| Type: | Package |
| Title: | 'Amber' Electronic Data Capture Client |
| Version: | 1.2.0 |
| Depends: | httr |
| Imports: | jsonlite, dplyr, tidyjson |
| Description: | 'Amber' is a server application for capturing electronic data records. Rich forms are used to collect data. This 'Amber' client allows to perform data extraction for reporting or data transfer at persistent location purposes. |
| License: | GPL-3 |
| URL: | https://github.com/obiba/amberr/, https://www.obiba.org/amberr/, https://www.obiba.org/pages/products/amber/ |
| BugReports: | https://github.com/obiba/amberr/issues/ |
| RoxygenNote: | 7.3.2 |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2025-04-03 07:19:08 UTC; yannick |
| Author: | Yannick Marcon 
[aut, cre],
OBiBa group [cph] |
| Maintainer: | Yannick Marcon <yannick.marcon@obiba.org> |
| Repository: | CRAN |
| Date/Publication: | 2025-04-03 07:30:02 UTC |
Make the Authorization header value.
Description
Make the Authorization header value.
Usage
.authzHeader(amber)
Issues a DELETE request to Amber for the specified resource
Description
Issues a DELETE request to Amber for the specified resource
Usage
.delete(amber, ..., query = list())
Issues a GET request to Amber for the specified resource
Description
Issues a GET request to Amber for the specified resource
Usage
.get(amber, ..., query = list())
Turns a dictionary in JSON format into a "Opal" one (variables and categories)
Description
Turns a dictionary in JSON format into a "Opal" one (variables and categories)
Usage
.makeDictionary(vars)
Converts a NULL value to NA
Description
Converts a NULL value to NA
Usage
.nullToNA(x)
Issues a POST form request to Amber for the specified resource
Description
Issues a POST form request to Amber for the specified resource
Usage
.post(amber, ..., query = list())
Display search result metrics
Description
Display search result metrics
Usage
.reportListMetrics(results)
Convert list to vector
Description
Convert list to vector
Usage
.unlist(x)
Utility method to build urls. Concatenates all arguments and adds a '/' separator between each element
Description
Utility method to build urls. Concatenates all arguments and adds a '/' separator between each element
Usage
.url(amber, ...)
Verbose flag
Description
Verbose flag
Usage
.verbose()
Get a campaign
Description
Get an interview design campaign by its name or identifier.
Usage
amber.campaign(amber, id, study = NULL, interviewDesign = NULL, query = list())
Arguments
amber |
An Amber object |
id |
Interview design's name or identifier |
study |
Study identifier (name or id), optional. |
interviewDesign |
Interview design identifier (name or id), optional. |
query |
A search query |
Value
A campaign object as a named list
See Also
Other studies functions:
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.campaign(a, id = "base", interviewDesign = "Adult trauma - baseline")
amber.logout(a)
## End(Not run)
Get the campaigns
Description
Get the interview design campaigns.
Usage
amber.campaigns(
amber,
study = NULL,
interviewDesign = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
interviewDesign |
Interview design identifier (name or id), optional. |
query |
A search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.campaigns(a)
amber.campaigns(a, study="Liftup", interviewDesign = "Treocapa")
amber.logout(a)
## End(Not run)
Export the case report records
Description
Export the case report records of one or several form(s).
