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Releases: Gilead-BioStats/gsm

v1.4.0

19 Dec 15:09
@mattroumaya mattroumaya
v1.4.0
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v1.4.0

gsm v1.4.0

This release introduces five new KRIs, the inclusion of interactive widgets ported over from the rbm-viz Javascript library, reporting updates, and various bug fixes and utility functions. Major changes are noted below!

Mapping/Assessment Functions for new KRIs

  • DataChg_Map_Raw & DataChg_Assess: Evaluates rate of reported data point with >1 changes.
  • DataEntry_Map_Raw & DataEntry_Assess: Evaluates rate of reported Data Entry Lag >10 days.
  • Screening_Map_Raw & Screening_Assess: Evaluates screen failure rate (SF) on mapped subject-level dataset to identify sites that may be over- or under-reporting patient discontinuations.
  • QueryAge_Map_Raw & QueryAge_Assess: Evaluates rate of reported Query Age >30 days.
  • QueryRate_Map_Raw & QueryRate_Assess: Evaluates query rates to identify sites that may be over- or under-reporting queries.

Interactive Widgets

  • When running any *_Assess() function, visualizations that are suffixed with JS are interactive htmlwidgets ported over from rbm-viz that can be explored in an IDE or web browser.

Reporting Updates

  • Interactive visualizations are now the default in the output of Study_Report().
  • Tables are now interactive and show flag directionality.
  • Only KRIs at the site-level are supported for now. QTLs and country-level KRI reporting is not currently supported.

What's Changed

Full Changelog: v1.3.2...v1.4.0

Contributors

samussiah, mattroumaya, and 2 other contributors
Assets 3
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v1.3.2

21 Nov 22:01
@mattroumaya mattroumaya
v1.3.2
1c2cbd9
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v1.3.2

gsm v1.3.2

This minor release includes updates to the data model that is passed to Gismo via Make_Snapshot()

  • All CTMS metadata is passed through via lMeta$status_study and lMeta$status_site
  • config_schedule/status_schedule are removed as inputs/outputs to Make_Snapshot()

What's Changed

Full Changelog: v1.3.1...v1.3.2

Contributors

mattroumaya
Assets 3
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v1.3.1

17 Nov 13:45
@mattroumaya mattroumaya
v1.3.1
8cb6033
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v1.3.1

gsm v1.3.1

This minor release adds a data frame to the output/data model of Make_Snapshot() that includes parameters and values for QTL analyses.

What's Changed

Full Changelog: v1.3.0...v1.3.1

Contributors

jwildfire, samussiah, and mattroumaya
Assets 3
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v1.3.0

11 Nov 17:51
@mattroumaya mattroumaya
v1.3.0
4e0143e
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v1.3.0

gsm v1.3.0

This release introduces new and refined statistical methods for qualified assessments.

  • A new statistical method Analyze_NormalApprox is now the default method used for the Adverse Event (AE), Disposition (DISP), Lab Abnormality (LB), and Protocol Deviation (PD) assessments.
  • Additionally, Flag_NormalApprox flags values, and Analyze_NormalApprox_PredictBounds creates upper and lower-boundaries for data visualization when a normal approximation is used.
  • QTLs are now supported for Disposition and Protocol Deviation assessments by providing a QTL workflow for Study_Assess() or Make_Snapshot().
  • Country-level workflow YAML files are now available in inst/workflow/country_workflow.
  • Significant documentation and vignette updates, including the Cookbook vignette, Contributor Guidelines, and a new Step-by-Step Analysis vignette.

What's Changed

Full Changelog: v1.2.0...v1.3.0

Contributors

jwildfire, samussiah, and 3 other contributors
Assets 3
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v1.2.0

10 Oct 14:52
@mattroumaya mattroumaya
v1.2.0
caa4fc1
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v1.2.0

gsm v1.2.0

This release includes qualified functionality for the following KRIs:

  • Lab Abnormality
  • Disposition
  • Adverse Event
  • Protocol Deviation

Notable updates include:

  • Addition of the Make_Snapshot() function, which allows a user to run multiple assessments on a given study, as well as create metadata needed as the inputs to the Gismo web app.
  • The Flag() function has been split into Flag_Poisson() and Flag_Fisher() functions to simplify flagging logic based on the type of statistical model that is being used.
  • The Transform_EventCount() function has been split into Transform_Rate() and Transform_Count() to be used based on the metric that is being evaluated.
  • *_Assess() functions have been refactored based on refinements to the data model. Notable changes include removing all lTags, and generally paring back some of the metadata captured in the assess functions which is either no longer needed, or will happen outside of the assessment function.

