TSFVIT06

Subjects With Treatment-emergent Orthostatic Hypotension During Treatment Period

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# Program Name:              tsfvit06

# Prep Environment

library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(junco)

# Define script level parameters:

tblid <- "TSFVIT06"
fileid <- tblid
titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

popfl <- "SAFFL"
trtvar <- "TRT01A"
ctrl_grp <- "Placebo"

# specify in the order you want to print on table
selparamcd <- c("ORTHYP", "DIABPO", "SYSBPO")

selparamcdN <- tibble(PARAMCD = selparamcd, PARAMCDN = seq_along(selparamcd))

### Per email June 12: DAS/SDS confirmed to NOT restrict to on-treatment values

# Process Data:

adsl <- pharmaverseadamjnj::adsl %>%
  filter(.data[[popfl]] == "Y") %>%
  select(USUBJID, all_of(c(popfl, trtvar)), SEX, AGEGR1, RACE, ETHNIC)


adsl$colspan_trt <- factor(
  ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"),
  levels = c("Active Study Agent", " ")
)


colspan_trt_map <- create_colspan_map(
  adsl,
  non_active_grp = ctrl_grp,
  non_active_grp_span_lbl = " ",
  active_grp_span_lbl = "Active Study Agent",
  colspan_var = "colspan_trt",
  trt_var = trtvar
)
ref_path <- c("colspan_trt", " ", trtvar, ctrl_grp)

### N is the number of subjects with postbaseline orthostatic measurements and without orthostatic hypotension at baseline
## do not use TRTEMFL as filter, as this will only select AVALC = Y records per definition of TRTEMFL
## instead : start from post-baseline records and retain one record per subject
## for those subjects with both Y and N records, keep the Y record
## for those subjects with only Y records or only N records, keep one Y, N record respectively
filtered_advs <- pharmaverseadamjnj::advs %>%
  filter(PARAMCD %in% selparamcd & APOBLFL == "Y") %>%
  filter(PARAMCD %in% selparamcd) %>%
  mutate(
    AVALC = case_when(
      (PARAMCD == "SYSBPO" | PARAMCD == "DIABPO") & CRIT1FL == "Y" ~ "Y",
      (PARAMCD == "SYSBPO" | PARAMCD == "DIABPO") &
        (CRIT1FL == "N" |
          CRIT1FL == NA) ~ "N",
      PARAMCD == "ORTHYP" ~ AVALC
    ),
    PARAM = case_when(
      PARAMCD == "SYSBPO" ~ "SBP (STD-SUP) <-20",
      PARAMCD == "DIABPO" ~ "DBP (STD-SUP) <-10",
      PARAMCD == "ORTHYP" ~ PARAM
    )
  ) %>%
  select(
    STUDYID,
    USUBJID,
    PARAMCD,
    PARAM,
    AVALC,
    AVISIT,
    APOBLFL,
    TRTEMFL,
    ONTRTFL
  ) %>%
  inner_join(adsl) %>%
  ### ensure to keep only 1 result per subject, keep N only in case no Y was observed
  arrange(USUBJID, PARAMCD, AVALC) %>%
  group_by(USUBJID, PARAMCD) %>%
  mutate(navalc = n_distinct(AVALC)) %>%
  filter(!(navalc > 1 & AVALC == "N")) %>%
  ## only keep one record
  slice_head(n = 1) %>%
  ungroup()

#### remove subjects abnormal for "ORTHYP" at baseline
bl_abn_orthyp <- pharmaverseadamjnj::advs %>%
  filter(PARAMCD == "ORTHYP" & ABLFL == "Y" & AVALC == "Y")

### actually remove the subjects with AVALC = Y for ORTHYP
### N is the number of subjects with postbaseline orthostatic measurements and without orthostatic hypotension at baseline
filtered_advs <- filtered_advs %>%
  filter(!(USUBJID %in% unique(bl_abn_orthyp$USUBJID)))

### get sorting as per order in selparamcdN
selparamcdN <- selparamcdN %>%
  left_join(unique(filtered_advs %>% select(PARAMCD, PARAM))) %>%
  arrange(PARAMCDN)

param_levels <- unique(as.character(selparamcdN$PARAM))

filtered_advs$PARAM <- factor(
  as.character(filtered_advs$PARAM),
  levels = param_levels
)


### Mapping for AVALC
### alternative approach to retrieve from metadata iso dataset
xlabel_map <- unique(filtered_advs %>% select(PARAM, PARAMCD)) %>%
  mutate(
    value = "Y",
    label = as.character(PARAM)
  ) %>%
  mutate(
    label = case_when(
      label ==
        "Orthostatic Hypotension" ~ "Total number of subjects with orthostatic hypotension",
      TRUE ~ label
    )
  )

