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Prerelease #312

Merged
merged 75 commits into from
Aug 20, 2024
Merged

Prerelease #312

merged 75 commits into from
Aug 20, 2024

Commits on May 9, 2024

  1. estimation module 

    - adding estimation module that includes CM/SCCS/Evidence synthesis
    @jreps
    jreps committed May 9, 2024
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  2. estimation module updates 

    - adding evidence synth into SCCS
- adding plots for SCCS and CM
    @jreps
    jreps committed May 9, 2024
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  3. estimation edits 

    - optimizing sccs negative control plot
- removing prints
    @jreps
    jreps committed May 9, 2024
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Commits on May 17, 2024

  1. - updating characterization 

    - updating characterization
    @jreps
    jreps committed May 17, 2024
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Commits on May 21, 2024

  1. improving characterization

    @jreps
    jreps committed May 21, 2024
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  2. Update characterization-incidence.R 

    - adding code to use CI TAR lookup if available
    @jreps
    jreps committed May 21, 2024
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  3. Merge branch 'develop' into estimation-updated

    @nhall6
    nhall6 committed May 21, 2024
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Commits on May 22, 2024

  1. minor exclude fixes 

    minor exclude fixes
    @jreps
    jreps committed May 22, 2024
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  2. Update characterization-riskFactors.R

    @jreps
    jreps committed May 22, 2024
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  3. fixes 

    fixes
    @jreps
    jreps committed May 22, 2024
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  4. Update characterization-caseSeries.R 

    adding two extra columns
    @jreps
    jreps committed May 22, 2024
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  5. Update characterization-caseSeries.R 

    restricting case series to during covariates
    @jreps
    jreps committed May 22, 2024
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  6. Update characterization-main.R 

    adding CI outcomes to char options
    @jreps
    jreps committed May 22, 2024
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Commits on May 23, 2024

  1. Update characterization-riskFactors.R 

    fixing multiple washout and min obs bug in risk factors
    @jreps
    jreps committed May 23, 2024
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Commits on Jun 1, 2024

  1. updating for new char tables 

    updating for new char tables
    @jreps
    jreps committed Jun 1, 2024
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Commits on Jun 3, 2024

  1. Update characterization-riskFactors.R

    @jreps
    jreps committed Jun 3, 2024
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  2. updating bug fixes and column cleanliness

    @nhall6
    nhall6 committed Jun 3, 2024
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  3. Merge branch 'estimation-updated' of https://github.com/OHDSI/OhdsiSh… 

    …inyModules into estimation-updated
    @nhall6
    nhall6 committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. Update characterization-timeToEvent.R 

    changing selection for tte
    @jreps
    jreps committed Jun 4, 2024
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Commits on Jun 6, 2024

  1. cleaning characterization tables 

    cleaning characterization tables
    @jreps
    jreps committed Jun 6, 2024
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  2. minor update 

    adding box to show selected tar/database for RF and case series.
    @jreps
    jreps committed Jun 6, 2024
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  3. Update characterization-dechallengeRechallenge.R 

    updating warning for dechal-rechal
    @jreps
    jreps committed Jun 6, 2024
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  4. Update characterization-dechallengeRechallenge.R 

    - only display warning when there are warnings
    @jreps
    jreps committed Jun 6, 2024
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  5. fixing column alignment and incidence error messages

    @nhall6
    nhall6 committed Jun 6, 2024
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  6. Merge branch 'estimation-updated' of https://github.com/OHDSI/OhdsiSh… 

    …inyModules into estimation-updated
    @nhall6
    nhall6 committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. adding drop down and slide filters

    @jreps
    jreps committed Jun 7, 2024
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  2. fixing scrolls 

    fixing scrolls
    @jreps
    jreps committed Jun 7, 2024
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Commits on Jun 11, 2024

  1. Update characterization-cohorts.R 

    fixing SMD calculation in cohorts
    @jreps
    jreps committed Jun 11, 2024
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  2. minor bug fixes 

    - fixing tar changing before generate in case series
- fixing columns showing in selection that should be hidden
    @jreps
    jreps committed Jun 11, 2024
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  3. updating table download 

    - updating csv export to excel export with a details sheet
    @jreps
    jreps committed Jun 11, 2024
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  4. Update components-data-viewer.R 

    changing saving file type
    @jreps
    jreps committed Jun 11, 2024
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  5. adding details to exported results 

    adding details to exported results for characterization cohorts and databases
    @jreps
    jreps committed Jun 11, 2024
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Commits on Jun 12, 2024

  1. Update components-data-viewer.R 

    fixing actions not being includes as it is an extra column that is added outside the coldDef
    @jreps
    jreps committed Jun 12, 2024
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  2. Update characterization-caseSeries.R 

    - adding details to case-series download
    @jreps
    jreps committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. fixing issue with SCCS not showing 

    fixing issue with SCCS not showing
    @jreps
    jreps committed Jun 13, 2024
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  2. fixing characterization 

    updating data downloads for char tables, fixing cohort names in CI, adding caption to custom CI plot
    @nhall6
    nhall6 committed Jun 13, 2024
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  3. Update characterization-main.R 

    sorting outcomes in char
    @jreps
    jreps committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. fixing estimation 

    - adding missing shiny::
- updating code to get T and Os for SCCS so it removed negative controls
    @jreps
    jreps committed Jun 14, 2024
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  2. adding fix for ci_lookup 

    adding fix for ci_lookup
    @jreps
    jreps committed Jun 14, 2024
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Commits on Jun 20, 2024

