---
title: "Complete Example 3"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{example3}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

options(rmarkdown.html_vignette.check_title = FALSE)

```
## Program

Below is another complete example showing how the **reporter** package
interacts with **tidyverse** and **sassy** functions to create an Adverse
Events report.

```{r eval=FALSE, echo=TRUE}
library(tidyverse)
library(sassy)

options("logr.autolog" = TRUE, 
        "logr.notes" = FALSE)

# Get temp location for log and report output
tmp <- tempdir()


# Get Data ----------------------------------------------------------------


# Open log
lf <- log_open(file.path(tmp, "example3.log"))

sep("Prepare Data")

# Get path to sample data
pkg <- system.file("extdata", package = "reporter")

# Create libname for csv data
libname(sdtm, pkg, "csv", quiet = TRUE) 

# Load data into workspace
lib_load(sdtm) 


sep("Prepare table data")
dat <- sdtm.AE %>% 
  inner_join(select(sdtm.DM, USUBJID, ARM, ARMCD),  
             c("USUBJID" = "USUBJID"), 
             keep = FALSE) %>% 
  filter(ARM != "SCREEN FAILURE")

put("Get population counts")
arm_pop <- dat %>% 
  select(USUBJID, ARM) %>%  
  distinct() %>% 
  count(ARM)  %>% 
  deframe() %>% put()

put ("Create lookup for AE severity")
sevn <- c(MILD = 1, MODERATE = 2, SEVERE = 3) %>% put()

put("Subset ADAE for needed rows and columns")
df_sub <- dat %>% 
  mutate(AESEVN = sevn[AESEV]) %>% 
  select(USUBJID, ARM, AESEV, AESEVN, AESOC, AEDECOD) %>% 
  distinct() %>% 
  put()


# Perform Calculations ----------------------------------------------------
sep("Perform Calculations")

put("Create template for needed ARM columns")
col_template <- paste0(c(rep("ARM A_", 3), rep("ARM B_", 3), rep("ARM C_", 3),
                         rep("ARM D_", 3)), rep(c(1, 2, 3), 3))



put("Identify and count highest severity grade for each subject")
df1 <- df_sub %>% arrange(USUBJID, AESOC, AEDECOD, AESEVN) %>% 
  group_by(USUBJID, ARM, AESOC, AEDECOD) %>% 
  mutate(max_sev = ifelse(row_number() == n(), TRUE, FALSE)) %>% 
  filter(max_sev == TRUE) %>% 
  group_by(ARM, AESOC, AEDECOD, AESEVN) %>% 
  summarize(cnt = n()) %>% 
  pivot_wider(names_from = c(ARM, AESEVN),
              values_from = cnt, 
              values_fill = 0) %>% 
  put()


put("Fill in missing columns where there were no events.")
for (nm in col_template) {
  if (!nm %in% names(df1))
    df1[[nm]] <- 0
}
put(df1)

put("Format counts and percents for each column")
df_events <- df1 %>% 
  transmute(AESOC = AESOC, 
            AEDECOD = str_to_title(AEDECOD),
            `ARM A_1` = fmt_cnt_pct(`ARM A_1`, arm_pop["ARM A"]),
            `ARM A_2` = fmt_cnt_pct(`ARM A_2`, arm_pop["ARM A"]),
            `ARM A_3` = fmt_cnt_pct(`ARM A_3`, arm_pop["ARM A"]),
            `ARM B_1` = fmt_cnt_pct(`ARM B_1`, arm_pop["ARM B"]),
            `ARM B_2` = fmt_cnt_pct(`ARM B_2`, arm_pop["ARM B"]),
            `ARM B_3` = fmt_cnt_pct(`ARM B_3`, arm_pop["ARM B"]),
            `ARM C_1` = fmt_cnt_pct(`ARM C_1`, arm_pop["ARM C"]),
            `ARM C_2` = fmt_cnt_pct(`ARM C_2`, arm_pop["ARM C"]),
            `ARM C_3` = fmt_cnt_pct(`ARM C_3`, arm_pop["ARM C"]),
            `ARM D_1` = fmt_cnt_pct(`ARM D_1`, arm_pop["ARM D"]), 
            `ARM D_2` = fmt_cnt_pct(`ARM D_2`, arm_pop["ARM D"]), 
            `ARM D_3` = fmt_cnt_pct(`ARM D_3`, arm_pop["ARM D"])) %>% 
  arrange(AESOC, AEDECOD) %>% 
  ungroup() %>% 
  put()


