Teal Module: Patient Prior Medication Teal Module — tm_t_pp_prior

This teal module produces a patient prior medication report using ADaM datasets.

Usage

tm_t_pp_prior_medication(
  label,
  dataname = "ADCM",
  parentname = "ADSL",
  patient_col = "USUBJID",
  atirel = NULL,
  cmdecod = NULL,
  cmindc = NULL,
  cmstdy = NULL,
  pre_output = NULL,
  post_output = NULL
)

Arguments

label: (character)
menu item label of the module in the teal app.
dataname: (character)
analysis data used in teal module.
parentname: (character)
parent analysis data used in teal module, usually this refers to ADSL.
patient_col: (character)
patient ID column to be used.
atirel: (teal.transform::choices_selected() or teal.transform::data_extract_spec())
ATIREL column of the ADCM dataset.
cmdecod: (teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMDECOD column of the ADCM dataset.
cmindc: (teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMINDC column of the ADCM dataset.
cmstdy: (teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMSTDY column of the ADCM dataset.
pre_output: optional, (shiny.tag)
with text placed before the output to put the output into context. For example a title.
post_output: optional, (shiny.tag)
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

Examples

library(scda)
synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
ADSL <- synthetic_cdisc_data_latest$adsl
ADCM <- synthetic_cdisc_data_latest$adcm

#' Modify ADCM
ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
ADCM$CMDOSE <- 1
ADCM$CMTRT <- ADCM$CMCAT
ADCM$CMDOSU <- "U"
ADCM$CMROUTE <- "CMROUTE"
ADCM$CMDOSFRQ <- "CMDOSFRQ"
ADCM$CMASTDTM <- ADCM$ASTDTM
ADCM$CMAENDTM <- ADCM$AENDTM
formatters::var_labels(
  ADCM[c("CMINDC", "CMTRT", "ASTDY")]
) <- c(
  "Indication",
  "Reported Name of Drug, Med, or Therapy",
  "Study Day of Start of Medication"
)
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADSL <- synthetic_cdisc_data_latest$adsl"
    ),
    cdisc_dataset("ADCM", ADCM,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADCM <- synthetic_cdisc_data_latest$adcm
        ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD))
        ADCM$CMDOSE <- 1
        ADCM$CMTRT <- ADCM$CMCAT
        ADCM$CMDOSU <- 'U'
        ADCM$CMROUTE <- 'CMROUTE'
        ADCM$CMDOSFRQ <- 'CMDOSFRQ'
        ADCM$CMASTDTM <- ADCM$ASTDTM
        ADCM$CMAENDTM <- ADCM$AENDTM
        formatters::var_labels(
          ADCM[c('CMINDC', 'CMTRT', 'ASTDY')]) <- c(
            'Indication',
            'Reported Name of Drug, Med, or Therapy',
            'Study Day of Start of Medication'
           )",
      keys = adcm_keys
    )
  ),
  modules = modules(
    tm_t_pp_prior_medication(
      label = "Prior medication",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = "ATIREL"
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      )
    )
  )
)
#> [INFO] 2022-10-14 09:11:07.4935 pid:3139 token:[] teal.modules.clinical Initializing tm_t_pp_prior_medication
if (FALSE) {
shinyApp(app$ui, app$server)
}