Package 'DQAgui' reference manual

Title:	Graphical User Interface for Data Quality Assessment
Description:	A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. Publication: Mang et al. (2021) <doi:10.1186/s12911-022-01961-z>.
Authors:	Lorenz A. Kapsner [cre, aut] , Jonathan M. Mang [aut] , MIRACUM - Medical Informatics in Research and Care in University Medicine [fnd], Universitätsklinikum Erlangen [cph]
Maintainer:	Lorenz A. Kapsner <[email protected]>
License:	GPL-3
Version:	0.2.4
Built:	2024-11-04 06:37:42 UTC
Source:	CRAN

button_send_datamap

Description

This function is an exported wrapper around the actual function to send the datamap. This actual function can be customized by the user.

Usage

button_send_datamap(rv)
button_send_datamap(rv)

Arguments

`rv`	The global rv object. rv$datamap needs to be valid.

Value

This functions is used to trigger logic when clicking the "Send Datamap" button on the dashboard (default: triggers the composing of an email by making use of the java-script command window.open('mailto: ...')). When customizing DQAgui, the function button_send_datamap can be overwritten in the namespace to trigger any other logic, wanted by the user.

Examples

if (interactive()) {
  button_send_datamap(rv=rv)
}

if (interactive()) {
  button_send_datamap(rv=rv)
}

Evaluates whether the load-data button needs to be shown or not.

Description

If there is a valid source system and a valid target system (this is also the case if the user set target == source), the result of this function will be TRUE and the button will be displayed via shinyjs. Otherwise the result is FALSE and the button will be hidden. This function also displays (or hides) the variables which can be assessed.

Usage

check_load_data_button(rv, session)
check_load_data_button(rv, session)

Arguments

`rv`	The global 'reactiveValues()' object, defined in server.R
`session`	Shiny session object

This function is used in the config-tab and displays the selected system to the user.

Description

This function is used in the config-tab and displays the selected system to the user.

Usage

feedback_txt(system, type)
feedback_txt(system, type)

Arguments

`system`	(String) e.g. "i2b2", "OMOP" or "CSV"
`type`	(String) "source" or "target"

Value

String containing the input params in a propper manner

get_db_settings

Description

get_db_settings

Usage

get_db_settings(input, target = TRUE, db_type, displayname_gui, rv)
get_db_settings(input, target = TRUE, db_type, displayname_gui, rv)

Arguments

`input`	Shiny server input object.
`target`	A boolean (default: TRUE).
`db_type`	(String) "postgres" or "oracle".
`displayname_gui`	(String) "i2b2 (Prod)"
`rv`	The global 'reactiveValues()' object, defined in server.R

Value

This functions returns a data table of key-value pairs for the database settings, which are parsed from the respective config tab from the shiny application.

Examples

if (interactive()) {
 get_db_settings(
  input = input,
  target = TRUE,
  db_type = "postgres"
 )
}

if (interactive()) {
 get_db_settings(
  input = input,
  target = TRUE,
  db_type = "postgres"
 )
}

Launch the DQA graphical user interface (GUI)

Description

Launch the DQA graphical user interface (GUI)

Usage

launch_app(
  port = 3838,
  utils_path = system.file("demo_data/utilities", package = "DQAstats"),
  mdr_filename = "mdr_example_data.csv",
  logfile_dir = tempdir(),
  parallel = FALSE,
  ncores = 2,
  demo_usage = FALSE
)
launch_app(
  port = 3838,
  utils_path = system.file("demo_data/utilities", package = "DQAstats"),
  mdr_filename = "mdr_example_data.csv",
  logfile_dir = tempdir(),
  parallel = FALSE,
  ncores = 2,
  demo_usage = FALSE
)

Arguments

`port`	The port, the MIRACUM DQA Tool is running on (default: 3838)
`utils_path`	The path to the utilities-folder, containing the metadata repository files (`mdr.csv` inside the folder `MDR`), JSON files with SQL statements (inside the folder `SQL`), config files for the database connection (`settings_default.yml`) and the email address used for the data map (`email.yml`), a JSON file containing site names (inside the folder `MISC`) and a markdown template to create the PDF report (`DQA_report.Rmd` inside the folder `RMD`).
`mdr_filename`	The filename of the mdr (e.g. "mdr_example_data.csv").
`logfile_dir`	Is the absolute path to the directory where the logfile will be stored. If not path is provided the tempdir() will be used.
`parallel`	A boolean. If `TRUE`, initializing a `future::plan()` for running the code (default: `FALSE`).
`ncores`	A integer. The number of cores to use. Caution: you would probably like to choose a low number when operating on large datasets. Default: 2.
`demo_usage`	A boolean. If `TRUE`, a box is shown on the dashboard with further instructions on how to use / configure the tool.