put("Get counts for All Adverse Events")
df2 <- df_sub %>% 
  select(USUBJID, ARM, AESEVN) %>% 
  arrange(USUBJID, AESEVN) %>% 
  group_by(USUBJID) %>% 
  mutate(max_sev = ifelse(row_number() == n(), TRUE, FALSE)) %>% 
  filter(max_sev == TRUE) %>% 
  group_by(ARM, AESEVN) %>% 
  summarize(cnt = n()) %>% 
  pivot_wider(names_from = c(ARM, AESEVN),
              values_from = cnt, 
              values_fill = 0) %>% 
  ungroup() %>% 
  put()

put("Fill in missing columns where there were no events.")
for (nm in col_template) {
  if (!nm %in% names(df2))
    df2[[nm]] <- 0
}
put(df2)

put("Format counts and percents for all adverse events.")
df_all <- df2 %>% 
  transmute(AESOC = "All System Organ Classes",
            AEDECOD = "All Adverse Events", 
            `ARM A_1` = fmt_cnt_pct(`ARM A_1`, arm_pop["ARM A"]),
            `ARM A_2` = fmt_cnt_pct(`ARM A_2`, arm_pop["ARM A"]),
            `ARM A_3` = fmt_cnt_pct(`ARM A_3`, arm_pop["ARM A"]),
            `ARM B_1` = fmt_cnt_pct(`ARM B_1`, arm_pop["ARM B"]),
            `ARM B_2` = fmt_cnt_pct(`ARM B_2`, arm_pop["ARM B"]),
            `ARM B_3` = fmt_cnt_pct(`ARM B_3`, arm_pop["ARM B"]),
            `ARM C_1` = fmt_cnt_pct(`ARM C_1`, arm_pop["ARM C"]),
            `ARM C_2` = fmt_cnt_pct(`ARM C_2`, arm_pop["ARM C"]),
            `ARM C_3` = fmt_cnt_pct(`ARM C_3`, arm_pop["ARM C"]),
            `ARM D_1` = fmt_cnt_pct(`ARM D_1`, arm_pop["ARM D"]), 
            `ARM D_2` = fmt_cnt_pct(`ARM D_2`, arm_pop["ARM D"]), 
            `ARM D_3` = fmt_cnt_pct(`ARM D_3`, arm_pop["ARM D"])) %>% 
  put()


# Final Data --------------------------------------------------------------

sep("Create final data frame")

final <- bind_rows(df_all, df_events) %>% put()


# Print Report ----------------------------------------------------------

sep("Create and print report")

put("Create table object")
tbl <- create_table(final, first_row_blank = TRUE, width = 9) %>% 
  column_defaults(from = `ARM A_1`, to = `ARM D_3`, width = 1) %>% 
  spanning_header("ARM A_1", "ARM A_3", label = "ARM A", n = arm_pop["ARM A"]) %>%
  spanning_header("ARM B_1", "ARM B_3", label = "ARM B", n = arm_pop["ARM B"]) %>%
  spanning_header("ARM C_1", "ARM C_3", label = "ARM C", n = arm_pop["ARM C"]) %>%
  spanning_header("ARM D_1", "ARM D_3", label = "ARM D", n = arm_pop["ARM D"]) %>%
  stub(vars = c("AESOC", "AEDECOD"), label = "System Organ Class\n   Preferred Term", width = 5) %>% 
  define(AESOC, blank_after = TRUE, label_row = TRUE) %>% 
  define(AEDECOD, indent = .25) %>% 
  define(`ARM A_1`, align = "center", label = "Mild") %>% 
  define(`ARM A_2`, align = "center", label = "Moderate") %>% 
  define(`ARM A_3`, align = "center", label = "Severe") %>% 
  define(`ARM B_1`, align = "center", label = "Mild", page_wrap = TRUE) %>% 
  define(`ARM B_2`, align = "center", label = "Moderate") %>% 
  define(`ARM B_3`, align = "center", label = "Severe") %>% 
  define(`ARM C_1`, align = "center", label = "Mild", page_wrap = TRUE) %>% 
  define(`ARM C_2`, align = "center", label = "Moderate") %>% 
  define(`ARM C_3`, align = "center", label = "Severe") %>% 
  define(`ARM D_1`, align = "center", label = "Mild", page_wrap = TRUE) %>% 
  define(`ARM D_2`, align = "center", label = "Moderate") %>% 
  define(`ARM D_3`, align = "center", label = "Severe") 


