PKCG03

Plot of Mean PK Concentration Over Time by Cohort

Output

Code
use_title <- "Plot of Mean (+/- SD) Plasma Concentrations Over Time by Treatment, \nPK Evaluable Patients"
use_subtitle <- "Analyte:"
use_footnote <- "Program: \nOutput:"

result <- g_lineplot(
  df = adpc,
  variables = control_lineplot_vars(
    x = "NFRLT",
    y = "AVAL",
    group_var = "ARM",
    paramcd = "PARAM",
    y_unit = "AVALU",
    subject_var = "USUBJID"
  ),
  alt_counts_df = adsl_f,
  y_lab = "Concentration",
  y_lab_add_paramcd = FALSE,
  y_lab_add_unit = TRUE,
  interval = "mean_sdi",
  whiskers = c("mean_sdi_lwr", "mean_sdi_upr"),
  title = use_title,
  subtitle = use_subtitle,
  caption = use_footnote,
  ggtheme = theme_nest()
)

plot <- result + theme(plot.caption = element_text(hjust = 0))
plot

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Code
use_title <- "Plot of Mean (+/- SD) Log-Scale Plasma Concentrations Over Time by Treatment, \nPK Evaluable Patients"
use_subtitle <- "Analyte:"
use_footnote <- "Program: \nOutput:"

adpc <- adpc %>%
  mutate(avalog = ifelse(AVAL != 0, AVAL, 0.001))

result <- g_lineplot(
  df = adpc,
  variables = control_lineplot_vars(
    x = "NFRLT",
    y = "avalog",
    group_var = "ARM",
    paramcd = "PARAM",
    y_unit = "AVALU",
    subject_var = "USUBJID"
  ),
  alt_counts_df = adsl_f,
  y_lab = "Concentration",
  y_lab_add_paramcd = FALSE,
  y_lab_add_unit = TRUE,
  interval = "mean_sdi",
  whiskers = c("mean_sdi_lwr", "mean_sdi_upr"),
  title = use_title,
  subtitle = use_subtitle,
  caption = use_footnote,
  ggtheme = theme_nest()
)

plot <- result + theme(plot.caption = element_text(hjust = 0)) +
  ggplot2::scale_y_log10(breaks = c(0.001, 0.01, 0.1, 1, 10), labels = c(0.001, 0.01, 0.1, 1, 10))
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Code
plot

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Code
library(tern)
library(dplyr)
library(ggplot2)
library(nestcolor)

adsl_f <- random.cdisc.data::cadsl %>%
  filter(SAFFL == "Y" & ARM != "B: Placebo") %>%
  df_explicit_na()

adpc <- random.cdisc.data::cadpc %>%
  mutate(Patient_ID = sub(".*id-", "", USUBJID)) %>%
  filter(PARAM == "Plasma Drug X") %>%
  droplevels() %>%
  df_explicit_na()

Reproducibility

Timestamp

[1] "2024-11-20 17:43:45 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
 broom               1.0.7       2024-09-26 [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)
 colorspace          2.1-1       2024-07-26 [1] RSPM
 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
 farver              2.1.2       2024-05-13 [1] RSPM
 fastmap             1.2.0       2024-05-15 [1] RSPM
 forcats             1.0.0       2023-01-29 [1] RSPM
 formatters        * 0.5.9.9003  2024-11-20 [1] https://p~
 generics            0.1.3       2022-07-05 [1] RSPM
 ggplot2           * 3.5.1       2024-04-23 [1] RSPM
 glue                1.8.0       2024-09-30 [1] RSPM
 gtable              0.3.6       2024-10-25 [1] RSPM
 htmltools           0.5.8.1     2024-04-04 [1] RSPM
 htmlwidgets         1.6.4       2023-12-06 [1] RSPM
 jsonlite            1.8.9       2024-09-20 [1] RSPM
 knitr               1.49        2024-11-08 [1] RSPM
 labeling            0.4.3       2023-08-29 [1] RSPM
 lattice             0.22-6      2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle           1.0.4       2023-11-07 [1] RSPM
 magrittr          * 2.0.3       2022-03-30 [1] RSPM
 Matrix              1.7-1       2024-10-18 [1] RSPM
 munsell             0.5.1       2024-04-01 [1] RSPM
 nestcolor         * 0.1.2.9017  2024-11-20 [1] https://p~
 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~
 rbibutils           2.3         2024-10-04 [1] RSPM
 Rdpack              2.6.2       2024-11-15 [1] RSPM
 rlang               1.1.4       2024-06-04 [1] RSPM
 rmarkdown           2.29        2024-11-04 [1] RSPM
 rtables           * 0.6.10.9005 2024-11-20 [1] https://p~
 scales              1.3.0       2023-11-28 [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
 survival            3.7-0       2024-06-05 [2] CRAN (R 4.4.1)
 tern              * 0.9.6.9016  2024-11-20 [1] https://p~
 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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