Usage
amber.case_report_export(
amber,
study = NULL,
form = NULL,
caseReportForm = NULL,
from = NULL,
to = NULL,
pId = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
form |
Form identifier (name or id), optional. |
caseReportForm |
Case report form identifier (name or id), optional. |
from |
From date (included), optional |
to |
To date (included), optional |
pId |
Patient/participant identifier |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A named list of data.frames, a data dictionary and a data data.frame per form revision (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find all case reports
amber.case_report_export(a)
# Find all case reports in a range of time
amber.case_report_export(a, from = "2022-01-12 00:00", to = "2022-02-13")
# Find all case reports for a specific participant/patient identifier
amber.case_report_export(a, pId = "1231")
# Find all case reports having their identifier matching a regular expression
amber.case_report_export(a, query = list(`data._id[$search]` = "^12"))
# Find all case reports which form data is equal to some value
# (will not work if the data are encrypted in the database)
amber.case_report_export(a, query = list(data.PATIENT.ORIGIN_REGION = "xyz"))
# Export records collected with a study's form in a specific version
amber.case_report_export(a,
study = "Trauma Registry",
form = "Adult trauma",
query = list(revision = 6))
# Export records collected with a specific case report form
tables <- amber.case_report_export(a, caseReportForm = "Adult trauma - test")
# Export records collected with a study's form in all versions used
tables <- amber.case_report_export(a,
study = "Trauma Registry",
form = "Adult trauma")
# Result contains both data and dictionary
tables
# Tables are named with the <case report form name>-<revision> pattern
names(tables)
# Merge datasets from different versions if relevant
dplyr::bind_rows(lapply(tables, function (t) {
t$data
}))
amber.logout(a)
## End(Not run)
Get a case report form
Description
Get a case report form by its name or identifier and its revision number (if any).
Usage
amber.case_report_form(
amber,
id,
study = NULL,
form = NULL,
revision = NULL,
query = list()
)
Arguments
amber |
An Amber object |
id |
Case report form's name or identifier |
study |
Study identifier (name or id), optional. |
form |
Form's name or identifier |
revision |
Revision number, optional, default is NULL (means that the case report form uses the latest form revision). |
query |
The search query, to desambiguate form lookup by name |
Value
A case report form object as a named list
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.case_report_form(a, id = "Adult trauma - baseline", form = "Adult trauma", revision = 10)
amber.case_report_form(a, id = "61e69a22fea2df2f3108b508")
amber.logout(a)
## End(Not run)
Get the case report forms
Description
Get the case reports of one or several form(s).
Usage
amber.case_report_forms(
amber,
study = NULL,
form = NULL,
revision = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
form |
Form identifier (name or id), optional. |
revision |
Revision number, optional, default is NULL (means that the case report form uses the latest form revision). |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.case_report_forms(a, form="61e69a22fea2df2f3108b508", skip=0, limit=10)
amber.case_report_forms(a, form="Adult trauma")
amber.case_report_forms(a, study="Trauma Registry", query = list(revision = 1))
amber.case_report_forms(a, query = list(revision = 1))
amber.logout(a)
## End(Not run)
Get the case report records
Description
Get the case report records of one or several form(s).
Usage
amber.case_reports(
amber,
study = NULL,
form = NULL,
caseReportForm = NULL,
from = NULL,
to = NULL,
pId = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
form |
Form identifier (name or id), optional. |
caseReportForm |
Case report form identifier (name or id), optional. |
from |
From date (included), optional |
to |
To date (included), optional |
pId |
Patient/participant identifier |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find all case reports
amber.case_reports(a)
# Find all case reports in a range of time
amber.case_reports(a, from = "2022-01-12 00:00", to = "2022-02-13")
# Find all case reports for a specific participant/patient identifier
amber.case_reports(a, pId = "1231")
# Find all case reports having their identifier matching a regular expression
amber.case_reports(a, query = list(`data._id[$search]` = "^12"))
# Find all case reports which form data is equal to some value
# (will not work if the data are encrypted in the database)
amber.case_reports(a, query = list(data.PATIENT.ORIGIN_REGION = "xyz"))
# Export records collected with a study's form in a specific version
amber.case_reports(a,
study = "Trauma Registry",
form = "Adult trauma",
query = list(revision = 6))
# Export records collected with a specific case report form
amber.case_reports(a, caseReportForm = "Adult trauma - test")
# Export records collected with a study's form in all versions used
amber.case_reports(a,
study = "Trauma Registry",
form = "Adult trauma")
amber.logout(a)
## End(Not run)
Get a form
Description
Get a form by name or identifier.
