NEWS.md

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

Changelog

0.11.1

30th July 2024

Change

• use personal access token instead of API key when accessing subscription database. Required as API keys were deprecated

0.11.0

15th October 2023

New

• add $dbPasswordExtraEncryption to allow additional encryption of database password
• $dbPasswordExtraEncryption public member allows definition of an additional user-selectable key to encrypt the database password. $dbPasswordExtraEncryption must be set before opening the database (i.e. before setting $BPdatabaseChoice to the desired server). $dbPasswordExtraEncryption will be immediately set to an empty string after being used by $BPdatabaseChoice
• note that the database password is always encrypted. $dbPasswordExtraEncryption allows a second layer of encryption to be added by the user
• $server.insert and $server.modify changed to allow additional, optional, setting of dbPasswordExtraEncryption
• if defining dbPassWordExtraEncryption with $server.modify, then dbPassword must be defined during the same call to $server.modify
• if dbPasswordExtraEncryption is set to NULL or an empty string (""), then dbPasswordExtraEncryption will not be used.
• the extra encryption key/password can be verified with $dbPasswordExtraVerify
• an extra column in Server table of the configuration database stores the 'hash' of the dbPasswordExtraEncryption key, but not the key itself.

Change

• add VisitID and VisitNotes to $db$visits
• add $db$visit_reason

0.10.1

7th October 2023

New

• add $db$reactions, $db$drugclasses, $db$ingredients, $db$ingredient_drugClass, $db$Product_ingredient, $db$products, $db$productnames

Change

• replace $db$dbversion with $dbversionN
• suppress warnings regarding selection of date format

0.10.0

16th October 2021

New

• add AppointmentType to self$db$appointments
• initialize_data_table, which initializes/modifies tables to configuration database, now exported
• $read_dMeasureModules discovers available dMeasure module packages
• returns result and stores in $dMeasureModules
• this functionality is transferred from DailyMeasure
• $open_configuration_db initializes/modifies configuration tables of dMeasure module packages
• if $dMeasureModules is defined first by calling $read_dMeasureModules
• calls function (not method) initialize_configuration_db of modules found in $dMeasureModules

Change

• Status in self$db$appointments has 'trimmed white space trimws applied.
• HomePhone, WorkPhone and MobilePhone in self$db$patients has 'trimmed white space trimws applied.

0.9.18

1st August 2021

New

• add NoPap, OptOut and OptOutReason to self$db$obgyndetail

0.9.17

11th July 2021

New

• add self$intellectualDisability_list - patients with a history of intellectual disability
• add self$refugeeAsylum_list - patients with a history of refugee or asylum seeker

0.9.16

3rd July 2021

New

• new config_db table Settings
• setting value pairs (character)
• new self$dateformat reactive
• date of formats to be used in GPstat! shiny GUI
• default value is 2021-01-17 (YYYY-mm-dd or %Y-%-m-%d)
• value read from config_db Settings table, with the setting value of dateformat
• associated choices self$dateformat_choices, a vector of character strings
• new self$dateformat_choice active variable.
• reads current value of self$dateformat OR
• writes to self$dateformat and writes to config_db Settings
• if shiny package not available, default is the first of self$dateformat_choices
• new self$formatdate
• returns function to format date, based on self$dateformat_choice
• if lubridate package is not available, returns function(x) {as.character(x)}
• reactive version is self$formatdateR, reacts to self$dateformat()
• suggestion of RN Dat Le, thanks
• add NotGivenHere to self$db$immunizations

Change

• self$list_asthma_details includes max_date parameter

Bugfix

• self$list_asthma_details incorrectly called self$list_contact_asthma

0.9.15

16th June 2021

Bugfix

• allow USERSTATUS == 3 for self$db$users
• empty user list data.frame had 'factorized' strings. change to normal strings

0.9.14

4th April 2021

New

• db$actions, fields : InternalID, UserID, Added, DueDate, Performed, ActionText, Comment

Bugfix

• remove references to CURRENTRX table, which is no longer accessible in Best Practice (probably since version Saffron)
• remove redundant definitions of self$db$vaccine_disease

0.9.13

21st November 2020

Changes

• self$db$users now based on USERS rather than BPS_Users to include 'inactive' users.

