# Complete Example 1

## Program

The previous examples in the libr documentation were intentionally simplified to focus on the workings of a particular function. It is helpful, however, to also view libr functions in the context of a complete program. The following example shows a complete program. The example illustrates how libr functions work together, and interact with tidyverse and sassy functions to create a report.

The data for this example has been included in the libr package as an external data file. It may be accessed using the `system.file()` function as shown below, or downloaded directly from the libr GitHub site here

    library(tidyverse)
    library(sassy)

    # Prepare Log -------------------------------------------------------------

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

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

    # Open log
    lf <- log_open(file.path(tmp, "example1.log"))

    # Load and Prepare Data ---------------------------------------------------

    sep("Prepare Data")

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

    # Define data library
    libname(sdtm, pkg, "csv", quiet = TRUE)

    # Loads data into workspace
    lib_load(sdtm)

    # Prepare data
    dm_mod <- sdtm.DM %>%
      select(USUBJID, SEX, AGE, ARM) %>%
      filter(ARM != "SCREEN FAILURE") %>%
      datastep({

        if (AGE >= 18 & AGE <= 24)
          AGECAT = "18 to 24"
        else if (AGE >= 25 & AGE <= 44)
          AGECAT = "25 to 44"
        else if (AGE >= 45 & AGE <= 64)
          AGECAT <- "45 to 64"
        else if (AGE >= 65)
          AGECAT <- ">= 65"

      }) %>% put()

    put("Get population counts")
    arm_pop <- count(dm_mod, ARM) %>% put()
    sex_pop <- count(dm_mod, SEX) %>% put()
    agecat_pop <- count(dm_mod, AGECAT) %>% put()

    # Convert agecat to factor so rows will sort correctly
    agecat_pop$AGECAT <- factor(agecat_pop$AGECAT, levels = c("18 to 24",
                                                              "25 to 44",
                                                              "45 to 64",
                                                              ">= 65"))
    # Sort agecat
    agecat_pop <- agecat_pop %>% arrange(AGECAT)

    # Create Plots ------------------------------------------------------------

    plt1 <- ggplot(data = arm_pop, aes(x = ARM, y = n)) +
      geom_col(fill = "#0000A0") +
      geom_text(aes(label = n), vjust = 1.5, colour = "white") +
      labs(x = "Treatment Group", y = "Number of Subjects (n)")

    plt2 <- ggplot(data = sex_pop, aes(x = SEX, y = n)) +
      geom_col(fill = "#00A000") +
      geom_text(aes(label = n), vjust = 1.5, colour = "white") +
      labs(x = "Biological Sex", y = "Number of Subjects (n)")

    plt3 <- ggplot(data = agecat_pop, aes(x = AGECAT, y = n)) +
      geom_col(fill = "#A00000") +
      geom_text(aes(label = n), vjust = 1.5, colour = "white") +
      labs(x = "Age Categories", y = "Number of Subjects (n)")

    # Report ------------------------------------------------------------------

    sep("Create and print report")

    page1 <- create_plot(plt1, 4.5, 7) %>%
      titles("Figure 1.1", "Distribution of Subjects by Treatment Group")

    page2 <- create_plot(plt2, 4.5, 7) %>%
      titles("Figure 1.2", "Distribution of Subjects by Biological Sex")

    page3 <- create_plot(plt3, 4.5, 7) %>%
      titles("Figure 1.2", "Distribution of Subjects by Age Category")

    rpt <- create_report(file.path(tmp, "./output/example1.rtf"), output_type = "RTF",
                         font = "Arial") %>%
      set_margins(top = 1, bottom = 1) %>%
      page_header("Sponsor: Company", "Study: ABC") %>%
      add_content(page1) %>%
      add_content(page2) %>%
      add_content(page3) %>%
      footnotes("Program: DM_Figure.R") %>%
      page_footer(paste0("Date Produced: ", fapply(Sys.time(), "%d%b%y %H:%M")),
                  right = "Page [pg] of [tpg]")

    res <- write_report(rpt)

