TSICM05

Prior Medications

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Output

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# Program Name:              tsicm05.R

# Prep Environment

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

# Define script level parameters:

# - Define output ID and file location

tblid <- "TSICM05"
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:

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

adcm <- pharmaverseadamjnj::adcm %>%
  filter(PREFL == "Y") %>%
  select(USUBJID, PREFL, 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$PREFL) == 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(
    "PREFL",
    afun = a_freq_j,
    extra_args = append(
      extra_args_1,
      list(label = "Subjects with >=1 prior 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$PREFL) == 0) {
  result <- safe_prune_table(
    result,
    prune_func = remove_rows(
      removerowtext = "Subjects with >=1 prior medication"
    )
  )
}

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

if (length(adcm$PREFL) != 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")

TSICM05: Prior 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 prior  medication	43 (81.1%)	56 (76.7%)	99 (78.6%)	49 (83.1%)	148 (80.0%)
Uncoded	42 (79.2%)	54 (74.0%)	96 (76.2%)	47 (79.7%)	143 (77.3%)
Uncoded: vitamin e	8 (15.1%)	10 (13.7%)	18 (14.3%)	12 (20.3%)	30 (16.2%)
Uncoded: multivitamin	8 (15.1%)	11 (15.1%)	19 (15.1%)	9 (15.3%)	28 (15.1%)
Uncoded: multivitamins	8 (15.1%)	5 (6.8%)	13 (10.3%)	6 (10.2%)	19 (10.3%)
Uncoded: vitamin c	5 (9.4%)	5 (6.8%)	10 (7.9%)	5 (8.5%)	15 (8.1%)
Uncoded: synthroid	3 (5.7%)	4 (5.5%)	7 (5.6%)	3 (5.1%)	10 (5.4%)
Uncoded: tylenol	3 (5.7%)	3 (4.1%)	6 (4.8%)	4 (6.8%)	10 (5.4%)
Uncoded: timoptic	5 (9.4%)	2 (2.7%)	7 (5.6%)	2 (3.4%)	9 (4.9%)
Uncoded: centrum silver	2 (3.8%)	2 (2.7%)	4 (3.2%)	2 (3.4%)	6 (3.2%)
Uncoded: ibuprofen	0	2 (2.7%)	2 (1.6%)	4 (6.8%)	6 (3.2%)
Uncoded: motrin	3 (5.7%)	1 (1.4%)	4 (3.2%)	2 (3.4%)	6 (3.2%)
Uncoded: ativan	0	3 (4.1%)	3 (2.4%)	2 (3.4%)	5 (2.7%)
Uncoded: ecotrin	0	3 (4.1%)	3 (2.4%)	2 (3.4%)	5 (2.7%)
Uncoded: estrogen nos	3 (5.7%)	0	3 (2.4%)	2 (3.4%)	5 (2.7%)
Uncoded: ginkgo biloba	1 (1.9%)	3 (4.1%)	4 (3.2%)	1 (1.7%)	5 (2.7%)
Uncoded: metamucil	3 (5.7%)	1 (1.4%)	4 (3.2%)	1 (1.7%)	5 (2.7%)
Uncoded: provera	1 (1.9%)	2 (2.7%)	3 (2.4%)	2 (3.4%)	5 (2.7%)
Uncoded: zestril	2 (3.8%)	1 (1.4%)	3 (2.4%)	2 (3.4%)	5 (2.7%)
Uncoded: zocor	1 (1.9%)	1 (1.4%)	2 (1.6%)	3 (5.1%)	5 (2.7%)
Uncoded: advil	4 (7.5%)	0	4 (3.2%)	0	4 (2.2%)
Uncoded: asa	3 (5.7%)	0	3 (2.4%)	1 (1.7%)	4 (2.2%)
Uncoded: claritin	0	3 (4.1%)	3 (2.4%)	1 (1.7%)	4 (2.2%)
Uncoded: dyazide	0	4 (5.5%)	4 (3.2%)	0	4 (2.2%)
Uncoded: vitamin b12	0	2 (2.7%)	2 (1.6%)	2 (3.4%)	4 (2.2%)
Uncoded: zinc	1 (1.9%)	1 (1.4%)	2 (1.6%)	2 (3.4%)	4 (2.2%)
Uncoded: betagan	1 (1.9%)	0	1 (0.8%)	2 (3.4%)	3 (1.6%)
Uncoded: centrum	1 (1.9%)	1 (1.4%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: furosemide	0	3 (4.1%)	3 (2.4%)	0	3 (1.6%)
Uncoded: garlic	2 (3.8%)	0	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: lopid	2 (3.8%)	1 (1.4%)	3 (2.4%)	0	3 (1.6%)
Uncoded: monopril	0	2 (2.7%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: ocuvite	1 (1.9%)	0	1 (0.8%)	2 (3.4%)	3 (1.6%)
Uncoded: potassium	0	2 (2.7%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: prilosec	0	2 (2.7%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: prinivil	1 (1.9%)	1 (1.4%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: tums	1 (1.9%)	1 (1.4%)	2 (1.6%)	1 (1.7%)	3 (1.6%)
Uncoded: vitamins	0	3 (4.1%)	3 (2.4%)	0	3 (1.6%)
Uncoded: accupril	2 (3.8%)	0	2 (1.6%)	0	2 (1.1%)
Uncoded: acetaminophen	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: altace	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: aspirin (e.c.)	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: b complex	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: benadryl	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: betacarotene	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: bufferin	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: calcium carbonate	0	0	0	2 (3.4%)	2 (1.1%)
Uncoded: capoten	0	2 (2.7%)	2 (1.6%)	0	2 (1.1%)
Uncoded: chloral hydrate	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: excedrin	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: glyburide	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: herbal preparation	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: hydrochlorothiazide	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: hydrocortisone,  topical	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: hytrin	1 (1.9%)	1 (1.4%)	2 (1.6%)	0	2 (1.1%)
Uncoded: lisinopril	0	2 (2.7%)	2 (1.6%)	0	2 (1.1%)
Uncoded: milk of magnesia	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: mylanta	0	0	0	2 (3.4%)	2 (1.1%)
Uncoded: prednisone	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: procardia	2 (3.8%)	0	2 (1.6%)	0	2 (1.1%)
Uncoded: propine	0	0	0	2 (3.4%)	2 (1.1%)
Uncoded: relafen	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: theragran-m	0	1 (1.4%)	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: trusopt	0	0	0	2 (3.4%)	2 (1.1%)
Uncoded: vitamin b	0	2 (2.7%)	2 (1.6%)	0	2 (1.1%)
Uncoded: vitamin d	1 (1.9%)	0	1 (0.8%)	1 (1.7%)	2 (1.1%)
Uncoded: aerobid	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: albuterol	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: alphagan	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: ampicillin	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: anti-oxidant	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: ascriptin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: beconase	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: benzalkonium  chloride	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: calcium magnesium	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: central-vite	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: charcoal, activated	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: cipro	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: cod-liver oil	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: daypro	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: debrox	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: dhea	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: diabeta	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: diabinese	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: diprolene cream	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: dipyridamole	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: docusate	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: docusate sodium	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: estradiol	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: eucerin creme	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: ex-lax	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: feldene	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: fibre, dietary	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: folic acid	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: fosamax	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: garamycin  ophthalmic	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: ginseng	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: glucotrol	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: hismanal	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: homeopatic  preparation	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: humulin n	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: hydrochlorothiazide  with triamterene	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: indocin	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: influenza virus  vaccine	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: iron	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: k-dur	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: keflex	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: levobunolol	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: levothroid	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: levoxine	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: levoxyl	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: lopressor	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: lorazepam	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: lotensin	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: maxzide	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: meclizine	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded:  medroxyprogesterone	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: metrogel	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: minerals nos	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: multivit	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: nasacort	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: nasal spray	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: neptazane	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: nitro patch	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: nitrodisc	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: nitroglycerin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: ocupress	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: papaya	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: perdiem	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: pilocarpine  hydrochloride	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: pilostat	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: pravastatin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: premphase	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: promethazine hcl  w/codeine	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: propulsid	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: psorcon	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: psyllium hydrophilic  mucilloid	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: quercetin	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: quinamm	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: quinapril	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: quinine sulfate	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: stresstabs	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: sudafed	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: sulindac	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: surfak	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: ticlid	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: timolol maleate	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: triamcinolone	0	0	0	1 (1.7%)	1 (0.5%)
Uncoded: tylenol extra  strength	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: tylenol w/codeine  no. 4	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: ultram	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: vitamin a	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: vitamin b6	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: vitamins with  minerals	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Uncoded: zephrex	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Uncoded: zestoretic	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Nervous system	3 (5.7%)	8 (11.0%)	11 (8.7%)	15 (25.4%)	26 (14.1%)
Acetylsalicylic acid	3 (5.7%)	8 (11.0%)	11 (8.7%)	14 (23.7%)	25 (13.5%)
Alprazolam	0	0	0	1 (1.7%)	1 (0.5%)
Sumatriptan	0	0	0	1 (1.7%)	1 (0.5%)
Alimentary tract and  metabolism	4 (7.5%)	8 (11.0%)	12 (9.5%)	7 (11.9%)	19 (10.3%)
Calcium	3 (5.7%)	4 (5.5%)	7 (5.6%)	6 (10.2%)	13 (7.0%)
Simeticone	0	2 (2.7%)	2 (1.6%)	0	2 (1.1%)
Algeldrate	0	0	0	1 (1.7%)	1 (0.5%)
Calcium carbonate	1 (1.9%)	0	1 (0.8%)	0	1 (0.5%)
Loperamide hydrochloride	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Metformin hydrochloride	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Genito urinary system and sex  hormones	3 (5.7%)	7 (9.6%)	10 (7.9%)	2 (3.4%)	12 (6.5%)
Estrogens conjugated	3 (5.7%)	7 (9.6%)	10 (7.9%)	2 (3.4%)	12 (6.5%)
Cardiovascular system	1 (1.9%)	6 (8.2%)	7 (5.6%)	2 (3.4%)	9 (4.9%)
Digoxin	1 (1.9%)	4 (5.5%)	5 (4.0%)	0	5 (2.7%)
Fluvastatin	0	2 (2.7%)	2 (1.6%)	0	2 (1.1%)
Nifedipine	0	0	0	2 (3.4%)	2 (1.1%)
Respiratory system	3 (5.7%)	0	3 (2.4%)	1 (1.7%)	4 (2.2%)
Naproxen sodium	3 (5.7%)	0	3 (2.4%)	1 (1.7%)	4 (2.2%)
Antineoplastic and  immunomodulating agents	0	0	0	1 (1.7%)	1 (0.5%)
Leuprorelin acetate	0	0	0	1 (1.7%)	1 (0.5%)
Blood and blood forming organs	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Ferrous sulfate	0	1 (1.4%)	1 (0.8%)	0	1 (0.5%)
Note: Prior medications are defined as any therapy used before the day of first dose (partial or complete) of study treatment.

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