Bugfix

• read_subscripton_db can now handle (much) more than 700 names in the list
• not many practices should have that many users, but mine does...
• change call to dbplyr::in_schema to opt out of quoting for schemas
• change required for dbplyr version 2.0.0
• filter_correspondence_named no longer removes CheckedBy, Notation and Action
• view_incoming no longer separates past and future appointments

0.9.12

19th August 2020

New

• add diabetes_type1_list and diabetes_type2_list methods
• add glucose_obs method
• add README.md
• store option for $list_contact_*, contact_*_list

Change

• db$correspondenceInRaw name changed to camel-case. string fields trimmed, date fields converted with as.Date
• replace various dplyr::filter(x == max(x)) with dplyr::arrange(desc(x), .by_group = TRUE) %>>% dplyr::filter(dplyr::row_number() == 1)
• arrange and slice breaks ties, where more than one x has the same 'max' value

Bugfix

• avoid rbinding tibble in $gluocse_obs
• $read_subscription_db handles situation where no relevant registrations are found

0.9.11

8th July 2020

• change license to Mozilla Public License 2.0

Bugfix

• if Action is NULL, in filter_investigations then no investigations will be listed
• if Action is NULL, in filter_correspondence then no correspondecne will be listed

0.9.10

1st July 2020

New

• dMeasureCustom - custom patient lists initialize_data_table function read from dMeasureCustom (if available) adds table to configuration SQLite database read_configuration_db function execute from dMeasureCustom (if available)

Changes

• Changes for new version of DTedit (v2)
• semantic_tag/semantic_button return empty string if tag/button is NA
• change db$currentrx to db$currentRx_raw. add db$currentRx
• remove adjust_date from check_subscription
• check_subscription_datechange_trigR flip-flops from positive to negative

Bugfix

• 'quote' contact_maxDate to prevent early evaluation
• $UserFullConfig uses only the first row in $db$practice to find PracticeName

0.9.9

4th May 2020

New

• db$patientsRaw (include HeadOfFamilyID)
• parent_list for those listed as head of family

Change

• increase tolerance of paste2 to unusual Unicode characters

0.9.8

29th April 2020

• dM$contact_maxDate (and $contact_maxDateR reactive version, and also private version)
• list_contact_count includes maxDate (in addition to minDate) allows restriction of date of last contact e.g. 'has not had contact in past 2 months'

0.9.7

25th April 2020

New

• db$asthmaplan and db$pcehrdocuments
• $list_contact_asthma, $contact_asthma_list and $contact_asthma_listR
• $asthmaplan_obs - list asthma plans
• $list_asthma_details - list asthma patients with vaccination and asthma plan status

Change

• list_fobt, list_cst, list_mammogram include_uptodate option (default TRUE)
• filter out cancelled and 'reversal' services in $db$servicesRaw
• add PayerCode to $db$servicesRaw

Fix

• incorrect labelling of renal disease indication for influenza vaccination

0.9.6

1st April 2020

New

• include_uptodate options for $list_vax, $list_influenza, $list_measlesVax, $list_zostavax

Fix

• correction to $list_influenza and $list_zostavax tag display logic (erroneously showed 'removed from reminder list')

0.9.5

30th March 2020

New

• add intID/intID_Date options to $list_zostavax, $list_influenza, $list_measlesVax, $list_vax

Change

• change from $asplenia_list to $asplenic_list
• adjustable $change_subscription (add adjust_days)

0.9.4

15th March 2020

New

• add $db$vaccines $db$vaccine_disease $db$vaxdiseases (none of them used, yet)

Changes

• change from MariaDB to Airtabler
• filter some 'dummy' entries from $list_appointments, such as 'DO NOT BOOK'
• $read_configuration_db throws warning and stops if $config_db is not a valid, even after an attempted opening (by $read_configuration_db)
• remove LicenseCheckDate from user configuration

Fix

• $server.update invalid Name logic fixed
• $userconfig.update and $userconfig.delete checks for $Fullname inclusion in description

0.9.3

7th March 2020

Improvements

• faster $list_appointments : doesn't retrieve entire patients table!
• reduce calls to $db$practice in $UserFullConfig
• strip whitespace from Fullname in $UserFullConfig
• $Driver definition in config database Server description (default is "SQL Server")

Fixes

• remove InternalID '0' patients from $appointments_filtered
• these are 'dummy' appointments
• deal with NA in ProviderNo
• add SENTTOWORKCOVER to $db$invoices SENTTOWORKCOVER is not a useful field, but for some reason some versions of MSSQL odbc client/server configurations require the extra field (not all fields work) to maintain non-zero status for UserID/InternalID after a select!
• removal of LicenseCheckData from user configuration

