Patient Profile Module

mod_patient_profile is a DaVinci Shiny module that displays patient information on a subject-level basis. It consists of three sections: summary, listings and plots.

The summary section shows visit-independent demographic information.
The listings section offers listings for visit-dependent information.
The plots section displays charts for events that happen over a span of time (adverse events, concomitant medications, ...) or line plots of point-like events (laboratory values, vital sign measurements).

Show/hide usage example

What follows is a sample call to the mod_patient_profile function. See the main article of this package for a tutorial on how to parameterize it.

dv.papo::mod_patient_profile(
  module_id = "papo",
  subject_level_dataset_name = "adsl",
  subjid_var = "USUBJID",
  summary = list(
    vars = c("SUBJID", "SITEID", "ARM", "TRTSDT", "TRTEDT", "AGE", "RACE", "SEX", "BMIBL"),
    column_count = 3L
  ),
  listings = list(
    "Concomitant Medication" = list(
      dataset = "cm"
    ),
    "Adverse Events" = list(
      dataset = "adae",
      default_vars = c("ASTDT", "ASTDY", "AENDT", "AENDY", "AEDECOD", "AESEV")
    )
  ),
  plots = list(
    timeline_info = c(trt_start_date = "TRTSDT", trt_end_date = "TRTEDT"),
    range_plots = list(
      "Concomitant Medication" = list(
        dataset = "cm",
        vars = c(
          start_date = "CMSTDT", end_date = "CMENDT",
          decode = "CMDECOD", grading = "CMDECOD"
        ),
        tooltip = c()
      ),
      "Adverse Events" = list(
        dataset = "adae",
        vars = c(
          start_date = "ASTDT", end_date = "AENDT", decode = "AEDECOD",
          grading = "AESEV", serious_ae = "AESER"
        ),
        tooltip = c("AE Start Day: " = "ASTDY", "AE End Day: " = "AENDY")
      )
    ),
    value_plots = list(
      "Lab Values" = list(
        dataset = "lb",
        vars = c(
          analysis_param = "PARAM", analysis_val = "AVAL", analysis_date = "ADT",
          analysis_indicator = "LBNRIND", range_low_limit = "A1LO", range_high_limit = "A1HI"
        ),
        tooltip = c()
      )
    ),
    vline_vars = c(
      "Informed Consent Date" = "RFICDT"
    )
  )
)

Usage

mod_patient_profile(
  module_id = "",
  subject_level_dataset_name = NULL,
  subjid_var = NULL,
  sender_ids = NULL,
  summary = NULL,
  listings = NULL,
  plots = NULL
)

Arguments

module_id

[character] Unique Shiny module identifier.

subject_level_dataset_name

[character] Subject-level dataset name.

subjid_var

[character] Unique subject identifier column.

sender_ids

[character(n)] (optional) Identifiers of modules allowed to request the display of target patient IDs.

summary

[list] (optional) Subject-level summary section. Composed of:

vars [character(n)] Values to display in the summary section. Indexes into dataset subject_level_dataset_name.
column_count [integer] Column count for the summary section.

listings

[list(n)] (optional) Listings section. Composed of:

dataset [character] Dataset name.
default_vars [character(n)] (optional) Default columns to display. If not specified, the first six columns are selected by default. Indexes into dataset dataset.

plots

[list] (optional) Plot section. Composed of:

timeline_info [list] Start and end study dates. Composed of:
- icf_date [character] (optional) Informed Consent Form signing Date. Indexes into dataset subject_level_dataset_name. Expects [Date|POSIXt] values.
- trt_start_date [character] Treatment Start Date, used also as Day 1 Reference Date. Indexes into dataset subject_level_dataset_name. Expects [Date|POSIXt] values.
- trt_end_date [character] Treatment End Date. Indexes into dataset subject_level_dataset_name. Expects [Date|POSIXt] values.
- part_end_date [character] (optional) Participation End Date. Indexes into dataset subject_level_dataset_name. Expects [Date|POSIXt] values.
range_plots [list(n)] Plots for range-like events (adverse events, concomitant medications, ...). Composed of:
- dataset [character] Dataset name.
- vars [list] Variables of interest for the event. Composed of:
 - start_date [character] Start date. Indexes into dataset dataset. Expects [Date|POSIXt] values.
 - end_date [character] End date. Indexes into dataset dataset. Expects [Date|POSIXt] values.
 - decode [character] Descriptive event label. Indexes into dataset dataset. Expects [character|factor] values.
 - grading [character] (optional) Degree of the event, used for color-coding the plot. Indexes into dataset dataset. Expects [character|factor] values.
 - serious_ae [character] (optional) Marker of event seriousness, usually reserved for adverse event datasets. Indexes into dataset dataset. Expects [logical|"Y"/"N"] values.
- tooltip [character(n)] Block of text to display as hover information over the left edge of each range. The names of this list are included as literal text and honor three basic HTML formatting elements: , ,  ). The columns the values refer to are populated with the value on the dataset relevant to any given row. Indexes into dataset dataset.
value_plots [list(n)] Plots for value-like (lab measurements, vital signs, ...) traces. Composed of:
- dataset [character] Dataset name.
- vars [list] Variables of interest for the trace. Composed of:
 - analysis_param [character] Parameter. Indexes into dataset dataset. Expects [character|factor] values.
 - analysis_val [character] Value. Indexes into dataset dataset. Expects [numeric] values.
 - analysis_date [character] Date. Indexes into dataset dataset. Expects [Date|POSIXt] values.
 - analysis_indicator [character] (optional) Analysis reference range indicator. Indexes into dataset dataset. Expects [character|factor] values.
 - range_low_limit [character] (optional) Lower limit of the reference range. Indexes into dataset dataset. Expects [numeric] values.
 - range_high_limit [character] (optional) Upper limit of the reference range. Indexes into dataset dataset. Expects [numeric] values.
 - summary_stats [character] (optional) Additional value column for summary statistics. Indexes into dataset dataset. Expects [numeric] values.
- tooltip [character(n)] Block of text to display as hover information over each point of the trace. The names of this list are included as literal text and honor three basic HTML formatting elements: , ,  ). The columns the values refer to are populated with the value on the dataset relevant to any given row. Indexes into dataset dataset.
vline_vars [character(n)] Place vertical dashed lines on days indicated by this dataset columns. Indexes into dataset subject_level_dataset_name. Expects [integer|Date|POSIXt] values.
vline_day_numbers [integer(n)] (optional) Place vertical dashed lines on days indicated by this parameter. Represents a CDISC (non-zero) Study Day.
palette [character(n)] (optional) If a name on this list matches the text on a plot element, the associated color will be applied to that element. This mapping takes precedence over the built-in palette. Contains either an HTML (#xxxxxx) or an R color.

Value

A list composed of the following elements:

ui: Shiny UI function.
server: Shiny server function.
module_id: Shiny unique identifier.

Usage

Arguments

Value

See also