Usage
amber.form(amber, id, study = NULL, query = list())
Arguments
amber |
An Amber object |
id |
Form's name or identifier |
study |
Study name or identifier, optional |
query |
The search query, to desambiguate form lookup by name |
Value
A form object as a named list
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.form(a, id = "Adult trauma")
amber.form(a, id = "61e69a22fea2df2f3108b508")
amber.logout(a)
## End(Not run)
Get a form revision
Description
Get a form revision by its form name or identifier and its revision number.
Usage
amber.form_revision(amber, form, revision, study = NULL)
Arguments
amber |
An Amber object |
form |
Form's name or identifier |
revision |
Revision number |
study |
Study identifier (name or id), optional. |
Value
A form revision object as a named list
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.form_revision(a, form = "Adult trauma", revision = 10)
amber.form_revision(a, form = "61e69a22fea2df2f3108b508", revision = 10)
amber.logout(a)
## End(Not run)
Get the form revisions
Description
Get the revisions of one or several form(s).
Usage
amber.form_revisions(
amber,
study = NULL,
form = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
form |
Form identifier (name or id), optional. |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.form_revisions(a, form="61e69a22fea2df2f3108b508", skip = 0, limit = 10)
amber.form_revisions(a, form="Adult trauma")
amber.form_revisions(a, study="Trauma Registry", query = list(revision = 1))
amber.form_revisions(a, query = list(revision = 1))
amber.logout(a)
## End(Not run)
Get the forms
Description
Get the forms
Usage
amber.forms(
amber,
study = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study name or identifier, optional |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.forms(a)
amber.forms(a, study="Trauma Registry", skip = 0, limit = 10)
amber.logout(a)
## End(Not run)
Get a group
Description
Get a user by name or identifier.
Usage
amber.group(amber, id)
Arguments
amber |
An Amber object |
id |
Group's name or identifier |
Value
A group object as a named list
See Also
Other users functions:
amber.groups(),
amber.user(),
amber.users()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.group(a, id = "obiba.org")
amber.group(a, id = "615abb061799dd6a2cdbbb10")
amber.logout(a)
## End(Not run)
Get the groups
Description
Get the groups
Usage
amber.groups(amber, query = list(), skip = 0, limit = 100, df = TRUE)
Arguments
amber |
An Amber object |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other users functions:
amber.group(),
amber.user(),
amber.users()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.groups(a, skip = 0, limit = 10)
amber.logout(a)
## End(Not run)
Get an interview design
Description
Get an interview design by its name or identifier.
Usage
amber.interview_design(amber, id, study = NULL, query = list())
Arguments
amber |
An Amber object |
id |
Interview design's name or identifier |
study |
Study identifier (name or id), optional. |
query |
A search query |
Value
An interview design object as a named list
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.interview_design(a, id = "Adult trauma - baseline")
amber.interview_design(a, id = "61e69a22fea2df2f3108b508")
amber.logout(a)
## End(Not run)
Get the interview designs
Description
Get the interview designs.
Usage
amber.interview_designs(
amber,
study = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
query |
A search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.interview_designs(a)
amber.interview_designs(a, study="Liftup")
amber.logout(a)
## End(Not run)
Export the interview records
Description
Export the interview records (data and dictionary) of interview step(s).
