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NEWS.md

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EHDEN HMB v2.3.5

  • Added database name of data partner in README.md file

EHDEN HMB v2.3.4

  • Added check in function getTteResKM(_procedureAnalysis.R). If no data are returned, skip export and subsequent data transformation.

EHDEN HMB v2.3.3

  • Edited hmb cohort definition. Added Observation domain block to Cohort Entry Events because of a change of concept 4302555 from Condition to Observation.

EHDEN HMB v2.3.2

  • Added code to remove double quotes from credentials in order to connect to server with DBI (function: cdmFromConAllDbs)

EHDEN HMB v2.3.1

  • Added Redshift connectivity in function cdmFromConAllDbs
  • Updated the KeyringSetup.R file to add two additional credentials: port and server

EHDEN HMB v2.3.0

  • Added function cdmFromConAllDbs to connect to different SQL servers with ODBC drivers

EHDEN HMB v2.2.0

  • Added if-clause for Snowflake specific SQL functions
  • Added code that checks if the output of function FeatureExtraction::getDbCovariateData is empty

EHDEN HMB v2.1.3

  • Updated renv.lock

EHDEN HMB v2.1.2

  • Edited info text in About page
  • Renamed age group label from age_30_45 to age_30_44
  • Added task to create png files of the KM plots for TTD and TTI

EHDEN HMB v2.1.1

  • Removed concept set undefinedIUD from analysis

EHDEN HMB v2.1.0

  • Moved hormonalLngIud concept from Procedure Analysis to Treatment Patterns
  • Edited info text in Treatment Patterns section

EHDEN HMB v2.0.0

  • Updated endometriosis, disorder of ovary, myomectomy, hysterectomy endometrial ablation and endometrial polyp concept sets
  • Merged concept sets hormonal IUD and lng IUD into one concept set named hormonalLngIud
  • Added new covariate concept set endometriosis of uterus
  • Added procedures in the Treatment Patterns analysis (Sequences)
  • Edited Treatment Patterns function code to include event cohorts that started the same day as the target cohort's end date
  • Reworked incidence analysis. Using the IncidencePrevalence package to calculate.
  • Added Age distribution plot in shiny app section Clinical Characteristics
  • Added new time window (at index i.e. 0 days from index date) for drug and procedure prevalence analysis
  • Changed the label of the first age group from 0-30 to 11-29
  • Created additional task named zip results

EHDEN HMB v1.1.1

  • Adjusted height and width parameters for KM plots pictures in the shiny app

EHDEN HMB v1.1.0

  • Reworked incidence analysis. Age groups' incidence is calclulated by the CohortIncidence package and not by stratified cohorts.

EHDEN HMB v1.0.2

  • Fixed cohort picker in shiny app
  • Updated renv.lock file for package dependency

EHDEN HMB v1.0.1

  • Corrected NEWS.md file
  • Added "result"" and "data"" folders in .gitignore file

EHDEN HMB v1.0.0

  • Removed HMB2 cohort definition
  • Added all drug cohorts to post-index utilization analysis
  • Split Oral Contraceptives concept set to 1) All oral contraceptives excluding estradiol+dienogest and 2) just estradiol+dienogest oral contraceptives
  • Added narrow definition of pain covariate (i.e. pain associated with HMB)
  • Added new Treatment Patterns analysis (without NSAIDs). Kept the initial analysis as sensitivity (with NSAIDs).
  • Added new Time to discontinuation analysis (without NSAIDs). Kept the initial analysis as sensitivity (with NSAIDs).
  • Added risk table with people at risk and censored underneath KM plots
  • Added subsets of Treatment Patterns analysis i.e. patterns of first 6 months, 1 year and 2 years after index date
  • Drug utilization has been extended to two different analyses: 'Within time window' and 'Complete follow-up'
  • Incidence analysis has been altered. Incidence rate is calculated by using the same stratified cohorts in both numerator and denominator

EHDEN HMB v0.9.0

  • Updated .gitignore with Github R template
  • Corrected links in README.md file
  • Corrected database names in sap.qmd and index.qmd file
  • Tidied up R scripts
  • Replaced SQL function EXTRACT with YEAR in the _buildStrata.R script to translate SQL code to Azure Synapse dialect
  • Converted dbplyr function to SQL code
  • Reworked initializeCohortTables function (Added drop table sql code)
  • Added database information Markdown in shiny app

EHDEN HMB v0.2.0

  • Add shiny app to preview results

EHDEN HMB v0.1.8

  • Fix pid and std file names in cohort definitions, changes anticipated build order

EHDEN HMB v0.1.7

  • Correct event in time to procedure intervention

EHDEN HMB v0.1.6

  • Minor bug fix to treatment patterns analysis
  • Correct typo in functions

EHDEN HMB v0.1.5

  • Correct bug in analysis settings (Issue #12)
  • Update package website
  • Add yearly incidence to Incidence Analysis (Issue #13)
  • Add R scripts for data exchange and CD preview (Issue #14)
  • Update cohort definitions from Siir
    • copperIUDproc
    • copperIUDdrug
    • disorderOfOvary

EHDEN HMB v0.1.4

  • Fix bug in baseline characteristics; typo in analysis settings (Issue #10)
  • Corrections to the study website

EHDEN HMB v0.1.3

  • Update cohort definitions
    • add baseline procedures
    • add baseline drugs
  • Include procedure prevalence at baseline [-365,0]

EHDEN HMB v0.1.2

  • Update cohort definitions
    • rerun drug exposure with Capr
    • rerun procedures with Capr
    • add time restraints to nsaids
    • add hmb cohort without hysterectomy censor
  • Add secondary treatment sequence including procedures

EHDEN HMB v0.1.1

  • Add study website
  • Update cohort definitions for denominator
  • Addition of executeStudy.R file to automate execution
  • Add age strata [under 30, 30-45, 45-55]

EHDEN HMB v0.1.0

  • First release of study code for EHDEN HMB
    • Add Incidence Analysis
    • Add Baseline Characteristics
    • Add Treatment Patterns
    • Add Procedure Analysis

EHDEN HMB v0.0.6

  • Add file StoreResults to upload cohort diagnostics zip to aws s3 bucket
  • Update KeyringSetup to match Ulysses
  • Update renv.lock to add aws.s3 and Ulysses v0.0.2
  • Minor correction to study task files

EHDEN HMB v0.0.5

  • Added in renv
  • Minor correction to HMB cohort for cohort diagnostics

EHDEN HMB v0.0.4

  • Fix errors in KeyringSetup.R file
  • Fix cohort diagnostics to use integer64 with id in cohortDefinitionSet

EHDEN HMB v0.0.3

  • Update How to run file with installation instructions for usethis and Ulysses
  • Fix extras/KeyringSetup.R file to correctly set up credentials and check them
  • Edit startSnowflakeSession function to handle string split of workDatabaseSchema
  • Edit study tasks to order snowflake start correctly and close connection at end of file

EHDEN HMB v0.0.2

  • Update cohort definition for HMB to fix error
  • Add cohort diagnostics script
  • Add HowToRun file and keyring file

EHDEN HMB v0.0.1

  • Add HMB cohort definition to repo
  • Start preparing documentation about study
  • Initialize OHDSI study
  • Add NEWS.md to track changes