Package 'micar' reference manual

Title:	'Mica' Data Web Portal Client
Description:	'Mica' is a server application used to create data web portals for large-scale epidemiological studies or multiple-study consortia. 'Mica' helps studies to provide scientifically robust data visibility and web presence without significant information technology effort. 'Mica' provides a structured description of consortia, studies, annotated and searchable data dictionaries, and data access request management. This 'Mica' client allows to perform data extraction for reporting purposes.
Authors:	Yannick Marcon [aut, cre] , OBiBa group [cph]
Maintainer:	Yannick Marcon <[email protected]>
License:	GPL-3
Version:	1.2.0
Built:	2025-02-09 04:44:57 UTC
Source:	https://github.com/obiba/micar

Get a data access request

Description

Get a specific data access request main form.

Usage

mica.dar(mica, id)
mica.dar(mica, id)

Arguments

`mica`	A Mica object
`id`	Data access request identifier

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar(m, "12345")
mica.logout(m)

## End(Not run)

Get data access request actions

Description

Get the actions history of a specific data access request.

Usage

mica.dar.actions(mica, id, df = TRUE)
mica.dar.actions(mica, id, df = TRUE)

Arguments

`mica`	A Mica object
`id`	Data access request identifier
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.actions(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.actions(m, "12345")
mica.logout(m)

## End(Not run)

Get a data access requests agreement forms

Description

Get a data access requests agreement forms.

Usage

mica.dar.agreements(mica, id, df = TRUE)
mica.dar.agreements(mica, id, df = TRUE)

Arguments

`mica`	A Mica object
`id`	Data access request identifier
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.agreements(m, '1234')
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.agreements(m, '1234')
mica.logout(m)

## End(Not run)

Get a amendment

Description

Get a specific data access request amendment.

Usage

mica.dar.amendment(mica, pid, id)
mica.dar.amendment(mica, pid, id)

Arguments

`mica`	A Mica object
`pid`	Data access request identifier
`id`	Amendment identifier

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendment(m, "12345", "12345-1")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendment(m, "12345", "12345-1")
mica.logout(m)

## End(Not run)

Get the data access request amendment form

Description

Get the data access request amendment form.

Usage

mica.dar.amendment.form(mica)
mica.dar.amendment.form(mica)

Arguments

mica

A Mica object

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendment.form(m)
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendment.form(m)
mica.logout(m)

## End(Not run)

Get amendment history

Description

Get the history of a specific data access request amendment.

Usage

mica.dar.amendment.history(mica, pid, id, df = TRUE)
mica.dar.amendment.history(mica, pid, id, df = TRUE)

Arguments

`mica`	A Mica object
`pid`	Data access request identifier
`id`	Amendment identifier
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendment.history(m, "12345", "12345-1")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendment.history(m, "12345", "12345-1")
mica.logout(m)

## End(Not run)

Get amendments

Description

Get the list of amendments of a specific data access request.

Usage

mica.dar.amendments(mica, pid, status = NULL, df = TRUE)
mica.dar.amendments(mica, pid, status = NULL, df = TRUE)

Arguments

`mica`	A Mica object
`pid`	Data access request identifier
`status`	Filter by status
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendments(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendments(m, "12345")
mica.logout(m)

## End(Not run)

Get amendments history

Description

Get the history of the amendments of a specific data access request.

Usage

mica.dar.amendments.history(mica, pid, df = TRUE)
mica.dar.amendments.history(mica, pid, df = TRUE)

Arguments

`mica`	A Mica object
`pid`	Data access request identifier
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendments.history(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.amendments.history(m, "12345")
mica.logout(m)

## End(Not run)

Get the data access request form

Description

Get the data access request form.

Usage

mica.dar.form(mica)
mica.dar.form(mica)

Arguments

mica

A Mica object

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.form(m)
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.form(m)
mica.logout(m)

## End(Not run)

Get data access request history

Description

Get the history of a specific data access request main form.

Usage

mica.dar.history(mica, id, df = TRUE)
mica.dar.history(mica, id, df = TRUE)

Arguments

`mica`	A Mica object
`id`	Data access request identifier
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.history(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.history(m, "12345")
mica.logout(m)

## End(Not run)

Get the data access requests preliminary form

Description

Get the data access requests preliminary form.

Usage

mica.dar.preliminaries(mica, status = NULL, df = TRUE)
mica.dar.preliminaries(mica, status = NULL, df = TRUE)

Arguments

`mica`	A Mica object
`status`	Filter by status
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.preliminaries(m)
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.preliminaries(m)
mica.logout(m)

## End(Not run)

Get a data access request preliminary form

Description

Get a specific data access request preliminary form.

Usage

mica.dar.preliminary(mica, id)
mica.dar.preliminary(mica, id)

Arguments

`mica`	A Mica object
`id`	Data access request identifier

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.preliminary(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.preliminary(m, "12345")
mica.logout(m)

## End(Not run)

Get data access request history preliminary form

Description

Get the history of a specific data access request preliminary form.

