Manipulating tbl data frame

Source: vignettes/tbl_manipulation.Rmd

Introduction

The tbl data frame is the main input to the gentlg function for creating the RTF/HTML outputs. This vignette will show you the tbl structure and how the tbl variables are in action for rendering the RTF/HTML outputs.

Basic tbl data frame

The basic variables of tbl includes label, col1, col2, …, coln, where

  • label: row text displayed on the 1st column of the table

  • col1: statistic results displayed on the 2nd column of the table

  • col2: statistic results displayed on the 3rd column of the table.

The example below shows you a very basic tbl data frame, and how this tbl is transformed through the gentlg function call to create the HTML output.

library(dplyr)
library(tidytlg)

tbl <- tibble::tribble(
               ~label,      ~col1,      ~col2,      ~col3,
  "Analysis Set: ITT",       "86",       "84",       "84",
        "Age (Years)",         NA,         NA,         NA,
                  "N",       "86",       "84",       "84"
)

knitr::kable(tbl)
label col1 col2 col3
Analysis Set: ITT 86 84 84
Age (Years) NA NA NA
N 86 84 84 

# render tbl
gentlg(huxme       = tbl,
          format      = "HTML",
          orientation = "landscape",
          opath       = ".",
          file        = "DEMO1",
          title       = "Basic tbl without formatting",
          colheader   = c("", "Placebo", "Active 1", "Active 2"),
          print.hux = FALSE,
          wcol        = .30)
DEMO1:   Basic tbl without formatting
Placebo
Active 1
Active 2
Analysis Set: ITT 86 84 84
Age (Years)
N 86 84 84
[demo1.html][] 23JUN2023, 12:58

Formatting table

The above example does not have any formatting in actions on the table. To enable formatting, additional variables will need to be created in the tbl data frame.

Add new row

For inserting a blank line prior to the 2nd row (i.e. Age (Years)), we will need to add the newrows variable with value = 1.

tbl <- tbl %>% 
  mutate(newrows = case_when(label == "Age (Years)" ~ 1,
                             TRUE ~ 0))

knitr::kable(tbl)
label col1 col2 col3 newrows
Analysis Set: ITT 86 84 84 0
Age (Years) NA NA NA 1
N 86 84 84 0 

# render tbl
gentlg(huxme       = tbl,
          format      = "HTML",
          orientation = "landscape",
          opath       = ".",
          file        = "DEMO2",
          title       = "Adding the variable of newrows",
          colheader   = c("", "Placebo", "Active 1", "Active 2"),
          print.hux = FALSE,
          wcol        = .30)
DEMO2:   Adding the variable of newrows
Placebo
Active 1
Active 2
Analysis Set: ITT 86 84 84
Age (Years)
N 86 84 84
[demo2.html][] 23JUN2023, 12:58

Add indentation

For adding 1 indentation to the N row, we will need to add the indentme variable with value = 1, which indicates 1 indentation (2 will result in 2 indentation, and so on).

tbl <- tbl %>% 
  mutate(indentme = case_when(label == "N" ~ 1,
                             TRUE ~ 0))

knitr::kable(tbl)
label col1 col2 col3 newrows indentme
Analysis Set: ITT 86 84 84 0 0
Age (Years) NA NA NA 1 0
N 86 84 84 0 1 

# render tbl
gentlg(huxme       = tbl,
          format      = "HTML",
          orientation = "landscape",
          opath       = ".",
          file        = "DEMO3",
          title       = "Adding the variable of indentme",
          colheader   = c("", "Placebo", "Active 1", "Active 2"),
          print.hux = FALSE,
          wcol        = .30)
DEMO3:   Adding the variable of indentme
Placebo
Active 1
Active 2
Analysis Set: ITT
 86 84 84
Age (Years)
N
 86 84 84
[demo3.html][] 23JUN2023, 12:58