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

    # Unload 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

Here is the log from the above program:

    =========================================================================
    Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpwLpEIV/log/example1.log
    Program Path: C:\packages\Testing\libr_example1.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 reporter_1.2.6 libr_1.2.1 fmtr_1.5.4 logr_1.2.7
                    sassy_1.0.5 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
    Log Start Time: 2021-11-20 23:06:50
    =========================================================================

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

    # library 'sdtm': 8 items
    - attributes: csv not loaded
    - path: C:/Users/dbosa/Documents/R/win-library/4.1/libr/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

    select: dropped 20 variables (STUDYID, DOMAIN, SUBJID, RFSTDTC, RFENDTC, <U+0085>)

    filter: removed 2 rows (2%), 85 rows remaining

    datastep: columns increased from 4 to 5

    # A tibble: 85 x 5
       USUBJID    SEX     AGE ARM   AGECAT
       <chr>      <chr> <dbl> <chr> <chr>
     1 ABC-01-049 M        39 ARM D 25 to 44
     2 ABC-01-050 M        47 ARM B 45 to 64
     3 ABC-01-051 M        34 ARM A 25 to 44
     4 ABC-01-052 F        45 ARM C 45 to 64
     5 ABC-01-053 F        26 ARM B 25 to 44
     6 ABC-01-054 M        44 ARM D 25 to 44
     7 ABC-01-055 F        47 ARM C 45 to 64
     8 ABC-01-056 M        31 ARM A 25 to 44
     9 ABC-01-113 M        74 ARM D >= 65
    10 ABC-01-114 F        72 ARM B >= 65
    # ... with 75 more rows

    Get population counts

    count: now 4 rows and 2 columns, ungrouped

    # A tibble: 4 x 2
      ARM       n
      <chr> <int>
    1 ARM A    20
    2 ARM B    21
    3 ARM C    21
    4 ARM D    23

    count: now 2 rows and 2 columns, ungrouped

    # A tibble: 2 x 2
      SEX       n
      <chr> <int>
    1 F        32
    2 M        53

    count: now 4 rows and 2 columns, ungrouped

    # A tibble: 4 x 2
      AGECAT       n
      <chr>    <int>
    1 >= 65       13
    2 18 to 24     5
    3 25 to 44    23
    4 45 to 64    44

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

    # A report specification: 3 pages
    - file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpwLpEIV/./output/example1.rtf'
    - output_type: RTF
    - units: inches
    - orientation: landscape
    - margins: top 1 bottom 1 left 1 right 1
    - line size/count: 9/40
    - page_header: left=Sponsor: Company right=Study: ABC
    - footnote 1: 'Program: DM_Figure.R'
    - page_footer: left=Date Produced: 20Nov21 23:06 center= right=Page [pg] of [tpg]
    - content:
    # A plot specification:
    - data: 4 rows, 2 cols
    - layers: 2
    - height: 4.5
    - width: 7
    - title 1: 'Figure 1.1'
    - title 2: 'Distribution of Subjects by Treatment Group'
    # A plot specification:
    - data: 2 rows, 2 cols
    - layers: 2
    - height: 4.5
    - width: 7
    - title 1: 'Figure 1.2'
    - title 2: 'Distribution of Subjects by Biological Sex'
    # A plot specification:
    - data: 4 rows, 2 cols
    - layers: 2
    - height: 4.5
    - width: 7
    - title 1: 'Figure 1.2'
    - title 2: 'Distribution of Subjects by Age Category'

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

    lib_sync: synchronized data in library 'sdtm'

    lib_unload: library 'sdtm' unloaded

    =========================================================================
    Log End Time: 2021-11-20 23:06:57
    Log Elapsed Time: 0 00:00:07
    =========================================================================

## Output

And here is the output:

Next: Complete Example 2