TSICM01

Concomitant Medications

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Output

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# Program Name:              tsicm01.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSICM01"
fileid <- tblid
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

trtvar <- "TRT01A"
popfl <- "SAFFL"

atcvar <- "CMLVL1"
atclevel <- "1"

combined_colspan_trt <- TRUE

if (combined_colspan_trt == TRUE) {
  # Set up levels and label for the required combined columns
  add_combo <- add_combo_facet(
    "Combined",
    label = "Combined",
    levels = c("Xanomeline High Dose", "Xanomeline Low Dose")
  )

  # choose if any facets need to be removed - e.g remove the combined column for placebo
  rm_combo_from_placebo <- cond_rm_facets(
    facets = "Combined",
    ancestor_pos = NA,
    value = " ",
    split = "colspan_trt"
  )

  mysplit <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
}

# Process Data:

# Read in required data
adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y") %>%
  select(USUBJID, all_of(trtvar), all_of(popfl))

adcm <- pharmaverseadamjnj::adcm %>%
  filter(ONTRTFL == "Y") %>%
  select(USUBJID, ONTRTFL, all_of(atcvar), CMDECOD)

# Convert medications to sentence case
adcm[[atcvar]] <- as.factor(stringr::str_to_sentence(adcm[[atcvar]]))
adcm$CMDECOD <- as.factor(stringr::str_to_sentence(adcm$CMDECOD))

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

# join data together
cm <- adcm %>% inner_join(., adsl, by = c("USUBJID"))

if (length(adcm$ONTRTFL) == 0) {
  cm <- adcm %>% right_join(., adsl, by = c("USUBJID"))
}

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

# Define layout and build table:

extra_args_1 <- list(.stats = "count_unique_fraction")

lyt <- rtables::basic_table(
  top_level_section_div = " ",
  show_colcounts = TRUE,
  colcount_format = "N=xx"
) %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  )

if (combined_colspan_trt == TRUE) {
  lyt <- lyt %>%
    split_cols_by(trtvar, split_fun = mysplit)
} else {
  lyt <- lyt %>%
    split_cols_by(trtvar)
}

lyt <- lyt %>%
  add_overall_col("Total") %>%
  analyze(
    "ONTRTFL",
    afun = a_freq_j,
    show_labels = "hidden",
    extra_args = append(
      extra_args_1,
      list(label = "Subjects with >=1 concomitant medication")
    )
  ) %>%
  split_rows_by(
    atcvar,
    child_labels = "hidden",
    split_label = paste0("ATC Level ", atclevel),
    label_pos = "topleft",
    split_fun = trim_levels_in_group("CMDECOD"),
    section_div = c(" "),
    indent_mod = 0L
  ) %>%
  summarize_row_groups(atcvar, cfun = a_freq_j, extra_args = extra_args_1) %>%
  analyze("CMDECOD", afun = a_freq_j, extra_args = extra_args_1) %>%
  append_topleft("  Standardized Medication Name")

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

# If there is no data remove top row and display "No data to display" text
if (length(adcm$ONTRTFL) == 0) {
  result <- safe_prune_table(
    result,
    prune_func = remove_rows(
      removerowtext = "Subjects with >=1 concomitant medication"
    )
  )
}

# Post-Processing step to sort by descending count on total column:

if (length(adcm$ONTRTFL) != 0) {
  result <- sort_at_path(
    result,
    c("root", atcvar),
    scorefun = jj_complex_scorefun(colpath = "Total")
  )
  result <- sort_at_path(
    result,
    c("root", atcvar, "*", "CMDECOD"),
    scorefun = jj_complex_scorefun(colpath = "Total")
  )
}

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Convert to tbl file and output table

tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid, orientation = "landscape")

