Manipulating tbl data frame

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)

	Placebo	Active 1	Active 2
DEMO1: Basic tbl without formatting
Analysis Set: ITT	86	84	84
Age (Years)
N	86	84	84
[demo1.html][] 18OCT2023, 14:12

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)

	Placebo	Active 1	Active 2
DEMO2: Adding the variable of newrows
Analysis Set: ITT	86	84	84

Age (Years)
N	86	84	84
[demo2.html][] 18OCT2023, 14:12

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)

	Placebo	Active 1	Active 2
DEMO3: Adding the variable of indentme
Analysis Set: ITT	86	84	84

Age (Years)
N	86	84	84
[demo3.html][] 18OCT2023, 14:12

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)

	Placebo	Active 1	Active 2
DEMO4: Adding the variable of boldme
Analysis Set: ITT	86	84	84

Age (Years)
N	86	84	84
[demo4.html][] 18OCT2023, 14:12

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	anbr
Age (Years)				HEADER	01
N	5	5	5	N	01
Mean (SD)	69.6 (14.40)	75.6 (6.73)	72.2 (9.23)	VALUE	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
Age (Years)				HEADER	01	0	1
N	5	5	5	N	01	1	2
Mean (SD)	69.6 (14.40)	75.6 (6.73)	72.2 (9.23)	VALUE	01	2	3


# 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)

	Placebo	Active 1	Active 2
DEMO5: Using row_type to set up indentation
Age (Years)
N	5	5	5
Mean (SD)	69.6 (14.40)	75.6 (6.73)	72.2 (9.23)
[demo5.html][] 18OCT2023, 14:12

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