Usage

mica.dar.preliminary.history(mica, id, df = TRUE)
mica.dar.preliminary.history(mica, id, df = TRUE)

Arguments

`mica`	A Mica object
`id`	Data access request identifier
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.preliminary.history(m, "12345")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dar.preliminary.history(m, "12345")
mica.logout(m)

## End(Not run)

Get the data access requests main form

Description

Get the data access requests main form.

Usage

mica.dars(mica, status = NULL, df = TRUE)
mica.dars(mica, status = NULL, df = TRUE)

Arguments

`mica`	A Mica object
`status`	Filter by status
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dars(m)
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("someuser", "somepassword", "https://mica-demo.obiba.org")
mica.dars(m)
mica.logout(m)

## End(Not run)

Get the datasets

Description

Get the datasets

Usage

mica.datasets(
  mica,
  query = "dataset()",
  select = list("*"),
  sort = list("id"),
  from = 0,
  limit = 10000,
  locale = "en",
  df = TRUE
)
mica.datasets(
  mica,
  query = "dataset()",
  select = list("*"),
  sort = list("id"),
  from = 0,
  limit = 10000,
  locale = "en",
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`select`	The fields to be extracted
`sort`	The fields to sort by
`from`	From item
`limit`	Max number of items
`locale`	The language for labels (default is "en")
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.datasets(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.datasets(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
mica.logout(m)

## End(Not run)

Open connection with Mica

Description

Open a connection with Mica and returns a Mica object. When the two-factor authentication mechanism is enabled, the user will be prompt for one-time password input.

Usage

mica.login(
  username = getOption("mica.username", "anonymous"),
  password = getOption("mica.password", "password"),
  url = getOption("mica.url"),
  opts = getOption("mica.opts", list())
)
mica.login(
  username = getOption("mica.username", "anonymous"),
  password = getOption("mica.password", "password"),
  url = getOption("mica.url"),
  opts = getOption("mica.opts", list())
)

Arguments

`username`	User name in mica. Can be provided by "mica.username" option.
`password`	User password in mica. Can be provided by "mica.password" option.
`url`	Mica url or list of mica urls. Can be provided by "mica.url" option. Secure http (https) connection is required.
`opts`	Curl options. Can be provided by "mica.opts" option.

Value

A Mica object.

Examples

## Not run: 
# login using credentials from mica.username and mica.password options
m <- mica.login("https://mica-demo.obiba.org")
# login by providing credentials
m <- mica.login("administrator", "password", "https://mica-demo.obiba.org")

## End(Not run)
## Not run: 
# login using credentials from mica.username and mica.password options
m <- mica.login("https://mica-demo.obiba.org")
# login by providing credentials
m <- mica.login("administrator", "password", "https://mica-demo.obiba.org")

## End(Not run)

Close connection with Mica

Description

Close connection and release resources of Mica.

Usage

mica.logout(mica)
mica.logout(mica)

Arguments

mica

A Mica object

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.logout(m)

## End(Not run)

Get the networks

Description

Get the networks

Usage

mica.networks(
  mica,
  query = "network()",
  select = list("*"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)
mica.networks(
  mica,
  query = "network()",
  select = list("*"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`select`	The fields to be extracted
`sort`	The fields to sort by
`from`	From item
`limit`	Max number of items
`locale`	The language for labels (default is "en")
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.networks(m, query="network(in(Mica_network.studyIds,clsa))")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.networks(m, query="network(in(Mica_network.studyIds,clsa))")
mica.logout(m)

## End(Not run)

Get the studies

Description

Get the studies

Usage

mica.studies(
  mica,
  query = "study()",
  select = list("acronym", "name", "objectives", "model",
    "populations.dataCollectionEvents.model.dataSources"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)
mica.studies(
  mica,
  query = "study()",
  select = list("acronym", "name", "objectives", "model",
    "populations.dataCollectionEvents.model.dataSources"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`select`	The fields to be extracted
`sort`	The fields to sort by
`from`	From item
`limit`	Max number of items
`locale`	The language for labels (default is "en")
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.studies(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))", 
  locale="en", from=0, limit=10)
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.studies(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))", 
  locale="en", from=0, limit=10)
mica.logout(m)

## End(Not run)

Get the study data collection events

Description

Get the study data collection events (DCEs). Note that the DCEs are not fetched directly, they are extracted from study search results.

