3    37.7
    #   Right
    #     mean    36.6    40.2    40.2    40.6
    # USA
    #   Left
    #     mean    40.4    39.7    39.2    40.1
    #   Right
    #     mean    36.9    39.8    38.5    39.0

tabulation_dplyr.R

As mentioned in the introduction to this vignette, please ignore the difference in arranging and formatting the data: it’s possible to condense the `rtable` more and it is possible to make the `tibble` look more like the reference table using the `gt` R package.

In terms of tabulation for this example there was arguably not much added by `rtables` over `dplyr`.

## Content Information

Unlike in `rtables` the different levels of summarization are discrete computations in `dplyr` which we will then need to combine

We first focus on the count and percentage information for handedness within each country (for each arm-gender pair), along with the analysis row mean values:

    c_h_df <- df %>%
      group_by(arm, gender, country, handed) %>%
      summarize(mean = mean(age), c_h_count = n()) %>%
      ## we need the sum below to *not* be by country, so that we're dividing by the column counts
      ungroup(country) %>%
      # now the `handed` grouping has been removed, therefore we can calculate percent now:
      mutate(n_col = sum(c_h_count), c_h_percent = c_h_count / n_col)
    # `summarise()` has grouped output by 'arm', 'gender', 'country'. You can
    # override using the `.groups` argument.
    c_h_df
    # # A tibble: 16 × 8
    # # Groups:   arm, gender [4]
    #    arm   gender country handed  mean c_h_count n_col c_h_percent
    #    <fct> <fct>  <fct>   <fct>  <dbl>     <int> <int>       <dbl>
    #  1 Arm A Female CAN     Left    38.9        32    96       0.333
    #  2 Arm A Female CAN     Right   36.6        13    96       0.135
    #  3 Arm A Female USA     Left    40.4        34    96       0.354
    #  4 Arm A Female USA     Right   36.9        17    96       0.177
    #  5 Arm A Male   CAN     Left    40.4        42   105       0.4
    #  6 Arm A Male   CAN     Right   40.2        22   105       0.210
    #  7 Arm A Male   USA     Left    39.7        19   105       0.181
    #  8 Arm A Male   USA     Right   39.8        22   105       0.210
    #  9 Arm B Female CAN     Left    40.3        26    92       0.283
    # 10 Arm B Female CAN     Right   40.2        20    92       0.217
    # 11 Arm B Female USA     Left    39.2        25    92       0.272
    # 12 Arm B Female USA     Right   38.5        21    92       0.228
    # 13 Arm B Male   CAN     Left    37.7        37   107       0.346
    # 14 Arm B Male   CAN     Right   40.6        25   107       0.234
    # 15 Arm B Male   USA     Left    40.1        25   107       0.234
    # 16 Arm B Male   USA     Right   39.0        20   107       0.187

tabulation_dplyr.R

which has 16 rows (cells) like the `average_age` data frame defined above. Next, we will derive the group information for countries:

    c_df <- df %>%
      group_by(arm, gender, country) %>%
      summarize(c_count = n()) %>%
      # now the `handed` grouping has been removed, therefore we can calculate percent now:
      mutate(n_col = sum(c_count), c_percent = c_count / n_col)
    # `summarise()` has grouped output by 'arm', 'gender'. You can override using the
    # `.groups` argument.
    c_df
    # # A tibble: 8 × 6
    # # Groups:   arm, gender [4]
    #   arm   gender country c_count n_col c_percent
    #   <fct> <fct>  <fct>     <int> <int>     <dbl>
    # 1 Arm A Female CAN          45    96     0.469
    # 2 Arm A Female USA          51    96     0.531
    # 3 Arm A Male   CAN          64   105     0.610
    # 4 Arm A Male   USA          41   105     0.390
    # 5 Arm B Female CAN          46    92     0.5
    # 6 Arm B Female USA          46    92     0.5
    # 7 Arm B Male   CAN          62   107     0.579
    # 8 Arm B Male   USA          45   107     0.421

