## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
echo = TRUE,
collapse = TRUE,
comment = "#>",
message = FALSE,
warning = FALSE
)
options(docx.add_datetime=FALSE)
library(junco)
library(rlistings)
library(tibble)
## ----setup-title, include=FALSE-----------------------------------------------
#Need to set up a dummy tittle and main footer
titles <- list(title = " ",
subtitles = NULL,
main_footer = "Dummy Note: On-treatment is defined as ~{optional treatment-emergent}")
#Need tempdir
out_dir <- file.path("..", "output")
if(!dir.exists(out_dir)) {
dir.create(out_dir)
}
NOT_CRAN <- !testthat:::on_cran()
## ----orientation_rtf----------------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
lyt <- basic_table(
show_colcounts = TRUE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",
show_colcounts = FALSE
) |>
### create table body row sections based on SEX
split_rows_by("SEX",
section_div = c(" "),
page_by = TRUE,
split_fun = drop_split_levels
) |>
summarize_row_groups("SEX",
cfun =a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
extrablankline = TRUE,
.stats = c("count_unique")
)
) |>
### analyze height
analyze("RESPONSE",
var_labels = c("Response"),
show_labels = "visible",
afun = a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
.stats = c("count_unique_fraction")
)
)
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----orientation_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE------
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/exampleorientation"),
# orientation = "landscape")
## ----orientation_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE-----
# export_as_docx_j(result,
# tblid = "exampleorientation",
# output_dir = out_dir,
# orientation = "landscape")
## ----orientation_rtf_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "exampleorientation", orientation = "landscape")
## ----fontsize_rtf-------------------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
lyt <- basic_table(
show_colcounts = TRUE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",
show_colcounts = FALSE
) |>
### create table body row sections based on SEX
split_rows_by("SEX",
section_div = c(" "),
page_by = TRUE,
split_fun = drop_split_levels
) |>
summarize_row_groups("SEX",
cfun =a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
extrablankline = TRUE,
.stats = c("count_unique")
)
) |>
### analyze height
analyze("RESPONSE",
var_labels = c("Response"),
show_labels = "visible",
afun = a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
.stats = c("count_unique_fraction")
)
)
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----fontsize_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE---------
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplefontsize"),
# fontspec = formatters::font_spec("Times", 8, 1.2))
#
## ----fontsize_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE--------
# export_as_docx_j(result,
# tblid = "examplefontsize",
# output_dir = out_dir,
# theme = theme_docx_default_j(font = "Times New Roman", font_size = 8L))
## ----fontsize_rtf_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "examplefontsize", fontspec = formatters::font_spec("Times", 8, 1.2))
## ----spanning_header_setup----------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
colspan_trt = factor(c("Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" ",
"Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" "),
levels = c(
"Active Study Agent",
" "
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
adsl
colspan_trt_map <- create_colspan_map(adsl,
non_active_grp = "Placebo",
non_active_grp_span_lbl = " ",
active_grp_span_lbl = "Active Study Agent",
colspan_var = "colspan_trt",
trt_var = "TRT01A")
colspan_trt_map
## ----spanning_header_full-----------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
colspan_trt = factor(c("Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" ",
"Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" "),
levels = c(
"Active Study Agent",
" "
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
# No combined column needed for spanning header example
mysplit <- make_split_fun()
colspan_trt_map <- create_colspan_map(adsl,
non_active_grp = "Placebo",
non_active_grp_span_lbl = " ",
active_grp_span_lbl = "Active Study Agent",
colspan_var = "colspan_trt",
trt_var = "TRT01A")
lyt <- basic_table(
show_colcounts = TRUE,
colcount_format = "N=xx"
) |>
split_cols_by("colspan_trt",
split_fun = trim_levels_to_map(map = colspan_trt_map)
) |>