  1. Update estimation-sccs-results-full.R

    @jreps
    jreps committed Jun 20, 2024
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  2. Update DESCRIPTION 

    adding Nathan Hall and Jamie Gilbert as co-authors
    @nhall6
    nhall6 authored Jun 20, 2024
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Commits on Jun 28, 2024

  1. minor updates 

    - fixed bug with control estimates plot not showing all results
- added ease value to control estimate plot
- added validation checks to print informative reason for missing plots
    @jreps
    jreps committed Jun 28, 2024
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  2. error handling for estimation plots 

    replacing estimation plot error message with useful notification
    @jreps
    jreps committed Jun 28, 2024
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  3. minor updates to estimation 

    - removing old sccs and cohort method files
- making estimation options be ordered by cohort name
- adding indication column into sccs diagnostics
- updating estimation outcome input to have the search options
    @jreps
    jreps committed Jun 28, 2024
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Commits on Jul 2, 2024

  1. characterization test updates 

    - updating characterization tests and fixing issues identified by tests
    @jreps
    jreps committed Jul 2, 2024
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Commits on Jul 9, 2024

  1. Update characterization-main.R 

    removing odd code
    @jreps
    jreps committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. passing R check 

    - passing tests 78% coverage
- cleaning checks but still some notes
    @jreps
    jreps committed Jul 10, 2024
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Commits on Jul 23, 2024

  1. Update characterization-incidence.R to use lookup tables.

    @chrisknoll
    chrisknoll committed Jul 23, 2024
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Commits on Jul 30, 2024

  1. Switch coldef json to CSV.

    @chrisknoll
    chrisknoll committed Jul 30, 2024
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  2. Removed dead code.

    @chrisknoll
    chrisknoll committed Jul 30, 2024
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  3. Fixes estimation bug when target has no comparator for CM

    @anthonysena
    anthonysena committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. fixing tests 

    - fixing tests
- updates for Characterization v1.1.0
- updating example app
    @jreps
    jreps committed Jul 31, 2024
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  2. fixing example sqlite database_ids 

    fixing example sqlite database_ids
    @jreps
    jreps committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Merge branch 'prerelease' into estimation-updated-cohortIncidence

    @jreps
    jreps authored Aug 1, 2024
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  2. Merge pull request #310 from OHDSI/estimation-updated-cohortIncidence 

    Estimation updated cohort incidence
    @jreps
    jreps authored Aug 1, 2024
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  3. CohortIncidence updates 

    - updating test database for new CohortIncidence
- fixing tests for new CohortIncidence
    @jreps
    jreps committed Aug 1, 2024
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  4. fixing check issues due to cohort incidence 

    fixing check issues due to cohort incidence
    @jreps
    jreps committed Aug 1, 2024
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  5. adding hot fixes from main 

    - adding hot fixes from main
- adding incidence results into example app
    @jreps
    jreps committed Aug 1, 2024
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  6. updating example app for CI 

    updating example app for CI
    @jreps
    jreps committed Aug 1, 2024
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  7. updating docs 

    - website update
- manual update
    @jreps
    jreps committed Aug 1, 2024
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Commits on Aug 6, 2024

  1. Update characterization-riskFactors.R 

    fixing minor bug in risk factor that happens when there is multiple outcomeWashoutdays
    @jreps
    jreps committed Aug 6, 2024
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Commits on Aug 9, 2024

  1. Fixing issue #315 , diagonal line along x = y

    @nhall6
    nhall6 committed Aug 9, 2024
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  2. Fixing issue #314 - adding T, C, and O IDs to the table to allow bett… 

    …er filtering to users
    @nhall6
    nhall6 committed Aug 9, 2024
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Commits on Aug 15, 2024

  1. addressing issue #307 

    adding global fuzzy string matching to table search
    @nhall6
    nhall6 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Characterization updates 

    - updating Characterization for new censoring
- adding counts to risk factor view
    @jreps
    jreps committed Aug 16, 2024
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  2. Merge pull request #316 from OHDSI/prerelease-issue#315 

    Fixing issue #315 , diagonal line along x = y
    @jreps
    jreps authored Aug 16, 2024
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  3. Merge pull request #317 from OHDSI/prerelease-issue#314 

    Fixing issue #314 - adding T, C, and O IDs to the table to allow better filtering capabilities for users in large studies
    @jreps
    jreps authored Aug 16, 2024
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Commits on Aug 19, 2024

  1. Update components-data-viewer.R 

    removing new dep on htmlwidgets
    @jreps
    jreps committed Aug 19, 2024
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  2. document updates 

    - updating version ready for release
- updating docs
- updating readme
    @jreps
    jreps committed Aug 19, 2024
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  3. Merge pull request #321 from OHDSI/prerelease-issue#307 

    addressing issue #307
    @jreps
    jreps authored Aug 19, 2024
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Commits on Aug 20, 2024

  1. Merge branch 'prerelease' into nhall6-author-updates

    @jreps
    jreps authored Aug 20, 2024
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  2. Merge branch 'develop' into prerelease

    @jreps
    jreps committed Aug 20, 2024
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  3. merging in develop 

    - merging in develop
- recreating docs after merge
    @jreps
    jreps committed Aug 20, 2024
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  4. fixing formatting of authors 

    fixing formatting of authors
    @jreps
    jreps committed Aug 20, 2024
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  5. Merge pull request #297 from OHDSI/nhall6-author-updates 

    Update DESCRIPTION
    @jreps
    jreps authored Aug 20, 2024
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