Usage

mica.study.dces(
  mica,
  query = "study()",
  select = list("populations.dataCollectionEvents"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)
mica.study.dces(
  mica,
  query = "study()",
  select = list("populations.dataCollectionEvents"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`select`	The fields to be extracted
`sort`	The fields to sort by
`from`	From item
`limit`	Max number of items. Note that this limit applies to the studies that are fetched, the resulting count of DCEs will be higher.
`locale`	The language for labels (default is "en")
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.study.dces(m, query="study(in(Mica_study.methods-design,cohort_study))")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.study.dces(m, query="study(in(Mica_study.methods-design,cohort_study))")
mica.logout(m)

## End(Not run)

Get the study populations

Description

Get the study populations. Note that the populations are not fetched directly, they are extracted from study search results.

Usage

mica.study.populations(
  mica,
  query = "study()",
  select = list("populations.name", "populations.description", "populations.model"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)
mica.study.populations(
  mica,
  query = "study()",
  select = list("populations.name", "populations.description", "populations.model"),
  sort = list("id"),
  from = 0,
  limit = 100,
  locale = "en",
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`select`	The fields to be extracted
`sort`	The fields to sort by
`from`	From item
`limit`	Max number of items. Note that this limit applies to the studies that are fetched, the resulting count of populations will be higher.
`locale`	The language for labels (default is "en")
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.study.populations(m, query="study(in(Mica_study.methods-design,cohort_study))")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.study.populations(m, query="study(in(Mica_study.methods-design,cohort_study))")
mica.logout(m)

## End(Not run)

Get the taxonomies

Description

Get the taxonomies, optionally filtered by taxonomy name and by term matching.

Usage

mica.taxonomies(
  mica,
  query = NULL,
  locale = "en",
  target = "variable",
  taxonomies = NULL,
  df = TRUE
)
mica.taxonomies(
  mica,
  query = NULL,
  locale = "en",
  target = "variable",
  taxonomies = NULL,
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`locale`	The language for labels (when NULL labels are not included in the result)
`target`	What the taxonomy is about: variable (default), dataset, study, network
`taxonomies`	Taxonomy names to subset. If NULL or empty all taxonomies are returned
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.taxonomies(m, target="variable", query="sex", locale="en",
  taxonomies = list("Mlstr_area", "Mlstr_additional"))
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.taxonomies(m, target="variable", query="sex", locale="en",
  taxonomies = list("Mlstr_area", "Mlstr_additional"))
mica.logout(m)

## End(Not run)

Get the variables

Description

Get the variables

Usage

mica.variables(
  mica,
  query = "variable()",
  select = list("*"),
  sort = list("id"),
  from = 0,
  limit = 10000,
  locale = "en",
  df = TRUE
)
mica.variables(
  mica,
  query = "variable()",
  select = list("*"),
  sort = list("id"),
  from = 0,
  limit = 10000,
  locale = "en",
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`select`	The fields to be extracted
`sort`	The fields to sort by
`from`	From item
`limit`	Max number of items
`locale`	The language for labels (default is "en")
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.variables(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.variables(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
mica.logout(m)

## End(Not run)

Get the vocabularies

Description

Get the taxonomy vocabularies, optionally filtered by taxonomy name and by term matching.

Usage

mica.vocabularies(
  mica,
  query = NULL,
  locale = "en",
  target = "variable",
  taxonomies = NULL,
  df = TRUE
)
mica.vocabularies(
  mica,
  query = NULL,
  locale = "en",
  target = "variable",
  taxonomies = NULL,
  df = TRUE
)

Arguments

`mica`	A Mica object
`query`	The search query
`locale`	The language for labels (when NULL labels are not included in the result)
`target`	What the taxonomy is about: variable (default), dataset, study, network
`taxonomies`	Taxonomy names to subset. If NULL or empty all taxonomies are returned
`df`	Return a data.frame (default is TRUE)

Examples

## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.vocabularies(m,target="variable", query="cancer", locale = "en")
mica.logout(m)

## End(Not run)
## Not run: 
m <- mica.login("https://mica-demo.obiba.org")
mica.vocabularies(m,target="variable", query="cancer", locale = "en")
mica.logout(m)

## End(Not run)

Package 'micar'

Help Index

Get a data access request

Description

Usage

Arguments

See Also

Examples

Get data access request actions

Description

Usage

Arguments

See Also

Examples

Get a data access requests agreement forms

Description

Usage

Arguments

See Also

Examples

Get a amendment

Description

Usage

Arguments

See Also

Examples

Get the data access request amendment form

Description

Usage

Arguments

See Also

Examples

Get amendment history

Description

Usage

Arguments

See Also

Examples

Get amendments

Description

Usage

Arguments

See Also

Examples

Get amendments history

Description

Usage

Arguments

See Also

Examples

Get the data access request form

Description

Usage

Arguments

See Also

Examples

Get data access request history

Description

Usage

Arguments

See Also

Examples

Get the data access requests preliminary form

Description

Usage

Arguments

See Also

Examples

Get a data access request preliminary form

Description

Usage

Arguments

See Also

Examples

Get data access request history preliminary form

Description

Usage

Arguments

See Also

Examples