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

## ----eval=FALSE, echo=TRUE----------------------------------------------------
#  library(dplyr)
#  library(tibble)
#  library(tidyr)
#  library(ards)
#  
#  # Create input data
#  adsl <- read.table(header = TRUE, text = '
#  STUDYID	DOMAIN	USUBJID	SUBJID	SITEID	BRTHDTC	AGE	AGEU	SEX	RACE	ARMCD	ARM
#  ABC	DM	ABC-01-049	49	1	11/12/1966	39	YEARS	M	"WHITE"		4	"ARM D"
#  ABC	DM	ABC-01-050	50	1	12/19/1958	47	YEARS	M	"WHITE"		2	"ARM B"
#  ABC	DM	ABC-01-051	51	1	5/2/1972	34	YEARS	M	"WHITE"		  1	"ARM A"
#  ABC	DM	ABC-01-052	52	1	6/27/1961	45	YEARS	F	"WHITE"	    3	"ARM C"
#  ABC	DM	ABC-01-053	53	1	4/7/1980	26	YEARS	F	"WHITE"		  2	"ARM B"
#  ABC	DM	ABC-01-054	54	1	9/13/1962	44	YEARS	M	"WHITE"		  4	"ARM D"
#  ABC	DM	ABC-01-055	55	1	6/11/1959	47	YEARS	F	"BLACK OR AFRICAN AMERICAN" 3	"ARM C"
#  ABC	DM	ABC-01-056	56	1	5/2/1975	31	YEARS	M	"WHITE"		  1	"ARM A"
#  ABC	DM	ABC-01-113	113	1	2/8/1932	74	YEARS	M	"WHITE"		  4	"ARM D"')
#  
#  # Create factors for categorical variables
#  # to get zero counts
#  adsl$SEX <- as.factor(adsl$SEX)
#  adsl$RACE <- as.factor(adsl$RACE)
#  adsl$ARM <- factor(adsl$ARM, levels = c("ARM A", "ARM B", "ARM C", "ARM D"))
#  
#  
#  # Initalize ARDS
#  init_ards(studyid = "ABC",
#            tableid = "01", adsns = "adsl",
#            population = "safety population",
#            time = "SCREENING", where = "saffl = TRUE", reset = TRUE)
#  
#  # Perform analysis on AGE variable
#  agedf <- adsl |>
#    select(AGE, ARM) |>
#    group_by(ARM, .drop = FALSE) |>  # Ensures zero counts in ARDS
#    summarize(n = n(),
#              mean = mean(AGE),
#              std = sd(AGE),
#              median = median(AGE),
#              min = min(AGE),
#              max = max(AGE)) |>
#    mutate(analvar = "AGE") |>
#    ungroup() |>
#    add_ards(statvars = c("n", "mean", "std", "median", "min", "max"),
#             statdesc = c("N", "Mean", "Std", "Median", "Min", "Max"),
#             anal_var = "AGE", trtvar = "ARM") |>
#    transmute(analvar, ARM,
#              n = sprintf("%d", n),
#              mean_sd = sprintf("%.1f (%.2f)", mean, std),
#              median = sprintf("%.1f", median),
#              min_max = sprintf("%.1f-%.1f", min, max)) |>
#    pivot_longer(c(n, mean_sd, median, min_max),
#                 names_to = "label", values_to = "stats") |>
#    pivot_wider(names_from = ARM,
#                values_from = c(stats)) |>
#    transmute(analvar, label = c("N", "Mean (Std)", "Median", "Min-Max"),
#              trtA = `ARM A`, trtB = `ARM B`, trtC = `ARM C`, trtD = `ARM D`)
#  
#  # View analysis results
#  agedf
#  #   # A tibble: 4 × 6
#  #   analvar label      trtA        trtB         trtC        trtD
#  #   <chr>   <chr>      <chr>       <chr>        <chr>       <chr>
#  # 1 AGE     N          2           2            2           3
#  # 2 AGE     Mean (Std) 32.5 (2.12) 36.5 (14.85) 46.0 (1.41) 52.3 (18.93)
#  # 3 AGE     Median     32.5        36.5         46.0        44.0
#  # 4 AGE     Min-Max    31.0-34.0   26.0-47.0    45.0-47.0   39.0-74.0
#  
#  # Get population counts
#  trt_pop <- count(adsl, ARM) |> deframe()
#  
#  trt_pop
#  # ARM A ARM B ARM C ARM D
#  #   2     2     2     3
#  
#  # Perform analysis on SEX variable
#  sexdf <- adsl |>
#    mutate(denom = trt_pop[paste0(adsl$ARM)]) |>
#    group_by(SEX, ARM, denom, .drop = FALSE) |>  # Help with zero counts
#    summarize(cnt = n()) |>
#    transmute(SEX, ARM, cnt, analvar = "SEX", label = SEX,
#              pct =  if_else(is.na(denom), 0, cnt / denom * 100)) |>
#    ungroup() |>
#    add_ards(statvars = c("cnt", "pct"), statdesc = "label",
#             anal_var = "SEX", trtvar = "ARM") |>
#    pivot_wider(names_from = ARM,
#                values_from = c(cnt, pct)) |>
#    