Value

Executing this function returns a DQAgui shiny application.

Examples

if (interactive()) {
  launch_app()
}

if (interactive()) {
  launch_app()
}

module_atemp_pl_server

Description

module_atemp_pl_server

Usage

module_atemp_pl_server(input, output, session, rv, input_re)
module_atemp_pl_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_atemp_pl_server,
  "moduleAtemporalPlausibilities",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_atemp_pl_server,
  "moduleAtemporalPlausibilities",
  rv = rv,
  input_re = reactive(input)
)
}

module_atemp_pl_ui

Description

module_atemp_pl_ui

Usage

module_atemp_pl_ui(id)
module_atemp_pl_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "atemp_plausi",
    module_atemp_pl_ui(
      "moduleAtemporalPlausibilities"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "atemp_plausi",
    module_atemp_pl_ui(
      "moduleAtemporalPlausibilities"
    )
  )
)
}

module_completeness_server

Description

module_completeness_server

Usage

module_completeness_server(input, output, session, rv, input_re)
module_completeness_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_completeness_server,
  "moduleCompleteness",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_completeness_server,
  "moduleCompleteness",
  rv = rv,
  input_re = reactive(input)
)
}

module_completeness_ui

Description

module_completeness_ui

Usage

module_completeness_ui(id)
module_completeness_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "completeness",
    module_completeness_ui(
      "moduleCompleteness"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "completeness",
    module_completeness_ui(
      "moduleCompleteness"
    )
  )
)
}

module_config_server

Description

module_config_server

Usage

module_config_server(input, output, session, rv, input_re)
module_config_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_config_server,
  "moduleConfig",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_config_server,
  "moduleConfig",
  rv = rv,
  input_re = reactive(input)
)
}

module_config_ui

Description

module_config_ui

Usage

module_config_ui(id)
module_config_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "config",
    module_config_ui(
      "moduleConfig"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "config",
    module_config_ui(
      "moduleConfig"
    )
  )
)
}

module_dashboard_server

Description

module_dashboard_server

Usage

module_dashboard_server(input, output, session, rv, input_re)
module_dashboard_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_dashboard_server,
  "moduleDashboard",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_dashboard_server,
  "moduleDashboard",
  rv = rv,
  input_re = reactive(input)
)
}

module_dashboard_ui

Description

module_dashboard_ui

Usage

module_dashboard_ui(id)
module_dashboard_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "dashboard",
    module_dashboard_ui(
      "moduleDashboard"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "dashboard",
    module_dashboard_ui(
      "moduleDashboard"
    )
  )
)
}

module_descriptive_server

Description

module_descriptive_server

Usage

module_descriptive_server(input, output, session, rv, input_re)
module_descriptive_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_descriptive_server,
  "moduleDescriptive",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_descriptive_server,
  "moduleDescriptive",
  rv = rv,
  input_re = reactive(input)
)
}

module_descriptive_ui

Description

module_descriptive_ui

Usage

module_descriptive_ui(id)
module_descriptive_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "descriptive",
    module_descriptive_ui(
      "moduleDescriptive"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "descriptive",
    module_descriptive_ui(
      "moduleDescriptive"
    )
  )
)
}

module_differences_server

Description

module_differences_server

Usage

module_differences_server(input, output, session, rv, input_re)
module_differences_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_differences_server,
  "moduleDifferences",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_differences_server,
  "moduleDifferences",
  rv = rv,
  input_re = reactive(input)
)
}

module_differences_ui

Description

module_differences_ui

Usage

module_differences_ui(id)
module_differences_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "differences",
    module_differences_ui(
      "moduleDifferences"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "differences",
    module_differences_ui(
      "moduleDifferences"
    )
  )
)
}

module_log_server

Description

module_log_server

Usage

module_log_server(input, output, session, rv, input_re)
module_log_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_log_server,
  "moduleLogging",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_log_server,
  "moduleLogging",
  rv = rv,
  input_re = reactive(input)
)
}

module_log_ui

Description

module_log_ui

Usage

module_log_ui(id)
module_log_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "logging",
    module_log_ui(
      "moduleLogging"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "logging",
    module_log_ui(
      "moduleLogging"
    )
  )
)
}

module_mdr_server

Description

module_mdr_server

Usage

module_mdr_server(input, output, session, rv, input_re)
module_mdr_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_mdr_server,
  "moduleMDR",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_mdr_server,
  "moduleMDR",
  rv = rv,
  input_re = reactive(input)
)
}

module_mdr_ui

Description

module_mdr_ui

Usage

module_mdr_ui(id)
module_mdr_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "mdr",
    module_mdr_ui(
      "moduleMDR"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "mdr",
    module_mdr_ui(
      "moduleMDR"
    )
  )
)
}