# Define layout and build table:

extra_args_rr <- list(
  method = "wald",
  denom = "n_df",
  ref_path = ref_path,
  .stats = c("count_unique_fraction")
)

lyt <- basic_table(
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  ) %>%
  split_cols_by(trtvar) %>%
  analyze(
    "AVALC",
    a_freq_j,
    show_labels = "hidden",
    table_names = "AVALC_N",
    extra_args = list(denom = "n_df", .stats = c("n_df"))
  ) %>%
  split_rows_by(
    "PARAM",
    label_pos = "topleft",
    split_fun = drop_split_levels,
    child_labels = "hidden",
    split_label = "Orthostatic hypotension, n (%)"
  ) %>%
  # as in shell, do not show denom in count/denom (%)
  ### indent will be fixed to 1, will be updated later in post-processing
  analyze(
    "AVALC",
    a_freq_j,
    extra_args = append(
      extra_args_rr,
      list(
        val = c("Y"),
        label_map = xlabel_map
      )
    ),
    indent_mod = 2L,
    show_labels = "hidden"
  )

result <- build_table(lyt, filtered_advs, alt_counts_df = adsl)

# Post-Processing:

## update indent for "SYSBPO" and "DIABPO"

adj_indent_mod <- function(result, path, indentupd) {
  indent_mod(tt_at_path(result, path)) <- indent_mod(tt_at_path(result, path)) +
    indentupd
  return(result)
}

result <- adj_indent_mod(
  result,
  path = c("PARAM", "Orthostatic Hypotension"),
  indentupd = -1L
)

result <- remove_col_count(result)

# Add titles and footnotes:

result <- set_titles(result, titles)

# Convert to tbl file and output table

tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid)

TSFVIT06: Subjects With Treatment-emergent Orthostatic Hypotension During [Treatment Period]; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
	Xanomeline High Dose	Xanomeline Low Dose	Placebo
Orthostatic hypotension, n (%)	N=53	N=73	N=59
N	28	39	37
Total number of subjects with orthostatic hypotension	25 (89.3%)	33 (84.6%)	34 (91.9%)
DBP (STD-SUP) <-10	25 (89.3%)	28 (71.8%)	32 (86.5%)
SBP (STD-SUP) <-20	19 (67.9%)	20 (51.3%)	26 (70.3%)

Key: STD=standing, SUP=supine
Note: N is the number of subjects with postbaseline orthostatic measurements and without orthostatic hypotension at baseline. N includes subjects with missing baseline evaluation. Orthostatic hypotension is defined as an absolute decrease in systolic (>20 mmHg) or diastolic (>10 mmHg) blood pressure after standing for at least 2 minutes relative to supine position.

