PKCG02
Plot of PK Concentration Over Time by Cohort/Treatment Group/Dose
Code
adpc_a <- adpc %>%
filter(
PARAM == "Plasma Drug X",
ARMCD == "ARM A"
) %>%
mutate(Patient_ID = sub(".*id-", "", USUBJID)) %>%
filter(Patient_ID %in% unique(Patient_ID)[1:10])
use_title1 <- "Plot of X Concentration (ug/mL) Over Time by Treatment: \nPK Evaluable Patients"
use_subtitle1 <- "Analyte: Plasma X (ug/mL) \nTreatment Group: ARM A"
use_footnote1 <- "Program: \nOutput:"
plot <- g_ipp(
df = adpc_a,
xvar = "NFRLT",
yvar = "AVAL",
xlab = "Norminal Time from First Dose (hr)",
ylab = "Concentration (ug/mL)",
id_var = "Patient_ID",
add_baseline_hline = FALSE,
yvar_baseline = "AVAL", # yvar_baseline cannot be NA or ignore
title = use_title1,
subtitle = use_subtitle1,
caption = use_footnote1,
plotting_choices = "all_in_one"
)
plot
Code
adpc_a <- adpc %>%
filter(
PARAM == "Plasma Drug X",
ARMCD == "ARM A"
) %>%
mutate(Patient_ID = sub(".*id-", "", USUBJID)) %>%
mutate(avalog = ifelse(AVAL != 0, AVAL, 0.001)) %>%
filter(Patient_ID %in% unique(Patient_ID)[1:10])
use_title3 <- "Log-scale Plot of X Concentration (ug/mL) Over Time by Treatment: \nPK Evaluable Patients"
use_subtitle3 <- "Analyte: Plasma X (ug/mL) \nTreatment Group: ARM A"
use_footnote3 <- "Program: \nOutput:"
result <- g_ipp(
df = adpc_a,
xvar = "NFRLT",
yvar = "avalog",
xlab = "Norminal Time from First Dose (hr)",
ylab = "Concentration (ug/mL)",
id_var = "Patient_ID",
add_baseline_hline = FALSE,
yvar_baseline = "AVAL", # yvar_baseline cannot be NA or ignore
title = use_title3,
caption = use_footnote3,
subtitle = use_subtitle3,
plotting_choices = "all_in_one"
)
plot <- result + ggplot2::scale_y_log10(breaks = c(0.001, 0.01, 0.1, 1, 10), labels = c(0.001, 0.01, 0.1, 1, 10))
plot
Timestamp
Session Info
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] nestcolor_0.1.2 ggplot2_3.5.1 dplyr_1.1.4 scda.2022_0.1.5
[5] scda_0.1.6 tern_0.9.4 rtables_0.6.7 magrittr_2.0.3
[9] formatters_0.5.6
loaded via a namespace (and not attached):
[1] Matrix_1.7-0 gtable_0.3.5 jsonlite_1.8.8 compiler_4.4.0
[5] brio_1.1.5 tidyselect_1.2.1 tidyr_1.3.1 splines_4.4.0
[9] scales_1.3.0 yaml_2.3.8 fastmap_1.1.1 lattice_0.22-6
[13] R6_2.5.1 labeling_0.4.3 generics_0.1.3 knitr_1.46
[17] rbibutils_2.2.16 htmlwidgets_1.6.4 backports_1.4.1 checkmate_2.3.1
[21] tibble_3.2.1 munsell_0.5.1 pillar_1.9.0 rlang_1.1.3
[25] utf8_1.2.4 testthat_3.2.1.1 broom_1.0.5 xfun_0.43
[29] cli_3.6.2 withr_3.0.0 Rdpack_2.6 digest_0.6.35
[33] grid_4.4.0 lifecycle_1.0.4 vctrs_0.6.5 evaluate_0.23
[37] glue_1.7.0 farver_2.1.1 codetools_0.2-20 survival_3.6-4
[41] fansi_1.0.6 colorspace_2.1-0 purrr_1.0.2 rmarkdown_2.26
[45] tools_4.4.0 pkgconfig_2.0.3 htmltools_0.5.8.1
.lock
file
Download the .lock
file and use renv::restore()
on it to recreate environment used to generate this website.
Code
parent_file_path <- knitr::current_input(dir = TRUE)
book_root_dir <- parent_file_path
while (!file.exists(file.path(book_root_dir, "_quarto.yml"))) book_root_dir <- dirname(book_root_dir)
lock_path <- file.path(
"../../assets/www/lock",
paste0(
gsub(
file.path(book_root_dir, ""),
"",
gsub(
"\\.rmarkdown$",
"",
knitr::current_input(dir = TRUE)
)
),
".lock"
)
)
withr::with_options(
list(renv.verbose = FALSE),
renv::snapshot(parent_file_path, lockfile = lock_path, prompt = FALSE, force = TRUE)
)