Usage
amber.interview_export(
amber,
study = NULL,
interviewDesign = NULL,
campaign = NULL,
from = NULL,
to = NULL,
completed = NULL,
code = NULL,
identifier = NULL,
state = NULL,
participantValid = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
interviewDesign |
Interview design identifier (name or id), optional. |
campaign |
Campaign identifier (name or id), optional. |
from |
From date (included), optional |
to |
To date (included), optional |
completed |
When TRUE export data from completed interviews only (default is NULL) |
code |
Participant interview code |
identifier |
Patient/participant study identifier |
state |
State of the interview: 'initiated', 'in_progress', 'completed' |
participantValid |
Participant is valid (logical): active and in the valid date range |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A named list of data.frames, a data dictionary and a data data.frame per form revision (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Extract data from all interviews
amber.interview_export(a)
# Extract data from all completed interviews
amber.interview_export(a, completed = TRUE)
# Extract data from all interviews in a range of time
amber.interview_export(a, from = "2022-01-12 00:00", to = "2022-02-13")
# Extract data from all interviews for a specific participant/patient
# study identifier
amber.interview_export(a, identifier = "1231")
# Extract data from all interviews having their participant study
# identifier matching a regular expression
amber.interview_export(a, query = list(`identifier[$search]` = "^12"))
# Extract data from all interviews having their participant attributes
# matching a value
# (will not work if the data are encrypted in the database)
amber.interview_export(a, query = list(data.country = "fr"))
# Export records collected with a study's interview design
tables <- amber.interview_export(a,
study = "liftup",
interviewDesign = "treocapa_lt")
# Result contains both data and dictionary
tables
# Tables are named with the <interview design name>-<form name>-<revision> pattern
names(tables)
# Merge datasets from different versions if relevant
dplyr::bind_rows(lapply(tables, function (t) {
t$data
}))
amber.logout(a)
## End(Not run)
Get the interview records
Description
Get the interviews of one or several interview design(s).
Usage
amber.interviews(
amber,
study = NULL,
interviewDesign = NULL,
campaign = NULL,
from = NULL,
to = NULL,
code = NULL,
identifier = NULL,
state = NULL,
participantValid = NULL,
query = list(),
skip = 0,
limit = 100,
mergeUpdatedFillingDates = FALSE,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
interviewDesign |
Interview design identifier (name or id), optional. |
campaign |
Campaign identifier (name or id), optional. |
from |
From date (included), optional |
to |
To date (included), optional |
code |
Participant interview code, optional |
identifier |
Participant identifier, optional |
state |
State of the interview: 'initiated', 'in_progress', 'completed' |
participantValid |
Participant is valid (logical): active and in the valid date range |
query |
A search query |
skip |
Number of items to skip |
limit |
Max number of items |
mergeUpdatedFillingDates |
Set the last update date as being the filling date, if filling date is empty (default is FALSE). |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find all interviews
amber.interviews(a)
# Find all interviews in a range of time
amber.interviews(a, from = "2022-01-12 00:00", to = "2022-02-13")
# Find all interviews for a specific participant/patient study identifier
amber.interviews(a, identifier = "1231")
# Find all interviews having their identifier matching a regular expression
amber.interviews(a, query = list(`data._id[$search]` = "^12"))
# Find all interviews which form data is equal to some value
# (will not work if the data are encrypted in the database)
amber.interviews(a, query = list(data.PATIENT.ORIGIN_REGION = "xyz"))
# Find interview records of a study
amber.interviews(a, study = "Trauma Registry")
amber.logout(a)
## End(Not run)
Get the actions of some interviews step
Description
Get the actions of the steps with a specific name.
Usage
amber.interviews_step_actions(steps, step_name)
Arguments
steps |
The data frame of interviews steps |
step_name |
The name of the step |
Value
A data.frame of step data
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find interview records of a study
itws <- amber.interviews(a, study = "Trauma Registry")
# Get steps
steps <- amber.interviews_steps(itws)
# Get actions of the step with name QUESTIONNAIRE
actions <- amber.interviews_step_actions(steps, 'QUESTIONNAIRE')
# Count the number of completed QUESTIONNAIRE steps ('complete' action type)
# in completed interviews ('completed' state)
actions %>% filter(state == 'completed', type == 'complete') %>% count()
amber.logout(a)
## End(Not run)
Get the data of some interviews step
Description
Get the data of the steps with a specific name.
