VSL01

Listing of Vital Signs: Safety-Evaluable Patients

Output

Code
lsting <- as_listing(
  out,
  key_cols = c("TRT01A", "CRTNPT", "AGSXRC", "AVISIT"),
  disp_cols = names(out),
  main_title = "Listing of Vital Signs: Safety-Evaluable Patients",
  main_footer = "Baseline is the patient's last observation prior to initiation of study drug. Abnormalities are flagged as high (H) or low (L) if outside the Roche standard reference range." 
)

head(lsting, 20)
Listing of Vital Signs: Safety-Evaluable Patients

——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                                                                                                   Diastolic Blood                                                                                                                                
                                                                                                                                                                      Pressure,                        Systolic Blood                                                                                             
                                                                                             Weight                                                                    Sitting       Diastolic Blood      Pressure,      Systolic Blood                                        Respiratory Rate                   
                                                                                             Result                        Temperature Result                          Result           Pressure,          Sitting         Pressure,      Pulse Rate Result                         Result                        
                                                                                 Study       (Kg);            Weight              (C);          Temperature Rate        (Pa);            Sitting            (Pa);           Sitting         (beats/min);        Pulse Rate      (breaths/min);    Respiratory Rate
Treatment   Center/Subject ID            Age/Sex/Race                Visit        Day    Range:(40-100)   Change from BL   Range:(36.1-37.2)     Change from BL    Range:(80-120)    Change from BL    Range:(120-180)   Change from BL    Range:(60-100)     Change from BL    Range:(12-20)      Change from BL 
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
A: Drug X       BRA-1/105       38/M/BLACK OR AFRICAN AMERICAN   WEEK 1 DAY 8     189         90.96            24.62              36.79               -1.88            101.10             -12.65          181.05/H             3.70             84.91              -2.05             18.34               1.13     
                                                                 WEEK 2 DAY 15    323         41.40           -24.93              36.52               -2.14            111.02              -2.72           132.47            -44.88             71.54             -15.42             9.81/L             -7.40     
                                                                 WEEK 3 DAY 22    492         60.55            -5.78             35.03/L              -3.64             88.35             -25.39          112.67/L           -64.68            33.75/L            -53.22            21.23/H              4.02     
                                                                 WEEK 4 DAY 29    550         69.69             3.36             35.71/L              -2.95            100.74             -13.00          194.88/H            17.53             97.51              10.54             12.50              -4.71     
                                                                 WEEK 5 DAY 36    628         81.64            15.30             36.01/L              -2.65           123.17/H              9.43           140.33            -37.02             62.50             -24.47            10.91/L             -6.30     
                BRA-1/134                 47/M/WHITE             WEEK 1 DAY 8     203         42.95           -12.51              36.39               -1.38            112.71              26.38           148.69            -52.75             69.12               3.72             15.31              -2.84     
                                                                 WEEK 2 DAY 15    326        20.36/L          -35.09             35.75/L              -2.03             98.42              12.09          188.08/H           -13.36             68.79               3.40             17.60              -0.55     
                                                                 WEEK 3 DAY 22    363         46.33            -9.12             35.43/L              -2.34             97.88              11.55           160.05            -41.39             90.21              24.81             18.15               0.00     
                                                                 WEEK 4 DAY 29    367         43.83           -11.62             36.01/L              -1.76             98.97              12.65           132.19            -69.25             88.39              23.00             19.62               1.48     
                                                                 WEEK 5 DAY 36    417        31.75/L          -23.71              36.35               -1.42           124.26/H             37.94           134.30            -67.14             88.64              23.25            20.08/H              1.94     
                BRA-1/42        36/M/BLACK OR AFRICAN AMERICAN   WEEK 1 DAY 8     265       115.27/H            8.42             37.35/H              -1.67            107.32               5.90           173.89             27.40             66.14              26.13             9.23/L              7.13     
                                                                 WEEK 2 DAY 15    313         45.84           -61.01             36.01/L              -3.01            110.97               9.55           144.75             -1.74           109.71/H             69.70             7.18/L              5.08     
                                                                 WEEK 3 DAY 22    325         85.70           -21.14             37.71/H              -1.31           124.13/H             22.71           89.08/L           -57.41             90.29              50.28            25.16/H             23.05     
                                                                 WEEK 4 DAY 29    535         44.64           -62.21              36.44               -2.58            79.51/L            -21.91           140.78             -5.71             82.44              42.43             14.06              11.95     
                                                                 WEEK 5 DAY 36    729         85.21           -21.64             35.78/L              -3.23            105.26               3.84           126.60            -19.89             88.71              48.70            25.98/H             23.87     
                BRA-1/93                  34/F/ASIAN             WEEK 1 DAY 8     402         47.51           -35.34             35.50/L              -0.83             94.27              17.98           98.82/L           -61.71             72.44              -7.85             14.97               0.22     
                                                                 WEEK 2 DAY 15    460         67.64           -15.21             37.96/H               1.62            109.98              33.69          104.21/L           -56.32           104.70/H             24.41             14.90               0.16     
                                                                 WEEK 3 DAY 22    464         53.06           -29.78              36.33               -0.01             90.17              13.87           139.66            -20.87           111.13/H             30.85            22.86/H              8.12     
                                                                 WEEK 4 DAY 29    496         61.68           -21.17             33.52/L              -2.82            112.76              36.47           128.82            -31.70             72.89              -7.39            20.77/H              6.03     
                                                                 WEEK 5 DAY 36    538         53.98           -28.86             35.71/L              -0.63             80.20               3.91           137.16            -23.37             96.63              16.35             18.10               3.36     
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————

