inst/doc/title_footer.R

In rtables: Reporting Tables

## ---- echo=FALSE, output="hide"-----------------------------------------------
knitr::opts_chunk$set(comment = "#")
suppressPackageStartupMessages(library(rtables))
suppressPackageStartupMessages(library(dplyr))


## -----------------------------------------------------------------------------
library(rtables)
library(dplyr)
lyt <- basic_table(title = "Study XXXXXXXX",
                   subtitles = c("subtitle YYYYYYYYYY", "subtitle2 ZZZZZZZZZ"),
                   main_footer = "Analysis was done using cool methods that are correct",
                   prov_footer = "file: /path/to/stuff/that/lives/there HASH:1ac41b242a") %>%
    split_cols_by("ARM") %>%
    split_rows_by("SEX", split_fun = drop_split_levels) %>%
    split_rows_by("STRATA1") %>%
    analyze("AGE", mean, format = "xx.x")

tbl <- build_table(lyt, DM)
cat(export_as_txt(tbl, paginate = TRUE, page_break = "\n\n\n"))

## -----------------------------------------------------------------------------
lyt2 <- basic_table(title = "Study XXXXXXXX",
                   subtitles = c("subtitle YYYYYYYYYY", "subtitle2 ZZZZZZZZZ"),
                   main_footer = "Analysis was done using cool methods that are correct",
                   prov_footer = "file: /path/to/stuff/that/lives/there HASH:1ac41b242a") %>%
    split_cols_by("ARM") %>%
    split_rows_by("SEX", page_by = TRUE, page_prefix = "Patient Subset - Gender", split_fun = drop_split_levels) %>%
    split_rows_by("STRATA1") %>%
    analyze("AGE", mean, format = "xx.x")

tbl2 <- build_table(lyt2, DM)
cat(export_as_txt(tbl2, paginate = TRUE, page_break = "\n\n~~~~ Page Break ~~~~\n\n"))

## -----------------------------------------------------------------------------
lyt3 <- basic_table(title = "Study XXXXXXXX",
                   subtitles = c("subtitle YYYYYYYYYY", "subtitle2 ZZZZZZZZZ"),
                   main_footer = "Analysis was done using cool methods that are correct",
                   prov_footer = "file: /path/to/stuff/that/lives/there HASH:1ac41b242a") %>%
    split_cols_by("ARM") %>%
    split_rows_by("SEX", page_by = TRUE, page_prefix = "Patient Subset - Gender", split_fun = drop_split_levels) %>%
    split_rows_by("STRATA1", page_by = TRUE, page_prefix = "Stratification - Strata") %>%
    analyze("AGE", mean, format = "xx.x")

tbl3 <- build_table(lyt3, DM)
cat(export_as_txt(tbl3, paginate = TRUE, page_break = "\n\n~~~~ Page Break ~~~~\n\n"))

## -----------------------------------------------------------------------------


afun <- function(df, .var, .spl_context) {
    val <- .spl_context$value[NROW(.spl_context)]
    rw_fnotes <-  if(val == "C") list("This is strata level C for these patients") else list()
    cl_fnotes <- if(val == "B" && df[1, "ARM", drop = TRUE] == "C: Combination")
                     list("these Strata B patients got the drug combination") else list()
    
    in_rows(mean = mean(df[[.var]]),
            .row_footnotes = rw_fnotes,
            .cell_footnotes = cl_fnotes,
            .formats = c(mean = "xx.x"))
}

lyt <- basic_table(title = "Study XXXXXXXX",
                   subtitles = c("subtitle YYYYYYYYYY", "subtitle2 ZZZZZZZZZ"),
                   main_footer = "Analysis was done using cool methods that are correct",
                   prov_footer = "file: /path/to/stuff/that/lives/there HASH:1ac41b242a") %>%
    split_cols_by("ARM") %>%
    split_rows_by("SEX", page_by = TRUE, page_prefix = "Patient Subset - Gender", split_fun = drop_split_levels) %>%
    split_rows_by("STRATA1") %>%
    analyze("AGE", afun, format = "xx.x")

tbl <- build_table(lyt, DM)
cat(export_as_txt(tbl, paginate = TRUE, page_break = "\n\n\n"))


## -----------------------------------------------------------------------------
## from ?tolower example slightly modified
.simpleCap <- function(x) {
    if(length(x) > 1)
        return(sapply(x, .simpleCap))
    s <- strsplit(tolower(x), " ")[[1]]
    paste(toupper(substring(s, 1, 1)), substring(s, 2),
          sep = "", collapse = " ")
}

adsl2 <- ex_adsl %>%
    filter(SEX %in% c("M", "F") &
           RACE %in% (levels(RACE)[1:3])) %>%
    ## we trim the level names here solely due to space considerations
    mutate(ethnicity = .simpleCap(gsub("(.*)OR.*", "\\1", RACE)),
           RACE = factor(RACE))
 
lyt2 <- basic_table() %>%
  split_cols_by("ARM") %>%
    split_cols_by("SEX", split_fun = drop_split_levels) %>%
    split_rows_by("RACE", labels_var = "ethnicity",
                  split_fun = drop_split_levels) %>%
    summarize_row_groups() %>%
    analyze(c("AGE", "STRATA1"))

tbl2 <- build_table(lyt2, adsl2)
tbl2

## -----------------------------------------------------------------------------

fnotes_at_path(tbl2, c("RACE", "ASIAN")) <- c("hi", "there")
tbl2

## -----------------------------------------------------------------------------

fnotes_at_path(tbl2, rowpath = NULL, c("ARM", "B: Placebo")) <- c("this is a placebo")
tbl2

## -----------------------------------------------------------------------------
row_paths_summary(tbl2)

## -----------------------------------------------------------------------------
fnotes_at_path(tbl2,
               rowpath = c("RACE", "ASIAN", "@content", "Asian"),
               colpath = c("ARM", "B: Placebo", "SEX", "F")) <- "These asian women got placebo treatments"
tbl2