Usage
amber.interviews_step_data(steps, step_name)
Arguments
steps |
The data frame of interviews steps |
step_name |
The name of the step |
Value
A data.frame of step data
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find interview records of a study
itws <- amber.interviews(a, study = "Trauma Registry")
# Get steps
steps <- amber.interviews_steps(itws)
# Get data of the step with name CONSENT
consent_data <- amber.interviews_step_data(steps, 'CONSENT')
# Count per agreement values (possible values are 0 or 1)
consent_data %>% count(AGREEMENT)
amber.logout(a)
## End(Not run)
Get the steps of interview records
Description
Get the steps of the provided interviews.
Usage
amber.interviews_steps(interviews)
Arguments
interviews |
The data frame of interviews |
Value
A data.frame of steps
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.participant(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find interview records of a study
itws <- amber.interviews(a, study = "Trauma Registry")
# Get steps
steps <- amber.interviews_steps(itws)
amber.logout(a)
## End(Not run)
Opan a connection with Amber
Description
Open a connection with Amber and returns an Amber object. When the two-factor authentication mechanism is enabled, the user will be prompt for one-time password input.
Usage
amber.login(
username = getOption("amber.username", "anonymous"),
password = getOption("amber.password", "password"),
url = getOption("amber.url"),
opts = getOption("amber.opts", list())
)
Arguments
username |
User name in Amber. Can be provided by "amber.username" option. |
password |
User password in Amber. Can be provided by "amber.password" option. |
url |
Amber url. Can be provided by "amber.url" option. Secure http (https) connection is required. |
opts |
Curl options. Can be provided by "amber.opts" option. |
Value
An Amber object
An amber connection object to be used in further function calls
Examples
## Not run:
# login using credentials from amber.username and amber.password options
a <- amber.login("https://amber-demo.obiba.org")
# login by providing credentials
a <- amber.login("administrator", "password", "https://amber-demo.obiba.org")
## End(Not run)
Close connection with Amber
Description
Close connection and release resources of Amber.
Usage
amber.logout(amber)
Arguments
amber |
An Amber object |
Value
No value
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.logout(a)
## End(Not run)
Get a participant
Description
Get an interview design campaign participant by its code or identifier.
Usage
amber.participant(
amber,
code,
study = NULL,
interviewDesign = NULL,
campaign = NULL,
query = list()
)
Arguments
amber |
An Amber object |
code |
Participant's code |
study |
Study identifier (name or id), optional. |
interviewDesign |
Interview design identifier (name or id), optional. |
campaign |
Campaign identifier (name or id), optional. |
query |
A search query |
Value
A participant object as a named list
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participants(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.campaign(a, id = "base", interviewDesign = "Adult trauma - baseline")
amber.logout(a)
## End(Not run)
Get the participants
Description
Get the participants of one or several interview design campaign(s).
Usage
amber.participants(
amber,
study = NULL,
interviewDesign = NULL,
campaign = NULL,
code = NULL,
identifier = NULL,
valid = NULL,
query = list(),
skip = 0,
limit = 100,
df = TRUE
)
Arguments
amber |
An Amber object |
study |
Study identifier (name or id), optional. |
interviewDesign |
Interview design identifier (name or id), optional. |
campaign |
Campaign identifier (name or id), optional. |
code |
Participant interview code, optional |
identifier |
Participant identifier, optional |
valid |
Participant is valid (logical): active and in the valid date range |
query |
A search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.studies(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
# Find all participants
amber.participants(a)
# Find all participants for a specific participant/patient study identifier
amber.participants(a, identifier = "1231")
# Find all participants which data is equal to some value
# (will not work if the data are encrypted in the database)
amber.participants(a, query = list(data.country = "fr"))
# Find the participants of a study interview campaign
amber.participants(a, study = "Liftup", campaign = "base")
amber.logout(a)
## End(Not run)
Get the studies
Description
Get the studies
Usage
amber.studies(amber, query = list(), skip = 0, limit = 100, df = TRUE)
Arguments
amber |
An Amber object |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.study()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.studies(a, skip=0, limit=10)
amber.logout(a)
## End(Not run)
Get a study
Description
Get a study by name or identifier.