split_cols_by("TRT01A",
show_colcounts = FALSE,
split_fun = mysplit
) |>
### create table body row sections based on SEX
split_rows_by("SEX",
section_div = c(" "),
page_by = TRUE,
split_fun = drop_split_levels
) |>
summarize_row_groups("SEX",
cfun =a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
extrablankline = TRUE,
.stats = c("count_unique")
)
) |>
### analyze height
analyze("RESPONSE",
var_labels = c("Response"),
show_labels = "visible",
afun = a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
.stats = c("count_unique_fraction")
)
)
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----spanning_header_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplespanningheader1"),
# orientation = "landscape")
## ----spanning_header_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "examplespanningheader1", orientation = "landscape")
## ----combined_column_setup----------------------------------------------------
add_combo <- add_combo_facet("Combined",
label = "Combined",
levels = c("Example Drug 5 mg", "Example Drug 10 mg", "Example Drug 20 mg")
)
mysplit <- make_split_fun(post = list(add_combo))
## ----combined_column_full-----------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
colspan_trt = factor(c("Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" ",
"Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" "),
levels = c(
"Active Study Agent",
" "
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
# Set up levels and label for the required combined column
add_combo <- add_combo_facet("Combined",
label = "Combined",
levels = c("Example Drug 5 mg", "Example Drug 10 mg", "Example Drug 20 mg")
)
mysplit <- make_split_fun(post = list(add_combo))
colspan_trt_map <- create_colspan_map(adsl,
non_active_grp = "Placebo",
non_active_grp_span_lbl = " ",
active_grp_span_lbl = "Active Study Agent",
colspan_var = "colspan_trt",
trt_var = "TRT01A")
lyt <- basic_table(
show_colcounts = TRUE,
colcount_format = "N=xx"
) |>
split_cols_by("colspan_trt",
split_fun = trim_levels_to_map(map = colspan_trt_map)
) |>
split_cols_by("TRT01A",
show_colcounts = FALSE,
split_fun = mysplit
) |>
### create table body row sections based on SEX
split_rows_by("SEX",
section_div = c(" "),
page_by = TRUE,
split_fun = drop_split_levels
) |>
summarize_row_groups("SEX",
cfun =a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
extrablankline = TRUE,
.stats = c("count_unique")
)
) |>
### analyze height
analyze("RESPONSE",
var_labels = c("Response"),
show_labels = "visible",
afun = a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
.stats = c("count_unique_fraction")
)
)
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----combined_column1_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplecombinedcolumn1"),
# orientation = "landscape")
## ----combined_column_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "examplecombinedcolumn1", orientation = "landscape")
## ----improved_combined_column_setup, eval=FALSE-------------------------------
# # choose if any facets need to be removed - e.g remove the combined column for placebo
# rm_combo_from_placebo <- cond_rm_facets(
# facets = "Combined",
# ancestor_pos = NA,
# value = " ",
# split = "colspan_trt"
# )
#
# mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
## ----improved_combined_column_full--------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
colspan_trt = factor(c("Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" ",
"Active Study Agent",
"Active Study Agent",
"Active Study Agent",
" "),
levels = c(
"Active Study Agent",
" "
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
# Set up levels and label for the required combined column
add_combo <- add_combo_facet("Combined",
label = "Combined",
levels = c("Example Drug 5 mg", "Example Drug 10 mg", "Example Drug 20 mg")
)
# choose if any facets need to be removed - e.g remove the combined column for placebo
rm_combo_from_placebo <- cond_rm_facets(
facets = "Combined",
ancestor_pos = NA,
value = " ",
split = "colspan_trt"
)
mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
colspan_trt_map <- create_colspan_map(adsl,
non_active_grp = "Placebo",
non_active_grp_span_lbl = " ",
active_grp_span_lbl = "Active Study Agent",
colspan_var = "colspan_trt",
trt_var = "TRT01A")
lyt <- basic_table(
show_colcounts = TRUE,
colcount_format = "N=xx"
) |>
split_cols_by("colspan_trt",
split_fun = trim_levels_to_map(map = colspan_trt_map)
) |>
split_cols_by("TRT01A",
show_colcounts = FALSE,
split_fun = mysplit
) |>
