Group Border
The reporter package can draw bottom lines to
separate different groups by setting group_border = TRUE in
define().
Here is an example:
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 \nand more and more", "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) %>%
footnotes("This is the footnote")
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) %>%
footnotes(c("This is the footnote 1")) %>%
page_header(left = "Test header", right = "Test header") %>%
set_margins(top = 1, bottom = 1)
res <- write_report(rpt)
Group Cohesion
In AE tables and summary statistics tables, there are groups for each
section, and sometimes we want to avoid splitting the same group across
multiple pages. With group cohesion, the reporter
package can keep the group on in the same page as much as possible by
setting group_cohesion = TRUE in define().
Here is an example:
library(reporter)
fp <- file.path(tempdir(), "example16b.pdf")
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")]
tbl <- create_table(dat, borders = "outside") %>%
define(group_1, group_cohesion = TRUE, label = "Group 1", blank_after = T) %>%
define(group_2, group_cohesion = TRUE, label = "Group 2")
rpt <- create_report(fp, output_type = "pdf", font = "Arial",
font_size = 10, orientation = "landscape") %>%
titles("Table 1.0", "My Nice Report with Group Cohesion") %>%
set_margins(top = 1, bottom = 1) %>%
add_content(tbl) %>%
footnotes("My footnote 1", "My footnote 2", borders = "none",
blank_row = "none")
res <- write_report(rpt)Page 1:
Page 2:
We can see that there is still space in the end of
page 1, but it’s not enough for the entire group B. To keep group B in
the same page, it is moved to the page 2.
Page 3:
After group B, the remaining space is not enough for
entire group C, and we cannot move the entire group C to page 3 or the
remaining space would be too much in page 2. As a result, group C will
be split from page 2 to page 3. However, because we set
group_cohesion = TRUE for both Group1 and Group2, when
Group1 is split, reporter will still keep Group2 on the
same page as much as possible. Therefore, we can see that the entire
“Flower C2” is moved to page 3 because the remaining space after “Flower
C1” is not enough for “Flower C2”.
Logic of Group Cohesion
The logic of group cohesion is very simple. If a group is to split,
the entire group will be moved to next page only if occupies at least
80% of the current page. Accordingly, Group B moves to the next page
because Group A occupies at least 80% of the page. Similarly, Group C2
moves to the next page because the combined data from Group B and Group
C1 reaches the 80% threshold. When group_cohesion = TRUE,
the default strength of group cohesion is 0.2, which means the required
proportion is 1 - 0.2 = 0.8. Users can change the required
proportion by assigning more strength such as
group_cohesion = 0.6, which means the requirement of
proportion is 0.4. Once the previous group has reached 40% of page, the
next group can be moved to next page if the remaining space is not
enough. That’s say, the more strength of group cohesion, the lower the
required proportion, and the less likely the group is to split.
Break Label
For the outputs with hierarchy levels such as AE tables. Taking SOC
as an example, when SOC continues onto the next page, we might want to
display the SOC again with suffix wording such as “Continued”. With
break_label = "Continued" in define(), the
reporter package will automatically generate the
repeated SOC with “Continued” at the top of next page.
Here is an example:
library(reporter)
fp <- file.path(tempdir(), "example16c.pdf")
# Prepare data
adae <- data.frame(
total = rep("Number of subject with adverse events", 66),
AESOC = c(NA,
rep("Gastrointestinal disorders", 13),
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("CHEILITIS", 4), rep("DIARRHOEA", 4), rep("STOMACH DISCOMFORT", 4),
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"
last_footnote <- paste0("Output: ",output_name," Source: adae")
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 = "(Cont.)") %>%
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("Severity of adverse event will be graded using CTCAE version 4.0 criteria.",
align = "left", blank_row = "none", valign = "top") %>%
footnotes("Reported Verbatim Term are displayed for Uncoded AEs.",
align = "left", blank_row = "none", valign = "top") %>%
footnotes(paste0("Program: ", program_path), italics = TRUE) %>%
footnotes(last_footnote, blank_row = "none", italics = TRUE )
sty <- create_style(font_name = "Arial",
font_size = 9)
# fp <- file.path("C:/Users/HuangC3/OneDrive - Parexel/Documents/reporter_bill/tests/testthat/user/example16c.pdf")
rpt <- create_report(fp,
orientation = "portrait",
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) %>%
footnotes("All the data is from dummy database.")
# Write the report
res <- write_report(rpt)Page 1:
Page 2:
SOC “Infections and infestations” continues onto the next page,
so it is repeated at the top of page 2 with suffix “(Continued)”.
Page 3:
Both SOC “Injury, poisoning and procedural
complications” and preferred term “MUSCLE INJURY” continue onto page 3,
so they’re repeated at the top with different suffix words.
