Clinical Tables with ‘flextable’, ‘tables’ and ‘rtables’
features: quick overview
with flextable()
‘flextable’ can easily create reporting table from data.frame. You can merge cells, add header rows or specify how data should be displayed in cells.
with as_flextable()
The as_flextable() function is used to transform specific objects into flextable objects.
species | island | ||||
|---|---|---|---|---|---|
Biscoe | Dream | Torgersen | Total | ||
Adelie | Count | 44 (12.8%) | 56 (16.3%) | 52 (15.1%) | 152 (44.2%) |
Mar. pct (1) | 26.2% ; 28.9% | 45.2% ; 36.8% | 100.0% ; 34.2% | ||
Chinstrap | Count | 0 (0.0%) | 68 (19.8%) | 0 (0.0%) | 68 (19.8%) |
Mar. pct | 0.0% ; 0.0% | 54.8% ; 100.0% | 0.0% ; 0.0% | ||
Gentoo | Count | 124 (36.0%) | 0 (0.0%) | 0 (0.0%) | 124 (36.0%) |
Mar. pct | 73.8% ; 100.0% | 0.0% ; 0.0% | 0.0% ; 0.0% | ||
Total | Count | 168 (48.8%) | 124 (36.0%) | 52 (15.1%) | 344 (100.0%) |
(1) Columns and rows percentages | |||||
package ‘doconv’ https://cran.r-project.org/package=doconv
Adverse Event Table preparation
link: https://rconsortium.github.io/rtrs-wg/commontables.html#tables-5
heading <- tabular(
Heading("")*1*
Heading("")*count ~
Heading()*ARM, data = ex_adsl)
body <- tabular(
Heading("Patients with at least one event")*1*
Heading("")*countpercentid*Arguments(ARM = ARM)*
Heading()*USUBJID +
Heading("Total number of events")*1*Heading("")*1 +
Heading()*AEBODSYS*
(Heading("Patients with at least one event")*
Percent(denom = ARM, fn = countpercentid)*
Heading()*USUBJID +
Heading("Total number of events")*1 +
Heading()*AEDECOD*DropEmpty(which = "row")*
Heading()*Percent(denom = ARM, fn = countpercentid)*
Heading()*USUBJID) ~
Heading()*ARM,
data = ex_adae)
tab <- rbind(heading, body)
Pagination with ‘flextable’
When working with Word or RTF, it is possible to prevents breaks between tables rows you want to stay together. Function paginate() let you define this pagination.
From https://ardata-fr.github.io/flextable-book/layout.html#pagination
Pagination with ‘rtables’
tbl_list <- basic_table() |>
split_cols_by("ARM") |>
split_rows_by(
"STRATA1",
split_fun = keep_split_levels(c("A", "B")),
page_by = TRUE, page_prefix = "Stratum") |>
split_rows_by(
"RACE",
split_fun = keep_split_levels(c("ASIAN", "WHITE"))) |>
summarize_row_groups() |>
analyze("AGE", afun = function(x, ...)
in_rows(
"mean (sd)" = rcell(c(mean(x), sd(x)), format = "xx.x (xx.x)"),
"range" = rcell(range(x), format = "xx.x - xx.x")
)) |>
build_table(formatters::ex_adsl) |>
paginate_table(lpp = 20)Now let’s use ‘officer’ to add tables into a Word document, one table per page.
Pagination with ‘tables’
Let’s create a quick example with ‘tables’.
Now let’s use ‘officer’ to add tables into a Word document, one table per page.
Word Computed fields and flextable
doc <- read_docx()
for (spl in splits) {
ft <- as_flextable(tab[spl, ],
spread_first_col = TRUE
) |>
add_footer_lines(
values =
as_paragraph(
"p. ",
as_word_field(x = "Page", width = .05),
" on ", as_word_field(x = "NumPages", width = .05)
)
)
doc <- body_add_flextable(doc, ft) |>
body_add_break()
}
doc <- body_remove(doc) |>
print(
target = "assets/files/tables-fields.docx"
)
Use section headers and footers
header_default <-
block_list(
fpar(ftext("p. "),
run_word_field(field = "Page"),
" on ",
run_word_field(field = "NumPages")))
footer_default <-
block_list(
fpar(
external_img(src = "assets/img/r-in-pharma-logo.png")))
ps <- prop_section(
header_default = header_default,
footer_default = footer_default)
doc <- read_docx()
for(spl in splits) {
ft <- as_flextable(tab[spl,],
spread_first_col = TRUE)
doc <- body_add_flextable(doc, ft)|>
body_add_break()
}
doc <- body_remove(doc) |>
body_set_default_section(value = ps) |>
print(target = "assets/files/tables-sections.docx")
Thank you
- Tables in Clinical Trials with R: https://rconsortium.github.io/rtrs-wg/
- The flextable book: https://ardata-fr.github.io/flextable-book/
- The flextable gallery: https://ardata.fr/flextable-gallery/
- source of the presentation: https://github.com/ardata-fr/r-in-pharma-2023-10-24
- presentation: https://ardata.fr/r-in-pharma-2023-10-24
References:
