DavidPatShuiFong/dMeasure
case finding in the EMR (Best Practice)

Package index
Search the DavidPatShuiFong/dMeasure package
Vignettes
Functions
306
Source code
20
Man pages
157
Home
/
GitHub
/
DavidPatShuiFong/dMeasure
/
dMeasure: dMeasure class

dMeasure: dMeasure class
In DavidPatShuiFong/dMeasure: case finding in the EMR (Best Practice)

dMeasureR Documentation

dMeasure class

Description

case-finding in EMR (Best Practice)

Details

dMeasure class

Methods

  • configuration_file_path : read (or initiate) YAML/SQL DB filepaths

  • open_configuration_db : open SQLite configuration database

  • read_configuration_db : read SQLite configuration database

  • open_emr_db : open Best Practice database

  • initialize_emr_tables : configure Best Practice datatables

  • location_list : list practice locations/groups

  • choose_location : change, or read, current location

Public fields

yaml_config_filepath

- filepath of YAML configuration

sql_config_filepath

- filepath of SQL configuration (NULL is not connected)

local_config

- in-memory copy of YAML configuration

Active bindings

local_config

- in-memory copy of YAML configuration

Methods

Public methods

Method list_fobt()

Usage
dMeasure$list_fobt(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  action = FALSE,
  screentag = FALSE,
  screentag_print = TRUE
)

Method list_cst_details()

Usage
dMeasure$list_cst_details(
  screen_cst_list,
  screen_cst_id = NULL,
  include_uptodate = TRUE
)

Method list_cst()

Usage
dMeasure$list_cst(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  action = FALSE,
  screentag = FALSE,
  screentag_print = TRUE
)

Method list_mammogram()

Usage
dMeasure$list_mammogram(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  action = FALSE,
  screentag = FALSE,
  screentag_print = TRUE
)

Method list_zostavax()

Usage
dMeasure$list_zostavax(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  intID = NULL,
  intID_Date = Sys.Date(),
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  vaxtag = FALSE,
  vaxtag_print = TRUE
)

Method list_measlesVax()

Usage
dMeasure$list_measlesVax(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  intID = NULL,
  intID_Date = Sys.Date(),
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  vaxtag = FALSE,
  vaxtag_print = TRUE
)

Method list_influenza()

Usage
dMeasure$list_influenza(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  intID = NULL,
  intID_Date = Sys.Date(),
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  vaxtag = FALSE,
  vaxtag_print = TRUE
)

Method list_vax()

Usage
dMeasure$list_vax(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  intID = NULL,
  intID_Date = Sys.Date(),
  appointments_list = NULL,
  include_uptodate = TRUE,
  lazy = FALSE,
  vaxtag = FALSE,
  vaxtag_print = TRUE,
  chosen = self$vaccine_choices
)

Method filter_investigations()

Usage
dMeasure$filter_investigations(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA
)

Method filter_investigations_appointment()

Usage
dMeasure$filter_investigations_appointment(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA,
  ignorePast = NA,
  lazy = FALSE
)

Method filter_investigations_named()

Usage
dMeasure$filter_investigations_named(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA,
  ignorePast = NA,
  lazy = FALSE
)

Method filter_correspondence()

Usage
dMeasure$filter_correspondence(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA
)

Method filter_correspondence_appointment()

Usage
dMeasure$filter_correspondence_appointment(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA,
  ignorePast = NA,
  lazy = FALSE
)

Method filter_correspondence_named()

Usage
dMeasure$filter_correspondence_named(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA,
  ignorePast = NA,
  lazy = FALSE
)

Method view_incoming()

Usage
dMeasure$view_incoming(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  Action = NA,
  Actioned = NA,
  ignorePast = NA,
  lazy = FALSE,
  screentag = FALSE,
  screentag_print = TRUE
)

Method filter_appointments()

Usage
dMeasure$filter_appointments(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  status = NA
)

Method filter_appointments_time()

Usage
dMeasure$filter_appointments_time(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  status = NA,
  lazy = FALSE
)

Method list_appointments()

Usage
dMeasure$list_appointments(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  status = NA,
  lazy = FALSE
)

Method list_visits()

Usage
dMeasure$list_visits(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  visit_type = NA,
  lazy = FALSE
)

Method diabetes_list()

Usage
dMeasure$diabetes_list(appointments = NULL)

Method diabetes_type1_list()

Usage
dMeasure$diabetes_type1_list(appointments = NULL)

Method diabetes_type2_list()

Usage
dMeasure$diabetes_type2_list(appointments = NULL)

Method asthma_list()

Usage
dMeasure$asthma_list(appointments = NULL)

Method list_asthma_details()

Usage
dMeasure$list_asthma_details(
  contact = FALSE,
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  ignoreOld = FALSE,
  include_uptodate = TRUE,
  lazy = FALSE
)

Method atsi_list()

Usage
dMeasure$atsi_list(appointments = NULL)

Method malignancy_list()

Usage
dMeasure$malignancy_list(appointments = NULL)

Method hiv_list()

Usage
dMeasure$hiv_list(appointments = NULL)

Method haemoglobinopathy_list()

Usage
dMeasure$haemoglobinopathy_list(appointments = NULL)

Method asplenic_list()

Usage
dMeasure$asplenic_list(appointments = NULL)

Method transplant_list()

Usage
dMeasure$transplant_list(appointments = NULL)

Method cvd_list()

Usage
dMeasure$cvd_list(appointments = NULL)

Method cardiacdisease_list()

Usage
dMeasure$cardiacdisease_list(appointments = NULL)

Method trisomy21_list()

Usage
dMeasure$trisomy21_list(appointments = NULL)

Method bmi30_list()

Usage
dMeasure$bmi30_list(appointments = NULL)

Method chroniclungdisease_list()

Usage
dMeasure$chroniclungdisease_list(appointments = NULL)

Method neurologic_list()

Usage
dMeasure$neurologic_list(appointments = NULL)

Method chronicliverdisease_list()

Usage
dMeasure$chronicliverdisease_list(appointments = NULL)

Method chronicrenaldisease_list()

Usage
dMeasure$chronicrenaldisease_list(appointments = NULL)

Method pregnant_list()

Usage
dMeasure$pregnant_list(appointments = NULL)

Method postnatal_list()

Usage
dMeasure$postnatal_list(
  appointments = NULL,
  include_edc = FALSE,
  days_min = 0,
  days_max = 180,
  outcome = c(0:7)
)

Method fifteenplus_list()

Usage
dMeasure$fifteenplus_list(appointments = NULL)

Method sixtyfiveplus_list()

Usage
dMeasure$sixtyfiveplus_list(appointments = NULL)

Method seventyfiveplus_list()

Usage
dMeasure$seventyfiveplus_list(appointments = NULL)

Method ATSI_35_44_list()

Usage
dMeasure$ATSI_35_44_list(appointments = NULL)

Method fortyfiveseventyfour_list()

Usage
dMeasure$fortyfiveseventyfour_list(appointments = NULL)

Method cst_eligible_list()

Usage
dMeasure$cst_eligible_list(appointments = NULL)

Method mammogram_eligible_list()

Usage
dMeasure$mammogram_eligible_list(appointments = NULL)

Method familialHypercholesterolaemia_list()

Usage
dMeasure$familialHypercholesterolaemia_list(appointments = NULL)

Method LVH_list()

Usage
dMeasure$LVH_list(appointments = NULL)

Method intellectualDisability_list()

Usage
dMeasure$intellectualDisability_list(appointments = NULL)

Method refugeeAsylum_list()

Usage
dMeasure$refugeeAsylum_list(appointments = NULL)

Method parent_list()

Usage
dMeasure$parent_list(appointments = NULL, months_min = 0, months_max = 12)

Method location.insert()

Usage
dMeasure$location.insert(description)

Method location.update()

Usage
dMeasure$location.update(description)

Method location.delete()

Usage
dMeasure$location.delete(description)

Method location.list()

Usage
dMeasure$location.list()

Method location.permission()

Usage
dMeasure$location.permission()

Method user_login()

Usage
dMeasure$user_login(password)

Method empty_password()

Usage
dMeasure$empty_password()

Method user_logout()

Usage
dMeasure$user_logout()

Method password.set()

Usage
dMeasure$password.set(newpassword, oldpassword = NULL)

Method password.reset()

Usage
dMeasure$password.reset(user, newpassword = "")

Method server.insert()

Usage
dMeasure$server.insert(description)

Method server.update()

Usage
dMeasure$server.update(description)

Method server.delete()

Usage
dMeasure$server.delete(description)

Method server.list()

Usage
dMeasure$server.list()

Method server.permission()

Usage
dMeasure$server.permission()

Method WriteLog()

Usage
dMeasure$WriteLog(message)

Method userrestriction.change()

Usage
dMeasure$userrestriction.change(restriction, state)

Method userconfig.insert()

Usage
dMeasure$userconfig.insert(description)

Method userconfig.update()

Usage
dMeasure$userconfig.update(description)

Method userconfig.delete()

Usage
dMeasure$userconfig.delete(description)

Method userconfig.list()

Usage
dMeasure$userconfig.list()

Method userrestriction.list()

Usage
dMeasure$userrestriction.list()

Method useradmin.permission()

Usage
dMeasure$useradmin.permission()

Method list_contact_appointments()

Usage
dMeasure$list_contact_appointments(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  status = NA,
  store = TRUE
)

Method list_contact_visits()

Usage
dMeasure$list_contact_visits(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  visit_type = NA,
  store = TRUE
)

Method list_contact_services()

Usage
dMeasure$list_contact_services(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  store = TRUE
)

Method list_contact_count()

Usage
dMeasure$list_contact_count(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_diabetes()