Usage
amber.study(amber, id)
Arguments
amber |
An Amber object |
id |
Study's name or identifier |
Value
A study object as a named list
See Also
Other studies functions:
amber.campaign(),
amber.campaigns(),
amber.case_report_export(),
amber.case_report_form(),
amber.case_report_forms(),
amber.case_reports(),
amber.form(),
amber.form_revision(),
amber.form_revisions(),
amber.forms(),
amber.interview_design(),
amber.interview_designs(),
amber.interview_export(),
amber.interviews(),
amber.interviews_step_actions(),
amber.interviews_step_data(),
amber.interviews_steps(),
amber.participant(),
amber.participants(),
amber.studies()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.study(a, id = "Trauma Registry")
amber.study(a, id = "6151b5234268f582926d37f44")
amber.logout(a)
## End(Not run)
Get subjects
Description
Get the users and groups as subjects: an identifier, a type and a name.
Usage
amber.subjects(amber, query = list(), df = TRUE)
Arguments
amber |
An Amber object |
query |
The search query |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a list of raw results when 'df' is FALSE)
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.subjects(a)
amber.logout(a)
## End(Not run)
Get a task
Description
Get a task by its identifier.
Usage
amber.task(amber, id)
Arguments
amber |
An Amber object |
id |
Task's identifier |
Value
An task object as a named list
See Also
Other tasks functions:
amber.task_logs(),
amber.tasks(),
amber.tasks_logs()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.task(a, id = "61e69a22fea2df2f3108b508")
amber.logout(a)
## End(Not run)
Get the logs of a task
Description
Get the logs of a task by its identifier.
Usage
amber.task_logs(amber, id, df = TRUE)
Arguments
amber |
An Amber object |
id |
Task's identifier |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other tasks functions:
amber.task(),
amber.tasks(),
amber.tasks_logs()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.task(a, id = "61e69a22fea2df2f3108b508")
amber.logout(a)
## End(Not run)
Get the tasks
Description
Get the tasks
Usage
amber.tasks(amber, query = list(), skip = 0, limit = 100, df = TRUE)
Arguments
amber |
An Amber object |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other tasks functions:
amber.task(),
amber.task_logs(),
amber.tasks_logs()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.tasks(a, skip = 0, limit = 10)
amber.logout(a)
## End(Not run)
Get the tasks logs
Description
Get the tasks logs
Usage
amber.tasks_logs(amber, query = list(), skip = 0, limit = 100, df = TRUE)
Arguments
amber |
An Amber object |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other tasks functions:
amber.task(),
amber.task_logs(),
amber.tasks()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.tasks_logs(a, skip = 0, limit = 10)
amber.logout(a)
## End(Not run)
Get a user
Description
Get a user by email or identifier.
Usage
amber.user(amber, id)
Arguments
amber |
An Amber object |
id |
User's email or identifier |
Value
A user object as a named list
See Also
Other users functions:
amber.group(),
amber.groups(),
amber.users()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.user(a, id = "jim@muse.com")
amber.user(a, id = "6151b512268f582926d37f90")
amber.logout(a)
## End(Not run)
Get the users
Description
Get the users
Usage
amber.users(amber, query = list(), skip = 0, limit = 100, df = TRUE)
Arguments
amber |
An Amber object |
query |
The search query |
skip |
Number of items to skip |
limit |
Max number of items |
df |
Return a data.frame (default is TRUE) |
Value
A data.frame (or a named list of raw results when 'df' is FALSE)
See Also
Other users functions:
amber.group(),
amber.groups(),
amber.user()
Examples
## Not run:
a <- amber.login("https://amber-demo.obiba.org")
amber.users(a, skip = 0, limit = 10)
amber.logout(a)
## End(Not run)