### create table body row sections based on SEX
split_rows_by("SEX",
section_div = c(" "),
page_by = TRUE,
split_fun = drop_split_levels
) |>
summarize_row_groups("SEX",
cfun =a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
extrablankline = TRUE,
.stats = c("count_unique")
)
) |>
### analyze height
analyze("RESPONSE",
var_labels = c("Response"),
show_labels = "visible",
afun = a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
.stats = c("count_unique_fraction")
)
)
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----combined_column2_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplecombinedcolumn2"),
# orientation = "landscape")
## ----improved_combined_column_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "examplecombinedcolumn2", orientation = "landscape")
## ----newline_data-------------------------------------------------------------
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
adsl
## ----newline_table_rtf--------------------------------------------------------
library(junco)
library(rtables)
adsl <- data.frame(TRT01A = c("Example Drug\\line 5 mg",
"Example Drug\\line 10 mg",
"Example Drug\\line 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
lyt <- basic_table(
show_colcounts = FALSE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",,
show_colcounts = FALSE
) |>
### analyze height
analyze("HEIGHT", afun = list_wrap_x(summary), format = "xx.xx")
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----newline_table_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/newlinetable"),
# orientation = "landscape")
## ----newline_table_docx-------------------------------------------------------
library(junco)
library(rtables)
adsl <- data.frame(TRT01A = c("Example Drug\n 5 mg",
"Example Drug\n 10 mg",
"Example Drug\n 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
lyt <- basic_table(
show_colcounts = FALSE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",,
show_colcounts = FALSE
) |>
### analyze height
analyze("HEIGHT", afun = list_wrap_x(summary), format = "xx.xx")
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----newline_table_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# export_as_docx_j(result,
# tblid = "examplenewline",
# output_dir = out_dir,
# orientation = "landscape")
## ----newline_table_rtf_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "newlinetable", orientation = "landscape")
## ----newline_listing_rtf------------------------------------------------------
library(junco)
library(rlistings)
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
) |>
formatters::var_relabel(TRT01A = "Actual Treatment for\\line Period 01") |>
formatters::var_relabel(SUBJECT = "Subject") |>
formatters::var_relabel(HEIGHT = "Height (in)")
result <- rlistings::as_listing(
df = adsl,
key_cols = c("TRT01A", "SUBJECT"),
disp_cols = "HEIGHT"
)
result <- set_titles(result, titles)
## ----newline_listing_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplelistingnewline2"),
# orientation = "landscape")
## ----newline_listing_docx-----------------------------------------------------
library(junco)
library(rlistings)
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
) |>
formatters::var_relabel(TRT01A = "Actual Treatment for\n Period 01") |>
formatters::var_relabel(SUBJECT = "Subject") |>
formatters::var_relabel(HEIGHT = "Height (in)")
result <- rlistings::as_listing(
df = adsl,
key_cols = c("TRT01A", "SUBJECT"),
disp_cols = "HEIGHT"
)
result <- set_titles(result, titles)
## ----newline_listing_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# export_as_docx_j(result,
# tblid = "examplelistingnewline2",
# output_dir = out_dir,
# orientation = "landscape")
## ----newline_listing_rtf_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "examplelistingnewline2", orientation = "landscape")
## ----border_matrix------------------------------------------------------------
library(junco)
adsl <- data.frame(span = c("Example Drug Low Dose",
"Example Drug Low Dose",
"Example Drug High Dose",
" "),
TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
lyt <- basic_table(
show_colcounts = FALSE,
colcount_format = "N=xx"
) |>
### first level in column header
split_cols_by("span",,
show_colcounts = FALSE
) |>
### second level in column header
split_cols_by("TRT01A",,
show_colcounts = FALSE
) |>
### analyze height
analyze("HEIGHT", afun = list_wrap_x(summary), format = "xx.xx")
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----border_matrix_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/bordertable"),
# orientation = "landscape")
## ----border_matrix_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "bordertable", orientation = "landscape")
## ----default_border_matrix----------------------------------------------------
header_border <- junco:::make_header_bordmat(obj = result)
header_border
## ----updated_border_matrix----------------------------------------------------
header_border[1, 4] <- 4
header_border
## ----custom_border_matrix_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/custombordertable"),
# orientation = "landscape",
# border_mat = header_border)
## ----custom_border_matrix_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# export_as_docx_j(result,
# tblid = "custombordertable",
# output_dir = out_dir,
# orientation = "landscape",
# border_mat = header_border)
## ----custom_border_matrix_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "custombordertable", orientation = "landscape", border_mat = header_border)
## ----default_markup_rtf-------------------------------------------------------
library(tibble)
dps_markup_df <- tibble::tribble(
~keyword,
~rtfstart,
~rtfend,
"super",
"\\super",
"\\nosupersub",
"sub",
"\\sub",
"\\nosupersub",
"optional",
"",
""
)
dps_markup_df
## ----superscript_example_data-------------------------------------------------
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
adsl
## ----superscript_table_rtf----------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = c("Example Drug~[super a] 5 mg",
"Example Drug~[super a] 10 mg",
"Example Drug~[super a] 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
lyt <- basic_table(
show_colcounts = FALSE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",,
show_colcounts = FALSE
) |>
### analyze height
analyze("HEIGHT", afun = list_wrap_x(summary), format = "xx.xx")
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----superscript_table_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/superscripttable"),
# orientation = "landscape",
# markup_df = dps_markup_df)
## ----default_markup_docx2-----------------------------------------------------
library(tibble)
docx_markup_df <- tibble::tribble(
~keyword,
~replace_by,
"super",
"flextable::as_sup",
"sub",
"flextable::as_sub",
"optional",
""
)
docx_markup_df
## ----superscript_table_docx---------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = c("Example Drug~[super a] 5 mg",
"Example Drug~[super a] 10 mg",
"Example Drug~[super a] 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
)
lyt <- basic_table(
show_colcounts = FALSE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",,
show_colcounts = FALSE
) |>
### analyze height
analyze("HEIGHT", afun = list_wrap_x(summary), format = "xx.xx")
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----superscript_table_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# export_as_docx_j(result,
# tblid = "superscripttable",
# output_dir = out_dir,
# orientation = "landscape",
# markup_df = docx_markup_df)
## ----superscript_table_rtf_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "superscripttable", orientation = "landscape", markup_df = dps_markup_df)
## ----superscript_listing_rtf--------------------------------------------------
library(junco)
library(rlistings)
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
) |>
formatters::var_relabel(TRT01A = "Actual Treatment for Period 01~[super a]") |>
formatters::var_relabel(SUBJECT = "Subject") |>
formatters::var_relabel(HEIGHT = "Height (in)")
result <- rlistings::as_listing(
df = adsl,
key_cols = c("TRT01A", "SUBJECT"),
disp_cols = "HEIGHT"
)
result <- set_titles(result, titles)
## ----superscript_listing_rtf_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplelistingsuperscript2"),
# orientation = "landscape")
## ----default_markup_docx------------------------------------------------------
library(tibble)
docx_markup_df <- tibble::tribble(
~keyword,
~replace_by,
"super",
"flextable::as_sup",
"sub",
"flextable::as_sub",
"optional",
""
)
docx_markup_df
## ----superscript_listing_docx-------------------------------------------------
library(junco)
library(rlistings)
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
) |>
formatters::var_relabel(TRT01A = "Actual Treatment for Period 01~[super a]") |>
formatters::var_relabel(SUBJECT = "Subject") |>
formatters::var_relabel(HEIGHT = "Height (in)")
result <- rlistings::as_listing(
df = adsl,
key_cols = c("TRT01A", "SUBJECT"),
disp_cols = "HEIGHT"
)
result <- set_titles(result, titles)
## ----superscript_listing_docx_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# export_as_docx_j(result,
# tblid = "examplelistingsuperscript2",
# output_dir = out_dir,
# orientation = "landscape",
# markup_df = docx_markup_df)
## ----superscript_listing_rtf_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result, "examplelistingsuperscript2", orientation = "landscape", markup_df = dps_markup_df)
## ----multiple_docs_data_prep--------------------------------------------------
library(tern)
library(dplyr)
library(rtables)
library(junco)
################################################################################
# Define script level parameters:
################################################################################
string_map <- default_str_map
trtvar <- "TRT01A"
popfl <- "SAFFL"
################################################################################
# Process Data:
################################################################################
adsl <- pharmaverseadamjnj::adsl %>%
filter(!!rlang::sym(popfl) == "Y") %>%
select(STUDYID, USUBJID, all_of(trtvar), all_of(popfl), RACE)
adae <- pharmaverseadamjnj::adae %>%
filter(TRTEMFL == "Y" & AEBODSYS == "Skin and subcutaneous tissue disorders") %>%
select(USUBJID, TRTEMFL, AEBODSYS, AEDECOD, RACE)
adsl$colspan_trt <- factor(ifelse(adsl[[trtvar]] == "Placebo", " ", "Active Study Agent"),
levels = c("Active Study Agent", " ")
)
colspan_trt_map <- create_colspan_map(adsl,
non_active_grp = "Placebo",
non_active_grp_span_lbl = " ",
active_grp_span_lbl = "Active Study Agent",
colspan_var = "colspan_trt",
trt_var = trtvar
)
# Add total for Race - adsl
totalrace1 <- adsl %>%
filter(RACE != "UNKNOWN" & !is.na(RACE)) %>%
mutate(RACE = "Total")
adsl <- bind_rows(totalrace1, adsl)
adsl <- adsl %>%
mutate(RACEcat = case_when(
RACE == "Total" ~ "Total",
RACE == "WHITE" ~ "White",
RACE == "BLACK OR AFRICAN AMERICAN" ~ "Black",
RACE == "ASIAN" ~ "Asian",
RACE != "UNKNOWN" & !is.na(RACE) ~ "Other"
)) %>%
filter(RACEcat %in% c("Total", "White", "Black", "Asian", "Other")) %>%
select(-RACE)
adsl$spanheader <- factor(ifelse(adsl$RACEcat == "Total", " ", "Race"),
levels = c(" ", "Race")
)
adsl$RACEcat <- factor(adsl$RACEcat, levels = c("Total", "White", "Black", "Asian", "Other"))
# Add total for Race - adae
totalrace2 <- adae %>%
filter(RACE != "UNKNOWN" & !is.na(RACE)) %>%
mutate(RACE = "Total")
adae <- bind_rows(totalrace2, adae)
adae <- adae %>%
mutate(RACEcat = case_when(
RACE == "Total" ~ "Total",
RACE == "WHITE" ~ "White",
RACE == "BLACK OR AFRICAN AMERICAN" ~ "Black",
RACE == "ASIAN" ~ "Asian",
RACE != "UNKNOWN" & !is.na(RACE) ~ "Other"
)) %>%
filter(RACEcat %in% c("Total", "White", "Black", "Asian", "Other")) %>%
select(-RACE)
adae$RACEcat <- factor(adae$RACEcat, levels = c("Total", "White", "Black", "Asian", "Other"))
# join data together
ae <- left_join(adsl, adae, by = c("USUBJID", "RACEcat"))
################################################################################
# Define layout and build table:
################################################################################
extra_args_1 <- list(denom = "n_altdf",
.stats = c("count_unique_fraction")
)
extra_args_2 <- list(denom = "n_altdf",
.stats = c("count_unique")
)
lyt <- basic_table(
top_level_section_div = " ",
show_colcounts = FALSE
) %>%
split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map))
lyt <- lyt %>%
split_cols_by(trtvar)
lyt <- lyt %>%
split_cols_by("spanheader", split_fun = trim_levels_in_group("RACEcat")) %>%
split_cols_by("RACEcat") %>%
analyze(popfl,
afun = a_freq_j,
show_labels = "hidden",
section_div = c(" "),
extra_args = append(extra_args_2,
list(
label = "Analysis set: Safety",
val = "Y",
section_div = c(" ")))
) %>%
analyze("TRTEMFL",
afun = a_freq_j,
show_labels = "hidden",
extra_args = append(extra_args_1,
list(label = "Subjects with >=1 AE",
val = "Y",
section_div = c(" ")))
) %>%
split_rows_by("AEBODSYS",
split_label = "System Organ Class",
split_fun = trim_levels_in_group("AEDECOD"),
label_pos = "topleft",
section_div = c(" "),
nested = FALSE
) %>%
summarize_row_groups("AEBODSYS",
cfun = a_freq_j,
extra_args = extra_args_1
) %>%
analyze("AEDECOD",
afun = a_freq_j,
extra_args = extra_args_1
) %>%
append_topleft(" Preferred Term, n (%)")
result <- build_table(lyt, ae, alt_counts_df = adsl)
result <- set_titles(result, titles)
#########################################################################################
# Post-Processing step to sort by descending count on chosen active treatment columns.
# For this table we can use a defined colpath so it takes the appropriate sub-column ("Total")
# for the last active treatment group/combined and use this for its sort order.
# If you only have 1 active treatment arm, consider using jj_complex_scorefun(spanningheadercolvar = NA, usefirstcol = TRUE)
# See function documentation for jj_complex_scorefun should your require a different sorting behavior.
#########################################################################################
# col_paths_summary(result)
if (length(adae$TRTEMFL) != 0) {
result <- sort_at_path(result, c("root", "AEBODSYS"),
scorefun = jj_complex_scorefun(colpath = c("colspan_trt", "Active Study Agent", trtvar, "Xanomeline High Dose", "spanheader", " ", "RACEcat", "Total"))
)
result <- sort_at_path(result, c("root", "AEBODSYS", "*", "AEDECOD"),
scorefun = jj_complex_scorefun(colpath = c("colspan_trt", "Active Study Agent", trtvar, "Xanomeline High Dose", "spanheader", " ", "RACEcat", "Total"))
)
}
## ----multiple_docs_table1-----------------------------------------------------
################################################################################
# Convert to tbl file and output table
################################################################################
## ----multiple_docs_table1_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(string_map = string_map, tt = result,
# file = paste0(out_dir, "/aetablemultipledocs1"), orientation = "landscape"
# )
## ----multiple_docs_table1_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
x <- tt_to_flextable_j(string_map = string_map, tt = result, "aetablemultipledocs1", orientation = "landscape", paginate= TRUE)
x[[1]]
knitr::asis_output("
")
x[[2]]
knitr::asis_output("
")
## ----multiple_docs_table2-----------------------------------------------------
################################################################################
# Convert to tbl file and output table
################################################################################
## ----multiple_docs_table2_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(string_map = string_map, tt = result,
# file = paste0(out_dir, "/aetablemultipledocs2"), orientation = "landscape",
# nosplitin = list(cols = c(trtvar))
# )
## ----multiple_docs_table2_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
x <- tt_to_flextable_j(string_map = string_map, tt = result, "aetablemultipledocs2", orientation = "landscape",
nosplitin = list(cols = c(trtvar)), paginate= TRUE)
x[[1]]
knitr::asis_output("
")
x[[2]]
knitr::asis_output("
")
x[[3]]
knitr::asis_output("
")
## ----multiple_docs_table3_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(string_map = string_map, tt = result,
# file = paste0(out_dir, "/aetablemultipledocs3"), orientation = "landscape",
# nosplitin = list(cols = c(trtvar)),
# combined_rtf = TRUE
# )
## ----multiple_docs_table3_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
x <- tt_to_flextable_j(string_map = string_map, tt = result, "aetablemultipledocs3", orientation = "landscape",
nosplitin = list(cols = c(trtvar)), combined_rtf = TRUE, paginate = TRUE)
x[[1]]
knitr::asis_output("
")
x[[2]]
knitr::asis_output("
")
x[[3]]
knitr::asis_output("
")
## ----page_break_table---------------------------------------------------------
library(junco)
adsl <- data.frame(TRT01A = factor(c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo",
"Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
levels = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"
)
),