Usage
dMeasure$list_contact_diabetes(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_chroniclungdisease()

Usage
dMeasure$list_contact_chroniclungdisease(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_asthma()

Usage
dMeasure$list_contact_asthma(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_15plus()

Usage
dMeasure$list_contact_15plus(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_65plus()

Usage
dMeasure$list_contact_65plus(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_45_74()

Usage
dMeasure$list_contact_45_74(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_75plus()

Usage
dMeasure$list_contact_75plus(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_ATSI_35_44()

Usage
dMeasure$list_contact_ATSI_35_44(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method list_contact_cst()

Usage
dMeasure$list_contact_cst(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  min_contact = NA,
  min_date = NA,
  max_date = NA,
  contact_type = NA,
  lazy = FALSE,
  store = TRUE
)

Method new()

Usage
dMeasure$new()

Method close()

Usage
dMeasure$close()

Method finalize()

Usage
dMeasure$finalize()

Method formatdate()

Usage
dMeasure$formatdate()

Method read_dMeasureModules()

Usage
dMeasure$read_dMeasureModules()

Method open_configuration_db()

Usage
dMeasure$open_configuration_db(
  configuration_file_path = self$configuration_file_path
)

Method read_configuration_db()

Usage
dMeasure$read_configuration_db(config_db = self$config_db)

Method BPdatabaseChoice_new()

Usage
dMeasure$BPdatabaseChoice_new()

Method read_subscription_db()

Usage
dMeasure$read_subscription_db(forcecheck = FALSE, users = NULL)

Method update_subscription()

Usage
dMeasure$update_subscription(
  Fullname = NA,
  License = NA,
  Identifier = NA,
  verify = TRUE
)

Method check_subscription()

Usage
dMeasure$check_subscription(
  clinicians = NA,
  date_from = NA,
  date_to = NA,
  adjust_days = 7
)

Method match_user()

Usage
dMeasure$match_user()

Method clinician_list()

Usage
dMeasure$clinician_list(view_name = "All", location = NULL)

Method choose_clinicians()

Usage
dMeasure$choose_clinicians(choices = "", view_name = "All")

Method open_emr_db()

Usage
dMeasure$open_emr_db(BPdatabaseChoice = NULL)

Method initialize_emr_tables()

Usage
dMeasure$initialize_emr_tables(emr_db)

Method choose_location()

Usage
dMeasure$choose_location(location = self$location)

Method choose_date()

Usage
dMeasure$choose_date(date_from = self$date_a, date_to = self$date_b)

Method list_allergy()

Usage
dMeasure$list_allergy(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  lazy = FALSE,
  qualitytag = FALSE,
  qualitytag_print = TRUE
)

Method list_socialHx()

Usage
dMeasure$list_socialHx(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  lazy = FALSE,
  qualitytag = FALSE,
  qualitytag_print = TRUE
)

Method list_familyHx()

Usage
dMeasure$list_familyHx(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  lazy = FALSE,
  qualitytag = FALSE,
  qualitytag_print = TRUE
)

Method list_dataQuality()

Usage
dMeasure$list_dataQuality(
  date_from = NA,
  date_to = NA,
  clinicians = NA,
  appointments_list = NULL,
  lazy = FALSE,
  qualitytag = FALSE,
  qualitytag_print = TRUE,
  chosen = self$dataQuality_choices
)

Method influenzaVax_obs()

Usage
dMeasure$influenzaVax_obs(intID, date_from = NA, date_to = NA)

Method HbA1C_obs()

Usage
dMeasure$HbA1C_obs(intID, date_from = NA, date_to = NA)

Method glucose_obs()

Usage
dMeasure$glucose_obs(intID, date_from = NA, date_to = NA)

Method smoking_obs()

Usage
dMeasure$smoking_obs(intID, date_from = NA, date_to = NA)

Method BloodPressure_obs()

Usage
dMeasure$BloodPressure_obs(intID, date_from = NA, date_to = NA)

Method asthmaplan_obs()

Usage
dMeasure$asthmaplan_obs(intID, date_from = NA, date_to = NA)

Method UrineAlbumin_obs()

Usage
dMeasure$UrineAlbumin_obs(intID, date_from = NA, date_to = NA)

Method PersistentProteinuria_obs()

Usage
dMeasure$PersistentProteinuria_obs(intID, date_from = NA, date_to = NA)

Method eGFR_obs()

Usage
dMeasure$eGFR_obs(intID, date_from = NA, date_to = NA)

Method Cholesterol_obs()

Usage
dMeasure$Cholesterol_obs(intID, date_from = NA, date_to = NA)

Method clone()

The objects of this class are cloneable with this method.

Usage
dMeasure$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.


DavidPatShuiFong/dMeasure documentation built on Aug. 2, 2024, 11:45 p.m.

Related to dMeasure in DavidPatShuiFong/dMeasure...

DavidPatShuiFong/dMeasure index
README.md

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close