WIP demo app with all modules #1408

m7pr · 2025-07-31T12:36:15Z

WIP

averissimo · 2025-08-01T08:10:21Z

Here are the missing modules:

tm_a_gee
tm_g_ci
tm_g_forest_rsp
tm_g_forest_tte
tm_g_ipp
tm_g_pp_patient_timeline
tm_g_pp_therapy
tm_t_abnormality_by_worst_grade
tm_t_ancova
tm_t_glm_counts
tm_t_tte

averissimo · 2025-08-04T11:36:00Z

Here's the full "manual" app for part 3:

# Load packages
pkgload::load_all("../teal.logger", export_all = FALSE)
pkgload::load_all("../teal.code", export_all = FALSE)
pkgload::load_all("../teal.data", export_all = FALSE)
pkgload::load_all("../teal.widgets", export_all = FALSE)
pkgload::load_all("../teal.slice", export_all = FALSE)
pkgload::load_all("../teal.reporter", export_all = FALSE)
pkgload::load_all("../teal", export_all = FALSE)
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)

# Example below

data <- teal_data()
data <- within(data, {
  library(dplyr)
  ADSL <- teal.modules.clinical::tmc_ex_adsl
  ADQS <- teal.modules.clinical::tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor(),
      AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
    ) %>%
    droplevels()

  # ci

  ADLB <- teal.modules.clinical::tmc_ex_adlb %>%
    filter(USUBJID %in% ADSL$USUBJID) %>%
    df_explicit_na()

  # forest

  ADRS <- teal.modules.clinical::tmc_ex_adrs %>%
    mutate(AVALC = tern::d_onco_rsp_label(AVALC) %>%
      formatters::with_label("Character Result/Finding")) %>%
    filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")

  # forest tte

  ADTTE <- teal.modules.clinical::tmc_ex_adtte
  ADSL$RACE <- droplevels(ADSL$RACE) %>% formatters::with_label("Race")

  # patient timeline
  ADAE <- teal.modules.clinical::tmc_ex_adae
  ADSL <- ADSL %>%
    filter(USUBJID %in% ADAE$USUBJID)

  ADCM <- teal.modules.clinical::tmc_ex_adcm %>%
    mutate(
      CMSTDY = case_when(
        CMCAT == "medcl B" ~ 20,
        CMCAT == "medcl C" ~ 150,
        TRUE ~ 1
      ) %>% with_label("Study Day of Start of Medication"),
      CMENDY = case_when(
        CMCAT == "medcl B" ~ 700,
        CMCAT == "medcl C" ~ 1000,
        TRUE ~ 500
      ) %>% with_label("Study Day of End of Medication"),
      CMASTDTM = ASTDTM,
      CMAENDTM = AENDTM
    )

    ADCM$CMASTDTM <- ADCM$ASTDTM
    ADCM$CMAENDTM <- ADCM$AENDTM  
})
teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]
ADRS <- data[["ADRS"]]
ADTTE <- data[["ADTTE"]]
ADQS <- data[["ADQS"]]
ADAE <- data[["ADAE"]]
ADCM <- data[["ADCM"]]

# Define arm reference and comparison

arm_ref_comp <- list(
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  ),
  ARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys
join_keys(data)["ADAE", "ADCM"] <- c("STUDYID", "USUBJID")