Changes

• subscription change : identifiers are changed to upper case

0.9.2

20th February 2020

Fixes

• self$UserFullConfig fix if self$db$users empty

0.9.1

19th February 2020

New

• self$db$Practice provides access to dbo.PRACTICE
• subscription changes
• self$subscription_db provides access to subscription servers (when open)
• self$read_subscription_db to read subscription information
• self$check_subscription to check subscription and date range
• can 'trigger' self$check_subscription_datechange_trigR
• self$UserConfigLicense and $UserConfigLicenseR - similar to $UserConfig, includes $LicenseDate and $Identifier

Changes

• private$.UserRestrictions does not collect() (delayed evaluation)
• private$.UserConfig does not collect() (delayed evaluation)
• private$.UserConfig also does not 'unroll' Locations/Attributes
• $UserConfig includes License, LicenseCheckDate
• private$.identified_user changed to active (self$.identified_user)
• adopts functionality of match_user function
• improved handling (emptying variables/tables) when databases closed or configuration filepath changed

0.8.2

24th December 2019

New

• list_measlesVax (measles vaccine eligibility)
• add self$vaccine_choices - list of available vaccine lists
• add postnatal_list

Bugfix

• default 'chosen' in list_dataQuality corrected
• correction in pregnant_list, allow is.na(ENDDATE) for current pregnancy improved date logic

0.8.1

18th December 2019

New

• list_familyHx (data quality method)
• db$familyhistory and db$familyhistorydetail : access to family history also db$relationcode - but this is not actually used at this time

Bugfix

• convert ResultValue and BPcode to numeric in db$ReportValues

also remove prceding "<" and ">" from ResultValue to allow numerical comparison against "<" and ">" values.

these features require a modified version of dbplyr + 'as.double' CASTs to DOUBLE, instead of NUMERIC (the latter casts to integers) + use TRY_CAST (a T-SQL/Microsoft SQL specific feature) instead of CAST, to allow graceful failure to NA instead of errors.

0.8.0

12th November 2019

New

• dataQuality module - list_dataQuality. currently includes list_allergy

Data quality assessment. Are allergies recorded for the listed patients?

social history (partial) - list_socialHx

list of quality choices in $dataQuality_choices

• paste2 - a version of paste which ignores NA, empty strings and character(0)

• addition of db$reactions addition of KnownAllergies to db$clinical

0.7.2

28th September 2019

Bugfixes

• add "Invoice" to appointment_status_types
• fix error if empty $contact_type when in $list_contact_count

0.7.1

27th September 2019

Bugfix

• process ReportDate to as.Date() in observeValues at table level failure to convert to as.Date will result in invalid dates being compared

other date fields in other tables also converted to as.Date() at table level

0.7.0

21st September 2019

Breaking changes

• Moved framingham_riskequation to package framinghamRiskEquation at https://github.com/DavidPatShuiFong/framinghamRiskEquation
• Moved billings methods to separate package (module) at https://github.com/DavidPatShuiFong/dMeasureBillings
• Moved chronic disease management methods (CDM) to separate package (module) at https://github.com/DavidPatShuiFong/dMeasureCDM

0.6.0

18th September 2019

New

• Addition of appointment versions of list_qim e.g. list_qim_cvdRisk_appointments

Breaking changes

• Move Quality Improvement Measures to separate package (module) 'dMeasureQIM'

Improvement

• Framingham risk equation function

Default is now cardiovascular (instead of coronary heart disease) risk

Bugfix

• GPMP R/V in CDM had reversed colours (yellow/green) and actions ('Overdue'). Fixed

0.5.0

9th September 2019

• Added vignette

• Change billings_list method to list_billings

• Integrates appointments, visits and billing contacts into single view

• Add 'own_billings' active field, if FALSE, then all of the patient's billings for the day are shown (not just those attributed to the same provider listed for that contact)

• Include 'status' in list_appointments return dataframe

• Fixes to server.delete and server.update methods

0.4.0

4th September 2019

• Practice Incentive Program (PIP) Quality Improvement Measures

• lists and reports available for all ten measures

• Mammogram added to cancer screening

• Cervical screening (including Pap) added to cancer screening

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