module_report_server

Description

module_report_server

Usage

module_report_server(input, output, session, rv, input_re)
module_report_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_report_server,
  "moduleReport",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_report_server,
  "moduleReport",
  rv = rv,
  input_re = reactive(input)
)
}

module_report_ui

Description

module_report_ui

Usage

module_report_ui(id)
module_report_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "report",
    module_report_ui(
      "moduleReport"
    )
  )
)
}
if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "report",
    module_report_ui(
      "moduleReport"
    )
  )
)
}

module_uniq_plaus_server

Description

module_uniq_plaus_server

Usage

module_uniq_plaus_server(input, output, session, rv, input_re)
module_uniq_plaus_server(input, output, session, rv, input_re)

Arguments

`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object
`rv`	The global 'reactiveValues()' object, defined in server.R
`input_re`	The Shiny server input object, wrapped into a reactive expression: `input_re = reactive({input})`

Value

The function returns a shiny server module.

Examples

if (interactive()) {
rv <- list()
shiny::callModule(
  module_uniq_plaus_server,
  "moduleUniquenessPlausibilities",
  rv = rv,
  input_re = reactive(input)
)
}

if (interactive()) {
rv <- list()
shiny::callModule(
  module_uniq_plaus_server,
  "moduleUniquenessPlausibilities",
  rv = rv,
  input_re = reactive(input)
)
}

module_uniq_plaus_ui

Description

module_uniq_plaus_ui

Usage

module_uniq_plaus_ui(id)
module_uniq_plaus_ui(id)

Arguments

`id`	A character. The identifier of the shiny object

Value

The function returns a shiny ui module.

Examples

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "uniq_plausis",
    module_uniq_plaus_ui(
      "moduleUniquenessPlausibilities"
    )
  )
)
}

if (interactive()) {
shinydashboard::tabItems(
  shinydashboard::tabItem(
    tabName = "uniq_plausis",
    module_uniq_plaus_ui(
      "moduleUniquenessPlausibilities"
    )
  )
)
}

This function is called when the user clicks on the button

Description

"Set target == source". It sets target settings = source settings.

Usage

set_target_equal_to_source(rv)
set_target_equal_to_source(rv)

Arguments

`rv`	The global 'reactiveValues()' object, defined in server.R

Sjows an error alert modal with the hint to look into the logfile.

Description

See title.

Usage

show_failure_alert(what_failed)
show_failure_alert(what_failed)

Arguments

what_failed

Short description of what failed.Like: "Getting the data failed." '

Value

Nothing - Just shows the alert modal.

Checks if an connection can be established to the system.

Description

After the button "Check connection" is pressed in the GUI, this function will be called and tries to connect to this system and feedbacks the result to the user. If the connection is successfully established, the button will be disabled and this connection will be stored as valid for the given source/target system.

Usage

test_connection_button_clicked(
  rv,
  source_target,
  db_type,
  input,
  output,
  session
)
test_connection_button_clicked(
  rv,
  source_target,
  db_type,
  input,
  output,
  session
)

Arguments

`rv`	The global 'reactiveValues()' object, defined in server.R
`source_target`	(String) "source" or "target"
`db_type`	(String) "postgres" or "oracle"
`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object

Value

true if the connection could be established and false otherwise (also if an error occurred)

This function checks if all necessary input parameters for source and target exist and are valid.

Description

This function checks if all necessary input parameters for source and target exist and are valid.

Usage

validate_inputs(rv, input, output, session)
validate_inputs(rv, input, output, session)

Arguments

`rv`	The global 'reactiveValues()' object, defined in server.R
`input`	Shiny server input object
`output`	Shiny server output object
`session`	Shiny session object

Package 'DQAgui'

Help Index

button_send_datamap

Description

Usage

Arguments

Value

Examples

Evaluates whether the load-data button needs to be shown or not.

Description

Usage

Arguments

This function is used in the config-tab and displays the selected system to the user.

Description

Usage

Arguments

Value

get_db_settings

Description

Usage

Arguments

Value

Examples

Launch the DQA graphical user interface (GUI)

Description

Usage

Arguments

Value

Examples

module_atemp_pl_server

Description

Usage

Arguments

Value

See Also

Examples

module_atemp_pl_ui

Description

Usage

Arguments

Value

See Also

Examples

module_completeness_server

Description

Usage

Arguments

Value

See Also

Examples

module_completeness_ui

Description

Usage

Arguments

Value

See Also

Examples

module_config_server

Description

Usage

Arguments

Value

See Also

Examples

module_config_ui

Description

Usage

Arguments

Value

See Also

Examples

module_dashboard_server

Description

Usage

Arguments

Value

See Also

Examples

module_dashboard_ui

Description