put("Create report object")
rpt <- create_report(file.path(tmp, "output/example3.rtf"), output_type = "RTF",
                     font = "Arial") %>% 
  options_fixed(font_size = 10) %>% 
  page_header("Sponsor: Company", "Study: ABC") %>% 
  titles("Table 5.0", "Adverse Events by Maximum Severity", bold = TRUE,
         font_size = 12) %>% 
  add_content(tbl) %>% 
  footnotes("Program: AE_Table.R",
            "Note: Adverse events were coded using MedDRA Version 9.1") %>% 
  page_footer(Sys.time(), "Confidential", "Page [pg] of [tpg]") 

put("Print report")
res <- write_report(rpt) %>% put()



# Clean Up ----------------------------------------------------------------
sep("Clean Up")

# Remove library from workspace
lib_unload(sdtm)

# Close log
log_close()


# View log
writeLines(readLines(lf, encoding = "UTF-8"))

# View report
# file.show(res$file_path)

```

## Log

The above program produces the following log:
```
=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpgrpGQ1/log/example3.log
Program Path: C:\packages\Testing\reporter_example3.R
Working Directory: C:/packages/Testing
User Name: dbosa
R Version: 4.1.2 (2021-11-01)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 19041
Base Packages: stats graphics grDevices utils datasets methods base
Other Packages: tidylog_1.0.2 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
                readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5 tidyverse_1.3.1
                magrittr_2.0.1 reporter_1.2.6 libr_1.2.1 fmtr_1.5.4 logr_1.2.7
                sassy_1.0.5 
Log Start Time: 2021-11-21 14:58:57
=========================================================================

=========================================================================
Prepare Data
=========================================================================

# library 'sdtm': 8 items
- attributes: csv not loaded
- path: C:/Users/dbosa/Documents/R/win-library/4.1/reporter/extdata
- items:
  Name Extension Rows Cols     Size        LastModified
1   AE       csv  150   27  88.3 Kb 2021-10-08 15:02:15
2   DA       csv 3587   18 528.1 Kb 2021-10-08 15:02:15
3   DM       csv   87   24  45.4 Kb 2021-10-08 15:02:15
4   DS       csv  174    9  33.9 Kb 2021-10-08 15:02:15
5   EX       csv   84   11  26.2 Kb 2021-10-08 15:02:15
6   IE       csv    2   14  13.2 Kb 2021-10-08 15:02:15
7   SV       csv  685   10  70.2 Kb 2021-10-08 15:02:15
8   VS       csv 3358   17 467.3 Kb 2021-10-08 15:02:15

lib_load: library 'sdtm' loaded

=========================================================================
Prepare table data
=========================================================================

select: dropped 21 variables (STUDYID, DOMAIN, SUBJID, RFSTDTC, RFENDTC, <U+0085>)

inner_join: added 2 columns (ARM, ARMCD)

            > rows only in x  (  0)

            > rows only in y  ( 30)