transmute(analvar, label,
#              trtA = sprintf("%1d (%3.0f%%)", `cnt_ARM A`, `pct_ARM A`),
#              trtB = sprintf("%1d (%3.0f%%)", `cnt_ARM B`, `pct_ARM B`),
#              trtC = sprintf("%1d (%3.0f%%)", `cnt_ARM C`, `pct_ARM C`),
#              trtD = sprintf("%1d (%3.0f%%)", `cnt_ARM D`, `pct_ARM D`))
#  
#  # View analysis results
#  sexdf
#  # # A tibble: 2 × 6
#  # analvar label trtA     trtB     trtC     trtD
#  #   <chr>   <fct> <chr>    <chr>    <chr>    <chr>
#  # 1 SEX     F     0 (  0%) 1 ( 50%) 2 (100%) 0 (  0%)
#  # 2 SEX     M     2 (100%) 1 ( 50%) 0 (  0%) 3 (100%)
#  
#  # Perform analysis on RACE
#  racedf <- adsl |>
#    mutate(denom = trt_pop[paste0(adsl$ARM)]) |>
#    group_by(RACE, ARM, denom, .drop = FALSE) |>  # Zero counts
#    summarize(cnt = n()) |>
#    transmute(RACE, ARM, cnt, analvar = "RACE", label = RACE,
#              pct =  if_else(is.na(denom), 0, cnt / denom * 100)) |>
#    ungroup() |>
#    add_ards(statvars = c("cnt", "pct"), statdesc = "label",
#             anal_var = "RACE", trtvar = "ARM") |>
#    pivot_wider(names_from = ARM,
#                values_from = c(cnt, pct)) |>
#    transmute(analvar, label,
#              trtA = sprintf("%1d (%3.0f%%)", `cnt_ARM A`, `pct_ARM A`),
#              trtB = sprintf("%1d (%3.0f%%)", `cnt_ARM B`, `pct_ARM B`),
#              trtC = sprintf("%1d (%3.0f%%)", `cnt_ARM C`, `pct_ARM C`),
#              trtD = sprintf("%1d (%3.0f%%)", `cnt_ARM D`, `pct_ARM D`))
#  
#  # View analysis results
#  racedf
#  # # A tibble: 2 × 6
#  # analvar   label                     trtA     trtB     trtC     trtD
#  #   <chr>   <fct>                     <chr>    <chr>    <chr>    <chr>
#  # 1 RACE    BLACK OR AFRICAN AMERICAN 0 (  0%) 0 (  0%) 1 ( 50%) 0 (  0%)
#  # 2 RACE    WHITE                     2 (100%) 2 (100%) 1 ( 50%) 3 (100%)
#  
#  # Combine all analysis into final data frame
#  final <- bind_rows(agedf, sexdf, racedf)
#  
#  # View final data frame
#  # - This data frame is ready for reporting
#  final
#  # # A tibble: 8 × 6
#  # analvar   label                     trtA        trtB         trtC        trtD
#  #   <chr>   <chr>                     <chr>       <chr>        <chr>       <chr>
#  # 1 AGE     N                         2           2            2           3
#  # 2 AGE     Mean (Std)                32.5 (2.12) 36.5 (14.85) 46.0 (1.41) 52.3 (18.93)
#  # 3 AGE     Median                    32.5        36.5         46.0        44.0
#  # 4 AGE     Min-Max                   31.0-34.0   26.0-47.0    45.0-47.0   39.0-74.0
#  # 5 SEX     F                         0 (  0%)    1 ( 50%)     2 (100%)    0 (  0%)
#  # 6 SEX     M                         2 (100%)    1 ( 50%)     0 (  0%)    3 (100%)
#  # 7 RACE    BLACK OR AFRICAN AMERICAN 0 (  0%)    0 (  0%)     1 ( 50%)    0 (  0%)
#  # 8 RACE    WHITE                     2 (100%)    2 (100%)     1 ( 50%)    3 (100%)
#  
#  
#  # Extract ARDS
#  # - This data frame can be saved to disc or inserted into a database
#  ards <- get_ards()
#  
#  # Remove some variables to improve readability
#  ards_reduced <- ards |>
#    select(trtvar, trtval, anal_var, anal_val,
#           statname, statval)
#  
#  # View results
#  ards_reduced
#  #    trtvar trtval anal_var                  anal_val statname    statval
#  # 1     ARM  ARM A      AGE                      <NA>        n   2.000000
#  # 2     ARM  ARM B      AGE                      <NA>        n   2.000000
#  # 3     ARM  ARM C      AGE                      <NA>        n   2.000000
#  # 4     ARM  ARM D      AGE                      <NA>        n   3.000000
#  # 5     ARM  ARM A      AGE                      <NA>     mean  32.500000
#  # 6     ARM  ARM B      AGE                      <NA>     mean  36.500000
#  # 7     ARM  ARM C      AGE                      <NA>     mean  46.000000
#  # 8     ARM  ARM D      AGE                      <NA>     mean  52.333333
#  # 9     ARM  ARM A      AGE                      <NA>      std   2.121320
#  # 10    ARM  ARM B      AGE                      <NA>      std  14.849242
#  # 11    ARM  ARM C      AGE                      <NA>      std   1.414214
#  # 12    ARM  ARM D      AGE                      <NA>      std  18.929694
#  # 13    ARM  ARM A      AGE                      <NA>   median  32.500000
#  # 14    ARM  ARM B      AGE                      <NA>   median  36.500000
#  # 15    ARM  ARM C      AGE                      <NA>   median  46.000000
#  # 16    ARM  ARM D      AGE                      <NA>   median  44.000000
#  # 17    ARM  ARM A      AGE                      <NA>      min  31.000000
#  # 18    ARM  ARM B      AGE                      <NA>      min  26.000000
#  # 19    ARM  ARM C      AGE                      <NA>      min  45.000000
#  # 20    ARM  ARM D      AGE                      <NA>      min  39.000000
#  # 21    ARM  ARM A      AGE                      <NA>      max  34.000000
#  # 22    ARM  ARM B      AGE                      <NA>      max  47.000000
#  # 23    ARM  ARM C      AGE                      <NA>      max  47.000000
#  # 24    ARM  ARM D      AGE                      <NA>      max  74.000000
#  # 25    ARM  ARM A      SEX                         F      cnt   0.000000
#  # 26    ARM  ARM B      SEX                         F      cnt   1.000000
#  # 27    ARM  ARM C      SEX                         F      cnt   2.000000
#  # 28    ARM  ARM D      SEX                         F      cnt   0.000000
#  # 29    ARM  ARM A      SEX                         M      cnt   2.000000
#  # 30    ARM  ARM B      SEX                         M      cnt   1.000000
#  # 31    ARM  ARM C      SEX                         M      cnt   0.000000
#  # 32    ARM  ARM D      SEX                         M      cnt   3.000000
#  # 33    ARM  ARM A      SEX                         F      pct   0.000000
#  # 34    ARM  ARM B      SEX                         F      pct  50.000000
#  # 35    ARM  ARM C      SEX                         F      pct 100.000000
#  # 36    ARM  ARM D      SEX                         F      pct   0.000000
#  # 37    ARM  ARM A      SEX                         M      pct 100.000000
#  # 38    ARM  ARM B      SEX                         M      pct  50.000000
#  # 39    ARM  ARM C      SEX                         M      pct   0.000000
#  # 40    ARM  ARM D      SEX                         M      pct 100.000000
#  # 41    ARM  ARM A     RACE BLACK OR AFRICAN AMERICAN      cnt   0.000000
#  # 42    ARM  ARM B     RACE BLACK OR AFRICAN AMERICAN      cnt   0.000000
#  # 43    ARM  ARM C     RACE BLACK OR AFRICAN AMERICAN      cnt   1.000000
#  # 44    ARM  ARM D     RACE BLACK OR AFRICAN AMERICAN      cnt   0.000000
#  # 45    ARM  ARM A     RACE                     WHITE      cnt   2.000000
#  # 46    ARM  ARM B     RACE                     WHITE      cnt   2.000000
#  # 47    ARM  ARM C     RACE                     WHITE      cnt   1.000000
#  # 48    ARM  ARM D     RACE                     WHITE      cnt   3.000000
#  # 49    ARM  ARM A     RACE BLACK OR AFRICAN AMERICAN      pct   0.000000
#  # 50    ARM  ARM B     RACE BLACK OR AFRICAN AMERICAN      pct   0.000000
#  # 51    ARM  ARM C     RACE BLACK OR AFRICAN AMERICAN      pct  50.000000
#  # 52    ARM  ARM D     RACE BLACK OR AFRICAN AMERICAN      pct   0.000000
#  # 53    ARM  ARM A     RACE                     WHITE      pct 100.000000
#  # 54    ARM  ARM B     RACE                     WHITE      pct 100.000000
#  # 55    ARM  ARM C     RACE                     WHITE      pct  50.000000
#  # 56    ARM  ARM D     RACE                     WHITE      pct 100.000000
#