What's Changed

Full Changelog: v1.1.0...v1.2.0

Contributors

jwildfire, samussiah, and 4 other contributors
Assets 3
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v1.1.0

15 Aug 18:42
@mattroumaya mattroumaya
v1.1.0
6711458
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v1.1.0

gsm v1.1.0

This release includes qualified functionality for the Disposition Assessment and experimental functionality for the Lab Abnormality assessment.

Additionally, updates include:

  • Mapping functions include custom grouping functionality by columns for SiteID, StudyID, or Region/CustomGroupID. This allows for Study (QTL) and Site (KRI) assessments to be run.
  • Analyze_Identity() allows for nominal and statistical assessments for all Assess functions.
  • New utility functions MakeStratifiedAssessment() and ConsolidateStrata() allow for stratified assessments to be run.
  • Visualize_Score() provides a standard visualization for Score or KRI.
  • Visualize_Workflow() provides a flowchart with a high-level overview of the data pipeline for a given assessment.

What's Changed

New Contributors

Full Changelog: v1.0.1...v1.1.0

Contributors

jwildfire, samussiah, and 3 other contributors
Assets 3
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v1.0.1

17 Jun 21:16
@samussiah samussiah
v1.0.1
d97bb02
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v1.0.1

Release Notes

This release explicitly captures the KRI of interest as part of the data model, standardizing the input to and output from the analysis functions. View a full list of resolved issues here.

What's Changed

New Contributors

Full Changelog: v1.0.0...v1.0.1

Contributors

jwildfire, samussiah, and 3 other contributors
Assets 3
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v1.0.0

02 Jun 18:02
@mattroumaya mattroumaya
v1.0.0
fa49650
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v1.0.0

Release Notes

This release includes qualified functionality for Adverse Event and Protocol Deviation Assessments.

Additionally, updates include:

  • Study_Assess() now has an argument lSubjFilters that filters subject-level data when running multiple assessments.
  • Study_AssessmentReport() is more concise, and now displays a yellow icon for checks that were not run.
  • Statistical models now include informative messages when bQuiet is FALSE.
  • Documentation and vignettes have been thoroughly reviewed and improved.

What's Changed

Full Changelog: v0.4.1...v1.0.0

Contributors

jwildfire, samussiah, and 2 other contributors
Assets 3
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v0.4.1

13 May 14:19
@samussiah samussiah
v0.4.1
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v0.4.1

gsm v0.4.1

v0.4.1 largely addresses function documentation and squashes a few bugs. View a complete list of resolved issues here.

What's Changed

Full Changelog: v0.4.0...v0.4.1

Contributors

jwildfire, samussiah, and 2 other contributors
Assets 3
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v0.4.0

02 May 21:16
@jwildfire jwildfire
v0.4.0
5daf7a3
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v0.4.0 Pre-release
Pre-release

gsm v0.4.0

This release includes a refactor to the gsm data workflow in preparation for a v1 release. Updates include:

  • *_Map_Raw() functions have default input parameters from {clindata}
  • *_Map_Raw() and *_Assess() functions now have options for verbose workflow commenting (when bQuiet == FALSE), and an option to return an error log (bReturnChecks == TRUE)
  • Default Mappings and Specifications now saved as metadata instead of hard-coded in functions. See inst/mappings/ and inst/specs/ in this package or clindata::mapping_rawplus
  • Added support for a study-level data pipeline with reporting via a new Study_Assess() function, which depends on supporting Study_*() functions and a series of utility functions (CheckInputs(), RunAssessment(), and RunStep())

What's Changed

New Contributors

Full Changelog: v0.3.0...v0.4.0

Contributors

jwildfire, samussiah, and 2 other contributors
Assets 3
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