## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE, echo=TRUE----------------------------------------------------
# library(reporter)
# 
# # Create temp file name
# tmp <- file.path(tempdir(), "example16a.pdf")
# 
# # Create data
# arm <- c(rep("A", 3), rep("B", 2), rep("C", 3), rep("D", 2))
# subjid <- 100:109
# name <- c("Quintana, Gabriel", "Allison, Blas", "Minniear, Presley",
#           "al-Kazemi, Najwa", "Schaffer, Ashley", "Laner, Tahma",
#           "Perry, Sean", "Crews, Deshawn Joseph", "Person, Ladon",
#           "Smith, Shaileigh")
# sex <- c("M", "F", "F", "M", "M", "F", "M", "F", "F", "M")
# age <- c(41, 53, 43, 39, 47, 52, 21, 38, 62, 26)
# 
# df <- data.frame(arm, subjid, name, sex, age, stringsAsFactors = FALSE)
# df <- rbind(df, df, df, df)
# 
# # Output with group_border
# tbl1 <- create_table(df, first_row_blank = FALSE, borders = "outside") %>%
#   define(subjid, label = "Subject ID for a patient", n = 10, align = "left",
#          width = 1) %>%
#   define(name, label = "Subject Name", width = 1) %>%
#   define(sex, label = "Sex", n = 10, align = "center") %>%
#   define(age, label = "Age", n = 10) %>%
#   define(arm, label = "Arm",
#          dedupe = TRUE,
#          group_border = TRUE)
# 
# 
# rpt <- create_report(tmp, output_type = "pdf", font = "Arial",
#                      font_size = 10) %>%
#   titles(c("Table 1.0", "This is a table with group border"), align = "center") %>%
#   add_content(tbl1) %>%
#   set_margins(top = 1, bottom = 1)
# 
# 
# res <- write_report(rpt)
# 

## ----eval=FALSE, echo=TRUE----------------------------------------------------
# library(reporter)
# 
# fp <- file.path(tempdir(), "example16b.pdf")
# 
# # Prepare data
# adae <- data.frame(
#   total = rep("Number of subject with adverse events", 53),
#   AESOC = c(NA,
#             rep("General disorders and administration site conditions", 9),
#             rep("Hepatobiliary disorders", 5),
#             rep("Infections and infestations", 25),
#             rep("Injury, poisoning and procedural complications", 13)),
#   AEDECOD = c(NA,
#               NA, rep("APPLICATION SITE ERYTHEMA", 4), rep("INFLUENZA LIKE ILLNESS", 4),
#               NA, rep("GALLBLADDER DISORDER", 4),
#               NA, rep("BRONCHITIS", 4), rep("NAIL INFECTION", 4), rep("PARONYCHIA", 4),
#               rep("RASH PUSTULAR", 4), rep("RESPIRATORY TRACT INFECTION", 4),
#               rep("RHINITIS", 4),
#               NA, rep("FALL", 4), rep("HEAT CRAMPS", 4), rep("MUSCLE INJURY", 4)
#   )
# )
# 
# adae$aedecod_seq <- rep(NA, nrow(adae))
# non_na_idx <- !is.na(adae$AEDECOD)
# adae$aedecod_seq[non_na_idx] <- ave(adae$AEDECOD[non_na_idx], adae$AEDECOD[non_na_idx], FUN = seq_along)
# 
# adae$AESEV <- adae$aedecod_seq
# adae$AESEV[adae$AESEV == "1"] <- NA
# adae$AESEV[adae$AESEV == "2"] <- "Mild"
# adae$AESEV[adae$AESEV == "3"] <- "Moderate"
# adae$AESEV[adae$AESEV == "4"] <- "Severe"
# 
# adae$trt1 <- "x ( x.x%)"
# adae$trt2 <- "x ( x.x%)"
# adae$trt3 <- "x ( x.x%)"
# 
# adae$aedecod_id <- rep(NA, nrow(adae))
# adae$aedecod_id[non_na_idx] <- ave(adae$AEDECOD[non_na_idx], adae$AESOC[non_na_idx],
#                                    FUN = function(x){as.numeric(factor(x, levels = unique(x)))})
# 
# adae$blank_grp <- paste(adae$total,
#                         adae$AESOC,
#                         ifelse(adae$aedecod_id == 1,NA,adae$AEDECOD),
#                         sep = "|")
# 
# adae <- adae[, setdiff(names(adae), c("aedecod_seq", "aedecod_id"))]
# 
# # Output
# custom_n_format <- function(x){
#   return(paste0("\n(N = ",x,")\nn(%)"))
# }
# 
# current_date <- gsub(" ","",toupper(format(Sys.Date(),"%d %b %Y")))
# current_time <- substr(Sys.time(),12,19)
# output_name <- "example16c.pdf"
# program_path <- "/dummy/tables/t-teae-soc-pt-gr-saf.R"
# 
# total_width <- 6
# trt_width <- 1.04
# item_width <- total_width - (trt_width*3)
# 
# tbl <- create_table(adae,
#                     borders = "outside",
#                     n_format = custom_n_format) %>%
# 
#   # ----- Column setting -----#
#   column_defaults(from = trt1, to = trt3, align = "center", width = trt_width) %>%
#   define(blank_grp, blank_before = T, visible = FALSE) %>%
#   stub(vars = c("total", "AESOC", "AEDECOD", "AESEV"),
#        label = "System Organ Class\n  Preferred Term\n    Grade",
#        width = item_width) %>%
#   define(AESOC, break_label = "(Continued)") %>%
#   define(AEDECOD, indent = 0.16, break_label = "(Continued)") %>%
#   define(AESEV, indent = 0.32) %>%
#   define(trt1, label = "Treatment A", n=11) %>%
#   define(trt2, label = "Treatment B", n=7) %>%
#   define(trt3, label = "Treatment C", n=15) %>%
# 
#   # ----- Footnote setting -----#
#   footnotes("Page [pg] of [tpg]", align = "right", blank_row = "none", valign = "top") %>%
#   footnotes("Safety Analysis Set includes all subjects who are received at least one dose of study drug.",
#             align = "left", blank_row = "none", valign = "top") %>%
#   footnotes("The analysis is performed on the maximum severity grade.",
#             align = "left", blank_row = "none", valign = "top") %>%
#   footnotes("Coded using MedDRA version 22.1.",
#             align = "left", blank_row = "none", valign = "top") %>%
#   footnotes(paste0("Program: ", program_path), italics = TRUE)
# 
# sty <- create_style(font_name = "Arial",
#                     font_size = 9)
# 
# rpt <- create_report(fp,
#                      orientation = "landscape",
#                      output_type = "PDF")  %>%
#   add_style(style = sty) %>%
#   set_margins(top = 1, bottom = 0.75, right = 1, left = 1.5) %>%
#   add_content(tbl) %>%
# 
#   # ----- Title setting -----#
#   titles("Table 14-6.1.3.1.  Treatment-emergent Adverse Events by System Organ Class,",
#          "Preferred Term and Grade",
#          "(Safety Analysis Set)",
#          bold = T,
#          font_size = 11)
# 
# # Write the report
# res <- write_report(rpt)
# 
# # Uncomment to view
# # file.show(res$path)
# 

