--- title: LBT14 subtitle: Laboratory Test Results Shift Table -- Highest NCI CTCAE Grade Post-Baseline by Baseline NCI CTCAE Grade --- ```{r setup, echo = FALSE, warning = FALSE, message = FALSE} library (dplyr)library (tern)<- random.cdisc.data:: cadsl<- random.cdisc.data:: cadlb<- df_explicit_na (adsl)<- df_explicit_na (adlb)# Please note that in real clinical data, population flag like SAFFL, and parameter category like PARCAT2 needs to be # selected properly. <- adsl %>% filter (SAFFL == "Y" )<- adlb %>% filter (SAFFL == "Y" )``` ```{r include = FALSE} <- c ("setup" )``` ## Output ## Standard Table (High) `WGRHIFL` ) must be selected appropriately in the pre-processing step. New grouping variables `ATOXGR_GP` (post-baseline) and `BTOXGR_GP` (baseline) are created to display the correct output.## {{< fa regular file-lines sm fw >}} Preview ```{r variant1, test = list(result_v1 = "result")} <- adlb %>% filter (WGRHIFL == "Y" )# Please note the step below can be skipped if you are using DTYPE PHANTOM <- h_adsl_adlb_merge_using_worst_flag (adsl_f, adlb_f, worst_flag = c ("WGRHIFL" = "Y" ))# Create new grouping variables ATOXGR_GP, BTOXGR_GP <- adlb_out %>% mutate (ATOXGR_GP = factor (case_when (%in% c (0 , - 1 , - 2 , - 3 , - 4 ) ~ "Not High" ,== 1 ~ "1" ,== 2 ~ "2" ,== 3 ~ "3" ,== 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not High" , "1" , "2" , "3" , "4" , "Missing" ))%>% mutate (BTOXGR_GP = factor (case_when (%in% c (0 , - 1 , - 2 , - 3 , - 4 ) ~ "Not High" ,== 1 ~ "1" ,== 2 ~ "2" ,== 3 ~ "3" ,== 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not High" , "1" , "2" , "3" , "4" , "Missing" ))<- basic_table (show_colcounts = TRUE ) %>% split_cols_by ("ACTARM" ) %>% split_rows_by ("PARAM" ,split_fun = drop_split_levels,label_pos = "topleft" ,split_label = "Parameter" %>% split_rows_by ("BTOXGR_GP" ,label_pos = "topleft" ,split_label = " Baseline NCI-CTCAE Grade" ,indent_mod = 2 L%>% summarize_num_patients (var = "USUBJID" , .stats = c ("unique_count" ), unique_count_suffix = FALSE ) %>% count_occurrences_by_grade ("ATOXGR_GP" , denom = "n" , drop = FALSE , .indent_mods = 3 L) %>% append_topleft (" Post-baseline NCI-CTCAE Grade" ) %>% build_table (df = adlb_out, alt_counts_df = adsl_f) %>% prune_table ()``` ```{r include = FALSE} <- c ("variant1" )``` ## Standard Table (Low) `WGRLOFL` ) must be selected appropriately in the pre-processing step. New grouping variables `ATOXGR_GP` (post-baseline) and `BTOXGR_GP` (baseline) are created to display the correct output.## {{< fa regular file-lines sm fw >}} Preview ```{r variant2, test = list(result_v2 = "result")} <- adlb %>% filter (WGRLOFL == "Y" )# Please note the step below can be skipped if you are using DTYPE PHANTOM <- h_adsl_adlb_merge_using_worst_flag (adsl_f, adlb_f, worst_flag = c ("WGRLOFL" = "Y" ))# Create new grouping variables ATOXGR_GP, BTOXGR_GP <- adlb_out %>% mutate (ATOXGR_GP = factor (case_when (%in% c (0 , 1 , 2 , 3 , 4 ) ~ "Not Low" ,== - 1 ~ "1" ,== - 2 ~ "2" ,== - 3 ~ "3" ,== - 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not Low" , "1" , "2" , "3" , "4" , "Missing" ))%>% mutate (BTOXGR_GP = factor (case_when (%in% c (0 , 1 , 2 , 3 , 4 ) ~ "Not Low" ,== - 1 ~ "1" ,== - 2 ~ "2" ,== - 3 ~ "3" ,== - 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not Low" , "1" , "2" , "3" , "4" , "Missing" ))<- basic_table (show_colcounts = TRUE ) %>% split_cols_by ("ACTARM" ) %>% split_rows_by ("PARAM" ,split_fun = drop_split_levels,label_pos = "topleft" ,split_label = "Parameter" %>% split_rows_by ("BTOXGR_GP" ,label_pos = "topleft" ,split_label = " Baseline NCI-CTCAE Grade" ,indent_mod = 2 L%>% summarize_num_patients (var = "USUBJID" , .stats = c ("unique_count" ), unique_count_suffix = FALSE ) %>% count_occurrences_by_grade ("ATOXGR_GP" , denom = "n" , drop = FALSE , .indent_mods = 3 L) %>% append_topleft (" Post-baseline NCI-CTCAE Grade" ) %>% build_table (df = adlb_out, alt_counts_df = adsl_f) %>% prune_table ()``` ```{r include = FALSE} <- c ("variant2" )``` ## Table Without Patients with <br/> Missing Baseline (High) ## {{< fa regular file-lines sm fw >}} Preview ```{r variant3, test = list(result_v3 = "result")} <- adlb %>% filter (WGRHIFL == "Y" )# Please note the step below can be skipped if you are using DTYPE PHANTOM <- h_adsl_adlb_merge_using_worst_flag (adsl_f, adlb_f, worst_flag = c ("WGRHIFL" = "Y" ))# Create new grouping variables ATOXGR_GP, BTOXGR_GP <- adlb_out %>% filter (BTOXGR != "<Missing>" ) %>% mutate (ATOXGR_GP = factor (case_when (%in% c (0 , - 1 , - 2 , - 3 , - 4 ) ~ "Not High" ,== 1 ~ "1" ,== 2 ~ "2" ,== 3 ~ "3" ,== 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not High" , "1" , "2" , "3" , "4" , "Missing" ))%>% mutate (BTOXGR_GP = factor (case_when (%in% c (0 , - 1 , - 2 , - 3 , - 4 ) ~ "Not High" ,== 1 ~ "1" ,== 2 ~ "2" ,== 3 ~ "3" ,== 4 ~ "4" levels = c ("Not High" , "1" , "2" , "3" , "4" ))<- basic_table (show_colcounts = TRUE ) %>% split_cols_by ("ACTARM" ) %>% split_rows_by ("PARAM" ,split_fun = drop_split_levels,label_pos = "topleft" ,split_label = "Parameter" %>% split_rows_by ("BTOXGR_GP" ,label_pos = "topleft" ,split_label = " Baseline NCI-CTCAE Grade" ,indent_mod = 2 L%>% summarize_num_patients (var = "USUBJID" , .stats = c ("unique_count" ), unique_count_suffix = FALSE ) %>% count_occurrences_by_grade ("ATOXGR_GP" , denom = "n" , drop = FALSE , .indent_mods = 3 L) %>% append_topleft (" Post-baseline NCI-CTCAE Grade" ) %>% build_table (df = adlb_out, alt_counts_df = adsl_f) %>% prune_table ()``` ```{r include = FALSE} <- c ("variant3" )``` ## Table with Missing Baseline <br/> Considered as Grade 0 (Low) `BTOXGR_GP` now is `"Not Low"` instead of `"Missing"` compared to *Standard Table (Low)*.## {{< fa regular file-lines sm fw >}} Preview ```{r variant4, test = list(result_v4 = "result")} <- adlb %>% filter (WGRLOFL == "Y" )# Please note the step below can be skipped if you are using DTYPE PHANTOM <- h_adsl_adlb_merge_using_worst_flag (adsl_f, adlb_f, worst_flag = c ("WGRLOFL" = "Y" ))# Create new grouping variables ATOXGR_GP, BTOXGR_GP <- adlb_out %>% mutate (ATOXGR_GP = factor (case_when (%in% c (0 , 1 , 2 , 3 , 4 ) ~ "Not Low" ,== - 1 ~ "1" ,== - 2 ~ "2" ,== - 3 ~ "3" ,== - 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not Low" , "1" , "2" , "3" , "4" ))%>% mutate (BTOXGR_GP = factor (case_when (%in% c (0 , 1 , 2 , 3 , 4 , "<Missing>" ) ~ "Not Low" ,== - 1 ~ "1" ,== - 2 ~ "2" ,== - 3 ~ "3" ,== - 4 ~ "4" levels = c ("Not Low" , "1" , "2" , "3" , "4" , "Missing" ))<- basic_table (show_colcounts = TRUE ) %>% split_cols_by ("ACTARM" ) %>% split_rows_by ("PARAM" ,split_fun = drop_split_levels,label_pos = "topleft" ,split_label = "Parameter" %>% split_rows_by ("BTOXGR_GP" ,label_pos = "topleft" ,split_label = " Baseline NCI-CTCAE Grade" ,indent_mod = 2 L%>% summarize_num_patients (var = "USUBJID" , .stats = c ("unique_count" ), unique_count_suffix = FALSE ) %>% count_occurrences_by_grade ("ATOXGR_GP" , denom = "n" , drop = FALSE , .indent_mods = 3 L) %>% append_topleft (" Post-baseline NCI-CTCAE Grade" ) %>% build_table (df = adlb_out, alt_counts_df = adsl_f) %>% prune_table ()``` ```{r include = FALSE} <- c ("variant4" )``` ## Table with Fill-In of Grades `prune_table()` is not applied.