            > matched rows     150

            >                 =====

            > rows total       150

filter: removed 5 rows (3%), 145 rows remaining

Get population counts

select: dropped 27 variables (STUDYID, DOMAIN, AESEQ, AETERM, AELLT, <U+0085>)

distinct: removed 90 rows (62%), 55 rows remaining

count: now 4 rows and 2 columns, ungrouped

ARM A ARM B ARM C ARM D 
   14    14    14    13 

Create lookup for AE severity

    MILD MODERATE   SEVERE 
       1        2        3 

Subset ADAE for needed rows and columns

mutate: new variable 'AESEVN' (double) with 3 unique values and 0% NA

select: dropped 24 variables (STUDYID, DOMAIN, AESEQ, AETERM, AELLT, <U+0085>)

distinct: removed 18 rows (12%), 127 rows remaining

# A tibble: 127 x 6
   USUBJID    ARM   AESEV    AESEVN AESOC                          AEDECOD              
   <chr>      <chr> <chr>     <dbl> <chr>                          <chr>                
 1 ABC-01-049 ARM D MODERATE      2 Investigations                 BLOOD GLUCOSE INCREA~
 2 ABC-01-049 ARM D MODERATE      2 Investigations                 BLOOD TRIGLYCERIDES ~
 3 ABC-01-049 ARM D MILD          1 Nervous system disorders       HEADACHE             
 4 ABC-01-049 ARM D MODERATE      2 Investigations                 LABORATORY TEST ABNO~
 5 ABC-01-049 ARM D MILD          1 Musculoskeletal and connectiv~ MUSCULOSKELETAL DISC~
 6 ABC-01-050 ARM B MILD          1 Skin and subcutaneous tissue ~ RASH                 
 7 ABC-01-050 ARM B MILD          1 Respiratory, thoracic and med~ UPPER RESPIRATORY TR~
 8 ABC-01-051 ARM A MILD          1 Nervous system disorders       HEADACHE             
 9 ABC-01-051 ARM A MILD          1 General disorders and adminis~ INFLUENZA LIKE ILLNE~
10 ABC-01-051 ARM A MILD          1 Respiratory, thoracic and med~ LOWER RESPIRATORY TR~
# ... with 117 more rows

=========================================================================
Perform Calculations
=========================================================================

Create template for needed ARM columns

Identify and count highest severity grade for each subject

group_by: 4 grouping variables (USUBJID, ARM, AESOC, AEDECOD)

mutate (grouped): new variable 'max_sev' (logical) with 2 unique values and 0% NA

filter (grouped): removed one row (1%), 126 rows remaining

group_by: 4 grouping variables (ARM, AESOC, AEDECOD, AESEVN)

summarize: now 101 rows and 5 columns, 3 group variables remaining (ARM, AESOC, AEDECOD)

pivot_wider: reorganized (ARM, AESEVN, cnt) into (ARM A_2, ARM A_1, ARM B_1, ARM B_2, ARM B_3, <U+0085>) [was 101x5, now 73x11]

# A tibble: 73 x 11
# Groups:   AESOC, AEDECOD [73]
   AESOC   AEDECOD `ARM A_2` `ARM A_1` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_2` `ARM C_1`
   <chr>   <chr>       <int>     <int>     <int>     <int>     <int>     <int>     <int>
 1 Gastro~ TOOTHA~         1         0         0         0         0         0         0
 2 Genera~ INFLUE~         0         1         0         0         0         0         0
 3 Infect~ GASTRO~         1         0         0         0         0         0         0
 4 Infect~ INFLUE~         1         0         0         0         0         0         0
 5 Infect~ ORAL C~         1         0         0         0         0         0         0
 6 Infect~ PNEUMO~         1         0         0         0         0         0         0
 7 Infect~ RESPIR~         0         1         0         0         0         1         2
 8 Infect~ SINUSI~         0         1         0         0         0         0         0
 9 Infect~ TOOTH ~         1         0         0         0         0         0         0
10 Infect~ UPPER ~         0         4         5         1         0         0         3
# ... with 63 more rows, and 2 more variables: ARM D_1 <int>, ARM D_2 <int>

Fill in missing columns where there were no events.