Baseline is the patient's last observation prior to initiation of study drug. Abnormalities are flagged as high (H) or low (L) if outside the Roche standard reference range.

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Code
library(dplyr)
library(rlistings)

advs <- random.cdisc.data::cadvs

get_param_unit_range <- function(dataset) {
  u_rng <- lapply(unique(dataset$PARAMCD), function(p) {
    dat <- dataset %>% filter(PARAMCD == p)
    list(
      unit = unique(dat$AVALU),
      range = paste0(unique(dat$ANRLO), "-", unique(dat$ANRHI))
    )
  })
  names(u_rng) <- unique(dataset$PARAMCD)
  u_rng
}

vs_u_rng <- get_param_unit_range(advs)

advs_sub <- advs %>%
  filter(!is.na(AVAL) & SAFFL == "Y" & ONTRTFL == "Y" & !is.na(VSSEQ)) %>%
  mutate(
    CRTNPT = paste(SITEID, sub("^.*-([[:alnum:]]+)$", "\\1", SUBJID), sep = "/"),
    AGSXRC = paste(AGE, SEX, RACE, sep = "/"),
    AVAL = format(round(AVAL, 2), nsmall = 2),
    AVAL_ANRIND = ifelse(ANRIND %in% c("NORMAL", ""), AVAL, paste(AVAL, substr(ANRIND, 1, 1), sep = "/")),
    CHG = format(round(CHG, 2), nsmall = 2)
  )

anl_vs <- advs_sub %>%
  select(SUBJID, CRTNPT, AGSXRC, TRT01A, PARAMCD, AVAL_ANRIND, CHG, ADY, AVISIT, ADTM) %>%
  tidyr::pivot_wider(
    id_cols = c(SUBJID, CRTNPT, AGSXRC, TRT01A, ADY, AVISIT, ADTM),
    names_from = PARAMCD,
    values_from = c(AVAL_ANRIND, CHG)
  )