tabulation_dplyr.R

Finally, we `left_join()` the two levels of summary to get a data.frame containing the full set of values which make up the body of our table (note, however, they are not in the same order):

    full_dplyr <- left_join(c_h_df, c_df) %>% ungroup()
    # Joining with `by = join_by(arm, gender, country, n_col)`

tabulation_dplyr.R

Alternatively, we could calculate only the counts in `c_h_df`, and use `mutate()` after the `left_join()` to divide the counts by the `n_col` values which are more naturally calculated within `c_df`. This would simplify `c_h_df`’s creation somewhat by not requiring the explicit `ungroup()`, but it prevents each level of summarization from being a self-contained set of computations.

The `rtables` call in contrast is:

    lyt <- basic_table(show_colcounts = TRUE) %>%
      split_cols_by("arm") %>%
      split_cols_by("gender") %>%
      split_rows_by("country") %>%
      summarize_row_groups() %>%
      split_rows_by("handed") %>%
      summarize_row_groups() %>%
      analyze("age", afun = mean, format = "xx.x")

    tbl <- build_table(lyt, df)
    tbl
    #                     Arm A                     Arm B
    #              Female        Male        Female        Male
    #              (N=96)      (N=105)       (N=92)      (N=107)
    # ————————————————————————————————————————————————————————————
    # CAN        45 (46.9%)   64 (61.0%)   46 (50.0%)   62 (57.9%)
    #   Left     32 (33.3%)   42 (40.0%)   26 (28.3%)   37 (34.6%)
    #     mean      38.9         40.4         40.3         37.7
    #   Right    13 (13.5%)   22 (21.0%)   20 (21.7%)   25 (23.4%)
    #     mean      36.6         40.2         40.2         40.6
    # USA        51 (53.1%)   41 (39.0%)   46 (50.0%)   45 (42.1%)
    #   Left     34 (35.4%)   19 (18.1%)   25 (27.2%)   25 (23.4%)
    #     mean      40.4         39.7         39.2         40.1
    #   Right    17 (17.7%)   22 (21.0%)   21 (22.8%)   20 (18.7%)
    #     mean      36.9         39.8         38.5         39.0

tabulation_dplyr.R

We can now spot check that the values are the same

    frm_rtables_h <- cell_values(
      tbl,
      rowpath = c("country", "CAN", "handed", "Right", "@content"),
      colpath = c("arm", "Arm B", "gender", "Female")
    )[[1]]
    frm_rtables_h
    # [1] 20.0000000  0.2173913

    frm_dplyr_h <- full_dplyr %>%
      filter(country == "CAN" & handed == "Right" & arm == "Arm B" & gender == "Female") %>%
      select(c_h_count, c_h_percent)

    frm_dplyr_h
    # # A tibble: 1 × 2
    #   c_h_count c_h_percent
    #       <int>       <dbl>
    # 1        20       0.217

    frm_rtables_c <- cell_values(
      tbl,
      rowpath = c("country", "CAN", "@content"),
      colpath = c("arm", "Arm A", "gender", "Male")
    )[[1]]

    frm_rtables_c
    # [1] 64.0000000  0.6095238

    frm_dplyr_c <- full_dplyr %>%
      filter(country == "CAN" & arm == "Arm A" & gender == "Male") %>%
      select(c_count, c_percent)

    frm_dplyr_c
    # # A tibble: 2 × 2
    #   c_count c_percent
    #     <int>     <dbl>
    # 1      64     0.610
    # 2      64     0.610

tabulation_dplyr.R

tabulation_dplyr.R

Further, the `rtable` syntax has hopefully also become a bit more straightforward to derive the cell values than with `dplyr` for this particular table.

## Summary

In this vignette learned that:

- many tables are quite easily created with `dplyr` and `data.frame` or `tibble` as data structure
  - `dplyr` keeps simple things simple
- if tables have group summaries then repeating of information is required
- `rtables` streamlines the construction of complex tables

We recommend that you continue reading the `clinical_trials` vignette where we create a number of more advanced tables using layouts.