# A tibble: 73 x 14
# Groups:   AESOC, AEDECOD [73]
   AESOC   AEDECOD `ARM A_2` `ARM A_1` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_2` `ARM C_1`
   <chr>   <chr>       <int>     <int>     <int>     <int>     <int>     <int>     <int>
 1 Gastro~ TOOTHA~         1         0         0         0         0         0         0
 2 Genera~ INFLUE~         0         1         0         0         0         0         0
 3 Infect~ GASTRO~         1         0         0         0         0         0         0
 4 Infect~ INFLUE~         1         0         0         0         0         0         0
 5 Infect~ ORAL C~         1         0         0         0         0         0         0
 6 Infect~ PNEUMO~         1         0         0         0         0         0         0
 7 Infect~ RESPIR~         0         1         0         0         0         1         2
 8 Infect~ SINUSI~         0         1         0         0         0         0         0
 9 Infect~ TOOTH ~         1         0         0         0         0         0         0
10 Infect~ UPPER ~         0         4         5         1         0         0         3
# ... with 63 more rows, and 5 more variables: ARM D_1 <int>, ARM D_2 <int>,
#   ARM A_3 <dbl>, ARM C_3 <dbl>, ARM D_3 <dbl>

Format counts and percents for each column

transmute (grouped): changed 73 values (100%) of 'AEDECOD' (0 new NA)

                     converted 'ARM A_1' from integer to character (0 new NA)

                     converted 'ARM A_2' from integer to character (0 new NA)

                     converted 'ARM A_3' from double to character (0 new NA)

                     converted 'ARM B_1' from integer to character (0 new NA)

                     converted 'ARM B_2' from integer to character (0 new NA)

                     converted 'ARM B_3' from integer to character (0 new NA)

                     converted 'ARM C_1' from integer to character (0 new NA)

                     converted 'ARM C_2' from integer to character (0 new NA)

                     converted 'ARM C_3' from double to character (0 new NA)

                     converted 'ARM D_1' from integer to character (0 new NA)

                     converted 'ARM D_2' from integer to character (0 new NA)

                     converted 'ARM D_3' from double to character (0 new NA)

ungroup: no grouping variables

# A tibble: 73 x 14
   AESOC   AEDECOD `ARM A_1` `ARM A_2` `ARM A_3` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_1`
   <chr>   <chr>   <chr>     <chr>     <chr>     <chr>     <chr>     <chr>     <chr>    
 1 Blood ~ Neutro~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 2 Cardia~ Palpit~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 3 Cardia~ Sinus ~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 4 Congen~ Dermoi~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 5 Ear an~ Vertigo 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~
 6 Endocr~ Parath~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~
 7 Gastro~ Diarrh~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~
 8 Gastro~ Food P~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 9 Gastro~ Tootha~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
10 Gastro~ Vomiti~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 2 ( 14.3~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
# ... with 63 more rows, and 5 more variables: ARM C_2 <chr>, ARM C_3 <chr>,
#   ARM D_1 <chr>, ARM D_2 <chr>, ARM D_3 <chr>

Get counts for All Adverse Events

select: dropped 3 variables (AESEV, AESOC, AEDECOD)

group_by: one grouping variable (USUBJID)

mutate (grouped): new variable 'max_sev' (logical) with 2 unique values and 0% NA

filter (grouped): removed 72 rows (57%), 55 rows remaining

group_by: 2 grouping variables (ARM, AESEVN)

summarize: now 9 rows and 3 columns, one group variable remaining (ARM)

pivot_wider: reorganized (ARM, AESEVN, cnt) into (ARM A_1, ARM A_2, ARM B_1, ARM B_2, ARM B_3, <U+0085>) [was 9x3, now 1x9]

ungroup: no grouping variables

# A tibble: 1 x 9
  `ARM A_1` `ARM A_2` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_1` `ARM C_2` `ARM D_1`
      <int>     <int>     <int>     <int>     <int>     <int>     <int>     <int>
1         6         8         8         4         2         8         6         7
# ... with 1 more variable: ARM D_2 <int>

Fill in missing columns where there were no events.