app <- init(
  data = data,
  modules = modules(
    tm_a_gee(
      label = "a_gee",
      dataname = "ADQS",
      aval_var = choices_selected("AVALBIN", fixed = TRUE),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
    ),
    tm_g_ci(
      label = "g_ci",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"), selected = c("ARMCD"), multiple = FALSE, fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(vars = "PARAMCD", choices = levels(ADLB$PARAMCD), selected = levels(ADLB$PARAMCD)[1], multiple = FALSE, label = "Select lab:"),
          filter_spec(vars = "AVISIT", choices = levels(ADLB$AVISIT), selected = levels(ADLB$AVISIT)[1], multiple = FALSE, label = "Select visit:")
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    ),
    tm_g_forest_tte(
      label = "g_forest_tte",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      )
    ),
    tm_g_forest_rsp(
      label = "g_forest_rsp",
      dataname = "ADRS",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADRS, "PARAMCD", "PARAM"),
        "INVET"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      ),
      plot_height = c(600L, 200L, 2000L),
      default_responses = list(
        BESRSPI = list(
          rsp = c("Stable Disease (SD)", "Not Evaluable (NE)"),
          levels = c(
            "Complete Response (CR)", "Partial Response (PR)", "Stable Disease (SD)",
            "Progressive Disease (PD)", "Not Evaluable (NE)"
          )
        ),
        INVET = list(
          rsp = c("Complete Response (CR)", "Partial Response (PR)"),
          levels = c(
            "Complete Response (CR)", "Not Evaluable (NE)", "Partial Response (PR)",
            "Progressive Disease (PD)", "Stable Disease (SD)"
          )
        ),
        OVRINV = list(
          rsp = c("Progressive Disease (PD)", "Stable Disease (SD)"),
          levels = c("Progressive Disease (PD)", "Stable Disease (SD)", "Not Evaluable (NE)")
        )
      )
    ),
    tm_g_ipp(
      label = "g_ipp",
      dataname = "ADLB",
      arm_var = choices_selected(
        value_choices(ADLB, "ARMCD"),
        "ARM A"
      ),
      paramcd = choices_selected(
        value_choices(ADLB, "PARAMCD"),
        "ALT"
      ),
      aval_var = choices_selected(
        variable_choices(ADLB, c("AVAL", "CHG")),
        "AVAL"
      ),
      avalu_var = choices_selected(
        variable_choices(ADLB, c("AVALU")),
        "AVALU",
        fixed = TRUE
      ),
      id_var = choices_selected(
        variable_choices(ADLB, c("USUBJID")),
        "USUBJID",
        fixed = TRUE
      ),
      visit_var = choices_selected(
        variable_choices(ADLB, c("AVISIT")),
        "AVISIT"
      ),
      baseline_var = choices_selected(
        variable_choices(ADLB, c("BASE")),
        "BASE",
        fixed = TRUE
      ),
      add_baseline_hline = FALSE,
      separate_by_obs = FALSE
    ),
    tm_g_pp_patient_timeline(
      label = "pp_patient_timeline",
      dataname_adae = "ADAE",
      dataname_adcm = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      cmdecod = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMDECOD"),
        selected = "CMDECOD",
      ),
      aeterm = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AETERM"),
        selected = c("AETERM")
      ),
      aetime_start = choices_selected(
        choices = variable_choices(data[["ADAE"]], "ASTDTM"),
        selected = c("ASTDTM")
      ),
      aetime_end = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AENDTM"),
        selected = c("AENDTM")
      ),
      dstime_start = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMASTDTM"),
        selected = c("CMASTDTM")
      ),
      dstime_end = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMAENDTM"),
        selected = c("CMAENDTM")
      ),
      aerelday_start = choices_selected(
        choices = variable_choices(data[["ADAE"]], "ASTDY"),
        selected = c("ASTDY")
      ),
      aerelday_end = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AENDY"),
        selected = c("AENDY")
      ),
      dsrelday_start = choices_selected(
        choices = variable_choices(data[["ADCM"]], "ASTDY"),
        selected = c("ASTDY")
      ),
      dsrelday_end = choices_selected(
        choices = variable_choices(data[["ADCM"]], "AENDY"),
        selected = c("AENDY")
      )
    ),
    tm_g_pp_therapy(
      label = "g_pp_therapy",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = c("ATIREL")
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmdose = choices_selected(
        choices = variable_choices(ADCM, "CMDOSE"),
        selected = "CMDOSE"
      ),
      cmtrt = choices_selected(
        choices = variable_choices(ADCM, "CMTRT"),
        selected = "CMTRT"
      ),
      cmdosu = choices_selected(
        choices = variable_choices(ADCM, "CMDOSU"),
        selected = c("CMDOSU")
      ),
      cmroute = choices_selected(
        choices = variable_choices(ADCM, "CMROUTE"),
        selected = "CMROUTE"
      ),
      cmdosfrq = choices_selected(
        choices = variable_choices(ADCM, "CMDOSFRQ"),
        selected = "CMDOSFRQ"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      ),
      cmendy = choices_selected(
        choices = variable_choices(ADCM, "AENDY"),
        selected = "AENDY"
      )
    ),
    tm_t_abnormality_by_worst_grade(
      label = "t_abnormality_by_worst_grade",
      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 = c("ALT", "CRP", "IGA")
      ),
      add_total = FALSE
    ),
    tm_t_ancova(
      label = "t_ancova",
      dataname = "ADQS",
      avisit = choices_selected(
        choices = value_choices(ADQS, "AVISIT"),
        selected = "WEEK 1 DAY 8"
      ),
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ACTARMCD", "ARMCD")),
        selected = "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      aval_var = choices_selected(
        choices = variable_choices(ADQS, c("CHG", "AVAL")),
        selected = "CHG"
      ),
      cov_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADQS, "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      interact_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      )
    ),
    tm_t_glm_counts(
      label = "t_glm_counts",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADTTE, c("ARM", "ARMCD", "ACTARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      aval_var = choices_selected(
        variable_choices(ADTTE, "AVAL"),
        "AVAL"
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, "SEX"),
        NULL
      ),
      offset_var = choices_selected(
        variable_choices(ADSL, "AGE"),
        NULL
      ),
      cov_var = choices_selected(
        variable_choices(ADTTE, "SITEID"),
        NULL
      )
    ),
    tm_t_tte(
      label = "t_tte",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("SEX", "BMRKR2")),
        "SEX"
      ),
      time_points = choices_selected(c(182, 243), 182),
      event_desc_var = choices_selected(
        variable_choices(ADTTE, "EVNTDESC"),
        "EVNTDESC",
        fixed = TRUE
      )
    )
  ),
  filter = teal_slices(
    teal_slice("ADSL", "SAFFL", selected = "Y", id = "ts1"),
    teal_slice("ADLB", "ONTRTFL", selected = "Y", id = "ts2"),
    teal_slice("ADLB", "AVISIT", selected = c("BASELINE", "WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22"), id = "ts3"),
    module_specific = TRUE,
    mapping = list(
      "g_ipp" = "ts3",
      "t_abnormality_by_worst_grade" = c("ts1", "ts2")
    )
  )
) |> shiny::runApp()

m7pr added 5 commits July 31, 2025 14:35

demo app

27bb83d

change random data genartion to custom data generation

b35dcb9

data creation

b5ae90e

some minor improvements to the modules calls

85a1fdd

fix init

8946e0f

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WIP demo app with all modules #1408

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m7pr commented Jul 31, 2025

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averissimo commented Aug 1, 2025

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averissimo commented Aug 4, 2025

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WIP demo app with all modules #1408

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