## {{< fa regular file-lines sm fw >}} Preview ```{r variant5, test = list(result_v5 = "result")} <- adlb %>% filter (WGRHIFL == "Y" )# Please note the step below can be skipped if you are using DTYPE PHANTOM <- h_adsl_adlb_merge_using_worst_flag (adsl_f, adlb_f, worst_flag = c ("WGRHIFL" = "Y" ))# Create new grouping variables ATOXGR_GP, BTOXGR_GP <- adlb_out %>% mutate (ATOXGR_GP = factor (case_when (%in% c (0 , - 1 , - 2 , - 3 , - 4 ) ~ "Not High" ,== 1 ~ "1" ,== 2 ~ "2" ,== 3 ~ "3" ,== 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not High" , "1" , "2" , "3" , "4" , "Missing" ))%>% mutate (BTOXGR_GP = factor (case_when (%in% c (0 , - 1 , - 2 , - 3 , - 4 ) ~ "Not High" ,== 1 ~ "1" ,== 2 ~ "2" ,== 3 ~ "3" ,== 4 ~ "4" ,== "<Missing>" ~ "Missing" levels = c ("Not High" , "1" , "2" , "3" , "4" , "Missing" ))<- basic_table (show_colcounts = TRUE ) %>% split_cols_by ("ACTARM" ) %>% split_rows_by ("PARAM" ,split_fun = drop_split_levels,label_pos = "topleft" ,split_label = "Parameter" %>% split_rows_by ("BTOXGR_GP" ,label_pos = "topleft" ,split_label = " Baseline NCI-CTCAE Grade" ,indent_mod = 2 L%>% summarize_num_patients (var = "USUBJID" , .stats = c ("unique_count" ), unique_count_suffix = FALSE ) %>% count_occurrences_by_grade ("ATOXGR_GP" , denom = "n" , drop = FALSE , .indent_mods = 3 L) %>% append_topleft (" Post-baseline NCI-CTCAE Grade" ) %>% build_table (df = adlb_out, alt_counts_df = adsl_f)``` ```{r include = FALSE} <- c ("variant5" )``` ## Data Setup `adlb` dataset needs to be filtered on correct flags like `WGRLOFL` , `WGRHIFL` , et al., otherwise the layout function will not return the correct counts. There is an option to create a record for a lab test where no record is found at that visit. If you specified `add_derived_type = "PHANTOM"` & `dtype_phantom_cond` , you don't have to use the `h_adsl_adlb_merge_using_worst_flag` function to preprocess your `adlb` dataset. Otherwise please follow the pre-processing steps below before applying the layout functions.```{r setup} #| code-fold: show ``` ## `teal` App ## {{< fa regular file-lines fa-sm fa-fw >}} Preview ```{r teal, opts.label = c("skip_if_testing", "app")} library (teal.modules.clinical)## Data reproducible code <- teal_data ()<- within (data, {<- random.cdisc.data:: cadsl<- random.cdisc.data:: cadlb<- c ("ADSL" , "ADLB" )datanames (data) <- datanamesjoin_keys (data) <- default_cdisc_join_keys[datanames]## Reusable Configuration For Modules <- data[["ADSL" ]]<- data[["ADLB" ]]## Setup App <- init (data = data,modules = modules (tm_t_shift_by_grade (label = "Grade Laboratory Abnormality Table" ,dataname = "ADLB" ,arm_var = choices_selected (choices = variable_choices (ADSL, subset = c ("ARM" , "ARMCD" )),selected = "ARM" paramcd = choices_selected (choices = value_choices (ADLB, "PARAMCD" , "PARAM" ),selected = "ALT" worst_flag_var = choices_selected (choices = variable_choices (ADLB, subset = c ("WGRLOVFL" , "WGRLOFL" , "WGRHIVFL" , "WGRHIFL" )),selected = c ("WGRHIFL" )worst_flag_indicator = choices_selected (value_choices (ADLB, "WGRLOVFL" ),selected = "Y" , fixed = TRUE anl_toxgrade_var = choices_selected (choices = variable_choices (ADLB, subset = c ("ATOXGR" )),selected = c ("ATOXGR" ),fixed = TRUE base_toxgrade_var = choices_selected (choices = variable_choices (ADLB, subset = c ("BTOXGR" )),selected = c ("BTOXGR" ),fixed = TRUE add_total = FALSE filter = teal_slices (teal_slice ("ADSL" , "SAFFL" , selected = "Y" ))shinyApp (app$ ui, app$ server)``` 