## ----eval=FALSE, echo=TRUE----------------------------------------------------
# define(AESOC, break_label = "(Continued)", group_cohesion = TRUE)
# define(AEDECOD, indent = 0.16, break_label = "(Continued)", group_cohesion = TRUE)

## ----eval=FALSE, echo=TRUE----------------------------------------------------
# library(reporter)
# 
# fp <- file.path(tempdir(), "example16b.pdf")
# 
# # Create data
# dat <- iris[1:91,]
# 
# dat$group_1 <- c(
#   rep("A", 14),
#   rep("B", 6),
#   rep("C", 22),
#   rep("D", 18),
#   rep("E", 31)
# )
# 
# dat$group_2 <- c(
#   rep("Flower A\nSubgroup A1", 14),
#   rep("Flower B\nSubgroup B1", 3),
#   rep("Flower B\nSubgroup B2", 3),
#   c(rep("Flower C1", 17)),
#   c(rep("Flower C2", 5)),
#   c(rep("Flower D", 16), rep("Flower D\nSubgroup D1", 2)),
#   c(rep("Flower E1", 2)),
#   c(rep("Flower E2", 29))
# )
# 
# dat <- dat[, c("group_1", "group_2", "Sepal.Length",
#                "Sepal.Width", "Petal.Length","Petal.Width")]
# 
# # Create table
# tbl <- create_table(dat, borders = "outside") %>%
#   define(group_1, group_cohesion = TRUE, label = "Region", blank_after = T,
#          width = 1.2) %>%
#   define(group_2, group_cohesion = TRUE, label = "Sector")
# 
# # Create report
# rpt <- create_report(fp, output_type = "pdf", font = "Arial",
#                      font_size = 10, orientation = "landscape") %>%
#   titles("Table 1.0", "Analysis of Iris Flowers") %>%
#   set_margins(top = 1, bottom = 1) %>%
#   add_content(tbl) %>%
#   footnotes("Program: /test/example16b.R",
#             "Output: /test/example16b.pdf")
# 
# # Output report
# res <- write_report(rpt)
#