TSICM01: Concomitant Medications; Safety Analysis Set (Study jjcs - core)
	Active Study Agent
ATC Level 1	Xanomeline High Dose	Xanomeline Low Dose	Combined	Placebo	Total
Standardized Medication Name	N=53	N=73	N=126	N=59	N=185
Subjects with ≥1 concomitant  medication	38 (71.7%)	43 (58.9%)	81 (64.3%)	35 (59.3%)	116 (62.7%)
Uncoded	34 (64.2%)	35 (47.9%)	69 (54.8%)	34 (57.6%)	103 (55.7%)
Uncoded: hydrocortisone,  topical	11 (20.8%)	12 (16.4%)	23 (18.3%)	4 (6.8%)	27 (14.6%)
Uncoded: cortisone	8 (15.1%)	4 (5.5%)	12 (9.5%)	4 (6.8%)	16 (8.6%)
Uncoded: benadryl	7 (13.2%)	6 (8.2%)	13 (10.3%)	1 (1.7%)	14 (7.6%)
Uncoded: ativan	2 (3.8%)	2 (2.7%)	4 (3.2%)	2 (3.4%)	6 (3.2%)
Uncoded: claritin	2 (3.8%)	2 (2.7%)	4 (3.2%)	1 (1.7%)	5 (2.7%)
Uncoded: lorazepam	1 (1.9%)	4 (5.5%)	5 (4.0%)	0	5 (2.7%)
Uncoded: calamine lotion	3 (5.7%)	1 (1.4%)	4 (3.2%)	0	4 (2.2%)
Uncoded: lidex	2 (3.8%)	2 (2.7%)	4 (3.2%)	0	4 (2.2%)
Uncoded: motrin	0	1 (1.4%)	1 (0.8%)	3 (5.1%)	4 (2.2%)
Uncoded: robitussin	1 (1.9%)	1 (1.4%)	2 (1.6%)	2 (3.4%)	4 (2.2%)
Uncoded: advil	2 (3.8%)	0	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: robitussin-dm	0	1 (1.4%)	1 (0.8%)	2 (3.4%)	3 (1.6%)
Uncoded: allegra	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: bactrim	0	0	0	2 (3.4%)	2 (1.1%)
Uncoded: erythromycin	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: ibuprofen	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: multivitamin	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: neosporin /usa/	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: prilosec	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: sudafed	0	0	0	2 (3.4%)	2 (1.1%)
Uncoded: sulfamethoxazole	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: tylenol	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: vitamin c	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: vitamin e	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: acetaminophen	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: albuterol	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: aloe vera	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: amoxicillin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: antihistamines for  systemic use	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: armour thyroid	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: augmentin	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: beconase	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: biaxin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: bromatane dx	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: cefaclor	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: ceftin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: cephalexin	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: cephalosporin c	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: chloral hydrate	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: cimetidine	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: cipro	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: coricidin d	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: corticosteroids,  dermatological  preparations	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: dalmane	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: demerol	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: diabeta	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: diltiazem  hydrochloride	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: diphenhydramine  hydrochloride	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: diprolene cream	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: donepezil  hydrochloride	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: doxycycline	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: droperidol	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: estrace	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: fluocinolone  acetonide	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: fluoroplex	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: furosemide	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: general anesthesia	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: glyburide	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: guiatuss	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: halotussin-dm	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: herbal preparation	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: hydrocodone	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: hydrocodone  w/apap	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: hydrocortisone  valerate	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: icy hot	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: influenza virus  vaccine	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: keflex	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: kenalog	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: lac-hydrin	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: lansoprazole	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: lipitor	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: lomotil	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: magnesium oxide	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: mavik	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: maxzide	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: melatonin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: metamucil	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: metronidazole	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: mevacor	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: monopril	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: mylanta	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: naproxen	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: neo-synephrine	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: olanzapine	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: pepcid	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: persantine	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: pertussin syrup	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: phenazopyridine	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: phenergan	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: pilocarpine  hydrochloride	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: pneumovax	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: polysporin	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: polysporin  ointment	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: potassium chloride	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: prednisone	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: premarin vaginal  cream	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: prempro	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: preparation h	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: promethazine hcl  w/codeine	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: propulsid	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: pseudoephedrine  hydrochloride	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: rocephin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: sinemet	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: sulfacetamide	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: terazol	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: topicort	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: toradol	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: triamcinolone	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: trimox	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: tums	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: tylenol extra  strength	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: tylenol sinus	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: tylenol w/codeine  no. 3	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: vicks formula 44d	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: vitamin b12	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: westcort	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: zantac	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: zithromax	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: zocor	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Systemic hormonal  preparations, excl.	7 (13.2%)	9 (12.3%)	16 (12.7%)	1 (1.7%)	17 (9.2%)
Hydrocortisone	7 (13.2%)	9 (12.3%)	16 (12.7%)	1 (1.7%)	17 (9.2%)
Nervous system	1 (1.9%)	3 (4.1%)	4 (3.2%)	2 (3.4%)	6 (3.2%)
Donepezil hydrochloride	1 (1.9%)	1 (1.4%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Acetylsalicylic acid	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Haloperidol	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Paroxetine hydrochloride	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Cardiovascular system	1 (1.9%)	3 (4.1%)	4 (3.2%)	0	4 (2.2%)
Doxazosin mesilate	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Digoxin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Losartan potassium	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Alimentary tract and  metabolism	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Cimetidine	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Loperamide hydrochloride	0	0	0	1 (1.7%)	1 (0.5%)
Dermatologicals	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Clobetasol propionate	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Respiratory system	0	0	0	1 (1.7%)	1 (0.5%)
Guaifenesin	0	0	0	1 (1.7%)	1 (0.5%)
Note: Concomitant medications are defined as any therapy used on or after the same day as the first dose of study treatment [up to last dose of study treatment +xx days}, including those that started before and continue on after the first dose of study treatment.

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