# A tibble: 1 x 12
  `ARM A_1` `ARM A_2` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_1` `ARM C_2` `ARM D_1`
      <int>     <int>     <int>     <int>     <int>     <int>     <int>     <int>
1         6         8         8         4         2         8         6         7
# ... with 4 more variables: ARM D_2 <int>, ARM A_3 <dbl>, ARM C_3 <dbl>, ARM D_3 <dbl>

Format counts and percents for all adverse events.

transmute: new variable 'AESOC' (character) with one unique value and 0% NA

           new variable 'AEDECOD' (character) with one unique value and 0% NA

           converted 'ARM A_1' from integer to character (0 new NA)

           converted 'ARM A_2' from integer to character (0 new NA)

           converted 'ARM A_3' from double to character (0 new NA)

           converted 'ARM B_1' from integer to character (0 new NA)

           converted 'ARM B_2' from integer to character (0 new NA)

           converted 'ARM B_3' from integer to character (0 new NA)

           converted 'ARM C_1' from integer to character (0 new NA)

           converted 'ARM C_2' from integer to character (0 new NA)

           converted 'ARM C_3' from double to character (0 new NA)

           converted 'ARM D_1' from integer to character (0 new NA)

           converted 'ARM D_2' from integer to character (0 new NA)

           converted 'ARM D_3' from double to character (0 new NA)

# A tibble: 1 x 14
  AESOC   AEDECOD  `ARM A_1` `ARM A_2` `ARM A_3` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_1`
  <chr>   <chr>    <chr>     <chr>     <chr>     <chr>     <chr>     <chr>     <chr>    
1 All Sy~ All Adv~ 6 ( 42.9~ 8 ( 57.1~ 0 (  0.0~ 8 ( 57.1~ 4 ( 28.6~ 2 ( 14.3~ 8 ( 57.1~
# ... with 5 more variables: ARM C_2 <chr>, ARM C_3 <chr>, ARM D_1 <chr>,
#   ARM D_2 <chr>, ARM D_3 <chr>

=========================================================================
Create final data frame
=========================================================================

# A tibble: 74 x 14
   AESOC   AEDECOD `ARM A_1` `ARM A_2` `ARM A_3` `ARM B_1` `ARM B_2` `ARM B_3` `ARM C_1`
   <chr>   <chr>   <chr>     <chr>     <chr>     <chr>     <chr>     <chr>     <chr>    
 1 All Sy~ All Ad~ 6 ( 42.9~ 8 ( 57.1~ 0 (  0.0~ 8 ( 57.1~ 4 ( 28.6~ 2 ( 14.3~ 8 ( 57.1~
 2 Blood ~ Neutro~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 3 Cardia~ Palpit~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 4 Cardia~ Sinus ~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 5 Congen~ Dermoi~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
 6 Ear an~ Vertigo 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~
 7 Endocr~ Parath~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~
 8 Gastro~ Diarrh~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~
 9 Gastro~ Food P~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
10 Gastro~ Tootha~ 0 (  0.0~ 1 (  7.1~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~ 0 (  0.0~
# ... with 64 more rows, and 5 more variables: ARM C_2 <chr>, ARM C_3 <chr>,
#   ARM D_1 <chr>, ARM D_2 <chr>, ARM D_3 <chr>

=========================================================================
Create and print report
=========================================================================

