Note: The direction of the shift table for each lab test is based on metadata and NCI CTCAE specifications. In addition, the worst laboratory flags must be selected appropriately to match the direction of abnormality. For example, if any lab requires a shift table for both directions, then both worst_flag_low and worst_flag_high must be specified in h_adlb_worsen. If all labs requires a shift table for only one direction, then the matching worst lab flag variable must be selected in h_adlb_worsen.
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Code
# In progress
Timestamp
Code
Sys.time()
[1] "2024-05-08 17:35:35 UTC"
Session Info
Code
sessionInfo()
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] tern_0.9.4 rtables_0.6.7 magrittr_2.0.3 formatters_0.5.6
[5] dplyr_1.1.4 scda.2022_0.1.5 scda_0.1.6
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] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3 knitr_1.46
[17] forcats_1.0.0 rbibutils_2.2.16 htmlwidgets_1.6.4 backports_1.4.1
[21] checkmate_2.3.1 tibble_3.2.1 munsell_0.5.1 pillar_1.9.0
[25] rlang_1.1.3 utf8_1.2.4 testthat_3.2.1.1 stringi_1.8.4
[29] broom_1.0.5 xfun_0.43 cli_3.6.2 Rdpack_2.6
[33] digest_0.6.35 grid_4.4.0 lifecycle_1.0.4 vctrs_0.6.5
[37] evaluate_0.23 glue_1.7.0 codetools_0.2-20 survival_3.6-4
[41] colorspace_2.1-0 fansi_1.0.6 purrr_1.0.2 rmarkdown_2.26
[45] tools_4.4.0 pkgconfig_2.0.3 htmltools_0.5.8.1
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---title: LBT08subtitle: Laboratory Test Results with Highest NCI CTCAE Grade at Any Time---------------------------------------------------------------------------{{< include ../../_utils/envir_hook.qmd >}}:::: {.panel-tabset}## Data Setup```{r setup, message = FALSE}#| code-fold: showlibrary(scda)library(scda.2022)library(dplyr)library(tern)adsl <- synthetic_cdisc_dataset("latest", "adsl")adlb <- synthetic_cdisc_dataset("latest", "adlb")adlb <- adlb %>% mutate( GRADDR = case_when( PARAMCD == "ALT" ~ "L", PARAMCD == "CRP" ~ "B", PARAMCD == "IGA" ~ "H" ) ) %>% filter(SAFFL == "Y" & ONTRTFL == "Y" & GRADDR != "")adsl <- df_explicit_na(adsl)adlb <- df_explicit_na(adlb)df <- h_adlb_worsen( adlb, worst_flag_low = c("WGRLOFL" = "Y"), worst_flag_high = c("WGRHIFL" = "Y"), direction_var = "GRADDR")attributes(df$GRADDR) <- list("label" = "Direction of Abnormality")```## Standard TableNote: The direction of the shift table for each lab test is based on metadata and NCI CTCAE specifications.In addition, the worst laboratory flags must be selected appropriately to match the direction of abnormality.For example, if any lab requires a shift table for both directions, then both `worst_flag_low` and `worst_flag_high` must be specified in `h_adlb_worsen`.If all labs requires a shift table for only one direction, then the matching worst lab flag variable must be selected in `h_adlb_worsen`.::: {.panel-tabset .nav-justified group="webr"}## {{< fa regular file-lines sm fw >}} Preview```{r variant1, test = list(result_v1 = "result")}result <- basic_table(show_colcounts = TRUE) %>% split_cols_by("ARMCD") %>% split_rows_by("PARAMCD", label_pos = "topleft", split_label = obj_label(df$PARAMCD)) %>% split_rows_by("GRADDR", label_pos = "topleft", split_label = obj_label(df$GRADDR)) %>% count_abnormal_lab_worsen_by_baseline( var = "ATOXGR", variables = list( id = "USUBJID", baseline_var = "BTOXGR", direction_var = "GRADDR" ) ) %>% append_topleft(" Highest NCI CTCAE Grade") %>% build_table(df = df, alt_counts_df = adsl)result````r webr_code_labels <- c("setup", "variant1")`{{< include ../../_utils/webr.qmd >}}:::{{< include ../../_utils/save_results.qmd >}}## `teal` App```{r teal, opts.label = c("skip_if_testing", "app")}#| code-fold: show# In progress```{{< include ../../repro.qmd >}}::::