PDT02
Major Protocol Deviations Related to Epidemic/Pandemic
Code
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ACTARM") %>%
analyze_num_patients(
vars = "USUBJID",
.stats = c("unique", "nonunique"),
.labels = c(
unique = "Total number of patients with at least one major protocol deviation related to epidemic/pandemic",
nonunique = "Total number of major protocol deviations related to epidemic/pandemic"
)
) %>%
split_rows_by(
"DVREAS",
split_fun = drop_split_levels,
nested = FALSE,
label_pos = "topleft",
split_label = obj_label(addv_pan$DVREAS)
) %>%
summarize_num_patients(
var = "USUBJID",
.stats = c("unique"),
.labels = "Site action due to epidemic/pandemic"
) %>%
count_occurrences(vars = "DVTERM") %>%
append_varlabels(addv_pan, "DVTERM", indent = 1L)
result <- build_table(lyt, addv_pan, alt_counts_df = adsl)
result
Primary Reason A: Drug X B: Placebo C: Combination
Description (N=134) (N=134) (N=132)
------------------------------------------------------------------------------------------------------------------------------------------
Total number of patients with at least one major protocol deviation related to epidemic/pandemic 8 (6.0%) 4 (3.0%) 4 (3.0%)
Total number of major protocol deviations related to epidemic/pandemic 8 5 4
Site action due to epidemic/pandemic 8 (6.0%) 4 (3.0%) 4 (3.0%)
Dose missed or significantly out of window 2 (1.5%) 0 1 (0.8%)
Failure to sign updated ICF within two visits 2 (1.5%) 1 (0.7%) 1 (0.8%)
Missed 2 or more efficacy assessments 1 (0.7%) 2 (1.5%) 0
Significant deviation from planned dose 3 (2.2%) 1 (0.7%) 2 (1.5%)
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] dplyr_1.1.4 tern_0.9.4.9007 rtables_0.6.7.9002
[4] magrittr_2.0.3 formatters_0.5.6.9004
loaded via a namespace (and not attached):
[1] Matrix_1.7-0 gtable_0.3.5
[3] jsonlite_1.8.8 compiler_4.4.0
[5] brio_1.1.5 tidyselect_1.2.1
[7] stringr_1.5.1 tidyr_1.3.1
[9] splines_4.4.0 scales_1.3.0
[11] yaml_2.3.8 fastmap_1.1.1
[13] lattice_0.22-6 ggplot2_3.5.1
[15] R6_2.5.1 generics_0.1.3
[17] knitr_1.46 forcats_1.0.0
[19] rbibutils_2.2.16 htmlwidgets_1.6.4
[21] backports_1.4.1 checkmate_2.3.1
[23] tibble_3.2.1 munsell_0.5.1
[25] pillar_1.9.0 rlang_1.1.3
[27] utf8_1.2.4 testthat_3.2.1.1
[29] stringi_1.8.3 broom_1.0.5
[31] xfun_0.43 cli_3.6.2
[33] Rdpack_2.6 digest_0.6.35
[35] grid_4.4.0 lifecycle_1.0.4
[37] vctrs_0.6.5 evaluate_0.23
[39] glue_1.7.0 codetools_0.2-20
[41] survival_3.6-4 random.cdisc.data_0.3.15.9003
[43] fansi_1.0.6 colorspace_2.1-0
[45] purrr_1.0.2 rmarkdown_2.26
[47] tools_4.4.0 pkgconfig_2.0.3
[49] 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)
)