Create table object

Create report object

Print report

# A report specification: 16 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpgrpGQ1/output/example3.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 0.5 bottom 0.5 left 1 right 1
- line size/count: 9/46
- page_header: left=Sponsor: Company right=Study: ABC
- title 1: 'Table 5.0'
- title 2: 'Adverse Events by Maximum Severity'
- footnote 1: 'Program: AE_Table.R'
- footnote 2: 'Note: Adverse events were coded using MedDRA Version 9.1'
- page_footer: left=2021-11-21 14:58:58 center=Confidential right=Page [pg] of [tpg]
- content: 
# A table specification:
- data: tibble 'final' 74 rows 14 cols
- show_cols: all
- use_attributes: all
- width: 9
- spanning_header: from='ARM A_1' to='ARM A_3' 'ARM A' level=1 
- spanning_header: from='ARM B_1' to='ARM B_3' 'ARM B' level=1 
- spanning_header: from='ARM C_1' to='ARM C_3' 'ARM C' level=1 
- spanning_header: from='ARM D_1' to='ARM D_3' 'ARM D' level=1 
- stub: AESOC AEDECOD 'System Organ Class
   Preferred Term' width=5 align='left' 
- define: AESOC dedupe='TRUE' 
- define: AEDECOD 
- define: ARM A_1 'Mild' align='center' 
- define: ARM A_2 'Moderate' align='center' 
- define: ARM A_3 'Severe' align='center' 
- define: ARM B_1 'Mild' align='center' page_wrap='TRUE' 
- define: ARM B_2 'Moderate' align='center' 
- define: ARM B_3 'Severe' align='center' 
- define: ARM C_1 'Mild' align='center' page_wrap='TRUE' 
- define: ARM C_2 'Moderate' align='center' 
- define: ARM C_3 'Severe' align='center' 
- define: ARM D_1 'Mild' align='center' page_wrap='TRUE' 
- define: ARM D_2 'Moderate' align='center' 
- define: ARM D_3 'Severe' align='center' 

# A report specification: 16 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpgrpGQ1/output/example3.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 0.5 bottom 0.5 left 1 right 1
- line size/count: 9/46
- page_header: left=Sponsor: Company right=Study: ABC
- title 1: 'Table 5.0'
- title 2: 'Adverse Events by Maximum Severity'
- footnote 1: 'Program: AE_Table.R'
- footnote 2: 'Note: Adverse events were coded using MedDRA Version 9.1'
- page_footer: left=2021-11-21 14:58:58 center=Confidential right=Page [pg] of [tpg]
- content: 
# A table specification:
- data: tibble 'final' 74 rows 14 cols
- show_cols: all
- use_attributes: all
- width: 9
- spanning_header: from='ARM A_1' to='ARM A_3' 'ARM A' level=1 
- spanning_header: from='ARM B_1' to='ARM B_3' 'ARM B' level=1 
- spanning_header: from='ARM C_1' to='ARM C_3' 'ARM C' level=1 
- spanning_header: from='ARM D_1' to='ARM D_3' 'ARM D' level=1 
- stub: AESOC AEDECOD 'System Organ Class
   Preferred Term' width=5 align='left' 
- define: AESOC dedupe='TRUE' 
- define: AEDECOD 
- define: ARM A_1 'Mild' align='center' 
- define: ARM A_2 'Moderate' align='center' 
- define: ARM A_3 'Severe' align='center' 
- define: ARM B_1 'Mild' align='center' page_wrap='TRUE' 
- define: ARM B_2 'Moderate' align='center' 
- define: ARM B_3 'Severe' align='center' 
- define: ARM C_1 'Mild' align='center' page_wrap='TRUE' 
- define: ARM C_2 'Moderate' align='center' 
- define: ARM C_3 'Severe' align='center' 
- define: ARM D_1 'Mild' align='center' page_wrap='TRUE' 
- define: ARM D_2 'Moderate' align='center' 
- define: ARM D_3 'Severe' align='center' 

=========================================================================
Clean Up
=========================================================================

lib_sync: synchronized data in library 'sdtm'

lib_unload: library 'sdtm' unloaded

=========================================================================
Log End Time: 2021-11-21 14:58:59
Log Elapsed Time: 0 00:00:01
=========================================================================

```

## Output

Here are the first 4 pages of the report produced by the sample program above:

<img src="../man/images/example3a.png"/>
<img src="../man/images/example3b.png"/>
<img src="../man/images/example3c.png"/>
<img src="../man/images/example3d.png"/>


Next: [Complete Example 4](reporter-example4.html)