USUBJID = c("1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"),
RESPONSE = factor(c("Yes",
"No",
"Yes",
"Yes",
"Yes",
"No",
"Yes",
"No"),
levels = c("Yes",
"No")
),
SEX = factor(c("Male",
"Female",
"Male",
"Female",
"Female",
"Male",
"Female",
"Male"),
levels = c("Male",
"Female")
)
) |>
var_relabel(RESPONSE = "Response")
lyt <- basic_table(
show_colcounts = TRUE,
colcount_format = "N=xx"
) |>
### first columns
split_cols_by("TRT01A",
show_colcounts = FALSE
) |>
### create table body row sections based on SEX
split_rows_by("SEX",
section_div = c(" "),
page_by = TRUE,
split_fun = drop_split_levels
) |>
summarize_row_groups("SEX",
cfun =a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
extrablankline = TRUE,
.stats = c("count_unique")
)
) |>
### analyze height
analyze("RESPONSE",
var_labels = c("Response"),
show_labels = "visible",
afun = a_freq_j,
extra_args = list(denom = "n_df",
denom_by = "SEX",
riskdiff = FALSE,
.stats = c("count_unique_fraction")
)
)
result <- build_table(lyt, adsl)
result <- set_titles(result, titles)
## ----page_break_table_export, eval=NOT_CRAN, message=FALSE, warning=FALSE-----
# tt_to_tlgrtf(result,
# file = paste0(out_dir, "/examplepagebreak"))
## ----page_break_table_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
male <- result[1:5, keep_titles = TRUE, keep_footers = FALSE]
tt_to_flextable_j(male, "examplepagebreak")
knitr::asis_output("
")
## ----page_break_table_display_part2, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
female <- result[6:10, keep_titles = TRUE, keep_footers = TRUE]
tt_to_flextable_j(female, "examplepagebreak")
## ----split_listing_part1------------------------------------------------------
library(junco)
library(rlistings)
adsl <- data.frame(TRT01A = c("Example Drug 5 mg",
"Example Drug 10 mg",
"Example Drug 20 mg",
"Placebo"),
SUBJECT = c("1",
"2",
"3",
"4"),
HEIGHT = c(70,
74,
60,
64
)
) |>
formatters::var_relabel(TRT01A = "Actual Treatment for Period 01~[super a]") |>
formatters::var_relabel(SUBJECT = "Subject") |>
formatters::var_relabel(HEIGHT = "Height (in)")
result <- rlistings::as_listing(
df = adsl,
key_cols = c("TRT01A", "SUBJECT"),
disp_cols = "HEIGHT"
)
result <- set_titles(result, titles)
keep <- result$TRT01A %in% c("Example Drug 5 mg", "Example Drug 10 mg")
result1 <- result[keep, ]
## ----split_listing_part1_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result1,
# file = paste0(out_dir, "/examplelistingmultiplefilesPART1OF2"),
# orientation = "landscape"
# )
## ----split_listing_docx_part1_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
#
# export_as_docx_j(result1,
# tblid = "examplelistingmultiplefilesPART1OF2",
# output_dir = out_dir,
# orientation = "landscape"
# )
## ----split_listing_part1_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result1, "examplelistingmultiplefilesPART1OF2",
orientation = "landscape")
## ----split_listing_part2------------------------------------------------------
keep <- result$TRT01A %in% c("Example Drug 20 mg", "Placebo")
result2 <- result[keep, ]
## ----split_listing_part2_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
# tt_to_tlgrtf(result2,
# file = paste0(out_dir, "/examplelistingmultiplefilesPART2OF2"),
# orientation = "landscape"
# )
## ----split_listing_docx_part2_export, eval=NOT_CRAN, message=FALSE, warning=FALSE----
#
# export_as_docx_j(result2,
# tblid = "examplelistingmultiplefilesPART2OF2",
# output_dir = out_dir,
# orientation = "landscape"
# )
## ----split_listing_part2_display, echo=FALSE, fig.align="center", out.width="100%", out.height="200px"----
tt_to_flextable_j(result2, "examplelistingmultiplefilesPART2OF2",
orientation = "landscape")