out <- anl_vs %>%
  select(
    CRTNPT, AGSXRC, TRT01A, AVISIT, ADY, AVAL_ANRIND_WEIGHT, CHG_WEIGHT, AVAL_ANRIND_TEMP, CHG_TEMP, AVAL_ANRIND_DIABP,
    CHG_DIABP, AVAL_ANRIND_SYSBP, CHG_SYSBP, AVAL_ANRIND_PULSE, CHG_PULSE, AVAL_ANRIND_RESP, CHG_RESP
  ) %>%
  var_relabel(
    CRTNPT = "Center/Subject ID",
    AGSXRC = "Age/Sex/Race",
    TRT01A = "Treatment",
    AVISIT = "Visit",
    ADY = "Study\nDay",
    AVAL_ANRIND_WEIGHT = paste0(
      "Weight\nResult\n(",
      vs_u_rng$WEIGHT$unit,
      ");\nRange:(",
      vs_u_rng$WEIGHT$range,
      ")"
    ),
    CHG_WEIGHT = "Weight\nChange from BL",
    AVAL_ANRIND_TEMP = paste0(
      "Temperature Result\n(",
      vs_u_rng$TEMP$unit,
      ");\nRange:(",
      vs_u_rng$TEMP$range,
      ")"
    ),
    CHG_TEMP = "Temperature Rate\nChange from BL",
    AVAL_ANRIND_DIABP = paste0(
      "Diastolic Blood\nPressure,\nSitting\nResult\n(",
      vs_u_rng$DIABP$unit,
      ");\nRange:(",
      vs_u_rng$DIABP$range,
      ")"
    ),
    CHG_DIABP = "Diastolic Blood\nPressure,\nSitting\nChange from BL",
    AVAL_ANRIND_SYSBP = paste0(
      "Systolic Blood\nPressure,\nSitting\n(",
      vs_u_rng$SYSBP$unit,
      ");\nRange:(",
      vs_u_rng$SYSBP$range,
      ")"
    ),
    CHG_SYSBP = "Systolic Blood\nPressure,\nSitting\nChange from BL",
    AVAL_ANRIND_PULSE = paste0(
      "Pulse Rate Result\n(",
      vs_u_rng$PULSE$unit,
      ");\nRange:(",
      vs_u_rng$PULSE$range,
      ")"
    ),
    CHG_PULSE = "Pulse Rate\nChange from BL",
    AVAL_ANRIND_RESP = paste0(
      "Respiratory Rate\nResult\n(",
      vs_u_rng$RESP$unit,
      ");\nRange:(",
      vs_u_rng$RESP$range,
      ")"
    ),
    CHG_RESP = "Respiratory Rate\nChange from BL"
  )

Reproducibility

Timestamp

[1] "2024-11-20 18:15:36 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-11-20
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version     date (UTC) lib source
 backports           1.5.0       2024-05-23 [1] RSPM
 brio                1.1.5       2024-04-24 [1] RSPM
 checkmate           2.3.2       2024-07-29 [1] RSPM
 cli                 3.6.3       2024-06-21 [1] RSPM
 codetools           0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
 curl                6.0.1       2024-11-14 [1] RSPM
 digest              0.6.37      2024-08-19 [1] RSPM
 dplyr             * 1.1.4       2023-11-17 [1] RSPM
 evaluate            1.0.1       2024-10-10 [1] RSPM
 fansi               1.0.6       2023-12-08 [1] RSPM
 fastmap             1.2.0       2024-05-15 [1] RSPM
 formatters        * 0.5.9.9003  2024-11-20 [1] https://p~
 generics            0.1.3       2022-07-05 [1] RSPM
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 htmltools           0.5.8.1     2024-04-04 [1] RSPM
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 knitr               1.49        2024-11-08 [1] RSPM
 lifecycle           1.0.4       2023-11-07 [1] RSPM
 magrittr            2.0.3       2022-03-30 [1] RSPM
 pillar              1.9.0       2023-03-22 [1] RSPM
 pkgcache            2.2.3       2024-09-12 [1] RSPM
 pkgconfig           2.0.3       2019-09-22 [1] RSPM
 processx            3.8.4       2024-03-16 [1] RSPM
 ps                  1.8.1       2024-10-28 [1] RSPM
 purrr               1.0.2       2023-08-10 [1] RSPM
 R6                  2.5.1       2021-08-19 [1] RSPM
 random.cdisc.data   0.3.16.9001 2024-11-20 [1] https://p~
 rlang               1.1.4       2024-06-04 [1] RSPM
 rlistings         * 0.2.9.9009  2024-11-20 [1] https://p~
 rmarkdown           2.29        2024-11-04 [1] RSPM
 sessioninfo         1.2.2       2021-12-06 [1] any (@1.2.2)
 stringi             1.8.4       2024-05-06 [1] RSPM
 stringr             1.5.1       2023-11-14 [1] RSPM
 testthat            3.2.1.1     2024-04-14 [1] RSPM
 tibble            * 3.2.1       2023-03-20 [1] RSPM
 tidyr               1.3.1       2024-01-24 [1] RSPM
 tidyselect          1.2.1       2024-03-11 [1] RSPM
 utf8                1.2.4       2023-10-22 [1] RSPM
 vctrs               0.6.5       2023-12-01 [1] RSPM
 withr               3.0.2       2024-10-28 [1] RSPM
 xfun                0.49        2024-10-31 [1] RSPM
 yaml                2.3.10      2024-07-26 [1] RSPM

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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