Enable bold font

To enable bolding on the row of Age (Years), the boldme variable with value = 1 will need to be added.

tbl <- tbl %>% 
  mutate(boldme = case_when(label == "Age (Years)" ~ 1,
                             TRUE ~ 0))

knitr::kable(tbl)
label col1 col2 col3 newrows indentme boldme
Analysis Set: ITT 86 84 84 0 0 0
Age (Years) NA NA NA 1 0 1
N 86 84 84 0 1 0 

# render tbl
gentlg(huxme       = tbl,
          format      = "HTML",
          orientation = "landscape",
          opath       = ".",
          file        = "DEMO4",
          title       = "Adding the variable of boldme",
          colheader   = c("", "Placebo", "Active 1", "Active 2"),
          print.hux = FALSE,
          wcol        = .30)
DEMO4:   Adding the variable of boldme
Placebo
Active 1
Active 2
Analysis Set: ITT
 86 84 84
Age (Years)
N
 86 84 84
[demo4.html][] 23JUN2023, 12:58

There is another formatting variable called newpage, where assigning newpage = 1 will start a new page in the output.

Fomatting functions

Besides manually adding the formatting variables to tbl, we have developed several formatting functions to facilitate the formatting process:

  • add_newrows: add newrows variable to the tbl based on row_type

  • add_indent: add indentme variable to the tbl based on row_type

  • add_newpage: add newpage variable to the tbl based on row_type.

The row_type variable is created in the tbl by calling the freq, nested_freq, and univar functions, which is used by the above functions for setting up the formatting variables. The tbl example below is obtained by calling the univar function for summarizing the age statistics in the CDISC ADSL dataset. After calling the univar function, we create the anbr (analysis number) variable as the identifier of this tbl chunk.

tbl <- cdisc_adsl %>% 
  univar(colvar = "TRT01PN", 
         rowvar = "AGE", 
         statlist = statlist(c("N", "MEANSD")),
         decimal = 0,
         row_header = "Age (Years)") %>% 
  mutate(anbr = "01") 

knitr::kable(tbl)
label 0 54 81 row_type group_level anbr
Age (Years) HEADER 0 01
N 5 5 5 N 0 01
Mean (SD) 69.6 (14.40) 75.6 (6.73) 72.2 (9.23) VALUE 0 01

The add_format function, which incorporates all 3 formatting functions above (add_indent, add_newrows, add_newpage), can then be applied to the tbl for creating the formatting variables.

tbl <- cdisc_adsl %>% 
  univar(colvar = "TRT01PN", 
         rowvar = "AGE", 
         statlist = statlist(c("N", "MEANSD")),
         decimal = 0,
         row_header = "Age (Years)") %>% 
  mutate(anbr = "01") %>%
  add_format()

knitr::kable(tbl)
label 0 54 81 row_type anbr indentme roworder newrows newpage
Age (Years) HEADER 01 0 1 0 0
N 5 5 5 N 01 1 2 0 0
Mean (SD) 69.6 (14.40) 75.6 (6.73) 72.2 (9.23) VALUE 01 2 3 0 0 

# render tbl
gentlg(huxme       = tbl,
          tlf         = "Table",
          format      = "HTML",
          orientation = "landscape",
          opath       = ".",
          file        = "DEMO5",
          title       = "Using row_type to set up indentation",
          colheader   = c("", "Placebo", "Active 1", "Active 2"),
          print.hux = FALSE,
          wcol        = .30)
DEMO5:   Using row_type to set up indentation
Placebo
Active 1
Active 2
Age (Years)
N
 5 5 5
Mean (SD)
 69.6 (14.40) 75.6 (6.73) 72.2 (9.23)
[demo5.html][] 23JUN2023, 12:58

The default indentation for each row_type is shown below.

row_type default indentation
TABLE_BY_HEADER 0
BY_HEADER[1-9] 0
HEADER 0
N 1
VALUE 2
NESTED 0