Download RTF file

--- title: TSFVIT06 subtitle: Subjects With Treatment-emergent Orthostatic Hypotension During Treatment Period --- ------------------------------------------------------------------------ {{< include ../../_utils/envir_hook.qmd >}} ```{r setup, echo = FALSE, warning = FALSE, message = FALSE} options(docx.add_datetime = FALSE, tidytlg.add_datetime = FALSE) envsetup_config_name <- "default" # Path to the combined config file envsetup_file_path <- file.path("../..", "envsetup.yml") Sys.setenv(ENVSETUP_ENVIRON = '') library(envsetup) loaded_config <- config::get(config = envsetup_config_name, file = envsetup_file_path) envsetup::rprofile(loaded_config) dpscomp <- compound dpspdr <- paste(protocol,dbrelease,rpteff,sep="__") aptcomp <- compound aptpdr <- paste(protocol,dbrelease,rpteff,sep="__") ###### Study specific updates (formerly in envre) dpscomp <- "standards" dpspdr <- "jjcs__NULL__jjcs - core" apt <- FALSE library(junco) default_str_map <- rbind(default_str_map, c("&ctcae", "5.0")) ``` ## Output :::: panel-tabset ## {{< fa regular file-lines sm fw >}} Preview ```{r variant1, results='hide', warning = FALSE, message = FALSE} # Program Name: tsfvit06 # Prep Environment library(envsetup) library(tern) library(dplyr) library(rtables) library(junco) # Define script level parameters: tblid <- "TSFVIT06" fileid <- tblid titles <- get_titles_from_file(input_path = '../../_data/', tblid) string_map <- default_str_map popfl <- "SAFFL" trtvar <- "TRT01A" ctrl_grp <- "Placebo" # specify in the order you want to print on table selparamcd <- c("ORTHYP", "DIABPO", "SYSBPO") selparamcdN <- tibble(PARAMCD = selparamcd, PARAMCDN = seq_along(selparamcd)) ### Per email June 12: DAS/SDS confirmed to NOT restrict to on-treatment values # Process Data: adsl <- pharmaverseadamjnj::adsl %>% filter(.data[[popfl]] == "Y") %>% select(USUBJID, all_of(c(popfl, trtvar)), SEX, AGEGR1, RACE, ETHNIC) adsl$colspan_trt <- factor( ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"), levels = c("Active Study Agent", " ") ) colspan_trt_map <- create_colspan_map( adsl, non_active_grp = ctrl_grp, non_active_grp_span_lbl = " ", active_grp_span_lbl = "Active Study Agent", colspan_var = "colspan_trt", trt_var = trtvar ) ref_path <- c("colspan_trt", " ", trtvar, ctrl_grp) ### N is the number of subjects with postbaseline orthostatic measurements and without orthostatic hypotension at baseline ## do not use TRTEMFL as filter, as this will only select AVALC = Y records per definition of TRTEMFL ## instead : start from post-baseline records and retain one record per subject ## for those subjects with both Y and N records, keep the Y record ## for those subjects with only Y records or only N records, keep one Y, N record respectively filtered_advs <- pharmaverseadamjnj::advs %>% filter(PARAMCD %in% selparamcd & APOBLFL == "Y") %>% filter(PARAMCD %in% selparamcd) %>% mutate( AVALC = case_when( (PARAMCD == "SYSBPO" | PARAMCD == "DIABPO") & CRIT1FL == "Y" ~ "Y", (PARAMCD == "SYSBPO" | PARAMCD == "DIABPO") & (CRIT1FL == "N" | CRIT1FL == NA) ~ "N", PARAMCD == "ORTHYP" ~ AVALC ), PARAM = case_when( PARAMCD == "SYSBPO" ~ "SBP (STD-SUP) <-20", PARAMCD == "DIABPO" ~ "DBP (STD-SUP) <-10", PARAMCD == "ORTHYP" ~ PARAM ) ) %>% select( STUDYID, USUBJID, PARAMCD, PARAM, AVALC, AVISIT, APOBLFL, TRTEMFL, ONTRTFL ) %>% inner_join(adsl) %>% ### ensure to keep only 1 result per subject, keep N only in case no Y was observed arrange(USUBJID, PARAMCD, AVALC) %>% group_by(USUBJID, PARAMCD) %>% mutate(navalc = n_distinct(AVALC)) %>% filter(!(navalc > 1 & AVALC == "N")) %>% ## only keep one record slice_head(n = 1) %>% ungroup() #### remove subjects abnormal for "ORTHYP" at baseline bl_abn_orthyp <- pharmaverseadamjnj::advs %>% filter(PARAMCD == "ORTHYP" & ABLFL == "Y" & AVALC == "Y") ### actually remove the subjects with AVALC = Y for ORTHYP ### N is the number of subjects with postbaseline orthostatic measurements and without orthostatic hypotension at baseline filtered_advs <- filtered_advs %>% filter(!(USUBJID %in% unique(bl_abn_orthyp$USUBJID))) ### get sorting as per order in selparamcdN selparamcdN <- selparamcdN %>% left_join(unique(filtered_advs %>% select(PARAMCD, PARAM))) %>% arrange(PARAMCDN) param_levels <- unique(as.character(selparamcdN$PARAM)) filtered_advs$PARAM <- factor( as.character(filtered_advs$PARAM), levels = param_levels ) ### Mapping for AVALC ### alternative approach to retrieve from metadata iso dataset xlabel_map <- unique(filtered_advs %>% select(PARAM, PARAMCD)) %>% mutate( value = "Y", label = as.character(PARAM) ) %>% mutate( label = case_when( label == "Orthostatic Hypotension" ~ "Total number of subjects with orthostatic hypotension", TRUE ~ label ) ) # Define layout and build table: extra_args_rr <- list( method = "wald", denom = "n_df", ref_path = ref_path, .stats = c("count_unique_fraction") ) lyt <- basic_table( show_colcounts = TRUE, colcount_format = "N=xx" ) %>% split_cols_by( "colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map) ) %>% split_cols_by(trtvar) %>% analyze( "AVALC", a_freq_j, show_labels = "hidden", table_names = "AVALC_N", extra_args = list(denom = "n_df", .stats = c("n_df")) ) %>% split_rows_by( "PARAM", label_pos = "topleft", split_fun = drop_split_levels, child_labels = "hidden", split_label = "Orthostatic hypotension, n (%)" ) %>% # as in shell, do not show denom in count/denom (%) ### indent will be fixed to 1, will be updated later in post-processing analyze( "AVALC", a_freq_j, extra_args = append( extra_args_rr, list( val = c("Y"), label_map = xlabel_map ) ), indent_mod = 2L, show_labels = "hidden" ) result <- build_table(lyt, filtered_advs, alt_counts_df = adsl) # Post-Processing: ## update indent for "SYSBPO" and "DIABPO" adj_indent_mod <- function(result, path, indentupd) { indent_mod(tt_at_path(result, path)) <- indent_mod(tt_at_path(result, path)) + indentupd return(result) } result <- adj_indent_mod( result, path = c("PARAM", "Orthostatic Hypotension"), indentupd = -1L ) result <- remove_col_count(result) # Add titles and footnotes: result <- set_titles(result, titles) # Convert to tbl file and output table tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid) ``` ```{r result1, echo=FALSE, message=FALSE, warning=FALSE, test = list(result_v1 = "result")} tt_to_flextable_j(result, tblid, string_map = string_map) ``` [Download RTF file](`r paste0(tolower(tblid), '.rtf')`) ::::